void process_subbrick (THD_3dim_dataset * dset, int ibrick)
{
const float EPSILON = 1.0e-10;
float factor; /* factor is new scale factor for this sub-brick */
void * vfim = NULL; /* sub-brick data pointer */
float * ffim = NULL; /* sub-brick data in floating point format */
char brick_label[THD_MAX_NAME]; /* sub-brick label */
ENTRY("process_subbrick") ;
if (!FDR_quiet) printf ("Processing sub-brick #%d \n", ibrick);
/*----- Allocate memory for float data -----*/
ffim = (float *) malloc (sizeof(float) * FDR_nxyz); MTEST (ffim);
/*----- Convert sub-brick to float stats -----*/
SUB_POINTER (dset, ibrick, 0, vfim);
EDIT_coerce_scale_type (FDR_nxyz, DSET_BRICK_FACTOR(dset,ibrick),
DSET_BRICK_TYPE(dset,ibrick), vfim, /* input */
MRI_float , ffim); /* output */
/*----- Calculate FDR z-scores for all voxels within this volume -----*/
process_volume (ffim, DSET_BRICK_STATCODE(dset,ibrick),
DSET_BRICK_STATAUX (dset,ibrick));
/*----- Replace old sub-brick with new z-scores -----*/
if( !FDR_float || DSET_BRICK_TYPE(dset,ibrick)==MRI_float ){
SUB_POINTER (dset, ibrick, 0, vfim);
factor = EDIT_coerce_autoscale_new (FDR_nxyz, MRI_float, ffim,
DSET_BRICK_TYPE(dset,ibrick), vfim);
if (factor < EPSILON) factor = 0.0;
else factor = 1.0 / factor;
if( DSET_BRICK_TYPE(dset,ibrick) == MRI_short )
EDIT_misfit_report( DSET_FILECODE(dset) , ibrick ,
FDR_nxyz , factor , vfim , ffim ) ;
} else { /*** if -float was given ***/
EDIT_substitute_brick( dset , ibrick , MRI_float , ffim ) ;
ffim = NULL ; factor = 0.0f ;
}
/*----- edit the sub-brick -----*/
if( FDR_qval ) strcpy (brick_label, "FDRq:");
else strcpy (brick_label, "FDRz:");
strcat (brick_label, DSET_BRICK_LABEL(dset, ibrick));
EDIT_BRICK_LABEL (dset, ibrick, brick_label);
EDIT_BRICK_FACTOR (dset, ibrick, factor);
if( !FDR_qval ) EDIT_BRICK_TO_FIZT (dset,ibrick);
else EDIT_BRICK_TO_NOSTAT(dset,ibrick);
/*----- Deallocate memory -----*/
if (ffim != NULL) { free (ffim); ffim = NULL; }
EXRETURN ;
}
void initialize_program
(
int argc, /* number of input arguments */
char ** argv /* array of input arguments */
)
{
float parameters [DIMENSION]; /* parameters for PDF estimation */
Boolean ok = TRUE; /* flag for successful PDF estimation */
int nx, ny, nz, nxy, nxyz, ixyz; /* voxel counters */
int n; /* histogram bin index */
short * sfim = NULL; /* pointer to anat data */
short * rfim = NULL; /* truncated data */
int icount;
int lower_cutoff = 25;
/*----- Get operator inputs -----*/
get_options (argc, argv);
/*----- Initialize local variables -----*/
if (anat == NULL) estPDF_error ("Unable to read anat dataset");
nx = DSET_NX(anat); ny = DSET_NY(anat); nz = DSET_NZ(anat);
nxy = nx*ny; nxyz = nxy*nz;
sfim = (short *) DSET_BRICK_ARRAY(anat,0) ;
if (sfim == NULL) estPDF_error ("Unable to read anat dataset");
rfim = (short *) malloc (sizeof(short) * nxyz); MTEST (rfim);
/*----- Just use voxels whose intensity is above the lower cutoff -----*/
icount = 0;
for (ixyz = 0; ixyz < nxyz; ixyz++)
if (sfim[ixyz] > lower_cutoff)
{
rfim[icount] = sfim[ixyz];
icount++;
}
printf ("%d voxels above lower cutoff = %d \n", icount, lower_cutoff);
/*----- Get PDF estimate and set voxel intensity limits -----*/
estpdf_short (icount, rfim, parameters);
min_val_float = parameters[4] - 2.0*parameters[5];
max_val_float = parameters[7] + 2.0*parameters[8];
if (! quiet)
{
printf ("\n");
printf ("Control inputs: \n");
printf ("anat filename = %s \n", anat_filename);
printf ("min value = %f \n", min_val_float);
printf ("max value = %f \n", max_val_float);
}
}
float * read_time_series
(
