/*****************************************************************************
Major portions of this software are copyrighted by the Medical College
of Wisconsin, 1994-2000, and are released under the Gnu General Public
License, Version 2. See the file README.Copyright for details.
******************************************************************************/
#include <string.h>
#include "mrilib.h"
#include <stdlib.h>
#include <ctype.h>
/*-------------------------- global data --------------------------*/
/** inputs **/
static THD_3dim_dataset * UC_dset = NULL ; /* dataset */
static MRI_IMAGE * UC_ref = NULL ; /* vector */
static char UC_prefix[THD_MAX_PREFIX] = "uc" ;
static int UC_be_quiet = 1 ;
static byte * UC_mask = NULL ;
static int UC_mask_nvox = 0 ;
static int UC_mask_hits = 0 ;
static int UC_nvec = 0 ;
static int UC_vdim = 0 ;
static float ** UC_vec = NULL ; /* UC_vec[k][i] is the i-th component */
/* of the k-th vector 0 <= i < UC_vdim */
/* 0 <= k < UC_nvec */
void UC_syntax(char * msg) ;
/*-------------------------------------------------------------------
detrend: routine to remove unwanted components from time series
---------------------------------------------------------------------*/
void detrend( int n , float vec[] )
{
register int ii ;
register float sum0 , sum1 , cf , lf ;
float sum2 , det ;
static int nold = -1 ; /* initialization flag */
static float cf0,cf1 , lf0,lf1 ; /* to be initialized */
/*** initialize coefficients for detrending ***/
if( n != nold ){
nold = n ; sum0 = sum1 = sum2 = 0.0 ;
for( ii=0 ; ii < n ; ii++ ){
sum0 += 1.0 ; sum1 += ii ; sum2 += ii*ii ;
}
det = sum0 * sum2 - sum1 * sum1 ;
cf0 = sum2 / det ; /* constant factor for sum0 */
cf1 = -sum1 / det ; /* constant factor for sum1 */
lf0 = cf1 ; /* linear factor for sum0 */
lf1 = sum0 / det ; /* linear factor for sum1 */
}
/*** remove mean and linear trend ***/
sum0 = sum1 = 0.0 ;
for( ii=0 ; ii < n ; ii++ ){
sum0 += vec[ii] ; sum1 += vec[ii] * ii ;
}
cf = cf0 * sum0 + cf1 * sum1 ;
lf = lf0 * sum0 + lf1 * sum1 ;
for( ii=0 ; ii < n ; ii++ ) vec[ii] -= cf + ii*lf ;
}
/*----------------------------------------------------------
normalize: routine to scale a time series to unit vector
------------------------------------------------------------*/
void normalize( int n , float vec[] )
{
register int ii ;
register float sqsum ;
detrend( n , vec ) ;
sqsum = 0.0 ;
for( ii=0 ; ii < n ; ii++ ) sqsum += vec[ii] * vec[ii] ;
if( sqsum < 1.e-10 ){
for( ii=0 ; ii < n ; ii++ ) vec[ii] = 0.0 ;
} else {
sqsum = 1.0 / sqrt(sqsum) ;
for( ii=0 ; ii < n ; ii++ ) vec[ii] *= sqsum ;
}
}
/*------------------------------------------------------------------*/
void UC_read_opts( int argc , char * argv[] )
{
int nopt = 1 ;
float val ;
int kk, nxyz, mm,nn ;
float * vv , * bb ;
while( nopt < argc && argv[nopt][0] == '-' ){
