int main( int argc , char * argv[] ) { int iarg=1 , dcode=0 , maxgap=2 , nftot=0 ; char * prefix="zfillin" , * dstr=NULL; THD_3dim_dataset * inset , * outset ; MRI_IMAGE * brim ; int verb=0 ; if( argc < 2 || strcmp(argv[1],"-help") == 0 ){ printf("Usage: 3dZFillin [options] dataset\n" "Extracts 1D rows in the given direction from a 3D dataset,\n" "searches for zeros that are 'close' to nonzero values in the row,\n" "and replaces the zeros with the closest nonzero neighbor.\n" "\n" "OPTIONS:\n" " -maxstep N = set the maximum distance to a neighbor\n" " [default=2].\n" " -dir D = set the direction of fill to 'D', which can\n" " be one of the following:\n" " A-P, P-A, I-S, S-I, L-R, R-L, x, y, z\n" " The first 6 are anatomical directions;\n" " the last 3 are reference to the dataset\n" " internal axes [no default value].\n" " -prefix P = set the prefix to 'P' for the output dataset.\n" "\n" "N.B.: * If the input dataset has more than one sub-brick,\n" " only the first one will be processed.\n" " * At this time, 3dZFillin only works on byte-valued datasets\n" "\n" "This program's only purpose is to fill up the Talairach Daemon\n" "bricks obtained from the UT San Antonio database.\n" "\n" ) ; PRINT_COMPILE_DATE ; exit(0) ; } mainENTRY("3dZFillin main") ; machdep() ; AFNI_logger("3dZfillin",argc,argv) ; PRINT_VERSION(3dZFillin") ; /*-- scan args --*/ while( iarg < argc && argv[iarg][0] == '-' ){ if( strncmp(argv[iarg],"-verb",5) == 0 ){ verb++ ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ prefix = argv[++iarg] ; if( !THD_filename_ok(prefix) ){ fprintf(stderr,"*** Illegal string after -prefix!\n"); exit(1) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-maxstep") == 0 ){ maxgap = strtol( argv[++iarg] , NULL , 10 ) ; if( maxgap < 1 ){ fprintf(stderr,"*** Illegal value after -maxgap!\n"); exit(1); } iarg++ ; continue ; } if( strcmp(argv[iarg],"-dir") == 0 ){ dstr = argv[++iarg] ; iarg++ ; continue ; } fprintf(stderr,"*** Illegal option: %s\n",argv[iarg]) ; exit(1) ; } if( dstr == NULL ){ fprintf(stderr,"*** No -dir option on command line!\n"); exit(1); } if( iarg >= argc ){ fprintf(stderr,"*** No input dataset on command line!\n"); exit(1); } inset = THD_open_dataset( argv[iarg] ) ; if( inset == NULL ){ fprintf(stderr,"*** Can't open dataset %s\n",argv[iarg]); exit(1); } outset = EDIT_empty_copy( inset ) ; EDIT_dset_items( outset , ADN_prefix , prefix , ADN_none ) ; if( THD_deathcon() && THD_is_file( DSET_HEADNAME(outset) ) ){ fprintf(stderr,"** Output file %s exists -- cannot overwrite!\n", DSET_HEADNAME(outset) ) ; exit(1) ; } tross_Copy_History( inset , outset ) ; tross_Make_History( "3dZFillin" , argc,argv , outset ) ; if( DSET_NVALS(inset) > 1 ){ fprintf(stderr,"++ WARNING: input dataset has more than one sub-brick!\n"); EDIT_dset_items( outset , ADN_ntt , 0 , ADN_nvals , 1 , ADN_none ) ; } if( DSET_BRICK_TYPE(outset,0) != MRI_byte ){ fprintf(stderr,"*** This program only works on byte datasets!\n"); exit(1) ; } switch( *dstr ){ case 'x': dcode = 1 ; break ; case 'y': dcode = 2 ; break ; case 'z': dcode = 3 ; break ; default: if( *dstr == ORIENT_tinystr[outset->daxes->xxorient][0] || *dstr == ORIENT_tinystr[outset->daxes->xxorient][1] ) dcode = 1 ; if( *dstr == ORIENT_tinystr[outset->daxes->yyorient][0] || *dstr == ORIENT_tinystr[outset->daxes->yyorient][1] ) dcode = 2 ; if( *dstr == ORIENT_tinystr[outset->daxes->zzorient][0] || *dstr == ORIENT_tinystr[outset->daxes->zzorient][1] ) dcode = 3 ; break ; } if( dcode == 0 ){ fprintf(stderr,"*** Illegal -dir direction!\n") ; exit(1) ; } if( verb ) fprintf(stderr,"++ Direction = axis %d in dataset\n",dcode) ; DSET_load(inset) ; CHECK_LOAD_ERROR(inset) ; brim = mri_copy( DSET_BRICK(inset,0) ) ; DSET_unload(inset) ; EDIT_substitute_brick( outset , 0 , brim->kind , mri_data_pointer(brim) ) ; nftot = THD_dataset_zfillin( outset , 0 , dcode , maxgap ) ; fprintf(stderr,"++ Number of voxels filled = %d\n",nftot) ; if (DSET_write(outset) != False) { fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(outset)) ; exit(0) ; } else { fprintf(stderr, "** 3dZFillin: Failed to write output!\n" ) ; exit(1) ; } }
void initialize_program (int argc, char * argv[]) { int iv; /* index number of sub-brick */ void * vfim = NULL; /* sub-brick data pointer */ float * ffim = NULL; /* sub-brick data in floating point format */ int ixyz; /* voxel index */ int nx, ny, nz, nxyz; /* numbers of voxels in input dataset */ int mx=0, my=0, mz=0, mxyz; /* numbers of voxels in mask dataset */ int nthr=0; /* number of voxels above mask threshold */ char message[80]; /* error message */ int ibin; /* p-value bin index */ /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ machdep() ; { int new_argc ; char ** new_argv ; addto_args( argc , argv , &new_argc , &new_argv ) ; if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; } } /*----- Save command line for history notes -----*/ commandline = tross_commandline( PROGRAM_NAME , argc,argv ) ; /*----- Does user request help menu? -----*/ if( argc < 2 || strcmp(argv[1],"-help") == 0 ) FDR_Syntax() ; /*----- Add to program log -----*/ AFNI_logger (PROGRAM_NAME,argc,argv); /*----- Read input options -----*/ read_options( argc , argv ) ; /*----- Open the mask dataset -----*/ if (FDR_mask_filename != NULL) { if (!FDR_quiet) printf ("Reading mask dataset: %s \n", FDR_mask_filename); DOPEN (FDR_dset, FDR_mask_filename); if (FDR_dset == NULL) { sprintf (message, "Cannot open mask dataset %s", FDR_mask_filename); FDR_error (message); } if (DSET_NVALS(FDR_dset) != 1) WARNING_message("Mask dataset: using sub-brick #0") ; /*----- Get dimensions of mask dataset -----*/ mx = DSET_NX(FDR_dset); my = DSET_NY(FDR_dset); mz = DSET_NZ(FDR_dset); mxyz = mx*my*mz; /*----- Allocate memory for float data -----*/ ffim = (float *) malloc (sizeof(float) * mxyz); MTEST (ffim); /*----- Convert mask dataset sub-brick to floats (in ffim) -----*/ iv = 0 ; SUB_POINTER (FDR_dset, iv, 0, vfim); EDIT_coerce_scale_type (mxyz, DSET_BRICK_FACTOR(FDR_dset,iv), DSET_BRICK_TYPE(FDR_dset,iv), vfim, /* input */ MRI_float , ffim); /* output */ /*----- Allocate memory for mask volume -----*/ FDR_mask = (byte *) malloc (sizeof(byte) * mxyz); MTEST (FDR_mask); /*----- Create mask of voxels above mask threshold -----*/ nthr = 0; for (ixyz = 0; ixyz < mxyz; ixyz++){ if (fabs(ffim[ixyz]) >= FDR_mask_thr){ FDR_mask[ixyz] = 1; nthr++; } else FDR_mask[ixyz] = 0; } if (!FDR_quiet) printf ("Number of voxels above mask threshold = %d \n", nthr); if (nthr < 1) FDR_error ("No voxels above mask threshold. Cannot continue."); /*----- Delete floating point sub-brick -----*/ if (ffim != NULL) { free (ffim); ffim = NULL; } /*----- Delete mask dataset -----*/ THD_delete_3dim_dataset (FDR_dset, False); FDR_dset = NULL ; } /*----- Get the input data -----*/ if (FDR_input1D_filename != NULL) { /*----- Read the input .1D file -----*/ if (!FDR_quiet) printf ("Reading input data: %s \n", FDR_input1D_filename); FDR_input1D_data = read_time_series (FDR_input1D_filename, &nxyz); if (FDR_input1D_data == NULL) { sprintf (message, "Unable to read input .1D data file: %s", FDR_input1D_filename); FDR_error (message); } if (nxyz < 1) { sprintf (message, "No p-values in input .1D data file: %s", FDR_input1D_filename); FDR_error (message); } FDR_nxyz = nxyz; FDR_nthr = nxyz; } else { /*----- Open the input 3D dataset -----*/ if (!FDR_quiet) printf ("Reading input dataset: %s \n", FDR_input_filename); FDR_dset = THD_open_dataset(FDR_input_filename); CHECK_OPEN_ERROR(FDR_dset,FDR_input_filename); /*----- Get dimensions of input dataset -----*/ nx = DSET_NX(FDR_dset); ny = DSET_NY(FDR_dset); nz = DSET_NZ(FDR_dset); nxyz = nx*ny*nz; /*----- Check for compatible dimensions -----*/ if (FDR_mask != NULL) { if ((nx != mx) || (ny != my) || (nz != mz)) FDR_error ("Mask and input dataset have incompatible dimensions"); FDR_nxyz = nxyz; FDR_nthr = nthr; } else { FDR_nxyz = nxyz; FDR_nthr = nxyz; } /*----- Check whether output dataset already exists -----*/ if( THD_deathcon() ) check_one_output_file (FDR_dset, FDR_output_prefix); } /*----- Initialize constant c(N) -----*/ if (FDR_cn < 0.0) { double cn; cn = 0.0; for (ixyz = 1; ixyz <= FDR_nthr; ixyz++) cn += 1.0 / ixyz; FDR_cn = cn; if (!FDR_quiet) printf ("c(N) = %f \n", FDR_cn); } /*----- Initialize voxel pointers -----*/ for (ibin = 0; ibin < FDR_MAX_LL; ibin++) FDR_head_voxel[ibin] = NULL; return ; }
