double corr(double *a, double *b, int n)
{
double v12, v11, v22, y1, y2, y ;
double *aa, *bb ;
ZALLOC(aa, n, double) ;
ZALLOC(bb, n, double) ;
y1 = asum(a,n)/ (double) n ;
y2 = asum(b,n)/ (double) n ;
vsp(aa, a, -y1, n) ;
vsp(bb, b, -y2, n) ;
v12 = vdot(aa, bb, n) ;
v11 = asum2(aa, n) ;
v22 = asum2(bb, n) ;
y = v11*v22 ;
if (y==0.0) fatalx("(corr) constant vector\n") ;
free(aa) ;
free(bb) ;
return (v12/sqrt(y)) ;
}
double corrx(double *a, double *b, int n)
// like corr but constant vec returns 0
{
double v12, v11, v22, y1, y2, y ;
double *aa, *bb ;
ZALLOC(aa, n, double) ;
ZALLOC(bb, n, double) ;
y1 = asum(a,n)/ (double) n ;
y2 = asum(b,n)/ (double) n ;
vsp(aa, a, -y1, n) ;
vsp(bb, b, -y2, n) ;
v12 = vdot(aa, bb, n) ;
v11 = asum2(aa, n) ;
v22 = asum2(bb, n) ;
free(aa) ;
free(bb) ;
y = v11*v22 ;
y += 1.0e-12 ;
return (v12/sqrt(y)) ;
}
double
oldtwestxx (double *lam, int m, double *pzn, double *pzvar)
{
double lsum, logsum;
double *ww;
double a, p, yn, var;
double ylike, ybase, y, ylmax, ynmax, yld, yld2, ainc, ym;
int k;
ZALLOC(ww, m, double);
copyarr (lam, ww, m);
lsum = asum (ww, m);
vlog (ww, ww, m);
logsum = asum (ww, m);
ylmax = -1.0e20;
yn = (double) m;
ybase = xxlikex (m, yn, logsum, lsum);
for (k = 1; k <= 100; ++k)
{
a = yn / 2.0;
ylike = xxlikex (m, a, logsum, lsum);
yld = xxliked (m, a, logsum, lsum);
ylike -= ybase;
if (verbose)
printf ("ynloop %12.3f %12.3f %12.3f\n", yn / (double) m, ylike, yld);
if (ylike < ylmax)
break;
ylmax = ylike;
ynmax = yn;
yn *= 1.1;
}
a = ynmax / 2.0;
for (k = 1; k <= 10; ++k)
{
// newton iteration
ylike = xxlikex (m, a, logsum, lsum);
yld = xxliked (m, a, logsum, lsum);
yld2 = xxliked2 (m, a, logsum, lsum);
ylike -= ybase;
ainc = -yld / yld2;
a += ainc;
if (verbose)
printf ("newton: %3d %15.9f %15.9f %15.9f\n", k, ylike, yld, ainc);
}
fflush (stdout);
yn = 2.0 * a;
ym = (double) m;
var = lsum / (2.0 * a * ym);
*pzn = yn;
*pzvar = var;
free (ww);
return 0;
}
VALUE nrmp( //
int n, //size of the array, sx.size==sy.size
const VALUE* x, //
VALUE2 p, //
int incx //
) {
if (p == 1.0) {
return asum(n, x, incx);
}
if (p == 2.0) {
return nrm2(n, x, incx);
}
VALUE zero = 0.0e+0;
VALUE norm = zero;
if (n <= 0 || incx <= 0) {
return norm;
} else if (n == 1) {
norm = Abs(x[0]);
} else {
for (int i = 0; i < (n - 1) * incx; i += incx) {
if (x[i] != zero) {
norm += pow(Abs(x[i]), p);
}
}
norm = pow(norm, 1.0 / double(p));
}
return norm;
} // << ------------------------------------------
TYPE nrm1( //
const ArrayListV<TYPE>& ax //[in]
) {
int n = ax.size();
const TYPE* x = ax.getPointer();
return asum(n, x, 1);
}
double dirmult(double *pp, int *aa, int len)
{
int t, i, m ;
double y1, y2, ysum ;
double top, bot ;
m = len ;
t = intsum(aa,m) ;
if (t < 1) return 0.0 ;
top = bot = 0.0 ;
ysum = asum(pp,m) ;
for (i=0; i<m; i++) {
top += lgamma(pp[i] + (double) aa[i]) ;
bot += lgamma(pp[i]) ;
}