/**** -verbose ****/
if( strncmp(argv[nopt],"-verbose",5) == 0 ){
UC_be_quiet = 0 ;
nopt++ ; continue ;
}
/**** -ref file.1D ****/
if( strncmp(argv[nopt],"-ref",4) == 0 ){
MRI_IMAGE * im ;
nopt++ ;
if( nopt >= argc ) UC_syntax("-ref needs an argument!") ;
im = mri_read( argv[nopt] ) ;
if( im == NULL ) UC_syntax("Can't read -ref file!") ;
if( im->kind == MRI_float ){
UC_ref = im ;
} else {
UC_ref = mri_to_float(im) ; mri_free(im) ;
}
im = mri_transpose(UC_ref) ; mri_free(UC_ref) ; UC_ref = im ;
nopt++ ; continue ;
}
/**** -prefix prefix ****/
if( strncmp(argv[nopt],"-prefix",6) == 0 ){
nopt++ ;
if( nopt >= argc ) UC_syntax("-prefix needs an argument!") ;
MCW_strncpy( UC_prefix , argv[nopt++] , THD_MAX_PREFIX ) ;
continue ;
}
/**** -mask mset ****/
if( strncmp(argv[nopt],"-mask",5) == 0 ){
THD_3dim_dataset * mset ; int ii ;
nopt++ ;
if( nopt >= argc ) UC_syntax("need arguments after -mask!") ;
mset = THD_open_dataset( argv[nopt] ) ;
if( mset == NULL ) UC_syntax("can't open -mask dataset!") ;
UC_mask = THD_makemask( mset , 0 , 1.0,0.0 ) ;
UC_mask_nvox = DSET_NVOX(mset) ;
DSET_delete(mset) ;
if( UC_mask == NULL ) UC_syntax("can't use -mask dataset!") ;
UC_mask_hits = THD_countmask( UC_mask_nvox , UC_mask ) ;
if( UC_mask_hits == 0 ) UC_syntax("mask is all zeros!") ;
if( !UC_be_quiet ) printf("--- %d voxels in mask\n",UC_mask_hits) ;
nopt++ ; continue ;
}
/**** unknown switch ****/
fprintf(stderr,"\n*** unrecognized option %s\n",argv[nopt]) ;
exit(1) ;
} /* end of loop over options */
/*--- a simple consistency check ---*/
/*--- last input is dataset name ---*/
if( nopt >= argc ) UC_syntax("no input dataset name?") ;
UC_dset = THD_open_dataset( argv[nopt] ) ;
if( !ISVALID_3DIM_DATASET(UC_dset) ){
fprintf(stderr,"\n*** can't open dataset file %s\n",argv[nopt]) ;
exit(1) ;
}
nxyz = DSET_NVOX(UC_dset) ;
if( UC_mask != NULL && nxyz != UC_mask_nvox )
UC_syntax("mask and input dataset size mismatch!") ;
/*--- load vectors ---*/
UC_nvec = (UC_mask_hits > 0) ? UC_mask_hits : nxyz ;
UC_vdim = DSET_NVALS(UC_dset) ;
if( UC_vdim < 4 )
UC_syntax("input dataset needs at least 4 sub-bricks!") ;
if( UC_ref == NULL || UC_ref->nx < UC_vdim )
UC_syntax("input ref not long enough for input dataset!") ;
vv = (float *) malloc( sizeof(float) * UC_nvec * UC_vdim ) ;
UC_vec = (float **) malloc( sizeof(float *) * UC_nvec ) ;
for( kk=0 ; kk < UC_nvec ; kk++ ) UC_vec[kk] = vv + (kk*UC_vdim) ;
if( !UC_be_quiet ) printf("--- reading dataset\n") ;
DSET_load(UC_dset) ; CHECK_LOAD_ERROR(UC_dset) ;
/* copy brick data into float storage */
if( !UC_be_quiet ) printf("--- loading vectors\n") ;
bb = (float *) malloc( sizeof(float) * nxyz ) ;
for( mm=0 ; mm < UC_vdim ; mm++ ){
EDIT_coerce_type( nxyz , DSET_BRICK_TYPE(UC_dset,mm) ,
DSET_ARRAY(UC_dset,mm) ,
MRI_float , bb ) ;
DSET_unload_one( UC_dset , mm ) ;
if( UC_mask == NULL ){