char * ts_filename, /* time series file name (plus column index) */
int * ts_length /* output value for time series length */
)
{
char message[THD_MAX_NAME]; /* error message */
char * cpt; /* pointer to column suffix */
char filename[THD_MAX_NAME]; /* time series file name w/o column index */
char subv[THD_MAX_NAME]; /* string containing column index */
MRI_IMAGE * im, * flim; /* pointers to image structures
-- used to read 1D ASCII */
float * far; /* pointer to MRI_IMAGE floating point data */
int nx; /* number of time points in time series */
int ny; /* number of columns in time series file */
int iy; /* time series file column index */
int ipt; /* time point index */
float * ts_data = NULL; /* input time series data */
/*----- First, check for empty filename -----*/
if (ts_filename == NULL)
FDR_error ("Missing input time series file name");
/*----- Read the time series file -----*/
flim = mri_read_1D(ts_filename) ;
if (flim == NULL)
{
sprintf (message, "Unable to read time series file: %s", ts_filename);
FDR_error (message);
}
far = MRI_FLOAT_PTR(flim);
nx = flim->nx;
ny = flim->ny; iy = 0 ;
if( ny > 1 ){
fprintf(stderr,"WARNING: time series %s has more than 1 column\n",ts_filename);
}
/*----- Save the time series data -----*/
*ts_length = nx;
ts_data = (float *) malloc (sizeof(float) * nx);
MTEST (ts_data);
for (ipt = 0; ipt < nx; ipt++)
ts_data[ipt] = far[ipt + iy*nx];
mri_free (flim); flim = NULL;
return (ts_data);
}
void get_options
(
int argc, /* number of input arguments */
char ** argv /* array of input arguments */
)
{
int nopt = 1; /* input option argument counter */
int ival, index; /* integer input */
float fval; /* float input */
char message[MAX_STRING_LENGTH]; /* error message */
/*----- does user request help menu? -----*/
if (argc < 2 || strncmp(argv[1], "-help", 5) == 0) display_help_menu();
/*----- main loop over input options -----*/
while (nopt < argc )
{
/*----- -anat filename -----*/
if (strncmp(argv[nopt], "-anat", 5) == 0)
{
nopt++;
if (nopt >= argc) estPDF_error ("need argument after -anat ");
anat_filename = malloc (sizeof(char) * MAX_STRING_LENGTH);
MTEST (anat_filename);
strcpy (anat_filename, argv[nopt]);
anat = THD_open_one_dataset (anat_filename);
if (!ISVALID_3DIM_DATASET (anat))
{
sprintf (message, "Can't open dataset: %s\n", anat_filename);
estPDF_error (message);
}
DSET_load(anat); CHECK_LOAD_ERROR(anat);
nopt++;
continue;
}
/*----- unknown command -----*/
sprintf(message,"Unrecognized command line option: %s\n", argv[nopt]);
estPDF_error (message);
}
}
voxel * create_voxel ()
{
voxel * voxel_ptr = NULL;
voxel_ptr = (voxel *) malloc (sizeof(voxel));
MTEST (voxel_ptr);
voxel_ptr->ixyz = 0;
voxel_ptr->pvalue = 0.0;
voxel_ptr->next_voxel = NULL;
return (voxel_ptr);
}
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) ;
}
void process_volume (float * ffim, int statcode, float * stataux)
{
int ixyz; /* voxel index */
int icount; /* count of sorted p-values */
float fval; /* voxel input statistical value */
float pval; /* voxel input stat. p-value */
float qval; /* voxel FDR q-value */
float zval; /* voxel FDR z-score */
float qval_min; /* smallest previous q-value */
voxel * head_voxel = NULL; /* linked list of voxels */
voxel * voxel_ptr = NULL; /* pointer to current voxel */
int ibin; /* p-value bin */
int * iarray = NULL; /* output array of voxel indices */
float * parray = NULL; /* output array of voxel p-values */
float * qarray = NULL; /* output array of voxel FDR q-values */
float * zarray = NULL; /* output array of voxel FDR z-scores */
