static void *
uio_int_handler(void *arg)
{
int ret;
void *(*ufunc)(void *);
void *uarg;
tsem_t *uio_sem;
int *exit_flag;
if (arg) {
void **args = arg;
ufunc = args[0];
uarg = args[1];
uio_sem = args[2];
exit_flag = args[3];
} else {
ufunc = uarg = NULL;
return NULL;
}
logd("%s start\n", __FUNCTION__);
while (uiomux && !*exit_flag) {
logd("wait for an interrupt...\n");
ret = uiomux_sleep(uiomux, VPU_UIO);
if (ret < 0) {
break;
}
logd("got an interrupt! (%d)\n", ret);
if (ufunc)
ufunc(uarg);
}
free (arg);
return NULL;
}
/*ARGSUSED1*/
void key (unsigned char key, int x, int y) {
switch (key) {
case 'b': bfunc(); break;
case 'c': cfunc(); break;
case 'l': lfunc(); break;
case 't': tfunc(); break;
case 'f': ffunc(); break;
case 'n': nfunc(); break;
case 'u': ufunc(); break;
case 'U': Ufunc(); break;
case 'p': pfunc(); break;
case 'P': Pfunc(); break;
case 'w': wfunc(); break;
case 'x': xfunc(); break;
case 'X': Xfunc(); break;
case 'y': yfunc(); break;
case '\033': exit(EXIT_SUCCESS); break;
default: break;
}
}
THD_3dim_dataset * MAKER_4D_to_typed_fim( THD_3dim_dataset * old_dset ,
char * new_prefix , int new_datum ,
int ignore , int detrend ,
generic_func * user_func ,
void * user_data )
{
THD_3dim_dataset * new_dset ; /* output dataset */
byte ** bptr = NULL ; /* one of these will be the array of */
short ** sptr = NULL ; /* pointers to input dataset sub-bricks */
float ** fptr = NULL ; /* (depending on input datum type) */
complex ** cptr = NULL ;
float * fxar = NULL ; /* array loaded from input dataset */
float * fac = NULL ; /* array of brick scaling factors */
float * fout = NULL ; /* will be array of output floats */
float * dtr = NULL ; /* will be array of detrending coeff */
float val , d0fac , d1fac , x0,x1;
double tzero=0 , tdelta , ts_mean , ts_slope ;
int ii , old_datum , nuse , use_fac , iz,izold, nxy,nvox , nbad ;
register int kk ;
void (*ufunc)(double,double,int,float *,double,double,void *,float *)
= (void (*)(double,double,int,float *,double,double,void *,float *)) user_func ;
/*----------------------------------------------------------*/
/*----- Check inputs to see if they are reasonable-ish -----*/
if( ! ISVALID_3DIM_DATASET(old_dset) ) return NULL ;
if( new_datum >= 0 &&
new_datum != MRI_byte &&
new_datum != MRI_short &&
new_datum != MRI_float ) return NULL ;
if( user_func == NULL ) return NULL ;
if( ignore < 0 ) ignore = 0 ;
/*--------- set up pointers to each sub-brick in the input dataset ---------*/
old_datum = DSET_BRICK_TYPE( old_dset , 0 ) ; /* get old dataset datum */
nuse = DSET_NUM_TIMES(old_dset) - ignore ; /* # of points on time axis */
if( nuse < 2 ) return NULL ;
if( new_datum < 0 ) new_datum = old_datum ; /* output datum = input */
if( new_datum == MRI_complex ) return NULL ; /* but complex = bad news */
DSET_load( old_dset ) ; /* must be in memory before we get pointers to it */
kk = THD_count_databricks( old_dset->dblk ) ; /* check if it was */
if( kk < DSET_NVALS(old_dset) ){ /* loaded correctly */
DSET_unload( old_dset ) ;
return NULL ;
}
switch( old_datum ){ /* pointer type depends on input datum type */
default: /** don't know what to do **/
DSET_unload( old_dset ) ;
return NULL ;
/** create array of pointers into old dataset sub-bricks **/
/*--------- input is bytes ----------*/
/* voxel #i at time #k is bptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_byte:
bptr = (byte **) malloc( sizeof(byte *) * nuse ) ;
if( bptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
bptr[kk] = (byte *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
/*--------- input is shorts ---------*/
/* voxel #i at time #k is sptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_short:
sptr = (short **) malloc( sizeof(short *) * nuse ) ;
if( sptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
sptr[kk] = (short *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