int main( int argc , char *argv[] ) { int nx,ny,nz , nxyz , ii,kk , num1,num2 , num_tt=0 , iv , piece , fim_offset; float dx,dy,dz , dxyz , num1_inv=0.0 , num2_inv , num1m1_inv=0.0 , num2m1_inv , dof , dd,tt,q1,q2 , f1,f2 , tt_max=0.0 ; THD_3dim_dataset *dset=NULL , *new_dset=NULL ; THD_3dim_dataset * base_dset; float *av1 , *av2 , *sd1 , *sd2 , *ffim , *gfim ; float *base_ary=NULL; void *vsp ; void *vdif ; /* output mean difference */ char cbuf[THD_MAX_NAME] ; float fbuf[MAX_STAT_AUX] , fimfac ; int output_datum ; float npiece , memuse ; float *dofbrik=NULL , *dofar=NULL ; THD_3dim_dataset *dof_dset=NULL ; /*-- read command line arguments --*/ if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ) TT_syntax(NULL) ; /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ mainENTRY("3dttest main"); machdep() ; PRINT_VERSION("3dttest") ; INFO_message("For most purposes, 3dttest++ should be used instead of 3dttest!") ; { int new_argc ; char ** new_argv ; addto_args( argc , argv , &new_argc , &new_argv ) ; if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; } } AFNI_logger("3dttest",argc,argv) ; TT_read_opts( argc , argv ) ; if( ! TT_be_quiet ) printf("3dttest: t-tests of 3D datasets, by RW Cox\n") ; /*-- read first dataset in set2 to get dimensions, etc. --*/ dset = THD_open_dataset( TT_set2->ar[0] ) ; /* 20 Dec 1999 BDW */ if( ! ISVALID_3DIM_DATASET(dset) ) ERROR_exit("Unable to open dataset file %s",TT_set2->ar[0]); nx = dset->daxes->nxx ; ny = dset->daxes->nyy ; nz = dset->daxes->nzz ; nxyz = nx * ny * nz ; dx = fabs(dset->daxes->xxdel) ; dy = fabs(dset->daxes->yydel) ; dz = fabs(dset->daxes->zzdel) ; dxyz = dx * dy * dz ; #ifdef TTDEBUG printf("*** nx=%d ny=%d nz=%d\n",nx,ny,nz) ; #endif /*-- make an empty copy of this dataset, for eventual output --*/ #ifdef TTDEBUG printf("*** making empty dataset\n") ; #endif new_dset = EDIT_empty_copy( dset ) ; tross_Make_History( "3dttest" , argc,argv , new_dset ) ; strcpy( cbuf , dset->self_name ) ; strcat( cbuf , "+TT" ) ; iv = DSET_PRINCIPAL_VALUE(dset) ; if( TT_datum >= 0 ){ output_datum = TT_datum ; } else { output_datum = DSET_BRICK_TYPE(dset,iv) ; if( output_datum == MRI_byte ) output_datum = MRI_short ; } #ifdef TTDEBUG printf(" ** datum = %s\n",MRI_TYPE_name[output_datum]) ; #endif iv = EDIT_dset_items( new_dset , ADN_prefix , TT_prefix , ADN_label1 , TT_prefix , ADN_directory_name , TT_session , ADN_self_name , cbuf , ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE , ADN_func_type , FUNC_TT_TYPE , ADN_nvals , FUNC_nvals[FUNC_TT_TYPE] , ADN_ntt , 0 , /* 07 Jun 2007 */ ADN_datum_all , output_datum , ADN_none ) ; if( iv > 0 ) ERROR_exit("%d errors in attempting to create output dataset!",iv ) ; if( THD_deathcon() && THD_is_file(new_dset->dblk->diskptr->header_name) ) ERROR_exit( "Output dataset file %s already exists--cannot continue!\a", new_dset->dblk->diskptr->header_name ) ; #ifdef TTDEBUG printf("*** deleting exemplar dataset\n") ; #endif THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; /** macro to test a malloc-ed pointer for validity **/ #define MTEST(ptr) \ if((ptr)==NULL) \ ( fprintf(stderr,"*** Cannot allocate memory for statistics!\n"), exit(0) ) /*-- make space for the t-test computations --*/ /* (allocate entire volumes) 13 Dec 2005 [rickr] */ npiece = 3.0 ; /* need at least this many */ if( TT_paired ) npiece += 1.0 ; else if( TT_set1 != NULL ) npiece += 2.0 ; npiece += mri_datum_size(output_datum) / (float) sizeof(float) ; npiece += mri_datum_size(output_datum) / (float) sizeof(float) ; #if 0 piece_size = TT_workmem * MEGA / ( npiece * sizeof(float) ) ; if( piece_size > nxyz ) piece_size = nxyz ; #ifdef TTDEBUG printf("*** malloc-ing space for statistics: %g float arrays of length %d\n", npiece,piece_size) ; #endif #endif av2 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(av2) ; sd2 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(sd2) ; ffim = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(ffim) ; num2 = TT_set2->num ; if( TT_paired ){ av1 = sd1 = NULL ; gfim = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(gfim) ; num1 = num2 ; } else if( TT_set1 != NULL ){ av1 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(av1) ; sd1 = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(sd1) ; gfim = NULL ; num1 = TT_set1->num ; } else { av1 = sd1 = NULL ; gfim = NULL ; num1 = 0 ; } vdif = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ; MTEST(vdif) ; vsp = (void *) malloc( mri_datum_size(output_datum) * nxyz ) ; MTEST(vsp) ; /* 27 Dec 2002: make DOF dataset (if prefix is given, and unpooled is on) */ if( TT_pooled == 0 && TT_dof_prefix[0] != '\0' ){ dofbrik = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(dofbrik) ; dof_dset = EDIT_empty_copy( new_dset ) ; tross_Make_History( "3dttest" , argc,argv , dof_dset ) ; EDIT_dset_items( dof_dset , ADN_prefix , TT_dof_prefix , ADN_directory_name , TT_session , ADN_type , ISHEAD(dset) ? HEAD_FUNC_TYPE : GEN_FUNC_TYPE, ADN_func_type , FUNC_BUCK_TYPE , ADN_nvals , 1 , ADN_datum_all , MRI_float , ADN_none ) ; if( THD_is_file(dof_dset->dblk->diskptr->header_name) ) ERROR_exit( "-dof_prefix dataset file %s already exists--cannot continue!\a", dof_dset->dblk->diskptr->header_name ) ; EDIT_substitute_brick( dof_dset , 0 , MRI_float , dofbrik ) ; } /* print out memory usage to edify the user */ if( ! TT_be_quiet ){ memuse = sizeof(float) * nxyz * npiece + ( mri_datum_size(output_datum) + sizeof(short) ) * nxyz ; if( dofbrik != NULL ) memuse += sizeof(float) * nxyz ; /* 27 Dec 2002 */ printf("--- allocated %d Megabytes memory for internal use (%d volumes)\n", (int)(memuse/MEGA), (int)npiece) ; } mri_fix_data_pointer( vdif , DSET_BRICK(new_dset,0) ) ; /* attach bricks */ mri_fix_data_pointer( vsp , DSET_BRICK(new_dset,1) ) ; /* to new dataset */ /** only short and float are allowed for output **/ if( output_datum != MRI_short && output_datum != MRI_float ) ERROR_exit("Illegal output data type %d = %s", output_datum , MRI_TYPE_name[output_datum] ) ; num2_inv = 1.0 / num2 ; num2m1_inv = 1.0 / (num2-1) ; if( num1 > 0 ){ num1_inv = 1.0 / num1 ; num1m1_inv = 1.0 / (num1-1) ; } /*----- loop over pieces to process the input datasets with -----*/ /** macro to open a dataset and make it ready for processing **/ #define DOPEN(ds,name) \ do{ int pv ; (ds) = THD_open_dataset((name)) ; /* 16 Sep 1999 */ \ if( !ISVALID_3DIM_DATASET((ds)) ) \ ERROR_exit("Can't open dataset: %s",(name)) ; \ if( (ds)->daxes->nxx!=nx || (ds)->daxes->nyy!=ny || (ds)->daxes->nzz!=nz ) \ ERROR_exit("Axes size mismatch: %s",(name)) ; \ if( !EQUIV_GRIDS((ds),new_dset) ) \ WARNING_message("Grid mismatch: %s",(name)) ; \ if( DSET_NUM_TIMES((ds)) > 1 ) \ ERROR_exit("Can't use time-dependent data: %s",(name)) ; \ if( TT_use_editor ) EDIT_one_dataset( (ds), &TT_edopt ) ; \ else DSET_load((ds)) ; \ pv = DSET_PRINCIPAL_VALUE((ds)) ; \ if( DSET_ARRAY((ds),pv) == NULL ) \ ERROR_exit("Can't access data: %s",(name)) ; \ if( DSET_BRICK_TYPE((ds),pv) == MRI_complex ) \ ERROR_exit("Can't use complex data: %s",(name)) ; \ break ; } while (0) #if 0 /* can do it directly now (without offsets) 13 Dec 2005 [rickr] */ /** macro to return pointer to correct location in brick for current processing **/ #define SUB_POINTER(ds,vv,ind,ptr) \ do{ switch( DSET_BRICK_TYPE((ds),(vv)) ){ \ default: ERROR_exit("Illegal datum! ***"); \ case MRI_short:{ short * fim = (short *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_byte:{ byte * fim = (byte *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; \ case MRI_float:{ float * fim = (float *) DSET_ARRAY((ds),(vv)) ; \ (ptr) = (void *)( fim + (ind) ) ; \ } break ; } break ; } while(0) #endif /** number of pieces to process **/ /* num_piece = (nxyz + piece_size - 1) / nxyz ; */ #if 0 nice(2) ; /** lower priority a little **/ #endif /* possibly open TT_base_dset now, and convert to floats */ if( TT_base_dname ) { DOPEN(base_dset, TT_base_dname) ; base_ary = (float *) malloc( sizeof(float) * nxyz ) ; MTEST(base_ary) ; EDIT_coerce_scale_type(nxyz , DSET_BRICK_FACTOR(base_dset,0) , DSET_BRICK_TYPE(base_dset,0),DSET_ARRAY(base_dset,0), /* input */ MRI_float ,base_ary ) ; /* output */ THD_delete_3dim_dataset( base_dset , False ) ; base_dset = NULL ; } /* only 1 'piece' now 13 Dec 2005 [rickr] */ for( piece=0 ; piece < 1 ; piece++ ){ fim_offset = 0 ; #ifdef TTDEBUG printf("*** start of piece %d: length=%d offset=%d\n",piece,nxyz,fim_offset) ; #else if( ! TT_be_quiet ){ printf("--- starting piece %d/%d (%d voxels) ",piece+1,1,nxyz) ; fflush(stdout) ; } #endif /** process set2 (and set1, if paired) **/ for( ii=0 ; ii < nxyz ; ii++ ) av2[ii] = 0.0 ; for( ii=0 ; ii < nxyz ; ii++ ) sd2[ii] = 0.0 ; for( kk=0 ; kk < num2 ; kk++ ){ /** read in the data **/ DOPEN(dset,TT_set2->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set2->ar[kk]); #endif #if 0 /* fimfac will be compute when the results are ready */ if( piece == 0 && kk == 0 ){ fimfac = DSET_BRICK_FACTOR(dset,iv) ; if( fimfac == 0.0 ) fimfac = 1.0 ; fimfacinv = 1.0 / fimfac ; #ifdef TTDEBUG printf(" ** set fimfac = %g\n",fimfac) ; #endif } #endif /** convert it to floats (in ffim) **/ EDIT_coerce_scale_type(nxyz , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),DSET_ARRAY(dset,iv), /* input */ MRI_float ,ffim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; /** get the paired dataset, if present **/ if( TT_paired ){ DOPEN(dset,TT_set1->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set1->ar[kk]); #endif EDIT_coerce_scale_type( nxyz , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),DSET_ARRAY(dset,iv), /* input */ MRI_float ,gfim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; if( TT_voxel >= 0 ) fprintf(stderr,"-- paired values #%02d: %f, %f\n", kk,ffim[TT_voxel],gfim[TT_voxel]) ; for( ii=0 ; ii < nxyz ; ii++ ) ffim[ii] -= gfim[ii] ; } else if( TT_voxel >= 0 ) fprintf(stderr,"-- set2 value #%02d: %f\n",kk,ffim[TT_voxel]); #ifdef TTDEBUG printf(" * adding into av2 and sd2\n") ; #endif /* accumulate into av2 and sd2 */ for( ii=0 ; ii < nxyz ; ii++ ){ dd = ffim[ii] ; av2[ii] += dd ; sd2[ii] += dd * dd ; } } /* end of loop over set2 datasets */ /** form the mean and stdev of set2 **/ #ifdef TTDEBUG printf(" ** forming mean and sigma of set2\n") ; #endif for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] *= num2_inv ; dd = (sd2[ii] - num2*av2[ii]*av2[ii]) ; sd2[ii] = (dd > 0.0) ? sqrt( num2m1_inv * dd ) : 0.0 ; } if( TT_voxel >= 0 ) fprintf(stderr,"-- s2 mean = %g, sd = %g\n", av2[TT_voxel],sd2[TT_voxel]) ; /** if set1 exists but is not paired with set2, process it now **/ if( ! TT_paired && TT_set1 != NULL ){ for( ii=0 ; ii < nxyz ; ii++ ) av1[ii] = 0.0 ; for( ii=0 ; ii < nxyz ; ii++ ) sd1[ii] = 0.0 ; for( kk=0 ; kk < num1 ; kk++ ){ DOPEN(dset,TT_set1->ar[kk]) ; iv = DSET_PRINCIPAL_VALUE(dset) ; #ifndef TTDEBUG if( ! TT_be_quiet ){ printf(".") ; fflush(stdout) ; } /* progress */ #else printf(" ** opened dataset file %s\n",TT_set1->ar[kk]); #endif EDIT_coerce_scale_type( nxyz , DSET_BRICK_FACTOR(dset,iv) , DSET_BRICK_TYPE(dset,iv),DSET_ARRAY(dset,iv), /* input */ MRI_float ,ffim ) ; /* output */ THD_delete_3dim_dataset( dset , False ) ; dset = NULL ; #ifdef TTDEBUG printf(" * adding into av1 and sd1\n") ; #endif for( ii=0 ; ii < nxyz ; ii++ ){ dd = ffim[ii] ; av1[ii] += dd ; sd1[ii] += dd * dd ; } if( TT_voxel >= 0 ) fprintf(stderr,"-- set1 value #%02d: %g\n",kk,ffim[TT_voxel]) ; } /* end of loop over set1 datasets */ /** form the mean and stdev of set1 **/ #ifdef TTDEBUG printf(" ** forming mean and sigma of set1\n") ; #endif for( ii=0 ; ii < nxyz ; ii++ ){ av1[ii] *= num1_inv ; dd = (sd1[ii] - num1*av1[ii]*av1[ii]) ; sd1[ii] = (dd > 0.0) ? sqrt( num1m1_inv * dd ) : 0.0 ; } if( TT_voxel >= 0 ) fprintf(stderr,"-- s1 mean = %g, sd = %g\n", av1[TT_voxel], sd1[TT_voxel]) ; } /* end of processing set1 by itself */ /***** now form difference and t-statistic *****/ #ifndef TTDEBUG if( ! TT_be_quiet ){ printf("+") ; fflush(stdout) ; } /* progress */ #else printf(" ** computing t-tests next\n") ; #endif #if 0 /* will do at end using EDIT_convert_dtype 13 Dec 2005 [rickr] */ /** macro to assign difference value to correct type of array **/ #define DIFASS switch( output_datum ){ \ case MRI_short: sdar[ii] = (short) (fimfacinv*dd) ; break ; \ case MRI_float: fdar[ii] = (float) dd ; break ; } #define TOP_SS 32700 #define TOP_TT (32700.0/FUNC_TT_SCALE_SHORT) #endif if( TT_paired || TT_use_bval == 1 ){ /** case 1: paired estimate or 1-sample **/ if( TT_paired || TT_n1 == 0 ){ /* the olde waye: 1 sample test */ f2 = 1.0 / sqrt( (double) num2 ) ; for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= (base_ary ? base_ary[ii] : TT_bval) ; /* final mean */ if( sd2[ii] > 0.0 ){ num_tt++ ; tt = av2[ii] / (f2 * sd2[ii]) ; sd2[ii] = tt; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { sd2[ii] = 0.0; } } if( TT_voxel >= 0 ) fprintf(stderr,"-- paired/bval mean = %g, t = %g\n", av2[TT_voxel], sd2[TT_voxel]) ; } else { /* 10 Oct 2007: -sdn1 was used with -base1: 'two' sample test */ f1 = (TT_n1-1.0) * (1.0/TT_n1 + 1.0/num2) / (TT_n1+num2-2.0) ; f2 = (num2 -1.0) * (1.0/TT_n1 + 1.0/num2) / (TT_n1+num2-2.0) ; for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= (base_ary ? base_ary[ii] : TT_bval) ; /* final mean */ q1 = f1 * TT_sd1*TT_sd1 + f2 * sd2[ii]*sd2[ii] ; if( q1 > 0.0 ){ num_tt++ ; tt = av2[ii] / sqrt(q1) ; sd2[ii] = tt ; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { sd2[ii] = 0.0 ; } } } /* end of -sdn1 special case */ #ifdef TTDEBUG printf(" ** paired or bval test: num_tt = %d\n",num_tt) ; #endif } else if( TT_pooled ){ /** case 2: unpaired 2-sample, pooled variance **/ f1 = (num1-1.0) * (1.0/num1 + 1.0/num2) / (num1+num2-2.0) ; f2 = (num2-1.0) * (1.0/num1 + 1.0/num2) / (num1+num2-2.0) ; for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= av1[ii] ; /* final mean */ q1 = f1 * sd1[ii]*sd1[ii] + f2 * sd2[ii]*sd2[ii] ; if( q1 > 0.0 ){ num_tt++ ; tt = av2[ii] / sqrt(q1) ; sd2[ii] = tt ; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; } else { sd2[ii] = 0.0 ; } } if( TT_voxel >= 0 ) fprintf(stderr,"-- unpaired, pooled mean = %g, t = %g\n", av2[TT_voxel], sd2[TT_voxel]) ; #ifdef TTDEBUG printf(" ** pooled test: num_tt = %d\n",num_tt) ; #endif } else { /** case 3: unpaired 2-sample, unpooled variance **/ /** 27 Dec 2002: modified to save DOF into dofar **/ if( dofbrik != NULL ) dofar = dofbrik + fim_offset ; /* 27 Dec 2002 */ for( ii=0 ; ii < nxyz ; ii++ ){ av2[ii] -= av1[ii] ; q1 = num1_inv * sd1[ii]*sd1[ii] ; q2 = num2_inv * sd2[ii]*sd2[ii] ; if( q1>0.0 && q2>0.0 ){ /* have positive variances? */ num_tt++ ; tt = av2[ii] / sqrt(q1+q2) ; sd2[ii] = tt ; /* final t-stat */ tt = fabs(tt) ; if( tt > tt_max ) tt_max = tt ; if( dofar != NULL ) /* 27 Dec 2002 */ dofar[ii] = (q1+q2)*(q1+q2) / (num1m1_inv*q1*q1 + num2m1_inv*q2*q2) ; } else { sd2[ii] = 0.0 ; if( dofar != NULL ) dofar[ii] = 1.0 ; /* 27 Dec 2002 */ } } if( TT_voxel >= 0 ) fprintf(stderr,"-- unpaired, unpooled mean = %g, t = %g\n", av2[TT_voxel], sd2[TT_voxel]) ; #ifdef TTDEBUG printf(" ** unpooled test: num_tt = %d\n",num_tt) ; #endif } #ifndef TTDEBUG if( ! TT_be_quiet ){ printf("\n") ; fflush(stdout) ; } #endif } /* end of loop over pieces of the input */ if( TT_paired ){ printf("--- Number of degrees of freedom = %d (paired test)\n",num2-1) ; dof = num2 - 1 ; } else if( TT_use_bval == 1 ){ if( TT_n1 == 0 ){ printf("--- Number of degrees of freedom = %d (1-sample test)\n",num2-1) ; dof = num2 - 1 ; } else { dof = TT_n1+num2-2 ; printf("--- Number of degrees of freedom = %d (-sdn1 2-sample test)\n",(int)dof) ; } } else { printf("--- Number of degrees of freedom = %d (2-sample test)\n",num1+num2-2) ; dof = num1+num2-2 ; if( ! TT_pooled ) printf(" (For unpooled variance estimate, this is only approximate!)\n") ; } printf("--- Number of t-tests performed = %d out of %d voxels\n",num_tt,nxyz) ; printf("--- Largest |t| value found = %g\n",tt_max) ; kk = sizeof(ptable) / sizeof(float) ; for( ii=0 ; ii < kk ; ii++ ){ tt = student_p2t( ptable[ii] , dof ) ; printf("--- Double sided tail p = %8f at t = %8f\n" , ptable[ii] , tt ) ; } /**----------------------------------------------------------------------**/ /** now convert data to output format 13 Dec 2005 [rickr] **/ /* first set mean */ fimfac = EDIT_convert_dtype(nxyz , MRI_float,av2 , output_datum,vdif , 0.0) ; DSET_BRICK_FACTOR(new_dset, 0) = (fimfac != 0.0) ? 1.0/fimfac : 0.0 ; dd = fimfac; /* save for debug output */ /* if output is of type short, limit t-stat magnitude to 32.7 */ if( output_datum == MRI_short ){ for( ii=0 ; ii < nxyz ; ii++ ){ if ( sd2[ii] > 32.7 ) sd2[ii] = 32.7 ; else if( sd2[ii] < -32.7 ) sd2[ii] = -32.7 ; } } fimfac = EDIT_convert_dtype(nxyz , MRI_float,sd2 , output_datum,vsp , 0.0) ; DSET_BRICK_FACTOR(new_dset, 1) = (fimfac != 0.0) ? 1.0/fimfac : 0.0 ; #ifdef TTDEBUG printf(" ** fimfac for mean, t-stat = %g, %g\n",dd, fimfac) ; #endif /**----------------------------------------------------------------------**/ INFO_message("Writing combined dataset into %s\n", DSET_BRIKNAME(new_dset) ) ; fbuf[0] = dof ; for( ii=1 ; ii < MAX_STAT_AUX ; ii++ ) fbuf[ii] = 0.0 ; (void) EDIT_dset_items( new_dset , ADN_stat_aux , fbuf , ADN_none ) ; #if 0 /* factors already set */ fbuf[0] = (output_datum == MRI_short && fimfac != 1.0 ) ? fimfac : 0.0 ; fbuf[1] = (output_datum == MRI_short ) ? 1.0 / FUNC_TT_SCALE_SHORT : 0.0 ; (void) EDIT_dset_items( new_dset , ADN_brick_fac , fbuf , ADN_none ) ; #endif if( !AFNI_noenv("AFNI_AUTOMATIC_FDR") ) ii = THD_create_all_fdrcurves(new_dset) ; else ii = 0 ; THD_load_statistics( new_dset ) ; THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ; if( ii > 0 ) ININFO_message("created %d FDR curves in header",ii) ; if( dof_dset != NULL ){ /* 27 Dec 2002 */ DSET_write( dof_dset ) ; WROTE_DSET( dof_dset ) ; } exit(0) ; }
int main( int argc , char * argv[] ) { THD_3dim_dataset *dset, *outset=NULL; int iarg=1, npad = 0, extent=0; char *prefix=NULL, *iname=NULL; char *oijkext = NULL; FILE *fout_ijkext=NULL; int extent_ijk=0; int extent_ijk_midslice=0; int imid=0, jmid=0, kmid=0; int extent_xyz_midslice=0; float xmid=0, ymid=0, zmid=0; /*-- startup bureaucracy --*/ mainENTRY("3dAutobox main"); machdep(); AFNI_logger("3dAutobox",argc,argv); PRINT_VERSION("3dAutobox") ; /*-- read command line options --*/ iarg = 1 ; while( iarg < argc && argv[iarg][0] == '-' ){ if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){ help_autobox(); exit(0) ; } if( strcmp(argv[iarg],"-prefix") == 0 ){ prefix = argv[++iarg] ; if( !THD_filename_ok(prefix) ){ fprintf(stderr,"** 3dAutobox: Illegal string after -prefix!\n"); exit(1) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-input") == 0 ){ iname = argv[++iarg] ; // This is a bad check, because it doesn't permit subbrick // selection! Will do check later. /*if( !THD_filename_ok(iname) ){ fprintf(stderr,"** 3dAutobox: Illegal string after -input!\n"); exit(1) ; }*/ iarg++ ; continue ; } if( strcmp(argv[iarg],"-noclust") == 0 ){ MRI_autobbox_clust(0) ; /* turn of clustering and clipping */ THD_autobbox_clip(0) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-npad") == 0 ){ npad = (int)strtod(argv[++iarg],NULL) ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-extent_ijk") == 0 ){ extent_ijk = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-extent_ijk_to_file") == 0 ){ if( ++iarg >= argc ) ERROR_exit("Need argument after '-extent_ijk_to_file'\n") ; oijkext = argv[iarg]; iarg++ ; continue ; } if( strcmp(argv[iarg],"-extent_ijk_midslice") == 0 ){ extent_ijk_midslice = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-extent_xyz_midslice") == 0 ){ extent_xyz_midslice = 1 ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-extent") == 0 ){ extent = 1 ; iarg++ ; continue ; } /*- washappenin, dood? -*/ ERROR_message("** 3dAutobox: %s makes no sense here.