float numer ;
/*------------ 18 Jan 2008: use the 'new' method? ------------*/
if( FDR_old < 1 ){
MRI_IMAGE *qim ; int flags=0 ;
qim = mri_new_vol_empty( FDR_nxyz,1,1 , MRI_float ) ;
mri_fix_data_pointer( ffim , qim ) ;
if( FDR_mask != NULL ){
float zz = (FUNC_IS_STAT(statcode)) ? 0.0f : 1.0f ;
for( ixyz=0 ; ixyz < FDR_nxyz ; ixyz++ )
if( !FDR_mask[ixyz] ) ffim[ixyz] = zz ;
}
if( FDR_curve ){ /* hidden option: produce t-z curve */
floatvec *fv = mri_fdr_curve( qim , statcode , stataux ) ;
if( fv == NULL ) ERROR_message("mri_fdr_curve fails!") ;
else {
printf("# FDR thresh-z curve\n") ;
for( ixyz=0 ; ixyz < fv->nar ; ixyz++ )
printf("%g %g\n", fv->x0+ixyz*fv->dx , fv->ar[ixyz] ) ;
}
exit(0) ;
} else { /* normal operation: convert to z(q) or q */
if( FDR_pmask == 0 ) flags |= 1 ; /* compatibility mode */
if( FDR_cn > 1.0f ) flags |= 2 ; /* dependency flag */
if( FDR_qval ) flags |= 4 ; /* qval flag */
(void)mri_fdrize( qim , statcode,stataux , flags ) ;
}
mri_clear_data_pointer(qim); mri_free(qim);
return ;
}
/*---------------- back to the 'old' method ------------------*/
/*----- Allocate memory for screen output arrays -----*/
if (FDR_list)
{
iarray = (int *) malloc (sizeof(int) * FDR_nthr); MTEST(iarray);
parray = (float *) malloc (sizeof(float) * FDR_nthr); MTEST(parray);
qarray = (float *) malloc (sizeof(float) * FDR_nthr); MTEST(qarray);
zarray = (float *) malloc (sizeof(float) * FDR_nthr); MTEST(zarray);
}
/*----- Loop over all voxels; sort p-values -----*/
icount = FDR_nthr;
for (ixyz = 0; ixyz < FDR_nxyz; ixyz++)
{
/*----- First, check if voxel is inside the mask -----*/
if( FDR_mask != NULL && !FDR_mask[ixyz] ) continue;
/*----- Convert stats to p-values -----*/
fval = fabs(ffim[ixyz]);
if (statcode <= 0)
pval = fval;
else
pval = THD_stat_to_pval (fval, statcode, stataux);
if (pval >= 1.0)
{
/*----- Count but don't sort voxels with p-value = 1 -----*/
icount--;
if (FDR_list)
{
iarray[icount] = ixyz;
parray[icount] = 1.0;
qarray[icount] = 1.0;
zarray[icount] = 0.0;
}
}
else
{
/*----- Place voxel in p-value bin -----*/
ibin = (int) (pval * (FDR_MAX_LL));
if (ibin < 0) ibin = 0;
if (ibin > FDR_MAX_LL-1) ibin = FDR_MAX_LL-1;
head_voxel = new_voxel (ixyz, pval, FDR_head_voxel[ibin]);
FDR_head_voxel[ibin] = head_voxel;
}
}
/*----- Calculate FDR q-values -----*/
qval_min = 1.0;
ibin = FDR_MAX_LL-1;
numer = (FDR_pmask) ? icount : FDR_nthr ; /* 18 Jan 2008 */
while (ibin >= 0)
{
voxel_ptr = FDR_head_voxel[ibin];
while (voxel_ptr != NULL)
{
/*----- Convert sorted p-values to FDR q-values -----*/
pval = voxel_ptr->pvalue;
qval = FDR_cn * (pval*numer) / icount;
if (qval > qval_min)
qval = qval_min;
else
qval_min = qval;
/*----- Convert FDR q-value to FDR z-score -----*/
if( !FDR_qval ){
if (qval < 1.0e-20) zval = 10.0;
else zval = normal_p2t(qval);
} else { zval = qval ; }
icount--;
/*----- Save calculated values -----*/
if (FDR_list)
{
iarray[icount] = voxel_ptr->ixyz;
parray[icount] = pval;
qarray[icount] = qval;
zarray[icount] = zval;
}
voxel_ptr->pvalue = zval;
voxel_ptr = voxel_ptr->next_voxel;
}
ibin--;
}
/*----- Write out the calculated values -----*/
if (FDR_list)
{
printf ("%12s %12s %12s %12s \n",
"Index", "p-value", "q-value", "z-score");
for (icount = 0; icount < FDR_nthr; icount++)
{
if (FDR_input1D_filename != NULL)
ixyz = iarray[icount] + 1;
else
ixyz = iarray[icount];
printf ("%12d %12.6f %12.6f %12.6f \n",
ixyz, parray[icount], qarray[icount], zarray[icount]);
}
/*----- Deallocate memory for output arrays -----*/
free (iarray); free (parray); free (qarray); free (zarray);
