char * THD_dataset_info( THD_3dim_dataset *dset , int verbose ) { THD_dataxes *daxes ; THD_fvec3 fv1 , fv2 , fv3 ; int ival , ntimes , nval_per , n1,n2,n3 , kv,npar ; float tf, angle=0.0; long long tb ; static char *RR="[R]" , *LL="[L]" , *PP="[P]" , *AA="[A]" , *SS="[S]" , *II="[I]" , *ZZ=" " ; char *xlbot , *xltop , *ylbot , *yltop , *zlbot , *zltop , *cpt ; char str[1024], soblq[1024] ; int nstr , obliquity; char *outbuf = NULL ; /* output buffer */ ENTRY("THD_dataset_info") ; if( ! ISVALID_3DIM_DATASET(dset) ) RETURN(NULL) ; daxes = dset->daxes ; if( DSET_IS_BRIK(dset) ) outbuf = THD_zzprintf(outbuf,"Dataset File: %s\n" , DSET_FILECODE(dset) ) ; else outbuf = THD_zzprintf(outbuf,"Dataset File: %s\n" , DSET_BRIKNAME(dset) ) ; outbuf = THD_zzprintf(outbuf,"Identifier Code: %s Creation Date: %s\n" , dset->idcode.str , dset->idcode.date ) ; outbuf = THD_zzprintf(outbuf, "Template Space: %s\n", dset->atlas_space); if( ISANAT(dset) ){ outbuf = THD_zzprintf(outbuf,"Dataset Type: %s (-%s)\n", ANAT_typestr[dset->func_type] , ANAT_prefixstr[dset->func_type] ) ; } else { outbuf = THD_zzprintf(outbuf,"Dataset Type: %s (-%s)\n", FUNC_typestr[dset->func_type] , FUNC_prefixstr[dset->func_type] ) ; } /* 25 April 1998: do byte order stuff */ switch( DSET_BYTEORDER(dset) ){ case LSB_FIRST: outbuf = THD_zzprintf(outbuf,"Byte Order: %s" , LSB_FIRST_STRING) ; break ; case MSB_FIRST: outbuf = THD_zzprintf(outbuf,"Byte Order: %s" , MSB_FIRST_STRING) ; break ; } if( THD_find_string_atr(dset->dblk,ATRNAME_BYTEORDER) == NULL ) /* 19 Sep 1999 */ outbuf = THD_zzprintf(outbuf," {assumed}") ; kv = mri_short_order() ; switch( kv ){ case LSB_FIRST: outbuf = THD_zzprintf(outbuf," [this CPU native = %s]\n" , LSB_FIRST_STRING) ; break ; case MSB_FIRST: outbuf = THD_zzprintf(outbuf," [this CPU native = %s]\n" , MSB_FIRST_STRING) ; break ; } /*-- 21 Jun 2002: print storage mode --*/ if( dset->dblk->diskptr != NULL ){ outbuf = THD_zzprintf(outbuf,"Storage Mode: %s\n", storage_mode_str(dset->dblk->diskptr->storage_mode)); } tb = dset->dblk->total_bytes ; if( tb > 0 ) outbuf = THD_zzprintf(outbuf,"Storage Space: %s (%s) bytes\n", commaized_integer_string(dset->dblk->total_bytes) , approximate_number_string(dset->dblk->total_bytes) ) ; /*-- keywords --*/ if( verbose >= 0 ){ cpt = DSET_KEYWORDS(dset) ; if( cpt != NULL && cpt[0] != '\0' ){ int j = strlen(cpt) ; if( j < 99 ){ outbuf = THD_zzprintf(outbuf,"Keywords: %s\n" , cpt ) ; } else { int k ; outbuf = THD_zzprintf(outbuf,"\n----- KEYWORDS -----\n") ; for( k=0 ; k < j ; k += ZMAX ) outbuf = THD_zzprintf(outbuf,SZMAX,cpt+k) ; outbuf = THD_zzprintf(outbuf,"\n") ; } } } /*-- idcodes --*/ if( verbose >= 0 ){ if( ! ISZERO_IDCODE(dset->anat_parent_idcode) ) outbuf = THD_zzprintf(outbuf,"Anatomy Parent: %s [%s]\n" , dset->anat_parent_name , dset->anat_parent_idcode.str ) ; else if( strlen(dset->anat_parent_name) > 0 ) outbuf = THD_zzprintf(outbuf,"Anatomy Parent: %s\n" , dset->anat_parent_name ) ; if( ! ISZERO_IDCODE(dset->warp_parent_idcode) ) outbuf = THD_zzprintf(outbuf,"Warp Parent: %s [%s]\n" , dset->warp_parent_name , dset->warp_parent_idcode.str) ; else if( strlen(dset->warp_parent_name) > 