\n", argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1); } if( argc < 2){ help_autobox(); exit(0); } /* got input ? */ if( iarg == argc-1 ) iname = argv[iarg] ; else if (iarg != argc) ERROR_exit("** 3dAutobox: %s is nonsense on the line \n" " I know you're John; stop pretending you have an accent!", argv[iarg]) ; if( !iname ) ERROR_exit("** 3dAutobox: Where is my input?") ; /*-- read data --*/ dset = THD_open_dataset(iname); // Check here instead of after -input. if( dset == NULL ) ERROR_exit("Can't open time series dataset '%s'.",iname); CHECK_OPEN_ERROR(dset,iname); if( DSET_BRICK_TYPE(dset,0) != MRI_short && DSET_BRICK_TYPE(dset,0) != MRI_byte && DSET_BRICK_TYPE(dset,0) != MRI_float ) ERROR_exit("** ILLEGAL dataset type: %s :-(", MRI_type_name[DSET_BRICK_TYPE(dset,0)]) ; DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ; { int nx=DSET_NX(dset), ny=DSET_NY(dset), nz=DSET_NZ(dset), nxy=nx*ny ; int xm=-1,xp=-1,ym=-1,yp=-1,zm=-1,zp=-1; THD_autobbox( dset , &xm,&xp , &ym,&yp , &zm,&zp, NULL ) ; xm -= npad; ym -= npad; zm -= npad; /* for LRF */ xp += npad; yp += npad; zp += npad; INFO_message("Auto bbox: x=%d..%d y=%d..%d z=%d..%d\n", xm,xp,ym,yp,zm,zp ) ; // [PT: Oct 18, 2018] New output text file, if desired if( oijkext ) { if( (fout_ijkext = fopen(oijkext, "w")) == NULL ) { fprintf(stderr, "\n\nError opening file %s.\n", oijkext); exit(1); } fprintf( fout_ijkext, "%8d %8d %8d %8d %8d %8d\n", xm, xp, ym, yp, zm, zp ); fclose(fout_ijkext); INFO_message("Wrote ijk extents file: %s", oijkext); } if( extent_ijk ) printf( "%8d %8d %8d %8d %8d %8d\n", xm, xp, ym, yp, zm, zp ); if( extent_ijk_midslice ) { imid = (xm + xp) / 2; // integer division fine, b/c we need ints jmid = (ym + yp) / 2; kmid = (zm + zp) / 2; printf( "%8d %8d %8d\n", imid, jmid, kmid ); } if ( (extent && !prefix) || (extent_xyz_midslice && !prefix) ) prefix = "EXTENT_ONLY"; if( prefix ){ outset = THD_zeropad( dset , -xm, xp-nx+1, -ym, yp-ny+1, -zm, zp-nz+1, prefix , ZPAD_IJK ) ; if( THD_deathcon() && THD_is_file(DSET_HEADNAME(outset)) ) ERROR_exit("3dAutobox: output file %s already exists :-(", DSET_HEADNAME(outset) ) ; if( outset == NULL ) ERROR_exit("3dAutobox: Some error occurred in processing :-(") ; tross_Copy_History( dset , outset ) ; /* 31 Jan 2001 - RWCox */ tross_Make_History( "3dAutobox" , argc,argv , outset ) ; if (!strstr(prefix,"EXTENT_ONLY")) { DSET_write(outset) ; INFO_message("3dAutobox: output dataset = %s", DSET_BRIKNAME(outset)) ; } if (extent) { float RL_AP_IS[6]; THD_dset_extent(outset, '-', RL_AP_IS); printf("Extent auto bbox: R=%f L=%f A=%f P=%f I=%f S=%f\n", RL_AP_IS[0],RL_AP_IS[1], RL_AP_IS[2],RL_AP_IS[3], RL_AP_IS[4],RL_AP_IS[5] ) ; } if( extent_xyz_midslice ) { INFO_message("aaa" ); float RL_AP_IS2[6]; THD_dset_extent(outset, '-', RL_AP_IS2); xmid = (RL_AP_IS2[0] + RL_AP_IS2[1]) / 2.; ymid = (RL_AP_IS2[2] + RL_AP_IS2[3]) / 2.; zmid = (RL_AP_IS2[4] + RL_AP_IS2[5]) / 2.; printf( "%10.5f %10.5f %10.5f\n", xmid, ymid, zmid ); } } } exit(0) ; }
int main( int argc , char * argv[] ) { int ninp , ids , nv , iv,jv,kv , ivout , new_nvals , have_fdr = 0, nfdr = 0 ; THD_3dim_dataset * new_dset=NULL , * dset ; char buf[256] ; double angle; /*----- identify program -----*/ #if 0 printf ("\n\nProgram %s \n", PROGRAM_NAME); printf ("Last revision: %s \n\n", LAST_MOD_DATE); #endif /*** read input options ***/ mainENTRY("3dbucket main"); machdep(); PRINT_VERSION("3dbucket") ; set_obliquity_report(0); /* silence obliquity */ /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ { int new_argc ; char ** new_argv ; addto_args( argc , argv , &new_argc , &new_argv ) ; if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; } } AFNI_logger("3dbucket",argc,argv) ; BUCK_read_opts( argc , argv ) ; /*** create new dataset (empty) ***/ ninp = BUCK_dsar->num ; if( ninp < 1 ){ fprintf(stderr,"*** No input datasets?\n") ; exit(1) ; } new_nvals = 0 ; for( ids=0 ; ids < ninp ; ids++ ) new_nvals += NSUBV(ids) ; if( BUCK_verb ) printf("-verb: output will have %d sub-bricks\n",new_nvals) ; new_dset = EDIT_empty_copy( DSUB(0) ) ; /* 23 May 2005: check for axis consistency */ /* 06 Feb 2008: and see if there are fdrcurves to perpetuate */ if( DSUB(0)->dblk->brick_fdrcurve ) have_fdr = 1 ; for( iv=1 ; iv < ninp ; iv++ ){ if( !EQUIV_DATAXES(new_dset->daxes,DSUB(iv)->daxes) ) fprintf(stderr,"++ WARNING: %s grid mismatch with %s\n", DSET_BRIKNAME(DSUB(0)) , DSET_BRIKNAME(DSUB(iv)) ) ; if( DSUB(iv)->dblk->brick_fdrcurve ) have_fdr = 1 ; angle = dset_obliquity_angle_diff(new_dset, DSUB(iv), -1.0); if (angle > 0.0) { WARNING_message( "dataset %s has an obliquity difference of %f degress with %s\n", new_dset , angle, DSUB(iv) ); } } /* if( ninp == 1 ) */ tross_Copy_History( DSUB(0) , new_dset ) ; tross_Make_History( "3dbucket" , argc,argv , new_dset ) ; EDIT_dset_items( new_dset , ADN_prefix , BUCK_output_prefix , ADN_directory_name, BUCK_session , ADN_type , BUCK_type , ADN_func_type , ISANATTYPE(BUCK_type) ? ANAT_BUCK_TYPE : FUNC_BUCK_TYPE, ADN_ntt , 0 , ADN_nvals , new_nvals , ADN_none ) ; /* can't re-write existing dataset, unless glueing is used */ if (! BUCK_glue){ if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) ){ fprintf(stderr,"*** Fatal error: file %s already exists!\n", DSET_HEADNAME(new_dset) ) ; exit(1) ; } } else { /* if glueing is used, make the 'new' dataset have the same idcode as the old one */ new_dset->idcode = DSUB(0) -> idcode ; /* copy the struct */ } THD_force_malloc_type( new_dset->dblk , DATABLOCK_MEM_MALLOC ) ; /* if there are fdr curves, allocate space 06 Feb 2008 [rickr] */ if( have_fdr ){ new_dset->dblk->brick_fdrcurve = (floatvec **)calloc(sizeof(floatvec *), new_nvals) ; if( !new_dset->dblk->brick_fdrcurve ){ fprintf(stderr,"** failed to alloc %d fdrcurves\n",new_nvals); exit(1); } if( BUCK_verb ) printf("-verb: adding fdrcurve list\n"); new_dset->dblk->brick_mdfcurve = (floatvec **)calloc(sizeof(floatvec *), /* 22 Oct 2008 */ new_nvals) ; } /*** loop over input datasets ***/ if( ninp > 1 ) myXtFree( new_dset->keywords ) ; ivout = 0 ; for( ids=0 ; ids < ninp ; ids++ ){ dset = DSUB(ids) ; nv = NSUBV(ids) ; if( ! BUCK_dry ){ DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ; } /** loop over sub-bricks to output **/ for( iv=0 ; iv < nv ; iv++ ){ jv = SUBV(ids,iv) ; /* which sub-brick to use */ if( ! BUCK_dry ){ EDIT_substitute_brick( new_dset , ivout , DSET_BRICK_TYPE(dset,jv) , DSET_ARRAY(dset,jv) ) ; /*----- preserve label when one exists --- Modified March 2010 ZSS*/ if (DSET_HAS_LABEL(dset, jv) ) sprintf (buf, "%s", DSET_BRICK_LABEL(dset,jv)); else sprintf(buf,"%.12s[%d]",DSET_PREFIX(dset),jv) ; EDIT_dset_items( new_dset , ADN_brick_label_one+ivout, buf , ADN_none ) ; #if 0 sprintf(buf,"%s[%d]",DSET_FILECODE(dset),jv) ; EDIT_dset_items( new_dset, ADN_brick_keywords_replace_one+ivout, buf, ADN_none ) ; #endif EDIT_dset_items( new_dset , ADN_brick_fac_one +ivout, DSET_BRICK_FACTOR(dset,jv), #if 0 ADN_brick_keywords_append_one+ivout, DSET_BRICK_KEYWORDS(dset,jv) , #endif ADN_none ) ; /** possibly write statistical parameters for this sub-brick **/ kv = DSET_BRICK_STATCODE(dset,jv) ; if( FUNC_IS_STAT(kv) ){ /* input sub-brick has stat params */ int npar = FUNC_need_stat_aux[kv] , lv ; float * par = (float *) malloc( sizeof(float) * (npar+2) ) ; float * sax = DSET_BRICK_STATAUX(dset,jv) ; par[0] = kv ; par[1] = npar ; for( lv=0 ; lv < npar ; lv++ ) par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ; EDIT_dset_items(new_dset , ADN_brick_stataux_one+ivout , par , ADN_none ) ; free(par) ; /* 2: if the input dataset has statistical parameters */ } else if( ISFUNC(dset) && /* dset has stat */ FUNC_IS_STAT(dset->func_type) && /* params */ jv == FUNC_ival_thr[dset->func_type] ){ /* thr sub-brick */ int npar , lv ; float * par , * sax ; kv = dset->func_type ; npar = FUNC_need_stat_aux[kv] ; par = (float *) malloc( sizeof(float) * (npar+2) ) ; sax = dset->stat_aux ; par[0] = kv ; par[1] = npar ; for( lv=0 ; lv < npar ; lv++ ) par[lv+2] = (sax != NULL) ? sax[lv] : 0.0 ; EDIT_dset_items(new_dset , ADN_brick_stataux_one+ivout , par , ADN_none ) ; free(par) ; } /** append any fdrcurve **/ if( have_fdr ){ /* fixed iv->jv (ick!), noticed by dglen 16 Mar 2010 [rickr] */ if(dset->dblk->brick_fdrcurve && dset->dblk->brick_fdrcurve[jv]){ COPY_floatvec(new_dset->dblk->brick_fdrcurve[ivout], dset->dblk->brick_fdrcurve[jv]) ; nfdr++; } else new_dset->dblk->brick_fdrcurve[ivout] = NULL ; if(dset->dblk->brick_mdfcurve && dset->dblk->brick_mdfcurve[jv]){ COPY_floatvec(new_dset->dblk->brick_mdfcurve[ivout], dset->dblk->brick_mdfcurve[jv]) ; } else new_dset->dblk->brick_mdfcurve[ivout] = NULL ; } /** print a message? **/ if( BUCK_verb ) printf("-verb: copied %s[%d] into %s[%d]\n" , DSET_FILECODE(dset) , jv , DSET_FILECODE(new_dset) , ivout ) ; } else { printf("-dry: would copy %s[%d] into %s[%d]\n" , DSET_FILECODE(dset) , jv , DSET_FILECODE(new_dset) , ivout ) ; } ivout++ ; } /** loop over all bricks in input dataset and unload them if they aren't going into the output (not required, but is done to economize on memory) **/ if( ! BUCK_dry && nv < DSET_NVALS(dset) ){ for( kv=0 ; kv < DSET_NVALS(dset) ; kv++ ){ /* all input sub-bricks */ for( iv=0 ; iv < nv ; iv++ ){ /* all output sub-bricks */ jv = SUBV(ids,iv) ; if( jv == kv ) break ; /* input matches output */ } if( iv == nv ){ mri_free( DSET_BRICK(dset,kv) ) ; #if 0 if( BUCK_verb ) printf("-verb: unloaded unused %s[%d]\n" , DSET_FILECODE(dset) , kv ) ; #endif } } } } /* end of loop over input datasets */ if( ! BUCK_dry ){ if( BUCK_verb ){ if( have_fdr ) fprintf(stderr,"-verb: added %d of %d fdr curves\n", nfdr, new_nvals); fprintf(stderr,"-verb: loading statistics\n") ; } THD_load_statistics( new_dset ) ; if( BUCK_glue ) putenv("AFNI_DECONFLICT=OVERWRITE") ; if( BUCK_glue && BUCK_ccode >= 0 ) THD_set_write_compression(BUCK_ccode) ; /* 16 Mar 2010 */ THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ; if( BUCK_verb ) fprintf(stderr,"-verb: wrote output: %s\n",DSET_BRIKNAME(new_dset)) ; } exit(0) ; }