for( kk=0 ; kk < nxyz ; kk++ ) UC_vec[kk][mm] = bb[kk] ;
} else {
for( nn=kk=0 ; kk < nxyz ; kk++ )
if( UC_mask[kk] ) UC_vec[nn++][mm] = bb[kk] ;
}
}
free(bb) ; DSET_unload( UC_dset ) ;
/* detrend and normalize vectors */
if( !UC_be_quiet ) printf("--- normalizing vectors\n") ;
for( kk=0 ; kk < UC_nvec ; kk++ )
normalize( UC_vdim , UC_vec[kk] ) ;
for( kk=0 ; kk < UC_ref->ny ; kk++ )
normalize( UC_vdim , MRI_FLOAT_PTR(UC_ref) + kk*UC_ref->nx ) ;
return ;
}
#include "uuu.c"
/*-----------------------------------------------------------------------
Compute the unusuality index of a reference vector in a set of vectors
-------------------------------------------------------------------------*/
float UC_unusuality( int ndim , float * ref , int nvec , float ** vec )
{
register int ii , kk ;
float psum,msum , * vv , val ;
float zmid , zmed , zsig , zplus,zminus , uval ;
static int nvold=-1 ;
static float * zval =NULL , *aval=NULL ;
static float pstar , zstar ;
if( ndim < 4 || nvec < 4 || ref == NULL || vec == NULL ) return 0.0 ;
/* initialize if number of vectors has changed */
if( nvold != nvec ){
if( zval != NULL ) free(zval) ;
if( aval != NULL ) free(aval) ;
zval = (float *) malloc(sizeof(float)*nvec) ;
aval = (float *) malloc(sizeof(float)*nvec) ;
nvold = nvec ;
pstar = 10.0 / nvec ;
zstar = qginv(0.5*pstar) ;
}
/* compute dot products */
for( kk=0 ; kk < nvec ; kk++ ){
psum = 0.0 ; vv = vec[kk] ;
for( ii=0 ; ii < ndim ; ii++ ) psum += ref[ii] * vv[ii] ;
zval[kk] = psum ;
}
{ char * ps = getenv("PTAIL") ;
float pp=0.0 ;
if( ps != NULL ) pp = strtod(ps,NULL) ;
set_unusuality_tail(pp) ;
}
psum = unusuality( nvec, zval ) ;
for( kk=0 ; kk < nvec ; kk++ ) zval[kk] = -zval[kk] ;
msum = unusuality( nvec, zval ) ;
uval = psum - msum ;
printf("psum=%.1f msum=%.1f total=%.1f uval=%.1f\n",
psum,msum,psum+msum,uval) ;
return (psum+msum) ;
}
/*---------------------------------------------------------------------------*/
void UC_syntax(char * msg)
{
if( msg != NULL ){ fprintf(stderr,"\n*** %s\n",msg) ; exit(1) ; }
printf(
"Unusual Component Analysis of 3D Datasets\n"
"Usage: 3duca [options] dataset ...\n"
"\n"
"The input dataset may have a sub-brick selector list.\n"
"Otherwise, all sub-bricks from a dataset will be used.\n"
"\n"
"OPTIONS:\n"
" -prefix pname \n"
" -verbose\n"
" -mask mset \n"
" -ref file.1D\n"
printf("\n" MASTER_SHORTHELP_STRING ) ;
) ;
exit(0) ;
}
/*------------------------------------------------------------------*/
int main( int argc , char * argv[] )
{
int kk ;
/*-- read command line arguments --*/
if( argc < 2 || strncmp(argv[1],"-help",5) == 0 ) UC_syntax(NULL) ;
(void) my_getenv("junk") ;
UC_read_opts( argc , argv ) ;
for( kk=0 ; kk < UC_ref->ny ; kk++ )
(void) UC_unusuality( UC_vdim,
MRI_FLOAT_PTR(UC_ref) + kk*UC_ref->nx,
UC_nvec, UC_vec ) ;
exit(0) ;
}
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