0 ) outbuf = THD_zzprintf(outbuf,"Warp Parent: %s\n" , dset->warp_parent_name ) ; } /*-- tagset --*/ if( verbose > 0 && dset->tagset != NULL && dset->tagset->num > 0 ){ int ii , ns=0 ; for( ii=0 ; ii < dset->tagset->num ; ii++ ) if( dset->tagset->tag[ii].set ) ns++ ; outbuf = THD_zzprintf(outbuf,"Tagset: %d set [out of %d total]\n", ns , dset->tagset->num ) ; } /* are we oblique ? */ if((obliquity = dset_obliquity(dset, &angle)) >= 0) { if(angle>0.0) { sprintf (soblq, "Data Axes Tilt: Oblique (%.3f deg. from plumb)\n" "Data Axes Approximate Orientation:", angle); } else { sprintf (soblq, "Data Axes Tilt: Plumb\n" "Data Axes Orientation:"); } { char *gstr = EDIT_get_geometry_string(dset) ; if( gstr != NULL && *gstr != '\0' ) outbuf = THD_zzprintf(outbuf,"Geometry String: \"%s\"\n",gstr) ; } } else { sprintf (soblq, "Data Axes Tilt: Unspecified, assumed plumb\n" "Data Axes Orientation:"); } outbuf = THD_zzprintf(outbuf, "%s\n" " first (x) = %s\n" " second (y) = %s\n" " third (z) = %s [-orient %c%c%c]\n" , soblq, ORIENT_typestr[daxes->xxorient] , ORIENT_typestr[daxes->yyorient] , ORIENT_typestr[daxes->zzorient] , ORIENT_typestr[daxes->xxorient][0] , ORIENT_typestr[daxes->yyorient][0] , ORIENT_typestr[daxes->zzorient][0] ) ; LOAD_FVEC3(fv1 , daxes->xxorg , daxes->yyorg , daxes->zzorg) ; fv1 = THD_3dmm_to_dicomm( dset , fv1 ) ; LOAD_FVEC3(fv2 , daxes->xxorg + (daxes->nxx-1)*daxes->xxdel , daxes->yyorg + (daxes->nyy-1)*daxes->yydel , daxes->zzorg + (daxes->nzz-1)*daxes->zzdel ) ; fv2 = THD_3dmm_to_dicomm( dset , fv2 ) ; if( fv1.xyz[0] > fv2.xyz[0] ) FSWAP( fv1.xyz[0] , fv2.xyz[0] ) ; if( fv1.xyz[1] > fv2.xyz[1] ) FSWAP( fv1.xyz[1] , fv2.xyz[1] ) ; if( fv1.xyz[2] > fv2.xyz[2] ) FSWAP( fv1.xyz[2] , fv2.xyz[2] ) ; LOAD_FVEC3(fv3 , daxes->xxdel , daxes->yydel , daxes->zzdel) ; fv3 = THD_3dmm_to_dicomm( dset , fv3 ) ; XLAB(xlbot,fv1.xyz[0]) ; YLAB(ylbot,fv1.xyz[1]) ; ZLAB(zlbot,fv1.xyz[2]) ; XLAB(xltop,fv2.xyz[0]) ; YLAB(yltop,fv2.xyz[1]) ; ZLAB(zltop,fv2.xyz[2]) ; n1 = DAXES_NUM(daxes,ORI_R2L_TYPE) ; n2 = DAXES_NUM(daxes,ORI_A2P_TYPE) ; n3 = DAXES_NUM(daxes,ORI_I2S_TYPE) ; outbuf = THD_zzprintf(outbuf, "R-to-L extent: %9.3f %s -to- %9.3f %s -step- %9.3f mm [%3d voxels]\n" "A-to-P extent: %9.3f %s -to- %9.3f %s -step- %9.3f mm [%3d voxels]\n" "I-to-S extent: %9.3f %s -to- %9.3f %s -step- %9.3f mm [%3d voxels]\n" , fv1.xyz[0],xlbot , fv2.xyz[0],xltop , fabs(fv3.xyz[0]) , n1 , fv1.xyz[1],ylbot , fv2.xyz[1],yltop , fabs(fv3.xyz[1]) , n2 , fv1.xyz[2],zlbot , fv2.xyz[2],zltop , fabs(fv3.xyz[2]) , n3 ) ; /*-- 01 Feb 2001: print the center of the dataset as well --*/ if( verbose > 0 ){ fv1.xyz[0] = 0.5*(fv1.xyz[0]+fv2.xyz[0]) ; XLAB(xlbot,fv1.xyz[0]) ; fv1.xyz[1] = 0.5*(fv1.xyz[1]+fv2.xyz[1]) ; YLAB(ylbot,fv1.xyz[1]) ; fv1.xyz[2] = 0.5*(fv1.xyz[2]+fv2.xyz[2]) ; ZLAB(zlbot,fv1.xyz[2]) ; outbuf = THD_zzprintf(outbuf, "R-to-L center: %9.3f %s\n" "A-to-P center: %9.3f %s\n" "I-to-S center: %9.3f %s\n" , fv1.xyz[0],xlbot , fv1.xyz[1],ylbot , fv1.xyz[2],zlbot ) ; } ntimes = DSET_NUM_TIMES(dset) ; nval_per = DSET_NVALS_PER_TIME(dset) ; if( ntimes > 1 ){ outbuf = THD_zzprintf(outbuf, "Number of