int main( int argc , char * argv[] ) { THD_dfvec3 *xx , *yy , dv ; int nvec=0 , ii,jj, iarg ; THD_dvecmat rt , rtinv ; THD_dmat33 pp,ppt , rr ; THD_dfvec3 tt ; THD_3dim_dataset *mset=NULL , *dset=NULL ; double *ww=NULL ; int nww=0 ; int keeptags=1 , wtval=0 , verb=0 , dummy=0 ; char * prefix = "tagalign" , *mfile=NULL ; float *fvol , cbot,ctop , dsum ; int nval , nvox , clipit , ival, RMETH=MRI_CUBIC; float matar[12] ; int use_3dWarp=1 , matrix_type=ROTATION ; mainENTRY("3dTagalign main"); /*--- help? ---*/ /*- scan args -*/ iarg = 1 ; RMETH=MRI_CUBIC; while( iarg < argc && argv[iarg][0] == '-' ){ /*-----*/ if( strcmp(argv[iarg],"-h") == 0 || strcmp(argv[iarg],"-help") == 0){ /* 22 Apr 2003 */ usage_3dTagalign(strlen(argv[iarg]) > 3 ? 2:1); exit(0); } /*-----*/ if( strcmp(argv[iarg],"-NN") == 0 ){ RMETH = MRI_NN ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-linear") == 0 ){ RMETH = MRI_LINEAR ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-cubic") == 0 ){ RMETH = MRI_CUBIC ; iarg++ ; continue ; } if( strcmp(argv[iarg],"-quintic") == 0 ){ RMETH = MRI_QUINTIC ; iarg++ ; continue ; } /*-----*/ if( strcmp(argv[iarg],"-rotate") == 0 ){ /* 22 Apr 2003 */ matrix_type = ROTATION ; use_3dWarp = 1 ; iarg++ ; continue ; } /*-----*/ if( strcmp(argv[iarg],"-affine") == 0 ){ /* 21 Apr 2003 */ matrix_type = AFFINE ; use_3dWarp = 1 ; iarg++ ; continue ; } /*-----*/ if( strcmp(argv[iarg],"-rotscl") == 0 ){ /* 22 Apr 2003 */ matrix_type = ROTSCL ; use_3dWarp = 1 ; iarg++ ; continue ; } #if 0 /*-----*/ if( strcmp(argv[iarg],"-3dWarp") == 0 ){ /* 21 Apr 2003 */ use_3dWarp = 1 ; iarg++ ; continue ; } #endif /*-----*/ if( strcmp(argv[iarg],"-master") == 0 ){ if( mset != NULL ) ERREX("Can only have one -master option") ; if( ++iarg >= argc ) ERREX("Need an argument after -master") ; mset = THD_open_dataset( argv[iarg] ) ; if( mset == NULL ) ERREX("Can't open -master dataset") ; if( mset->tagset == NULL ) ERREX("No tags in -master dataset") ; if( TAGLIST_COUNT(mset->tagset) < 3 ) ERREX("Not enough tags in -master dataset") ; for( nvec=ii=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ ) if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ) nvec++ ; if( nvec < 3 ) ERREX("Not enough tags set in -master dataset") ; if( nvec < TAGLIST_COUNT(mset->tagset) ) fprintf(stderr,"++ WARNING: not all tags are set in -master dataset\n") ; if( verb ) fprintf(stderr,"++ Found %d tags in -master dataset\n",nvec) ; iarg++ ; continue ; } #if 0 /*-----*/ if( strcmp(argv[iarg],"-wtval") == 0 ){ if( ww != NULL ) ERREX("Can't have -wtval after -wt1D") ; wtval++ ; iarg++ ; continue ; } /*-----*/ if( strcmp(argv[iarg],"-wt1D") == 0 ){ MRI_IMAGE * wtim ; float * wtar ; if( wtval ) ERREX("Can't have -wt1D after -wtval") ; if( ww != NULL ) ERREX("Can't have two -wt1D options!") ; if( ++iarg >= argc ) ERREX("Need an argument after -wt1D") ; wtim = mri_read_1D( argv[iarg] ) ; if( wtim == NULL ) ERREX("Can't read -wtim file") ; if( wtim->ny > 1 ) ERREX("-wtim file has more than one columm") ; wtar = MRI_FLOAT_PTR(wtim) ; ww = (double *) malloc(sizeof(double)*wtim->nx) ; nww = wtim->nx ; for( ii=0 ; ii < nww ; ii++ ){ ww[ii] = (double) wtar[ii] ; if( ww[ii] < 0.0 ) ERREX("Negative value found in -wt1D file") ; } mri_free(wtim) ; iarg++ ; continue ; } #endif /*-----*/ if( strcmp(argv[iarg],"-nokeeptags") == 0 ){ keeptags = 0 ; iarg++ ; continue ; } /*-----*/ if( strncmp(argv[iarg],"-verb",5) == 0 ){ verb++ ; iarg++ ; continue ; } /*-----*/ if( strcmp(argv[iarg],"-dummy") == 0 ){ dummy++ ; iarg++ ; continue ; } /*-----*/ if( strcmp(argv[iarg],"-prefix") == 0 ){ if( ++iarg >= argc ) ERREX("Need an argument after -prefix") ; prefix = argv[iarg] ; if( !THD_filename_ok(prefix) ) ERREX("-prefix string is illegal") ; iarg++ ; continue ; } /*-----*/ if( strcmp(argv[iarg],"-matvec") == 0 ){ if( ++iarg >= argc ) ERREX("Need an argument after -matvec") ; mfile = argv[iarg] ; if( !THD_filename_ok(mfile) ) ERREX("-matvec string is illegal") ; iarg++ ; continue ; } /*-----*/ fprintf(stderr,"** Unknown option: %s\n",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1) ; } /* end of scanning command line for options */ if( argc < 2 ){ ERROR_message("Too few options"); usage_3dTagalign(0); exit(1) ; } if( mset == NULL ) ERREX("No -master option found on command line") ; #if 0 if( ww != NULL && nww < nvec ) ERREX("Not enough weights found in -wt1D file") ; /*-- if -wtval, setup weights from master tag values --*/ if( wtval ){ ww = (double *) malloc(sizeof(double)*nvec) ; nww = nvec ; for( ii=jj=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ ){ if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ){ ww[jj] = (double) TAG_VAL(TAGLIST_SUBTAG(mset->tagset,ii)) ; if( ww[jj] < 0.0 ) ERREX("Negative value found in -master tag values") ; jj++ ; } } } #endif /*-- read input dataset (to match to master dataset) --*/ if( iarg >= argc ) ERREX("No input dataset?") ; dset = THD_open_dataset( argv[iarg] ) ; if( dset == NULL ) ERREX("Can't open input dataset") ; if( dset->tagset == NULL ) ERREX("No tags in input dataset") ; if( TAGLIST_COUNT(dset->tagset) != TAGLIST_COUNT(mset->tagset) ) ERREX("Tag counts don't match in -master and input") ; /* check if set tags match exactly */ for( ii=0 ; ii < TAGLIST_COUNT(mset->tagset) ; ii++ ){ if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) != TAG_SET(TAGLIST_SUBTAG(dset->tagset,ii)) ) ERREX("Set tags don't match in -master and input") ; } /*-- load vector lists: xx=master, yy=input --*/ xx = (THD_dfvec3 *) malloc( sizeof(THD_dfvec3) * nvec ) ; yy = (THD_dfvec3 *) malloc( sizeof(THD_dfvec3) * nvec ) ; dsum = 0.0 ; for( ii=jj=0 ; ii < nvec ; ii++ ){ if( TAG_SET(TAGLIST_SUBTAG(mset->tagset,ii)) ){ LOAD_DFVEC3( xx[jj] , /* N.B.: */ TAG_X( TAGLIST_SUBTAG(mset->tagset,ii) ) , /* these are */ TAG_Y( TAGLIST_SUBTAG(mset->tagset,ii) ) , /* in Dicom */ TAG_Z( TAGLIST_SUBTAG(mset->tagset,ii) ) ) ; /* order now */ LOAD_DFVEC3( yy[jj] , TAG_X( TAGLIST_SUBTAG(dset->tagset,ii) ) , TAG_Y( TAGLIST_SUBTAG(dset->tagset,ii) ) , TAG_Z( TAGLIST_SUBTAG(dset->tagset,ii) ) ) ; dv = SUB_DFVEC3( xx[jj] , yy[jj] ) ; dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1] + dv.xyz[2]*dv.xyz[2] ; jj++ ; } } dsum = sqrt(dsum/nvec) ; fprintf(stderr,"++ RMS distance between tags before = %.2f mm\n" , dsum ) ; /*-- compute best transformation from mset to dset coords --*/ switch( matrix_type ){ default: case ROTATION: rt = DLSQ_rot_trans( nvec , yy , xx , ww ) ; /* in thd_rot3d.c */ break ; case AFFINE: rt = DLSQ_affine ( nvec , yy , xx ) ; /* 21 Apr 2003 */ break ; case ROTSCL: rt = DLSQ_rotscl ( nvec , yy , xx , (DSET_NZ(dset)==1) ? 2 : 3 ) ; break ; } rtinv = INV_DVECMAT(rt) ; /*-- check for floating point legality --*/ nval = 0 ; for( ii=0 ; ii < 3 ; ii++ ){ dsum = rt.vv.xyz[ii] ; nval += thd_floatscan(1,&dsum) ; for( jj=0 ; jj < 3 ; jj++ ){ dsum = rt.mm.mat[ii][jj] ; nval += thd_floatscan(1,&dsum) ; } } if( nval > 0 ){ fprintf(stderr,"** Floating point errors during calculation\n" "** of transform matrix and translation vector\n" ) ; exit(1) ; } /*-- check for rotation matrix legality --*/ dsum = DMAT_DET(rt.mm) ; if( dsum == 0.0 || (matrix_type == ROTATION && fabs(dsum-1.0) > 0.01) ){ fprintf(stderr,"** Invalid transform matrix computed: tags dependent?