/*--------- input is floats ---------*/
/* voxel #i at time #k is fptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_float:
fptr = (float **) malloc( sizeof(float *) * nuse ) ;
if( fptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
fptr[kk] = (float *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
/*--------- input is complex ---------*/
/* voxel #i at time #k is cptr[k][i] */
/* for i=0..nvox-1 and k=0..nuse-1. */
case MRI_complex:
cptr = (complex **) malloc( sizeof(complex *) * nuse ) ;
if( cptr == NULL ) return NULL ;
for( kk=0 ; kk < nuse ; kk++ )
cptr[kk] = (complex *) DSET_ARRAY(old_dset,kk+ignore) ;
break ;
} /* end of switch on input type */
/*---- allocate space for 1 voxel timeseries ----*/
fxar = (float *) malloc( sizeof(float) * nuse ) ; /* voxel timeseries */
if( fxar == NULL ){ FREE_WORKSPACE ; return NULL ; }
/*--- get scaling factors for sub-bricks ---*/
fac = (float *) malloc( sizeof(float) * nuse ) ; /* factors */
if( fac == NULL ){ FREE_WORKSPACE ; return NULL ; }
use_fac = 0 ;
for( kk=0 ; kk < nuse ; kk++ ){
fac[kk] = DSET_BRICK_FACTOR(old_dset,kk+ignore) ;
if( fac[kk] != 0.0 ) use_fac++ ;
else fac[kk] = 1.0 ;
}
if( !use_fac ) FREEUP(fac) ;
/*--- setup for detrending ---*/
dtr = (float *) malloc( sizeof(float) * nuse ) ;
if( dtr == NULL ){ FREE_WORKSPACE ; return NULL ; }
d0fac = 1.0 / nuse ;
d1fac = 12.0 / nuse / (nuse*nuse - 1.0) ;
for( kk=0 ; kk < nuse ; kk++ )
dtr[kk] = kk - 0.5 * (nuse-1) ; /* linear trend, orthogonal to 1 */
/*---------------------- make a new dataset ----------------------*/
new_dset = EDIT_empty_copy( old_dset ) ; /* start with copy of old one */
/*-- edit some of its internal parameters --*/
ii = EDIT_dset_items(
new_dset ,
ADN_prefix , new_prefix , /* filename prefix */
ADN_malloc_type , DATABLOCK_MEM_MALLOC , /* store in memory */
ADN_datum_all , new_datum , /* atomic datum */
ADN_nvals , 1 , /* # sub-bricks */
ADN_ntt , 0 , /* # time points */
ADN_type , ISHEAD(old_dset) /* dataset type */
? HEAD_FUNC_TYPE
: GEN_FUNC_TYPE ,
ADN_func_type , FUNC_FIM_TYPE , /* function type */
ADN_none ) ;
if( ii != 0 ){
ERROR_message("Error creating dataset '%s'",new_prefix) ;
THD_delete_3dim_dataset( new_dset , False ) ; /* some error above */
FREE_WORKSPACE ; return NULL ;
}
/*------ make floating point output brick
(only at the end will scale to byte or shorts) ------*/
nvox = old_dset->daxes->nxx * old_dset->daxes->nyy * old_dset->daxes->nzz ;
fout = (float *) malloc( sizeof(float) * nvox ) ; /* ptr to brick */
if( fout == NULL ){
THD_delete_3dim_dataset( new_dset , False ) ;
FREE_WORKSPACE ; return NULL ;
}
/*----- set up to find time at each voxel -----*/
tdelta = old_dset->taxis->ttdel ;
if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tdelta *= 0.001 ;
if( tdelta == 0.0 ) tdelta = 1.0 ;
izold = -666 ;
nxy = old_dset->daxes->nxx * old_dset->daxes->nyy ;
/*----------------------------------------------------*/
/*----- Setup has ended. Now do some real work. -----*/
/* start notification */
#if 0
user_func( 0.0 , 0.0 , nvox , NULL,0.0,0.0 , user_data , NULL ) ;
#else
ufunc( 0.0 , 0.0 , nvox , NULL,0.0,0.0 , user_data , NULL ) ;
#endif
/***** loop over voxels *****/
for( ii=0 ; ii < nvox ; ii++ ){ /* 1 time series at a time */
/*** load data from input dataset, depending on type ***/
switch( old_datum ){
/*** input = bytes ***/
case MRI_byte:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = bptr[kk][ii] ;
break ;
/*** input = shorts ***/
case MRI_short:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = sptr[kk][ii] ;
break ;
/*** input = floats ***/
case MRI_float:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = fptr[kk][ii] ;
break ;
/*** input = complex (note we use absolute value) ***/
case MRI_complex:
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] = CABS(cptr[kk][ii]) ;