time steps = %d" , ntimes ) ; STATUS("timestep") ; outbuf = THD_zzprintf(outbuf, " Time step = %.5f%s Origin = %.5f%s" , dset->taxis->ttdel , UNITS_TYPE_LABEL(dset->taxis->units_type) , dset->taxis->ttorg , UNITS_TYPE_LABEL(dset->taxis->units_type) ) ; if( dset->taxis->nsl > 0 ) outbuf = THD_zzprintf(outbuf," Number time-offset slices = %d Thickness = %.3f", dset->taxis->nsl , fabs(dset->taxis->dz_sl) ) ; outbuf = THD_zzprintf(outbuf,"\n") ; STATUS("nsl done") ; if( verbose > 0 && dset->taxis->nsl > 0 && dset->taxis->toff_sl != NULL ){ outbuf = THD_zzprintf(outbuf,"Time-offsets per slice:") ; for( ival=0 ; ival < dset->taxis->nsl ; ival++ ) outbuf = THD_zzprintf(outbuf, " %.3f" , dset->taxis->toff_sl[ival] ) ; outbuf = THD_zzprintf(outbuf,"\n") ; } } else { outbuf = THD_zzprintf(outbuf, "Number of values stored at each pixel = %d\n" , nval_per ) ; } #if 0 if( verbose > 0 && ntimes > 1 ) nval_per = dset->dblk->nvals ; else nval_per = 1 ; /* 12 Feb 2002 */ #else nval_per = dset->dblk->nvals ; if( verbose < 0 && nval_per > 5 ) nval_per = 3 ; #endif /* print out stuff for each sub-brick */ for( ival=0 ; ival < nval_per ; ival++ ){ STATUS("ival a") ; sprintf( str , " -- At sub-brick #%d '%s' datum type is %s" , ival , DSET_BRICK_LAB(dset,ival) , MRI_TYPE_name[DSET_BRICK_TYPE(dset,ival)] ) ; nstr = strlen(str) ; tf = DSET_BRICK_FACTOR(dset,ival) ; if( ISVALID_STATISTIC(dset->stats) ){ if( tf != 0.0 ){ sprintf( str+nstr , ":%13.6g to %13.6g [internal]\n" "%*s[*%13.6g] %13.6g to %13.6g [scaled]\n" , dset->stats->bstat[ival].min/tf , dset->stats->bstat[ival].max/tf , nstr-16," " , tf , dset->stats->bstat[ival].min , dset->stats->bstat[ival].max ) ; } else { sprintf( str+nstr , ":%13.6g to %13.6g\n" , dset->stats->bstat[ival].min , dset->stats->bstat[ival].max ) ; } } else if( tf != 0.0 ){ sprintf( str+nstr , " [*%g]\n",tf) ; } else { sprintf( str+nstr , "\n") ; } STATUS("ival b") ; outbuf = THD_zzprintf(outbuf,"%s",str) ; /** 30 Nov 1997: print sub-brick stat params **/ kv = DSET_BRICK_STATCODE(dset,ival) ; if( FUNC_IS_STAT(kv) ){ STATUS("ival c") ; outbuf = THD_zzprintf(outbuf," statcode = %s",FUNC_prefixstr[kv] ) ; npar = FUNC_need_stat_aux[kv] ; if( npar > 0 ){ outbuf = THD_zzprintf(outbuf,"; statpar =") ; for( kv=0 ; kv < npar ; kv++ ) outbuf = THD_zzprintf(outbuf," %g",DSET_BRICK_STATPAR(dset,ival,kv)) ; } outbuf = THD_zzprintf(outbuf,"\n") ; STATUS("ival d") ; } cpt = DSET_BRICK_KEYWORDS(dset,ival) ; if( cpt != NULL && cpt[0] != '\0' ){ outbuf = THD_zzprintf(outbuf," keywords = %.66s\n",cpt) ; } STATUS("ival z") ; } if( verbose < 0 && nval_per < dset->dblk->nvals ) /* 21 Sep 2007 */ outbuf = THD_zzprintf(outbuf, "** For info on all %d sub-bricks, use '3dinfo -verb' **\n", dset->dblk->nvals) ; /** print out dataset global statistical parameters **/ if( ISFUNC(dset) && FUNC_need_stat_aux[dset->func_type] > 0 ){ outbuf = THD_zzprintf(outbuf,"Auxiliary functional statistical parameters:\n %s\n", FUNC_label_stat_aux[dset->func_type] ) ; for( ival=0 ; ival < FUNC_need_stat_aux[dset->func_type] ; ival++ ) outbuf = THD_zzprintf(outbuf," %g",dset->stat_aux[ival]) ; outbuf = THD_zzprintf(outbuf,"\n") ; } /** If