\n" "** computed [matrix] and [vector] follow:\n" ) ; for( ii=0 ; ii < 3 ; ii++ ) fprintf(stderr," [ %10.5f %10.5f %10.5f ] [ %10.5f ] \n", rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] ); exit(1) ; } /*-- print summary --*/ if( verb ){ fprintf(stderr,"++ Matrix & Vector [Dicom: x=R-L; y=A-P; z=I-S]\n") ; for( ii=0 ; ii < 3 ; ii++ ) fprintf(stderr," %10.5f %10.5f %10.5f %10.5f\n", rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] ); } if( matrix_type == ROTATION || matrix_type == ROTSCL ){ double theta, costheta , dist , fac=1.0 ; if( matrix_type == ROTSCL ){ fac = DMAT_DET(rt.mm); fac = fabs(fac); if( DSET_NZ(dset) == 1 ) fac = sqrt(fac) ; else fac = cbrt(fac) ; } costheta = 0.5 * sqrt(1.0 + DMAT_TRACE(rt.mm)/fac ) ; theta = 2.0 * acos(costheta) * 180/3.14159265 ; dist = SIZE_DFVEC3(rt.vv) ; fprintf(stderr,"++ Total rotation=%.2f degrees; translation=%.2f mm; scaling=%.2f\n", theta,dist,fac) ; } if( mfile ){ FILE * mp ; if( THD_is_file(mfile) ) fprintf(stderr,"++ Warning: -matvec will overwrite file %s\n",mfile) ; mp = fopen(mfile,"w") ; if( mp == NULL ){ fprintf(stderr,"** Can't write to -matvec %s\n",mfile) ; } else { for( ii=0 ; ii < 3 ; ii++ ) fprintf(mp," %10.5f %10.5f %10.5f %10.5f\n", rt.mm.mat[ii][0],rt.mm.mat[ii][1],rt.mm.mat[ii][2],rt.vv.xyz[ii] ); fclose(mp) ; if( verb ) fprintf(stderr,"++ Wrote matrix+vector to %s\n",mfile) ; } } if( dummy ){ fprintf(stderr,"++ This was a -dummy run: no output dataset\n") ; exit(0) ; } /*-- 21 Apr 2003: transformation can be done the old way (a la 3drotate), or the new way (a la 3dWarp). --*/ #if 0 if( !use_3dWarp ){ /**** the old way ****/ /*-- now must scramble the rotation matrix and translation vector from Dicom coordinate order to dataset brick order --*/ pp = DBLE_mat_to_dicomm( dset ) ; ppt = TRANSPOSE_DMAT(pp) ; rr = DMAT_MUL(ppt,rt.mm) ; rr = DMAT_MUL(rr,pp) ; tt = DMATVEC(ppt,rt.vv) ; /*-- now create the output dataset by screwing with the input dataset (this code is adapted from 3drotate.c) --*/ DSET_mallocize(dset) ; DSET_load( dset ) ; CHECK_LOAD_ERROR(dset) ; dset->idcode = MCW_new_idcode() ; dset->dblk->diskptr->storage_mode = STORAGE_BY_BRICK ; /* 14 Jan 2004 */ EDIT_dset_items( dset , ADN_prefix , prefix , ADN_label1 , prefix , ADN_none ) ; if( !THD_ok_overwrite() && (THD_deathcon() && THD_is_file(dset->dblk->diskptr->header_name) )){ fprintf(stderr, "** Output file %s already exists -- cannot continue!\n", dset->dblk->diskptr->header_name ) ; exit(1) ; } tross_Make_History( "3dTagalign" , argc,argv , dset ) ; /*-- if desired, keep old tagset --*/ if( keeptags ){ THD_dfvec3 rv ; dsum = 0.0 ; for( jj=ii=0 ; ii < TAGLIST_COUNT(dset->tagset) ; ii++ ){ if( TAG_SET(TAGLIST_SUBTAG(dset->tagset,ii)) ){ rv = DMATVEC( rt.mm , yy[jj] ) ; /* operating on */ rv = ADD_DFVEC3( rt.vv , rv ) ; /* Dicom order */ dv = SUB_DFVEC3( xx[jj] , rv ) ; dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1] + dv.xyz[2]*dv.xyz[2] ; UNLOAD_DFVEC3( rv , TAG_X( TAGLIST_SUBTAG(dset->tagset,ii) ) , TAG_Y( TAGLIST_SUBTAG(dset->tagset,ii) ) , TAG_Z( TAGLIST_SUBTAG(dset->tagset,ii) ) ) ; jj++ ; } } dsum = sqrt(dsum/nvec) ; fprintf(stderr,"++ RMS distance between tags after = %.2f mm\n" , dsum ) ; } else { myXtFree(dset->tagset) ; /* send it to the dustbin */ } /*-- rotate sub-bricks --*/ if( verb ) fprintf(stderr,"++ computing output BRIK") ; nvox = DSET_NVOX(dset) ; nval = DSET_NVALS(dset) ; fvol = (float *) malloc( sizeof(float) * nvox ) ; THD_rota_method( MRI_HEPTIC ) ; clipit = 1 ; for( ival=0 ; ival < nval ; ival++ ){ /*- get sub-brick out of dataset -*/ EDIT_coerce_type( nvox , DSET_BRICK_TYPE(dset,ival),DSET_ARRAY(dset,ival) , MRI_float,fvol ) ; if( clipit ){ register int ii ; register float bb,tt ; bb = tt = fvol[0] ; for( ii=1 ; ii < nvox ; ii++ ){ if( fvol[ii] < bb ) bb = fvol[ii] ; else if( fvol[ii] > tt ) tt = fvol[ii] ; } cbot = bb ; ctop = tt ; } if( verb && nval < 5 ) fprintf(stderr,".") ; /*- rotate it -*/ THD_rota_vol_matvec( DSET_NX(dset) , DSET_NY(dset) , DSET_NZ(dset) , fabs(DSET_DX(dset)) , fabs(DSET_DY(dset)) , fabs(DSET_DZ(dset)) , fvol , rr , tt ) ; if( verb ) fprintf(stderr,".") ; if( clipit ){ register int ii ; register float bb,tt ; bb = cbot ; tt = ctop ; for( ii=0 ; ii < nvox ; ii++ ){ if( fvol[ii] < bb ) fvol[ii] = bb ; else if( fvol[ii] > tt ) fvol[ii] = tt ; } } if( verb && nval < 5 ) fprintf(stderr,".") ; /*- put it back into dataset -*/ EDIT_coerce_type( nvox, MRI_float,fvol , DSET_BRICK_TYPE(dset,ival),DSET_ARRAY(dset,ival) ); } /* end of loop over sub-brick index */ if( verb ) fprintf(stderr,":") ; /* save matrix+vector into dataset, too */ UNLOAD_DMAT(rt.mm,matar[0],matar[1],matar[2], matar[4],matar[5],matar[6], matar[8],matar[9],matar[10] ) ; UNLOAD_DFVEC3(rt.vv,matar[3],matar[7],matar[11]) ; THD_set_atr( dset->dblk, "TAGALIGN_MATVEC", ATR_FLOAT_TYPE, 12, matar ) ; /* write dataset to disk */ dset->dblk->master_nvals = 0 ; /* in case this was a mastered dataset */ DSET_write(dset) ; if( verb ) fprintf(stderr,"\n") ; } else #endif { /**** the new way: use 3dWarp type transformation ****/ THD_3dim_dataset *oset ; THD_vecmat tran ; #if 0 DFVEC3_TO_FVEC3( rt.vv , tran.vv ) ; DMAT_TO_MAT ( rt.mm , tran.mm ) ; #else DFVEC3_TO_FVEC3( rtinv.vv , tran.vv ) ; DMAT_TO_MAT ( rtinv.mm , tran.mm ) ; #endif mri_warp3D_method( RMETH ) ; oset = THD_warp3D_affine( dset, tran, mset, prefix, 0, WARP3D_NEWDSET ) ; if( oset == NULL ){ fprintf(stderr,"** ERROR: THD_warp3D() fails!\n"); exit(1); } tross_Copy_History( dset , oset ) ; tross_Make_History( "3dTagalign" , argc,argv , oset ) ; UNLOAD_DMAT(rt.mm,matar[0],matar[1],matar[2], matar[4],matar[5],matar[6], matar[8],matar[9],matar[10] ) ; UNLOAD_DFVEC3(rt.vv,matar[3],matar[7],matar[11]) ; THD_set_atr( oset->dblk, "TAGALIGN_MATVEC", ATR_FLOAT_TYPE, 12, matar ) ; /*-- if desired, keep old tagset --*/ if( keeptags ){ THD_dfvec3 rv ; oset->tagset = myXtNew(THD_usertaglist) ; *(oset->tagset) = *(dset->tagset) ; dsum = 0.0 ; for( jj=ii=0 ; ii < TAGLIST_COUNT(oset->tagset) ; ii++ ){ if( TAG_SET(TAGLIST_SUBTAG(oset->tagset,ii)) ){ rv = DMATVEC( rt.mm , yy[jj] ) ; rv = ADD_DFVEC3( rt.vv , rv ) ; dv = SUB_DFVEC3( xx[jj] , rv ) ; dsum += dv.xyz[0]*dv.xyz[0] + dv.xyz[1]*dv.xyz[1] + dv.xyz[2]*dv.xyz[2] ; UNLOAD_DFVEC3( rv , TAG_X( TAGLIST_SUBTAG(oset->tagset,ii) ) , TAG_Y( TAGLIST_SUBTAG(oset->tagset,ii) ) , TAG_Z( TAGLIST_SUBTAG(oset->tagset,ii) ) ) ; jj++ ; } } dsum = sqrt(dsum/nvec) ; fprintf(stderr,"++ RMS distance between tags after = %.2f mm\n" , dsum ) ; } DSET_write(oset) ; } /* end of 3dWarp-like work */ exit(0) ; }
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() ) ; }
int main( int argc , char * argv[] ) { int iv,nvals , nvec , ii,jj,kk , nvox ; THD_3dim_dataset * new_dset=NULL ; double * choleski ; float ** refvec , * fv , * fc , * fit ; MRI_IMAGE * flim ; /*** read input options ***/ if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) DT_Syntax() ; /*-- 20 Apr 2001: addto the arglist, if user wants to [RWCox] --*/ mainENTRY("3dDetrend main"); machdep() ; PRINT_VERSION("3dDetrend"); AFNI_logger("3dDetrend",argc,argv) ; { int new_argc ; char ** new_argv ; addto_args( argc , argv , &new_argc , &new_argv ) ; if( new_argv != NULL ){ argc = new_argc ; argv = new_argv ; } } DT_read_opts( argc , argv ) ; /*** create new dataset (empty) ***/ new_dset = EDIT_empty_copy( DT_dset ) ; /* make a copy of its header */ /* modify its header */ tross_Copy_History( DT_dset , new_dset ) ; tross_Make_History( "3dDetrend" , argc,argv , new_dset ) ; EDIT_dset_items( new_dset , ADN_prefix , DT_output_prefix , ADN_directory_name, DT_session , ADN_none ) ; /* can't re-write existing dataset */ if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) ) ERROR_exit("File %s already exists!\n",DSET_HEADNAME(new_dset) ) ; /* read input in, and attach its bricks to the output dataset */ /* (not good in a plugin, but OK in a standalone program!) */ if( DT_verb ) INFO_message("Loading input dataset bricks\n") ; DSET_mallocize( new_dset ) ; DSET_mallocize( DT_dset ) ; DSET_load( DT_dset ) ; CHECK_LOAD_ERROR(DT_dset) ; nvals = DSET_NVALS(new_dset) ; for( iv=0 ; iv < nvals ; iv++ ) EDIT_substitute_brick( new_dset , iv , DSET_BRICK_TYPE(DT_dset,iv) , DSET_ARRAY(DT_dset,iv) ) ; if( DT_norm && DSET_BRICK_TYPE(new_dset,0) != MRI_float ){ INFO_message("Turning -normalize option off (input not in float format)"); DT_norm = 0 ; } /* load reference (detrending) vectors; setup to do least squares fitting of each voxel */ nvec = 0 ; for( ii=0 ; ii < IMARR_COUNT(DT_imar) ; ii++ ) /* number of detrending vectors */ nvec += IMARR_SUBIMAGE(DT_imar,ii)->ny ; refvec = (float **) malloc( sizeof(float *)*nvec ) ; for( kk=ii=0 ; ii < IMARR_COUNT(DT_imar) ; ii++ ){ fv = MRI_FLOAT_PTR( IMARR_SUBIMAGE(DT_imar,ii) ) ; for( jj=0 ; jj < IMARR_SUBIMAGE(DT_imar,ii)->ny ; jj++ ) /* compute ptr */ refvec[kk++] = fv + ( jj * IMARR_SUBIMAGE(DT_imar,ii)->nx ) ; /* to vectors */ } fit = (float *) malloc( sizeof(float) * nvals ) ; /* will get fit to voxel data */ /*--- do the all-voxels-together case ---*/ if( !DT_byslice ){ choleski = startup_lsqfit( nvals , NULL , nvec , refvec ) ; if( choleski == NULL ) ERROR_exit("Choleski factorization fails: linearly dependent vectors!