}
/*----- Place FDR z-scores into float array -----*/
save_all_voxels (ffim);
/*----- Deallocate linked-list memory -----*/
delete_all_voxels();
}
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 ;
}
void read_options ( int argc , char * argv[] )
{
int nopt = 1 ; /* count of input arguments */
char message[80]; /* error message */
if( AFNI_yesenv("AFNI_FLOATIZE") ) FDR_float = 1 ;
/*----- main loop over input options -----*/
while( nopt < argc )
{
/*----- -input fname -----*/
if (strcmp(argv[nopt], "-input") == 0)
{
nopt++;
if (nopt >= argc) FDR_error ("need argument after -input ");
FDR_input_filename = (char *) malloc (sizeof(char)*THD_MAX_NAME);
MTEST (FDR_input_filename);
strcpy (FDR_input_filename, argv[nopt]);
nopt++;
continue;
}
/*----- -input1D dname -----*/
if (strcmp(argv[nopt], "-input1D") == 0)
{
nopt++;
if (nopt >= argc) FDR_error ("need argument after -input1D ");
FDR_input1D_filename = (char *) malloc (sizeof(char)*THD_MAX_NAME);
MTEST (FDR_input1D_filename);
strcpy (FDR_input1D_filename, argv[nopt]);
nopt++;
continue;
}
/*----- -mask_file mname -----*/
if (strcmp(argv[nopt], "-mask_file") == 0 || strcmp(argv[nopt],"-mask") == 0)
{
nopt++;
if (nopt >= argc) FDR_error ("need argument after -mask_file ");
FDR_mask_filename = (char *) malloc (sizeof(char)*THD_MAX_NAME);
MTEST (FDR_mask_filename);
strcpy (FDR_mask_filename, argv[nopt]);
nopt++;
continue;
}
/*----- -mask_thr m -----*/
if( strcmp(argv[nopt],"-mask_thr") == 0 ){
float fval;
nopt++ ;
if( nopt >= argc ){
FDR_error (" need 1 argument after -mask_thr");
}
sscanf (argv[nopt], "%f", &fval);
if (fval < 0.0){
FDR_error (" Require mask_thr >= 0.0 ");
}
FDR_mask_thr = fval;
nopt++; continue;
}
/*---- -force & -old & -pmask & -float etc. [18 Jan 2008] -----*/
if( strcmp(argv[nopt],"-force") == 0 ){
FDR_force = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-qval") == 0 ){
FDR_qval = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-old") == 0 ){
FDR_old = 1 ; FDR_pmask = 0 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-new") == 0 ){
FDR_old = -1 ; FDR_pmask = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-pmask") == 0 ){
FDR_pmask = 1 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-nopmask") == 0 ){
FDR_pmask = 0 ; nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-float") == 0 ){
FDR_float = 1 ; nopt++ ; continue ;
}
#if 0
if( strcmp(argv[nopt],"-curve") == 0 ){ /* hidden option */
FDR_curve = 1 ; nopt++ ; continue ;
}
#endif
/*----- -cind -----*/
if( strcmp(argv[nopt],"-cind") == 0 ){
FDR_cn = 1.0;
nopt++ ; continue ;
}
/*----- -cdep -----*/
if( strcmp(argv[nopt],"-cdep") == 0 ){
FDR_cn = -1.0;
nopt++ ; continue ;
}
/*----- -quiet -----*/
if( strcmp(argv[nopt],"-quiet") == 0 ){
FDR_quiet = 1;
nopt++ ; continue ;
}
if( strcmp(argv[nopt],"-verb") == 0 ){
FDR_quiet = 0 ; nopt++ ; continue ;
}
/*----- -list -----*/
if( strcmp(argv[nopt],"-list") == 0 ){
FDR_list = 1;
nopt++ ; continue ;
}
/*----- -prefix prefix -----*/
if( strcmp(argv[nopt],"-prefix") == 0 ||
strcmp(argv[nopt],"-output") == 0 ){
nopt++ ;
if( nopt >= argc ){
FDR_error (" need argument after -prefix!");
}
FDR_output_prefix = (char *) malloc (sizeof(char) * THD_MAX_PREFIX);
MCW_strncpy( FDR_output_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
continue ;
}
/*----- unknown command -----*/
sprintf(message,"Unrecognized command line option: %s\n", argv[nopt]);
FDR_error (message);
} /*----- end of loop over command line arguments -----*/
if( FDR_old == 0 && FDR_pmask ){ /* the new way is on by default */