present, print out History **/ { char *chn ; int j,k ; chn = tross_Get_History(dset) ; if( chn != NULL ){ j = strlen(chn) ; outbuf = THD_zzprintf(outbuf,"\n----- HISTORY -----\n") ; for( k=0 ; k < j ; k += ZMAX ) outbuf = THD_zzprintf(outbuf,SZMAX,chn+k) ; free(chn) ; outbuf = THD_zzprintf(outbuf,"\n") ; } } /** If present, print out Notes **/ if( verbose >= 0 ){ ATR_int *notecount; int num_notes, i, j, mmm ; char *chn , *chd ; notecount = THD_find_int_atr(dset->dblk, "NOTES_COUNT"); if( notecount != NULL ){ num_notes = notecount->in[0] ; if( verbose == 0 && num_notes > 5 ) num_notes = 5 ; mmm = (verbose > 0) ? ZMAX : 1200 ; /* 400 it was! Come on Bob, have a heart! -ZSS */ for (i=1; i<= num_notes; i++) { chn = tross_Get_Note( dset , i ) ; if( chn != NULL ){ j = strlen(chn) ; if( j > mmm ) chn[mmm] = '\0' ; chd = tross_Get_Notedate(dset,i) ; if( chd == NULL ){ chd = AFMALL(char,16) ; strcpy(chd,"no date") ; } outbuf = THD_zzprintf(outbuf,"\n----- NOTE %d [%s] -----\n%s\n",i,chd,chn) ; free(chn) ; free(chd) ; }
char * STAVG_main( PLUGIN_interface * plint ) { MCW_idcode * idc ; /* input dataset idcode */ THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */ char * new_prefix , * str , * str2; /* strings from user */ int meth; /* chosen computation method */ int new_datum , /* control parameters */ old_datum , ntime ; int te, ne, tinc, kim, nia; int numepochs, minlength, maxlength, lastindex, navgpts; int nvox , perc , new_units, old_units ; int ii, ibot,itop , kk, jj; int no1, user_maxlength, delta; int *pEpochLength, *pTimeIndex; int nx, ny, nz, npix; float *pNumAvg; float old_dtime; MRI_IMAGE * stimim; MRI_IMARR *avgimar; 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) */ float * fxar = NULL ; /* array loaded from input dataset */ float * stimar = NULL ; float ** fout = NULL ; /* will be array of output floats */ float * tar = NULL ; /* will be array of taper coefficients */ float * nstimar; /*--------------------------------------------------------------------*/ /*----- Check inputs from AFNI to see if they are reasonable-ish -----*/ /*--------- go to first input line ---------*/ PLUTO_next_option(plint) ; idc = PLUTO_get_idcode(plint) ; /* get dataset item */ old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */ if( old_dset == NULL ) return "*************************\n" "Cannot find Input Dataset\n" "*************************" ; ntime = DSET_NUM_TIMES(old_dset) ; if( ntime < 2 ) return "*****************************\n" "Dataset has only 1 time point\n" "*****************************" ; ii = DSET_NVALS_PER_TIME(old_dset) ; if( ii > 1 ) return "************************************\n" "Dataset has > 1 value per time point\n" "************************************" ; old_datum = DSET_BRICK_TYPE( old_dset , 0 ) ; /* get old dataset datum type */ new_datum = old_datum; old_dtime = DSET_TIMESTEP(old_dset); old_units = DSET_TIMEUNITS(old_dset); nvox = old_dset->daxes->nxx * old_dset->daxes->nyy * old_dset->daxes->nzz; npix = old_dset->daxes->nxx * old_dset->daxes->nyy; nx = old_dset->daxes->nxx; new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */ if( ! PLUTO_prefix_ok(new_prefix) ) /* check if it is OK */ return "************************\n" "Output Prefix is illegal\n" "************************" ; /*--------- go to next input line ---------*/ PLUTO_next_option(plint); stimim = PLUTO_get_timeseries(plint); if( stimim == NULL ) return "Please specify stimulus timing"; if( stimim->nx < ntime ){ return "**************************************\n" "Not enough pts in stimulus time-series\n" "**************************************"; } stimar = MRI_FLOAT_PTR(stimim); delta = PLUTO_get_number(plint); if( abs(delta) > ntime ){ return "************************\n" "Delta shift is too large\n" "************************"; } /*initialize variables if not user specified */ user_maxlength = ntime; no1 = 0; /*--------- go to next input line ---------*/ PLUTO_next_option(plint); str = PLUTO_get_string(plint) ; /* get string item (the method) */ meth = PLUTO_string_index( str , /* find it in list it is from */ _STAVG_NUM_METHODS , method_strings ) ; /*--------- see if the 4th option line is present --------*/ str = PLUTO_get_optiontag( plint ) ; if( str != NULL ){ user_maxlength = (int) PLUTO_get_number(plint) ; str2 = PLUTO_get_string(plint) ; /* get string item (the method) */ no1 = PLUTO_string_index( str2 , /* find it in list it is from */ 2 , yes_no_strings) ; } /*------------------------------------------------------*/ /*---------- At this point, the inputs are OK ----------*/ PLUTO_popup_meter( plint ) ; /* popup a progress meter */ /*________________[ Main Code ]_________________________*/ fout = avg_epochs( old_dset, stimar, user_maxlength, 1, meth, plint ); if( fout == NULL ) return " \nError in avg_epochs() function!\n " ; if( RMB_DEBUG ) fprintf(stderr, "Done with avg_epochs\n"); maxlength = M_maxlength; /*______________________________________________________*/ new_dset = EDIT_empty_copy( old_dset ) ; /* start with copy of old one */ { char * his = PLUTO_commandstring(plint) ; tross_Copy_History( old_dset , new_dset ) ; tross_Append_History( new_dset , his ) ; free( his ) ; } /*-- 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 , maxlength , /* # sub-bricks */ ADN_ntt , maxlength , /* # time points */ /* ADN_ttorg , old_dtime , */ /* time origin */ /* ADN_ttdel , old_dtime , */ /* time step */ /* ADN_ttdur , old_dtime , */ /* time duration */ /* ADN_nsl , 0 , */ /* z-axis time slicing */ /* ADN_tunits , old_units , */ /* time units */ ADN_none ) ; if( ii != 0 ){ THD_delete_3dim_dataset( new_dset , False ) ; FREE_WORKSPACE ; return "***********************************\n" "Error while creating output dataset\n" "***********************************" ; } /*------------------------------------------------------------*/ /*------- The output is now in fout[kk][ii], for kk=0..maxlength-1 , 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 bricks to the dataset ***/ case MRI_float: for( kk=0 ; kk < maxlength ; kk++ ) EDIT_substitute_brick( new_dset , kk , MRI_float , fout[kk] ) ; break ; /*** output is shorts: we have to create a scaled sub-brick from fout ***/ case MRI_short:{ short * bout ; float fac ; for( kk=0 ; kk < maxlength ; kk++ ){ /* loop over sub-bricks */ /*-- get output sub-brick --*/ bout = (short *) malloc( sizeof(short) * nvox ) ; if( bout == NULL ){ fprintf(stderr,"\nFinal malloc error in plug_stavg!