\n") ; /* loop over voxels, fitting and detrending (or replacing) */ nvox = DSET_NVOX(new_dset) ; if( DT_verb ) INFO_message("Computing voxel fits\n") ; for( kk=0 ; kk < nvox ; kk++ ){ flim = THD_extract_series( kk , new_dset , 0 ) ; /* data */ fv = MRI_FLOAT_PTR(flim) ; fc = delayed_lsqfit( nvals, fv, nvec, refvec, choleski ) ; /* coef */ for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = 0.0 ; for( jj=0 ; jj < nvec ; jj++ ) for( ii=0 ; ii < nvals ; ii++ ) fit[ii] += fc[jj] * refvec[jj][ii] ; /* fit */ if( !DT_replace ) /* remove */ for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = fv[ii] - fit[ii] ; if( DT_norm ) THD_normalize( nvals , fit ) ; /* 23 Nov 1999 */ THD_insert_series( kk, new_dset, nvals, MRI_float, fit, 0 ) ; free(fc) ; mri_free(flim) ; } free(choleski) ; /*- end of all-voxels-together case -*/ } #ifdef ALLOW_BYSLICE else { /*- start of slice case [08 Dec 1999] -*/ int ksl , nslice , tt , nx,ny , nxy , kxy ; MRI_IMAGE * vim ; /* make separate space for the slice-wise detrending vectors */ for( kk=ii=0 ; ii < DT_nvector ; ii++ ){ for( jj=0 ; jj < IMARR_SUBIMAGE(DT_imar,ii)->ny ; jj++ ) /* replace ptrs */ refvec[kk++] = (float *) malloc( sizeof(float) * nvals ) ; /* to vectors */ } nslice = DSET_NZ(new_dset) ; nxy = DSET_NX(new_dset) * DSET_NY(new_dset) ; /* loop over slices */ for( ksl=0 ; ksl < nslice ; ksl++ ){ if( DT_verb ) INFO_message("Computing voxel fits for slice %d\n",ksl) ; /* extract slice vectors from input interlaced vectors */ for( kk=ii=0 ; ii < DT_nvector ; ii++ ){ /* loop over vectors */ vim = IMARR_SUBIMAGE(DT_imar,ii) ; /* ii-th vector image */ nx = vim->nx ; ny = vim->ny ; /* dimensions */ for( jj=0 ; jj < ny ; jj++ ){ /* loop over columns */ fv = MRI_FLOAT_PTR(vim) + (jj*nx) ; /* ptr to column */ for( tt=0 ; tt < nvals ; tt++ ) /* loop over time */ refvec[kk][tt] = fv[ksl+tt*nslice] ; /* data point */ } } /* initialize fitting for this slice */ choleski = startup_lsqfit( nvals , NULL , nvec , refvec ) ; if( choleski == NULL ) ERROR_exit("Choleski fails: linearly dependent vectors at slice %d\n",ksl) ; /* loop over voxels in this slice */ for( kxy=0 ; kxy < nxy ; kxy++ ){ kk = kxy + ksl*nxy ; /* 3D index */ flim = THD_extract_series( kk , new_dset , 0 ) ; /* data */ fv = MRI_FLOAT_PTR(flim) ; fc = delayed_lsqfit( nvals, fv, nvec, refvec, choleski ) ; /* coef */ for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = 0.0 ; for( jj=0 ; jj < nvec ; jj++ ) for( ii=0 ; ii < nvals ; ii++ ) fit[ii] += fc[jj] * refvec[jj][ii] ; /* fit */ if( !DT_replace ) /* remove */ for( ii=0 ; ii < nvals ; ii++ ) fit[ii] = fv[ii] - fit[ii] ; if( DT_norm ) THD_normalize( nvals , fit ) ; /* 23 Nov 1999 */ THD_insert_series( kk, new_dset, nvals, MRI_float, fit, 0 ) ; free(fc) ; mri_free(flim) ; } free(choleski) ; } /* end of loop over slices */ } /*- end of -byslice case -*/ #endif /*-- done done done done --*/ DSET_write(new_dset) ; if( DT_verb ) WROTE_DSET(new_dset) ; exit(0) ; }
int main( int argc , char * argv[] ) { int iarg ; THD_3dim_dataset *inset , *outset ; int add_I=0 , add_S=0 , add_A=0 , add_P=0 , add_L=0 , add_R=0 ; int RLsiz=0, APsiz=0, ISsiz=0 ; /* 23 Mar 2004 */ char * prefix="zeropad" ; int add_z=0 ; /* 07 Feb 2001 */ int mm_flag=0 ; /* 13 Feb 2001 */ int flag ; THD_3dim_dataset *mset=NULL ; /* 14 May 2002 */ /*-- help? --*/ mainENTRY("3dZeropad main"); machdep(); AFNI_logger("3dZeropad",argc,argv); PRINT_VERSION("3dZeropad") ; /*-- read command line options --*/ if( argc == 1){ usage_3dZeropad(1); exit(0); } /* Bob's help shortcut */ iarg = 1 ; while( iarg < argc && argv[iarg][0] == '-' ){ if( strcmp(argv[iarg],"-help") == 0 || strcmp(argv[iarg],"-h") == 0){ usage_3dZeropad(strlen(argv[iarg])>3 ? 2:1); exit(0); } /*- -I, -S, etc. -*/ if( strlen(argv[iarg]) == 2 ){ switch( argv[iarg][1] ){ case 'I': add_I = (int) strtod(argv[++iarg],NULL) ; break ; case 'S': add_S = (int) strtod(argv[++iarg],NULL) ; break ; case 'A': add_A = (int) strtod(argv[++iarg],NULL) ; break ; case 'P': add_P = (int) strtod(argv[++iarg],NULL) ; break ; case 'L': add_L = (int) strtod(argv[++iarg],NULL) ; break ; case 'R': add_R = (int) strtod(argv[++iarg],NULL) ; break ; /* 07 Feb 2001: slice-direction is special */ case 'z': case 'Z': add_z = (int) strtod(argv[++iarg],NULL) ; break ; default: fprintf(stderr,"** 3dZeropad: Illegal option: %s\n",argv[iarg]) ; exit(1) ; } if( mset != NULL ){ fprintf(stderr,"** 3dZeropad: Can't use %s with -master!\n",argv[iarg-1]) ; exit(1) ; } iarg++ ; continue ; /* skip to next argument */ } /*- -RL, -AP, -IS [23 Mar 2004] -*/ if( strcmp(argv[iarg],"-RL") == 0 || strcmp(argv[iarg],"-LR") == 0 ){ if( add_R || add_L || mset != NULL ){ fprintf(stderr,"** 3dZeropad: Can't use -RL with -R, -L, or -master!\n"); exit(1) ; } RLsiz = (int) strtod(argv[++iarg],NULL) ; if( RLsiz < 1 ){ fprintf(stderr,"** 3dZeropad: value after -RL is illegal!\n") ; exit(1) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-AP") == 0 || strcmp(argv[iarg],"-PA") == 0 ){ if( add_A || add_P || mset != NULL ){ fprintf(stderr,"** 3dZeropad: Can't use -AP with -A, -P, or -master!\n"); exit(1) ; } APsiz = (int) strtod(argv[++iarg],NULL) ; if( APsiz < 1 ){ fprintf(stderr,"** 3dZeropad: value after -AP is illegal!\n") ; exit(1) ; } iarg++ ; continue ; } if( strcmp(argv[iarg],"-IS") == 0 || strcmp(argv[iarg],"-SI") == 0 ){ if( add_S || add_I || mset != NULL ){ fprintf(stderr,"** 3dZeropad: Can't use -IS with -I, -S, or -master!\n"); exit(1) ; } ISsiz = (int) strtod(argv[++iarg],NULL) ; if( ISsiz < 1 ){ fprintf(stderr,"** 3dZeropad: value after -IS is illegal!\n") ; exit(1) ; } iarg++ ; continue ; } /*- -mm -*/ if( strcmp(argv[iarg],"-mm") == 0 ){ if( mset != NULL ){ fprintf(stderr,"** 3dZeropad: Can't use %s with -master!\n",argv[iarg]) ; exit(1) ; } mm_flag = 1 ; iarg++ ; continue ; } /*- -prefix -*/ if( strcmp(argv[iarg],"-prefix") == 0 ){ prefix = argv[++iarg] ; if( !THD_filename_ok(prefix) ){ fprintf(stderr,"** 3dZeropad: Illegal string after -prefix!\n"); exit(1) ; } iarg++ ; continue ; } /*-- -master [14 May 2002] --*/ if( strcmp(argv[iarg],"-master") == 0 ){ if( add_I || add_S || add_A || mm_flag || add_P || add_R || add_L || add_z || RLsiz || APsiz || ISsiz ){ fprintf(stderr,"** 3dZeropad: Can't use -master with -I,-S,-A,-P,-R,-L, or -mm!\n"); exit(1) ; } if( mset != NULL ){ fprintf(stderr,"** 3dZeropad: Can't use -master twice!\n"); exit(1); } mset = THD_open_dataset( argv[++iarg] ) ; if( !ISVALID_DSET(mset) ){ fprintf(stderr,"** 3dZeropad: Can't open -master %s\n",argv[iarg]); exit(1); } THD_make_cardinal(mset); /* deoblique 21 Oct, 2011 [rickr] */ iarg++ ; continue ; } /*- what the hell? -*/ fprintf(stderr,"** 3dZeropad: Illegal option: %s\n",argv[iarg]) ; suggest_best_prog_option(argv[0], argv[iarg]); exit(1) ; } if (iarg < 2) { ERROR_message("Too few options, try %s -help for details\n",argv[0]); exit(1); } /*- check to see if the user asked for something, anything -*/ if( mset == NULL ){ if( add_I==0 && add_S==0 && add_P==0 && add_A==0 && add_L==0 && add_R==0 && add_z==0 && RLsiz==0 && APsiz==0 && ISsiz==0 ){ fprintf(stderr,"++ 3dZeropad: All inputs are zero? Making a copy!\n") ; } } /* check for conflicts [23 Mar 2004] */ if( RLsiz > 0 && (add_R || add_L || add_z) ){ fprintf(stderr,"** 3dZeropad: Can't use -R or -L or -z with -RL!\n"); exit(1); } if( APsiz > 0 && (add_A || add_P || add_z) ){ fprintf(stderr,"** 3dZeropad: Can't use -A or -P or -z with -AP!\n"); exit(1); } if( ISsiz > 0 && (add_I || add_S || add_z) ){ fprintf(stderr,"** 3dZeropad: Can't use -I or -S or -z with -IS!\n"); exit(1); } /*-- read the input dataset --*/ if( iarg >= argc ){ fprintf(stderr,"** 3dZeropad: No input dataset on command line!\n"); exit(1); } #if 0 if( strncmp(argv[iarg],"3dcalc(",7) == 0 ){ fprintf(stderr,"** 3dZeropad: Can't use '3dcalc()' input datasets here!\n"); exit(1); } #endif inset = THD_open_dataset( argv[iarg] ) ; if( inset == NULL ){ fprintf(stderr,"** 3dZeropad: Can't open dataset %s\n",argv[iarg]); exit(1); } THD_make_cardinal(inset); /* deoblique 21 Oct, 2011 [rickr] */ #if 0 if( DSET_IS_MASTERED(inset) ){ fprintf(stderr,"** 3dZeropad: Can't use partial datasets!\n"); exit(1); } #endif /*-- 14 May 2002: use master dataset now? --*/ if( mset != NULL ){ THD_dataxes *max=mset->daxes, *iax=inset->daxes ; int nerr=0 ; float mxbot,mybot,mzbot , mxtop,mytop,mztop , mdx,mdy,mdz ; float ixbot,iybot,izbot , ixtop,iytop,iztop , idx,idy,idz ; int mnx,mny,mnz , inx,iny,inz ; int add_xb,add_xt , add_yb,add_yt , add_zb,add_zt ; /* check if datasets are oriented the same */ if( max->xxorient != iax->xxorient || max->yyorient != iax->yyorient || max->zzorient != iax->zzorient ){ fprintf(stderr, "** 3dZeropad: Master (%s) and Input (%s) dataset not oriented the same!\n", DSET_PREFIX(mset), DSET_PREFIX(inset)); nerr++ ; } /* check if datasets have same voxel dimensions */ mdx = max->xxdel ; mdy = max->yydel ; mdz = max->zzdel ; idx = iax->xxdel ; idy = iax->yydel ; idz = iax->zzdel ; mnx = max->nxx ; mny = max->nyy ; mnz = max->nzz ; inx = iax->nxx ; iny = iax->nyy ; inz = iax->nzz ; if( fabs(mdx-idx) > 0.01*fabs(mdx) || fabs(mdy-idy) > 0.01*fabs(mdy) || fabs(mdz-idz) > 0.01*fabs(mdz) ){ fprintf(stderr,"** 3dZeropad: Master and Input datasets don't have same voxel size!