fprintf(stderr,"\n"
"++ The 'new' method of FDR calculation is on by default; in particular:\n"
" + * Voxel p-values of exactly 1 (e.g., from t=0 or F=0 or correlation=0)\n"
" + are ignored by default; in the old mode of operation, they were\n"
" + included in the count which goes into the FDR algorithm. The old\n"
" + process tends to increase the q-values and so decrease the z-scores.\n"
" + * If you wish to do the FDR conversion using the old mode, use '-old'\n"
" + on the command line. For more information, use '3dFDR -help'.\n"
" + * If you don't want to see this message again, use the '-new' option.\n"
"++ RWCox - 18 Jan 2008\n\n"
) ;
}
if( FDR_old < 1 && FDR_pmask == 0 && FDR_mask != NULL ){ /* 29 Jan 2008 */
fprintf(stderr,"\n"
"++ In the 'new' method of FDR calculation, options '-nopmask' and\n"
" + -mask_file are incompatible. Am now turning '-pmask' back on\n"
" + so that the mask can be used.\n"
"++ RWCox - 29 Jan 2008\n\n"
) ;
FDR_pmask = 1 ;
}
return ;
}
void print2D_current(TString caseAna, TString channel, TString fsrFlag, TString accFlag, TString norm_type){
double sigma_Z = 524.699999999999932;
if (fsrFlag == "post") sigma_Z = 516.5;
cout << "Reading " << "covariance_finalResults_2D_mu_"+fsrFlag+"FSR_"+accFlag+"_normalized.root" << endl;
TFile fin("covariance_finalResults_2D_mu_"+fsrFlag+"FSR_"+accFlag+"_normalized.root","read");
TMatrixD *Morig=(TMatrixD*)fin.Get("totalCov_TM");
TMatrixD *Corig=(TMatrixD*)fin.Get("totalCorr_TM");
fin.Close();
// copy
TMatrixD M(*Morig);
TMatrixD MAlexey(*Morig);
TMatrixD MTEST(*Morig);
delete Morig; // no longer need original
// get errors to apply the correlation cut-off
int dim=M.GetNcols();
TVectorD S(dim);
for (int i=0; i<dim; i++) {
S[i]=sqrt(M(i,i));
}
//
// Now ready to print the matrix
//
// define ranges
const int nMassBins=6;
const int nYBins[nMassBins]={ 24, 24, 24, 24, 24, 12 };
const int massLimits[nMassBins+1] = { 20, 30, 45, 60, 120, 200, 1500 };
double diagonals_preFSR[132] = {0.00220474, 0.00211757, 0.00208329, 0.00196359, 0.00188362, 0.00178958, 0.00170293, 0.00147753, 0.00132556, 0.00123584, 0.00114805, 0.00112789, 0.00114458, 0.00130523, 0.00135017, 0.00140954, 0.0014109, 0.00147887, 0.00140234, 0.00126359, 0.00112224, 0.000942219, 0.000836654, 0.000407358, 0.00178671, 0.001573, 0.00152372, 0.00145345, 0.00142417, 0.00143499, 0.00144411, 0.00147708, 0.00148128, 0.00142131, 0.00140812, 0.00131649, 0.0012678, 0.0012579, 0.00119449, 0.00116062, 0.0011051, 0.00101312, 0.00100221, 0.000896522, 0.000852432, 0.000762897, 0.000637827, 0.000318889,0.000619175, 0.00063628, 0.000683457, 0.000663991, 0.000833326, 0.000576589, 0.000604494, 0.000665053, 0.000562349, 0.000571806, 0.000574754, 0.000641049, 0.000559305, 0.000510976, 0.000465562, 0.000552576, 0.000426906, 0.000394093, 0.000473651, 0.000490072, 0.000487637, 0.000310961, 0.000382431, 0.000199051, 0.00820416, 0.00817875, 0.00823994, 0.00826059, 0.0083192, 0.00826397, 0.00818159, 0.00799829, 0.0079163, 0.00798274, 0.00788228, 0.00776324, 0.00757453, 0.00723493, 0.00688138, 0.00638258, 0.00615382, 0.00560927, 0.00511678, 0.00477886, 0.00480081, 0.00446441, 0.0035405, 0.00140224, 0.000313394, 0.000313743, 0.000317145, 0.000302152, 0.000274664, 0.000282591, 0.000290322, 0.000263838, 0.000275426, 0.000243859, 0.000232308, 0.000223118, 0.000221724, 0.000214459, 0.000212437, 0.000205239, 0.000199126, 0.000188036, 0.000177693, 0.000186241, 0.000147574, 0.000143643, 0.00010251, 5.09799e-05, 0.000139172, 0.000115512, 0.000103777, 9.132e-05, 7.77451e-05, 7.36202e-05, 6.34563e-05, 5.60115e-05, 5.03875e-05, 4.09827e-05, 3.82219e-05, 1.55491e-05};