break ;
} /* end of switch over input type */
/*** scale? ***/
if( use_fac )
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] *= fac[kk] ;
/** compute mean and slope **/
x0 = x1 = 0.0 ;
for( kk=0 ; kk < nuse ; kk++ ){
x0 += fxar[kk] ; x1 += fxar[kk] * dtr[kk] ;
}
x0 *= d0fac ; x1 *= d1fac ; /* factors to remove mean and trend */
ts_mean = x0 ;
ts_slope = x1 / tdelta ;
/** detrend? **/
if( detrend )
for( kk=0 ; kk < nuse ; kk++ ) fxar[kk] -= (x0 + x1 * dtr[kk]) ;
/** compute start time of this timeseries **/
iz = ii / nxy ; /* which slice am I in? */
if( iz != izold ){ /* in a new slice? */
tzero = THD_timeof( ignore ,
old_dset->daxes->zzorg
+ iz*old_dset->daxes->zzdel , old_dset->taxis ) ;
izold = iz ;
if( DSET_TIMEUNITS(old_dset) == UNITS_MSEC_TYPE ) tzero *= 0.001 ;
}
/*** compute output ***/
#if 0
user_func( tzero,tdelta , nuse,fxar,ts_mean,ts_slope , user_data , fout+ii ) ;
#else
ufunc( tzero,tdelta , nuse,fxar,ts_mean,ts_slope , user_data , fout+ii ) ;
#endif
} /* end of outer loop over 1 voxels at a time */
DSET_unload( old_dset ) ; /* don't need this no more */
/* end notification */
#if 0
user_func( 0.0 , 0.0 , 0 , NULL,0.0,0.0 , user_data , NULL ) ;
#else
ufunc( 0.0 , 0.0 , 0 , NULL,0.0,0.0 , user_data , NULL ) ;
#endif
nbad = thd_floatscan( nvox , fout ) ; /* 08 Aug 2000 */
if( nbad > 0 )
fprintf(stderr,
"++ Warning: %d bad floats computed in MAKER_4D_to_typed_fim\n\a",
nbad ) ;
/*------------------------------------------------------------*/
/*------- The output is now in fout[ii], ii=0..nvox-1.
We must now put this into the output dataset -------*/
switch( new_datum ){
/*** output is floats is the simplest:
we just have to attach the fout brick to the dataset ***/
case MRI_float:
EDIT_substitute_brick( new_dset , 0 , MRI_float , fout ) ;
fout = NULL ; /* so it won't be freed later */
break ;
/*** output is shorts:
we have to create a scaled sub-brick from fout ***/
case MRI_short:{
short * bout ;
float sfac ;
/*-- get output sub-brick --*/
bout = (short *) malloc( sizeof(short) * nvox ) ;
if( bout == NULL ){
fprintf(stderr,
"\nFinal malloc error in MAKER_4D_to_fim - is memory exhausted?\n\a");
EXIT(1) ;
}
/*-- find scaling and then scale --*/
sfac = MCW_vol_amax( nvox,1,1 , MRI_float , fout ) ;
if( sfac > 0.0 ){
sfac = 32767.0 / sfac ;
EDIT_coerce_scale_type( nvox,sfac ,
MRI_float,fout , MRI_short,bout ) ;
sfac = 1.0 / sfac ;
}
/*-- put output brick into dataset, and store scale factor --*/
EDIT_substitute_brick( new_dset , 0 , MRI_short , bout ) ;
EDIT_dset_items( new_dset , ADN_brick_fac , &sfac , ADN_none ) ;
}
break ;
/*** output is bytes (byte = unsigned char)
we have to create a scaled sub-brick from fout ***/
case MRI_byte:{
byte * bout ;
float sfac ;
/*-- get output sub-brick --*/
bout = (byte *) malloc( sizeof(byte) * nvox ) ;
if( bout == NULL ){
fprintf(stderr,
"\nFinal malloc error in MAKER_4D_to_fim - is memory exhausted?\n\a");
EXIT(1) ;
}
/*-- find scaling and then scale --*/
sfac = MCW_vol_amax( nvox,1,1 , MRI_float , fout ) ;
if( sfac > 0.0 ){
sfac = 255.0 / sfac ;
EDIT_coerce_scale_type( nvox,sfac ,
MRI_float,fout , MRI_byte,bout ) ;
sfac = 1.0 / sfac ;
}
/*-- put output brick into dataset, and store scale factor --*/
EDIT_substitute_brick( new_dset , 0 , MRI_byte , bout ) ;
EDIT_dset_items( new_dset , ADN_brick_fac , &sfac , ADN_none ) ;
}
break ;
} /* end of switch on output data type */
/*-------------- Cleanup and go home ----------------*/
FREE_WORKSPACE ;
return new_dset ;
}
double MathFunction::Evaluate(double t, int diff) const //if diff=1, then differentiate w.r.t. time
{
//t .. time or input parameter
double val = 0;
switch (funcmode)
{
case TMFempty: //no function
{
//val = 0;
break;
}
case TMFpolynomial: //polynomial, coeffs contain polynomial coeffs a_1 * 1 + a_2 * t + a_3 * t^2 + ...