\n\a") ; return("Final malloc error in plug_stavg!"); ; /* exit(1) ;*/ } /*-- find scaling and then scale --*/ /*fac = MCW_vol_amax( nvox,1,1 , MRI_float , fout[kk] ) ;*/ fac = 1.0; EDIT_coerce_scale_type( nvox,fac , MRI_float,fout[kk] , MRI_short,bout ) ; free( fout[kk] ) ; /* don't need this anymore */ /*-- put output brick into dataset, and store scale factor --*/ EDIT_substitute_brick( new_dset , kk , MRI_short , bout ) ; } } break ; /*** output is bytes (byte = unsigned char) we have to create a scaled sub-brick from fout ***/ case MRI_byte:{ byte * bout ; float fac ; for( kk=0 ; kk < maxlength ; kk++ ){ /* loop over sub-bricks */ /*-- get output sub-brick --*/ bout = (byte *) malloc( sizeof(byte) * nvox ) ; if( bout == NULL ){ fprintf(stderr,"\nFinal malloc error in plug_stavg!\n\a") ; return("Final malloc error in plug_stavg!"); ; /* exit(1) ;*/ } /*-- find scaling and then scale --*/ fac = 1.0; EDIT_coerce_scale_type( nvox,fac , MRI_float,fout[kk] , MRI_byte,bout ) ; free( fout[kk] ) ; /* don't need this anymore */ /*-- put output brick into dataset, and store scale factor --*/ EDIT_substitute_brick( new_dset , kk , MRI_byte , bout ) ; } } break ; } /* end of switch on output data type */ /*-------------- Cleanup and go home ----------------*/ PLUTO_set_meter( plint , 100 ) ; /* set progress meter to 100% */ PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ; FREE_WORKSPACE ; return NULL ; /* null string returned means all was OK */ }
char * IMREG_main( PLUGIN_interface * plint ) { MCW_idcode * idc ; /* input dataset idcode */ THD_3dim_dataset * old_dset , * new_dset ; /* input and output datasets */ char * new_prefix , * str ; /* strings from user */ int base , ntime , datum , nx,ny,nz , ii,kk , npix ; float dx,dy,dz ; MRI_IMARR * ims_in , * ims_out ; MRI_IMAGE * im , * imbase ; byte ** bptr = NULL , ** bout = NULL ; short ** sptr = NULL , ** sout = NULL ; float ** fptr = NULL , ** fout = NULL ; float * dxar = NULL , * dyar = NULL , * phiar = NULL ; /*--------------------------------------------------------------------*/ /*----- Check inputs from AFNI to see if they are reasonable-ish -----*/ /*--------- go to first input line ---------*/ PLUTO_next_option(plint) ; idc = PLUTO_get_idcode(plint) ; /* get dataset item */ old_dset = PLUTO_find_dset(idc) ; /* get ptr to dataset */ if( old_dset == NULL ) return "*************************\n" "Cannot find Input Dataset\n" "*************************" ; ntime = DSET_NUM_TIMES(old_dset) ; if( ntime < 2 ) return "*****************************\n" "Dataset has only 1 time point\n" "*****************************" ; ii = DSET_NVALS_PER_TIME(old_dset) ; if( ii > 1 ) return "************************************\n" "Dataset has > 1 value per time point\n" "************************************" ; nx = old_dset->daxes->nxx ; dx = old_dset->daxes->xxdel ; ny = old_dset->daxes->nyy ; dy = old_dset->daxes->yydel ; npix = nx*ny ; nz = old_dset->daxes->nzz ; dz = old_dset->daxes->zzdel ; if( nx != ny || fabs(dx) != fabs(dy) ) { #ifdef IMREG_DEBUG fprintf(stderr,"\nIMREG: nx=%d ny=%d nz=%d dx=%f dy=%f dz=%f\n", nx,ny,nz,dx,dy,dz ) ; #endif return "***********************************\n" "Dataset does not have square slices\n" "***********************************" ; } new_prefix = PLUTO_get_string(plint) ; /* get string item (the output prefix) */ if( ! PLUTO_prefix_ok(new_prefix) ) /* check if it is OK */ return "************************\n" "Output Prefix is illegal\n" "************************" ; /*--------- go to next input line ---------*/ PLUTO_next_option(plint) ; base = PLUTO_get_number(plint) ; if( base >= ntime ) return "********************\n" "Base value too large\n" "********************" ; /*--------- see if the 3rd option line is present --------*/ str = PLUTO_get_optiontag( plint ) ; if( str != NULL ) { float fsig , fdxy , fdph ; fsig = PLUTO_get_number(plint) * 0.42466090 ; fdxy = PLUTO_get_number(plint) ; fdph = PLUTO_get_number(plint) ; mri_align_params( 0 , 0.0,0.0,0.0 , fsig,fdxy,fdph ) ; /* fprintf(stderr,"Set fine params = %f %f %f\n",fsig,fdxy,fdph) ; */ } /*------------- ready to compute new dataset -----------*/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: loading dataset\n") ; #endif DSET_load( old_dset ) ; /*** 1) Copy the dataset in toto ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: Copying dataset\n") ; #endif new_dset = PLUTO_copy_dset( old_dset , new_prefix ) ; if( new_dset == NULL ) return "****************************\n" "Failed to copy input dataset\n" "****************************" ; /*** 2) Make an array of empty images ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: making empty images\n") ; #endif datum = DSET_BRICK_TYPE(new_dset,0) ; INIT_IMARR(ims_in) ; for( ii=0 ; ii < ntime ; ii++ ) { im = mri_new_vol_empty( nx , ny , 1 , datum ) ; ADDTO_IMARR(ims_in,im) ; } imbase = mri_new_vol_empty( nx , ny , 1 , datum ) ; dxar = (float *) malloc( sizeof(float) * ntime ) ; dyar = (float *) malloc( sizeof(float) * ntime ) ; phiar = (float *) malloc( sizeof(float) * ntime ) ; /*** 3) Get pointers to sub-bricks in old and new datasets ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: getting input brick pointers\n") ; #endif switch( datum ) { /* pointer type depends on input datum type */ case MRI_byte: bptr = (byte **) malloc( sizeof(byte *) * ntime ) ; bout = (byte **) malloc( sizeof(byte *) * ntime ) ; for( ii=0 ; ii < ntime ; ii++ ) { bptr[ii] = (byte *) DSET_ARRAY(old_dset,ii) ; bout[ii] = (byte *) DSET_ARRAY(new_dset,ii) ; } break ; case MRI_short: sptr = (short **) malloc( sizeof(short *) * ntime ) ; sout = (short **) malloc( sizeof(short *) * ntime ) ; for( ii=0 ; ii < ntime ; ii++ ) { sptr[ii] = (short *) DSET_ARRAY(old_dset,ii) ; sout[ii] = (short *) DSET_ARRAY(new_dset,ii) ; } #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: sptr[0] = %p sout[0] = %p\n",sptr[0],sout[0]) ; #endif break ; case MRI_float: fptr = (float **) malloc( sizeof(float *) * ntime ) ; fout = (float **) malloc( sizeof(float *) * ntime ) ; for( ii=0 ; ii < ntime ; ii++ ) { fptr[ii] = (float *) DSET_ARRAY(old_dset,ii) ; fout[ii] = (float *) DSET_ARRAY(new_dset,ii) ; } break ; } /*** 4) Loop over slices ***/ PLUTO_popup_meter(plint) ; for( kk=0 ; kk < nz ; kk++ ) { /*** 4a) Setup ims_in images to point to input slices ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: slice %d -- setup input images\n",kk) ; #endif for( ii=0 ; ii < ntime ; ii++ ) { im = IMARR_SUBIMAGE(ims_in,ii) ; switch( datum ) { case MRI_byte: mri_fix_data_pointer( bptr[ii] + kk*npix, im ) ; break ; case MRI_short: mri_fix_data_pointer( sptr[ii] + kk*npix, im ) ; break ; case MRI_float: mri_fix_data_pointer( fptr[ii] + kk*npix, im ) ; break ; } } /*** 4b) Setup im to point to base image ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: slice %d -- setup base image\n",kk) ; #endif switch( datum ) { case MRI_byte: mri_fix_data_pointer( bptr[base] + kk*npix, imbase ) ; break ; case MRI_short: mri_fix_data_pointer( sptr[base] + kk*npix, imbase ) ; break ; case MRI_float: mri_fix_data_pointer( fptr[base] + kk*npix, imbase ) ; break ; } /*** 4c) Register this slice at all times ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: slice %d -- register\n",kk) ; #endif ims_out = mri_align_dfspace( imbase , NULL , ims_in , ALIGN_REGISTER_CODE , dxar,dyar,phiar ) ; if( ims_out == NULL ) fprintf(stderr,"IMREG: mri_align_dfspace return NULL\n") ; /*** 4d) Put the output back in on top of the input; note that the output is always in MRI_float format ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: slice %d -- put output back into dataset\n",kk) ; #endif for( ii=0 ; ii < ntime ; ii++ ) { switch( datum ) { case MRI_byte: im = mri_to_mri( MRI_byte , IMARR_SUBIMAGE(ims_out,ii) ) ; memcpy( bout[ii] + kk*npix , MRI_BYTE_PTR(im) , sizeof(byte)*npix ) ; mri_free(im) ; break ; case MRI_short: #ifdef IMREG_DEBUG if( ii==0 )fprintf(stderr,"IMREG: conversion to short at ii=%d\n",ii) ; #endif im = mri_to_mri( MRI_short , IMARR_SUBIMAGE(ims_out,ii) ) ; #ifdef IMREG_DEBUG if( ii==0 )fprintf(stderr,"IMREG: copying to %p from %p\n",sout[ii] + kk*npix,MRI_SHORT_PTR(im)) ; #endif memcpy( sout[ii] + kk*npix , MRI_SHORT_PTR(im) , sizeof(short)*npix ) ; #ifdef IMREG_DEBUG if( ii==0 )fprintf(stderr,"IMREG: freeing\n") ; #endif mri_free(im) ; break ; case MRI_float: im = IMARR_SUBIMAGE(ims_out,ii) ; memcpy( fout[ii] + kk*npix , MRI_FLOAT_PTR(im) , sizeof(float)*npix ) ; break ; } } PLUTO_set_meter(plint, (100*(kk+1))/nz ) ; /*** 4e) Destroy the output images ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: destroying aligned output\n") ; #endif DESTROY_IMARR( ims_out ) ; } /*** 5) Destroy the empty images and other workspaces ***/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: destroy workspaces\n") ; #endif mri_clear_data_pointer(imbase) ; mri_free(imbase) ; for( ii=0 ; ii < ntime ; ii++ ) { im = IMARR_SUBIMAGE(ims_in,ii) ; mri_clear_data_pointer(im) ; } DESTROY_IMARR(ims_in) ; FREE_WORKSPACE ; /*------------- let AFNI know about the new dataset ------------*/ #ifdef IMREG_DEBUG fprintf(stderr,"IMREG: send result to AFNI\n") ; #endif PLUTO_add_dset( plint , new_dset , DSET_ACTION_MAKE_CURRENT ) ; return NULL ; /* null string returned means all was OK */ }