double rdiagonals_preFSR[132] = {0.0339971, 0.0337208, 0.032773, 0.0335877, 0.0340049, 0.0344678, 0.0351017, 0.0345766, 0.0344008, 0.0339871, 0.0334087, 0.0332816, 0.0322232, 0.0322838, 0.0310592, 0.0313493, 0.0294624, 0.0289783, 0.0268042, 0.0240434, 0.0209985, 0.0160163, 0.0104074, 0.00394112, 0.0512196, 0.0488462, 0.049328, 0.0489294, 0.0497668, 0.0516309, 0.0498744, 0.0488812, 0.0501116, 0.0487699, 0.0490278, 0.0486872, 0.0467183, 0.049095, 0.0459175, 0.0444989, 0.0413405, 0.0367446, 0.0315492, 0.0262498, 0.0209891, 0.0150392, 0.00890852, 0.00310112, 0.0213773, 0.0213444, 0.021062, 0.0216232, 0.020339, 0.0222888, 0.0218933, 0.0214533, 0.0215288, 0.0212879, 0.0205312, 0.0196386, 0.0185561, 0.0186806, 0.0170245, 0.0159697, 0.0140271, 0.0122443, 0.0112471, 0.00938589, 0.0077171, 0.00489739, 0.00342707, 0.00116623,0.604588, 0.600796, 0.601957, 0.596068, 0.595779, 0.590047, 0.584797, 0.57086, 0.557382, 0.54488, 0.526063, 0.503772, 0.475897, 0.445807, 0.417606, 0.374982, 0.339285, 0.292885, 0.250475, 0.20262, 0.156481, 0.108768, 0.0637553, 0.0202485,
0.00662107, 0.0068695, 0.00674016, 0.00671329, 0.006447, 0.00671166, 0.00630126, 0.00632929, 0.00613147, 0.00581744, 0.00577516, 0.00531591, 0.00516504, 0.00479951, 0.00464618, 0.00416784, 0.00371484, 0.0030139, 0.00238956, 0.00220813, 0.00138641, 0.000996914, 0.000525727, 0.000204149, 0.00100991, 0.00115943, 0.00124304, 0.000994088, 0.00101695, 0.00100447, 0.000906887, 0.000616144, 0.000469744, 0.000288772, 0.000184214, 4.10414e-05};
double diagonals_postFSR[132] = {0.00221175, 0.00212597, 0.00208369, 0.00198295, 0.00190802, 0.00182345, 0.00173207, 0.00152478, 0.00137675, 0.00128194, 0.00120738, 0.00120436, 0.00121263, 0.00136807, 0.00139429, 0.00146451, 0.00146562, 0.00152889, 0.00145013, 0.00130909, 0.00114496, 0.000954991, 0.000795812, 0.000393729, 0.00180454, 0.00159939, 0.00153431, 0.0014354, 0.00142042, 0.00147654, 0.00148879, 0.00150211, 0.00153454, 0.00146574, 0.00145038, 0.00138594, 0.00132894, 0.00133732, 0.00126548, 0.00123125, 0.00114978, 0.00107037, 0.00102759, 0.000934409, 0.000851672, 0.000725795, 0.00065131, 0.000296067, 0.000737911, 0.000735332, 0.000724041, 0.000716565, 0.000688831, 0.000705611, 0.000704845, 0.000703817, 0.00069591, 0.000703824, 0.000680863, 0.000665061, 0.000653354, 0.000634177, 0.00058112, 0.000541761, 0.00050425, 0.000485744, 0.000442929, 0.00040406, 0.000364285, 0.000309282, 0.000245493, 0.000136572, 0.0080247, 0.00800476, 0.00806034, 0.00808799, 0.00815336, 0.00810854, 0.00802642, 0.00785401, 0.00778262, 0.00780448, 0.00776131, 0.00766702, 0.00747821, 0.00715004, 0.00681454, 0.00633735, 0.00606506, 0.00554794, 0.00507419, 0.0048055, 0.0047721, 0.00445233, 0.00353591, 0.00137453, 0.00034878, 0.000349607, 0.00034785, 0.00033325, 0.000310629, 0.000321449, 0.000324078, 0.000303162, 0.000315696, 0.000284189, 0.000275219, 0.000264221, 0.000260037, 0.000252548, 0.00025174, 0.000243753, 0.000234663, 0.000214962, 0.000204784, 0.00020642, 0.000165171, 0.000152023, 0.000113424, 6.24019e-05, 0.000150168, 0.000129036, 0.000117808, 0.000102805, 9.06346e-05, 8.79511e-05, 7.67355e-05, 6.53114e-05, 5.9421e-05, 4.99151e-05, 4.55147e-05, 1.97611e-05};
double rdiagonals_postFSR[132] = {0.0336475, 0.0332778, 0.0326289, 0.0332891, 0.0337836, 0.0342364, 0.034789, 0.0342068, 0.0340713, 0.0336801, 0.0329994, 0.0330048, 0.031868, 0.0319083, 0.0308544, 0.0309242, 0.0290639, 0.0285542, 0.02643, 0.0235605, 0.020521, 0.0155586, 0.0100116, 0.00371247, 0.0515544, 0.0491292, 0.0497977, 0.0493683, 0.0501341, 0.0520321, 0.0501604, 0.0493229, 0.0503617, 0.049072, 0.0493856, 0.0488609, 0.0470033, 0.0491916, 0.0459866, 0.0445097, 0.0411828, 0.0365744, 0.0313967, 0.0260833, 0.0207742, 0.0148265, 0.00878173, 0.00297568,