{
//if (t > 1) t = 1; //hack!!!!
if (vectime.Length() == 2)
{
if (t < vectime(1)) t = vectime(1);
else if (t > vectime(2)) t = vectime(2);
}
double pt = 1;
if (!diff)
{
for (int i=1; i <= coeff.Length(); i++)
{
val += coeff(i) * pt;
pt *= t;
}
}
else if (diff==1) //a_2 * 1 + a_3 * 2* t + a_4 * 3* t^2 + ...
{
for (int i=2; i <= coeff.Length(); i++)
{
val += coeff(i) * pt * ((double)i-1);
pt *= t;
}
}
break;
}
case TMFpiecewiseconst: //time points, not interpolated, differentiation not possible
{
if (vectime.Length() != 0 && !diff)
{
int index = 1;
index = FindIndexPiecewise(t);
val = valX(index);
}
break;
}
case TMFpiecewiselinear: //time points linearly interpolated
{
if (vectime.Length() != 0 && !diff)
{
int index = 1;
index = FindIndexPiecewise(t);
val = InterpolatePiecewise(t, index);
}
break;
}
case TMFpiecewisequad: //time points quadratic interpolated, not yet implemented!
{
if (vectime.Length() != 0)
{
int i = 1;
while (i <= vectime.Length() && t > vectime(i)) {
i++;
}
if (i > vectime.Length())
{
i = vectime.Length();
if (diff)
val = valY(i); //vel
else
val = valX(i); //pos
}
else
{
double t1 = 0, t2;
double x1 = 0;
double x2 = 0;
double v1 = 0;
double v2 = 0;
if (i >= 2)
{
t1 = vectime(i-1);
x1 = valX(i-1); //pos
v1 = valY(i-1); //vel
}
double dt = vectime(i)-t1;
if (dt <= 0) dt = 1;
x2 = valX(i); //pos
v2 = valY(i); //vel
t2 = vectime(i);
if (diff)
val = (1.-(t-t1)/dt)*v1 + (1.+(t-t2)/dt)*v2; //linearly interpolate velocity
else
{
val = x1 + (t-t1)*v1 + 0.5*(v2-v1)*Sqr(t-t1)/dt; //linearly interpolate velocity
}
}
}
break;
}
case TMFharmonic: //harmonic function
{
if (valX.Length() != 0 && valX.Length() == valY.Length() && valX.Length() == valZ.Length())
{
val = 0;
for (int i=1; i <= valX.Length(); i++)
{
if (!diff)
val += valZ(i)*sin(valX(i)*t+valY(i));
else
val += valZ(i)*valX(i)*cos(valX(i)*t+valY(i));
}
}
break;
}
case TMFsin:
{
//input variable:t
//Evaluate val = coeff(1) * Sin(coeff(2)*t + coeff(3))
val = coeff(1) * sin(coeff(2)*t + coeff(3));
break;
}
case TMFcos: //***
{
//input variable:t
val = coeff(1) * cos(coeff(2)*t + coeff(3));
break;
}
case TMFstaticDynamicFricion: //***
{
assert(0 && "ERROR in mathfunc.cpp: SetStaticDynamicFricionFunction not anymore supported by MathFunction, use TMFExpression instead!");
////input variable: velocity
//if(coeff(3) > 0.0 && fabs(t) <= coeff(3))
//{
// val = coeff(4)/(coeff(3))*t;
//}else
//{
// //if(-1e-10<t && t<1e-10)t=0.0;
// val = coeff(1)*Sgn(t) + coeff(2)*t;
//}
//break;
}
case TMFuserdefined: //***
{
val = ufunc(t,coeff);
break;
}
case TMFexpression:
{
//val = mbsPI->EvaluateParsedFunction1D(parsedFunctionExpression, parsedFunctionVariables, t); //$JG2013-4-29: old slow code of YV
val = pf.Evaluate(t); //$JG2013-4-29: new code, faster: Parsed function is only evaluated, not interpreted!
break;
}
default:
;
}
return val;
}