\n"); nerr++ ; } if( nerr ) exit(1) ; /* calculate coords at top and bottom of each dataset */ mxbot = max->xxorg ; mxtop = mxbot + mnx*mdx ; mybot = max->yyorg ; mytop = mybot + mny*mdy ; mzbot = max->zzorg ; mztop = mzbot + mnz*mdz ; ixbot = iax->xxorg ; ixtop = ixbot + inx*idx ; iybot = iax->yyorg ; iytop = iybot + iny*idy ; izbot = iax->zzorg ; iztop = izbot + inz*idz ; /* calculate amount to add/trim at each face */ add_xb = (int) rint((ixbot-mxbot)/idx) ; add_xt = (int) rint((mxtop-ixtop)/idx) ; add_yb = (int) rint((iybot-mybot)/idy) ; add_yt = (int) rint((mytop-iytop)/idy) ; add_zb = (int) rint((izbot-mzbot)/idz) ; add_zt = (int) rint((mztop-iztop)/idz) ; /* map trims from x,y,z to RL,AP,IS coords */ switch( iax->xxorient ){ case ORI_R2L_TYPE: add_R = add_xb ; add_L = add_xt ; break ; case ORI_L2R_TYPE: add_L = add_xb ; add_R = add_xt ; break ; case ORI_I2S_TYPE: add_I = add_xb ; add_S = add_xt ; break ; case ORI_S2I_TYPE: add_S = add_xb ; add_I = add_xt ; break ; case ORI_A2P_TYPE: add_A = add_xb ; add_P = add_xt ; break ; case ORI_P2A_TYPE: add_P = add_xb ; add_A = add_xt ; break ; } switch( iax->yyorient ){ case ORI_R2L_TYPE: add_R = add_yb ; add_L = add_yt ; break ; case ORI_L2R_TYPE: add_L = add_yb ; add_R = add_yt ; break ; case ORI_I2S_TYPE: add_I = add_yb ; add_S = add_yt ; break ; case ORI_S2I_TYPE: add_S = add_yb ; add_I = add_yt ; break ; case ORI_A2P_TYPE: add_A = add_yb ; add_P = add_yt ; break ; case ORI_P2A_TYPE: add_P = add_yb ; add_A = add_yt ; break ; } switch( iax->zzorient ){ case ORI_R2L_TYPE: add_R = add_zb ; add_L = add_zt ; break ; case ORI_L2R_TYPE: add_L = add_zb ; add_R = add_zt ; break ; case ORI_I2S_TYPE: add_I = add_zb ; add_S = add_zt ; break ; case ORI_S2I_TYPE: add_S = add_zb ; add_I = add_zt ; break ; case ORI_A2P_TYPE: add_A = add_zb ; add_P = add_zt ; break ; case ORI_P2A_TYPE: add_P = add_zb ; add_A = add_zt ; break ; } fprintf(stderr,"++ 3dZeropad -master => -I %d -S %d -A %d -P %d -R %d -L %d\n", add_I,add_S,add_A,add_P,add_R,add_L ) ; DSET_delete(mset) ; } /*-- 07 Feb 2001: if -z was used, fix that now --*/ if( add_z != 0 ){ switch( inset->daxes->zzorient ){ case ORI_R2L_TYPE: case ORI_L2R_TYPE: if( add_R != 0 && add_R != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -R\n"); if( add_L != 0 && add_L != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -L\n"); add_R = add_L = add_z ; break ; case ORI_P2A_TYPE: case ORI_A2P_TYPE: if( add_P != 0 && add_P != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -P\n"); if( add_A != 0 && add_A != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -A\n"); add_P = add_A = add_z ; break ; case ORI_I2S_TYPE: case ORI_S2I_TYPE: if( add_I != 0 && add_I != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -I\n"); if( add_I != 0 && add_S != add_z ) fprintf(stderr,"++ 3dZeropad: -z overrides -S\n"); add_I = add_S = add_z ; break ; } } /*-- 23 Mar 2004: expand/contract if ordered --*/ if( RLsiz > 0 ){ int nold=0 ; if( inset->daxes->xxorient == ORI_R2L_TYPE || inset->daxes->xxorient == ORI_L2R_TYPE ) nold = inset->daxes->nxx ; else if( inset->daxes->yyorient == ORI_R2L_TYPE || inset->daxes->yyorient == ORI_L2R_TYPE ) nold = inset->daxes->nyy ; else if( inset->daxes->zzorient == ORI_R2L_TYPE || inset->daxes->zzorient == ORI_L2R_TYPE ) nold = inset->daxes->nzz ; if( nold > 0 ){ add_R = (RLsiz-nold) / 2 ; add_L = RLsiz-(nold+add_R) ; } } if( APsiz > 0 ){ int nold=0 ; if( inset->daxes->xxorient == ORI_A2P_TYPE || inset->daxes->xxorient == ORI_P2A_TYPE ) nold = inset->daxes->nxx ; else if( inset->daxes->yyorient == ORI_A2P_TYPE || inset->daxes->yyorient == ORI_P2A_TYPE ) nold = inset->daxes->nyy ; else if( inset->daxes->zzorient == ORI_A2P_TYPE || inset->daxes->zzorient == ORI_P2A_TYPE ) nold = inset->daxes->nzz ; if( nold > 0 ){ add_A = (APsiz-nold) / 2 ; add_P = APsiz-(nold+add_A) ; } } if( ISsiz > 0 ){ int nold=0 ; if( inset->daxes->xxorient == ORI_I2S_TYPE || inset->daxes->xxorient == ORI_S2I_TYPE ) nold = inset->daxes->nxx ; else if( inset->daxes->yyorient == ORI_I2S_TYPE || inset->daxes->yyorient == ORI_S2I_TYPE ) nold = inset->daxes->nyy ; else if( inset->daxes->zzorient == ORI_I2S_TYPE || inset->daxes->zzorient == ORI_S2I_TYPE ) nold = inset->daxes->nzz ; if( nold > 0 ){ add_I = (ISsiz-nold) / 2 ; add_S = ISsiz-(nold+add_I) ; } } /*-- 04 Oct 2000: all the real work is now in thd_zeropad.c --*/ flag = ZPAD_PURGE ; if( mm_flag ) flag |= ZPAD_MM ; outset = THD_zeropad( inset , add_I, add_S, add_A, add_P, add_L, add_R, prefix , flag ) ; if( THD_deathcon() && THD_is_file(DSET_HEADNAME(outset)) ){ fprintf(stderr, "** 3dZeropad: output file %s already exists - FATAL ERROR!\n", DSET_HEADNAME(outset) ) ; exit(1) ; } if( outset == NULL ){ fprintf(stderr,"** 3dZeropad: Some error occurred in processing!\n") ; exit(1) ; } tross_Copy_History( inset , outset ) ; /* 31 Jan 2001 - RWCox */ tross_Make_History( "3dZeropad" , argc,argv , outset ) ; if (DSET_write(outset) != False) { fprintf(stderr,"++ output dataset: %s\n",DSET_BRIKNAME(outset)) ; exit(0) ; } else { fprintf(stderr, "** 3dZeropad: Failed to write output!\n" ) ; exit(1) ; } }
int main( int argc , char * argv[] ) { int ninp , ids , nv , iv,jv,kv , ivout , new_nvals ; THD_3dim_dataset * new_dset=NULL , * dset ; char buf[256] ; /*----- Identify software -----*/ #if 0 printf ("\n\n"); printf ("Program: %s \n", PROGRAM_NAME); printf ("Author: %s \n", PROGRAM_AUTHOR); printf ("Initial Release: %s \n", PROGRAM_INITIAL); printf ("Latest Revision: %s \n", PROGRAM_LATEST); printf ("\n"); #endif /*** read input options ***/ if( argc < 2 || strncmp(argv[1],"-help",4) == 0 ) B2F_Syntax() ; mainENTRY("3dbuc2fim main"); machdep(); AFNI_logger(PROGRAM_NAME,argc,argv); PRINT_VERSION("3dbuc2fim") ; AUTHOR(PROGRAM_AUTHOR); B2F_read_opts( argc , argv ) ; /*** create new dataset (empty) ***/ ninp = B2F_dsar->num ; if( ninp < 1 ){ fprintf(stderr,"*** No input datasets?\n") ; exit(1) ; } new_nvals = 0 ; for( ids=0 ; ids < ninp ; ids++ ) new_nvals += NSUBV(ids) ; /*----- Check for acceptable number of sub-bricks -----*/ if (new_nvals < 1) { fprintf(stderr,"*** Less than 1 sub-brick specified\n") ; exit(1) ; } if (new_nvals > 2) { fprintf(stderr,"*** More than 2 sub-bricks specified\n") ; exit(1) ; } if( B2F_verb ) printf("-verb: output will have %d sub-bricks\n",new_nvals) ; new_dset = EDIT_empty_copy( DSUB(0) ) ; if( ninp == 1 ) tross_Copy_History( DSUB(0) , new_dset ) ; tross_Make_History( "3dbuc2fim" , argc,argv , new_dset ) ; /*----- Set default value for function type. This will be changed later, if the second sub-brick has a statistic type. -----*/ if (new_nvals == 1) B2F_func_type = FUNC_FIM_TYPE; else B2F_func_type = FUNC_THR_TYPE; EDIT_dset_items (new_dset , ADN_prefix , B2F_output_prefix , ADN_directory_name, B2F_session , ADN_type , HEAD_FUNC_TYPE, ADN_func_type , B2F_func_type, ADN_ntt , 0 , ADN_nvals , new_nvals , ADN_none ) ; if( THD_deathcon() && THD_is_file(DSET_HEADNAME(new_dset)) ){ fprintf(stderr,"*** Fatal error: file %s already exists!\n", DSET_HEADNAME(new_dset) ) ; exit(1) ; } THD_force_malloc_type( new_dset->dblk , DATABLOCK_MEM_MALLOC ) ; /*** loop over input datasets ***/ if( ninp > 1 ) myXtFree( new_dset->keywords ) ; ivout = 0 ; for( ids=0 ; ids < ninp ; ids++ ){ dset = DSUB(ids) ; nv = NSUBV(ids) ; DSET_load(dset) ; CHECK_LOAD_ERROR(dset) ; /** loop over sub-bricks to output **/ for( iv=0 ; iv < nv ; iv++ ){ jv = SUBV(ids,iv) ; /* which sub-brick to use */ EDIT_substitute_brick( new_dset , ivout , DSET_BRICK_TYPE(dset,jv) , DSET_ARRAY(dset,jv) ) ; /*----- If this sub-brick is from a bucket dataset, preserve the label for this sub-brick -----*/ if (dset->func_type == FUNC_BUCK_TYPE) sprintf (buf, "%s", DSET_BRICK_LABEL(dset,jv)); else sprintf(buf,"%.12s[%d]",DSET_PREFIX(dset),jv) ; EDIT_dset_items( new_dset , ADN_brick_label_one+ivout, buf , ADN_none ) ; #if 0 sprintf(buf,"%s[%d]",DSET_FILECODE(dset),jv) ; EDIT_dset_items( new_dset, ADN_brick_keywords_replace_one+ivout, buf, ADN_none ) ; #endif EDIT_dset_items( new_dset , ADN_brick_fac_one +ivout, DSET_BRICK_FACTOR(dset,jv), #if 0 ADN_brick_keywords_append_one+ivout, DSET_BRICK_KEYWORDS(dset,jv) , #endif ADN_none ) ; /** possibly write statistical parameters for this sub-brick **/ kv = DSET_BRICK_STATCODE(dset,jv) ; if( FUNC_IS_STAT(kv) ){ /* input sub-brick has stat params */ int npar = MAX_STAT_AUX , lv ; float * par = (float *) malloc( sizeof(float) * (npar) ) ; float * sax = DSET_BRICK_STATAUX(dset,jv) ; for( lv=0 ; lv < npar ; lv++ ) par[lv] = (sax != NULL && lv < FUNC_need_stat_aux[kv]) ? sax[lv] : 0.0; if (ivout == 1) { EDIT_dset_items(new_dset , ADN_func_type , kv, ADN_stat_aux, par , ADN_none ) ; } free(par) ; /* 2: if the input dataset has statistical parameters */ } else if( ISFUNC(dset) && /* dset has stat */ FUNC_IS_STAT(dset->func_type) && /* params */ jv == FUNC_ival_thr[dset->func_type] ){ /* thr sub-brick */ int npar , lv ; float * par , * sax ; kv = dset->func_type ; npar = MAX_STAT_AUX ; par = (float *) malloc( sizeof(float) * (npar+2) ) ; sax = dset->stat_aux ; for( lv=0 ; lv < npar ; lv++ ) par[lv] = (sax != NULL) ? sax[lv] : 0.0 ; if (ivout == 1) { for( lv=0 ; lv < npar+2 ; lv++ ) printf ("par[%d] = %f \n", lv, par[lv]); EDIT_dset_items(new_dset , ADN_func_type , kv, ADN_stat_aux, par , ADN_none ) ; } free(par) ; } /** print a message? **/ if( B2F_verb ) printf("-verb: copied %s[%d] into %s[%d]\n" , DSET_FILECODE(dset) , jv , DSET_FILECODE(new_dset) , ivout ) ; ivout++ ; } /** loop over all bricks in input dataset and unload them if they aren't going into the output (not required, but is done to economize on memory) **/ if( nv < DSET_NVALS(dset) ){ for( kv=0 ; kv < DSET_NVALS(dset) ; kv++ ){ /* all input sub-bricks */ for( iv=0 ; iv < nv ; iv++ ){ /* all output sub-bricks */ jv = SUBV(ids,iv) ; if( jv == kv ) break ; /* input matches output */ } if( iv == nv ){ mri_free( DSET_BRICK(dset,kv) ) ; #if 0 if( B2F_verb ) printf("-verb: unloaded unused %s[%d]\n" , DSET_FILECODE(dset) , kv ) ; #endif } } } } /* end of loop over input datasets */ if( B2F_verb ) fprintf(stderr,"-verb: loading statistics\n") ; THD_load_statistics( new_dset ) ; THD_write_3dim_dataset( NULL,NULL , new_dset , True ) ; if( B2F_verb ) fprintf(stderr,"-verb: wrote output: %s\n",DSET_BRIKNAME(new_dset)) ; exit(0) ; }