0.0256592, 0.0257041, 0.0253218, 0.0260294, 0.0248893, 0.0266365, 0.0262303, 0.0256931, 0.0256673, 0.0252969, 0.0246081, 0.0236905, 0.0221783, 0.02201, 0.02022, 0.0187476, 0.0164779, 0.0144995, 0.0130875, 0.0109181, 0.00889321, 0.00575018, 0.00387918, 0.00127005,
0.602668, 0.59906, 0.600088, 0.594422, 0.594111, 0.588837, 0.583597, 0.569714, 0.556393, 0.543969, 0.525012, 0.502787, 0.475247, 0.445218, 0.416989, 0.374532, 0.338999, 0.29251, 0.250117, 0.202428, 0.156312, 0.108611, 0.0636249, 0.0201009,
0.00631477, 0.00651359, 0.00642427, 0.00636077, 0.00614697, 0.0063431, 0.00597265, 0.00601271, 0.00586154, 0.00557037, 0.00550196, 0.00508115, 0.0049044, 0.00452822, 0.00440214, 0.00397127, 0.00353436, 0.0028604, 0.00227513, 0.00209037, 0.00131489, 0.000937039, 0.000501518, 0.000191148,
0.000957856, 0.00111243, 0.00119348, 0.00095393, 0.000971326, 0.000964124, 0.000861841, 0.000586147, 0.000449087, 0.000277411, 0.000177376, 3.9162e-05};
double sigmaZerrNoLumi = 0.;
TString accFlag1 = accFlag;
if (accFlag == "fullAcc") accFlag1= "fullSpace";
if (fsrFlag == "pre" && accFlag == "inAcc") sigmaZerrNoLumi = pow(0.4,2) +pow(5.1,2) +pow(1.2,2);
if (fsrFlag == "post" && accFlag == "inAcc") sigmaZerrNoLumi =pow(0.4,2) +pow(4.9,2) +pow(1.1,2);
int fi_min=0;
for (int iM=0; iM<nMassBins; iM++) {
int fj_min=fi_min;
for (int jM=iM; jM<nMassBins; ++jM) {
TString fname=Form("cov_%d_%d_vs_%d_%d_%s_%s_%s.out",
massLimits[iM],massLimits[iM+1],
massLimits[jM],massLimits[jM+1],string(fsrFlag).c_str(),string(accFlag).c_str(),string(norm_type).c_str());
std::ofstream fout(fname.Data());
fout << "Covariances of the Drell-Yan differential cross section in the muon channel as a function of the dilepton mass for mass bins "
<< Form("(%d,%d) and (%d,%d)\n",
massLimits[iM],massLimits[iM+1],
massLimits[jM],massLimits[jM+1]);
if (norm_type == "rshape") {
string thiss = " # "+string(fsrFlag)+"FSR "+string(accFlag1)+" r-shape suppressed\n";
fout << thiss.c_str();
} else if (norm_type == "absolute") {
string thiss = " # "+string(fsrFlag)+"FSR "+string(accFlag1)+" absolute suppressed\n";
fout << thiss.c_str();
} else {
string thiss = " # "+string(fsrFlag)+"FSR "+string(accFlag1)+" (sigma/sigma_Z) suppressed\n";
fout << thiss.c_str();
}
fout << "M : 20 - 1500 GeV\n";
if (accFlag != "fullAcc") {
fout << "ABS(ETA(MU)) <= 2.4\n";
}
fout << "PT(MU1) : >=9 GEV\n"
<< "PT(MU2) : >=14 GEV\n"
<< "RE : P P --> DYmumu X\n"
<< "SQRT(S) : 7000.0 GEV\n"
<< "mass-rapidity-bin-index= rapBin + sum_{im=1}^{massBin-1} nYBins(im) \n"
<< "x: mass-rapidity-bin-index\n"
<< "y: mass-rapidity-bin-index\n";
if (norm_type == "rshape") {
fout << "z: cov(r_x,r_y)\n";
} else if (norm_type == "absolute") {
fout << "z: cov(sigma_x,sigma_y) [pb^2]\n";
} else {
fout << "z: cov(sigma_x/sigmaZ,sigma_y/sigmaZ)\n";
}
// print top row
fout << " ";
int allZeroes=1;
for (int fj=fj_min; fj<fj_min+nYBins[jM]; fj++) fout << Form(" %6d",fj+1);
fout << "\n";
// print the matrix
for (int fi=fi_min+nYBins[iM]-1; fi>=fi_min; fi--) {
fout << Form("%4d",fi+1) << " ";
for (int fj=fj_min; fj<fj_min+nYBins[jM]; fj++) {
double corr_ij = MAlexey(fi,fj)/sqrt(MAlexey(fi,fi)*MAlexey(fj,fj));
double prod = 0;
if (fsrFlag == "pre" && accFlag == "inAcc") prod = diagonals_preFSR[fi]*diagonals_preFSR[fj];
if (fsrFlag == "post" && accFlag == "inAcc") prod = diagonals_postFSR[fi]*diagonals_postFSR[fj];
if (fi!=fj) M(fi,fj) = prod*corr_ij;
else M(fi,fj) = prod;
double val = M(fi,fj);
if (norm_type == "absolute") {
if (fsrFlag == "pre" && accFlag == "inAcc") val = sigma_Z*sigma_Z*val + rdiagonals_preFSR[fi]*rdiagonals_preFSR[fj]*sigmaZerrNoLumi;
if (fsrFlag == "post" && accFlag == "inAcc") val = sigma_Z*sigma_Z*val + rdiagonals_postFSR[fi]*rdiagonals_postFSR[fj]*sigmaZerrNoLumi;
}
if (norm_type == "normalized" || norm_type == "absolute") {
if (jM != nMassBins-1 && iM != nMassBins-1) {val *= 0.1*0.1;}
else if (((jM == nMassBins-1) && !(iM == nMassBins-1)) || (!(jM == nMassBins-1) && (iM == nMassBins-1))) {
val *= 0.1*0.2;
} else {
val *= 0.2*0.2;
}
}
//FIXME correlation cut-off
//if (fabs(MAlexey(fi,fj)/sqrt(MAlexey(fi,fi)*MAlexey(fj,fj)))<0.01) val=0.;
fout << " " << Form("% 6.1e",val);
if (fabs(M(fi,fj))!=0.) allZeroes=0;
}
fout << "\n";
}
fj_min+=nYBins[jM];
fout.close();
if (allZeroes) {
std::cout << "all entries are 0 in file <" << fname << ">\n";
}
}
fi_min+=nYBins[iM];
}
for (int fj=0; fj<132; fj++) {
for (int fi=0; fi < 132; fi++) {
double corr_ij = MAlexey(fi,fj)/sqrt(MAlexey(fi,fi)*MAlexey(fj,fj));
double prod = 0;
if (fsrFlag == "pre") prod = diagonals_preFSR[fi]*diagonals_preFSR[fj];
if (fsrFlag == "post") prod = diagonals_postFSR[fi]*diagonals_postFSR[fj];
if (fi!=fj) M(fi,fj) = prod*corr_ij;
else M(fi,fj) = prod;
double val = M(fi,fj);
if (norm_type == "absolute") {
if (fsrFlag == "pre") val = sigma_Z*sigma_Z*val + rdiagonals_preFSR[fi]*rdiagonals_preFSR[fj]*sigmaZerrNoLumi;
if (fsrFlag == "post") val = sigma_Z*sigma_Z*val + rdiagonals_postFSR[fi]*rdiagonals_postFSR[fj]*sigmaZerrNoLumi;
}
if (norm_type == "normalized" || norm_type == "absolute") {
if (fi < 120 && fj < 120) {val *= 0.1*0.1;}
else if (((fi >=120) && !(fj >= 120)) || (!(fi >= 120) && (fj >= 120))) {
val *= 0.1*0.2;
} else {
val *= 0.2*0.2;
}
}
//FIXME correlation cut-off
if (fabs(MAlexey(fi,fj)/sqrt(MAlexey(fi,fi)*MAlexey(fj,fj)))<0.01) val=0.;
MTEST(fi,fj) = val;
}
}
TFile * fFile = new TFile("OUTcovariance_2D_mu_"+fsrFlag+"FSR_"+accFlag+"_"+norm_type+".root","RECREATE");
MTEST.Write("totalCov_TM");
Corig->Write("totalCorr_TM");
fFile->Close();
//validation
cout << "Validation " << fsrFlag << " " << accFlag << " " << norm_type << endl;
//check positive definiteness by checning the signs of all eigenvalues
cout << "Test matrix determinant " << MTEST.Determinant() << endl;
for (int i = 0; i < 132; i++) {
for (int j = 0; j < 132; j++) {
if (fabs(MTEST(i,j)-MTEST(j,i)) > fabs(MTEST(i,j))/10000.) cout << "Warning " << i << " " << j << " " << MTEST(i,j) << " " << MTEST(j,i) << endl;
}
}
for (int i = 0; i < 132; i++) {
for (int j = 0; j < 132; j++) {
if (i!=j) continue;
double val = 0;
if (fsrFlag == "pre") val =diagonals_preFSR[j];
if (fsrFlag == "post") val = diagonals_postFSR[j];
if (norm_type == "absolute") {
if (fsrFlag == "pre") val = sqrt(sigma_Z*sigma_Z*val*val + rdiagonals_preFSR[fi]*rdiagonals_preFSR[fj]*sigmaZerrNoLumi);
if (fsrFlag == "post") val = sqrt(sigma_Z*sigma_Z*val*val + rdiagonals_postFSR[fi]*rdiagonals_postFSR[fj]*sigmaZerrNoLumi);
}
if (norm_type == "normalized" || norm_type == "absolute") {
if (i < 120 && j < 120) {val *= 0.1;}
else if (((i >=120) && !(j >= 120)) || (!(i >= 120) && (j >= 120))) {
val *= sqrt(0.1*0.2);
} else {
val *= 0.2;
}
}
if (fabs(sqrt(MTEST(j,j)) - val) > fabs(sqrt(MTEST(j,j)))/10000.) cout << "Warning " << sqrt(MTEST(j,j)) << " " << val << " " << fabs(sqrt(MTEST(j,j)) - val) << endl;
}
}
}