top += lgamma(ysum) ;
bot += lgamma(ysum + (double) t) ;
y1 = top-bot ;
return y1 -y2 ;
}
double variance(double *a, int n)
{
double *aa ;
double y1, y2 ;
ZALLOC(aa, n, double) ;
y1 = asum(a,n)/ (double) n ;
vsp(aa, a, -y1, n) ;
y2 = asum(aa,n)/ (double) n ;
free(aa) ;
return y2 ;
}
double trace(double *a, int n)
{
double *diags, t ;
ZALLOC(diags,n,double) ;
getdiag(diags,a,n) ; /* extract diagonal */
t = asum(diags,n) ;
free(diags) ;
return t ;
}
double anova(double *vec, int len, int *xtypes, int numeg)
// anova 1 but f statistic
{
int i, k ;
double y1, top, bot, ftail ;
double *w0, *w1, *popsize, *wmean ;
static int ncall2 = 0 ;
if (numeg >= len) fatalx("bad anova\n") ;
ZALLOC(w0, len, double) ;
ZALLOC(w1, len, double) ;
ZALLOC(wmean, numeg, double) ;
ZALLOC(popsize, numeg, double) ;
y1 = asum(vec, len)/ (double) len ; // mean
vsp(w0, vec, -y1, len) ;
for (i=0; i<len; i++) {
k = xtypes[i] ;
++popsize[k] ;
wmean[k] += w0[i] ;
}
/* debug */
if (numeg == 2) {
++ncall2 ;
for (i=0; i<len; ++i) {
if (ncall2<0) break ;
k = xtypes[i] ;
// printf("yy %4d %4d %12.6f %12.6f\n", i, k, vec[i], w0[i]) ;
}
}
vsp(popsize, popsize, 1.0e-12, numeg) ;
vvd(wmean, wmean, popsize, numeg) ;
vvt(w1, wmean, wmean, numeg) ;
top = vdot(w1, popsize, numeg) ;
for (i=0; i<len ; i++) {
k = xtypes[i] ;
w1[i] = w0[i] - wmean[k] ;
}
bot = asum2(w1, len) / (double) (len-numeg) ;
bot *= (double) (numeg-1) ;
ftail = rtlf(numeg-1, len-numeg, top/bot) ;
free(w0) ;
free(w1) ;
free(popsize) ;
free(wmean) ;
return ftail ;
}
double binomtail(int n, int t, double p, char c)
{
/**
c = '+': P(S>=t)
c = '-': P(S<t)
WARNING <= t use binomtail(n, t+1, ...
*/
double *bindis ;
double val ;
ZALLOC(bindis, n+1, double) ;
genlogbin(bindis, n, p) ;
vexp(bindis, bindis, n+1) ;
if (c=='+')
val = asum(bindis+t, n-t+1) ;
else
val = asum(bindis, t) ;
free(bindis) ;
return val ;
}
double bal1 (double *a, int n)
// WARNING a is input and output
{
double y ;
y = asum(a, n) ;
if (y<=0.0) fatalx("bad bal1\n") ;
vst(a, a, 1.0/y, n) ;
return y ;
}
double pdinv(double *cinv, double *coeff, int n)
// cinv and coeff can be same
// cinv can be NULL
// return log det (coeff)
{
double *tt;
double *p ;
double t, sum, y ;
int i,j, k ;
/**
pmat(coeff, n) ;
*/
ZALLOC (tt, n*n, double);
ZALLOC (p, n, double );
copyarr(coeff,tt,n*n);
choldc (tt, n, p) ;
for (i=0; i<n; i++) {
tt[i*n+i] = 1.0/p[i] ;
for (j=i+1; j<n; j++) {
sum=0.0 ;
for (k=i; k<j; k++) {
sum -= tt[j*n+k]*tt[k*n+i] ;
}
tt[j*n+i] = sum/p[j] ;
}
}
for (i=0; i<n; i++)
for (j=i; j<n; j++) {
sum=0.0 ;
if (cinv == NULL) break ;
for (k=j; k<n; k++) {
sum += tt[k*n+j]*tt[k*n+i] ;
}
cinv[i*n+j] = cinv[j*n+i] = sum ;
}
vlog(p, p, n) ;
y = 2.0*asum(p, n) ;
free(tt) ;
free(p) ;
return y ;
}
double chitest(double *a, double *p, int n)
/* a is n boxes. Goodness of fit test to p */
{
double *x, *b, *pp ;
double y1=0.0, y2=0.0 ;
int i ;
ZALLOC(pp, n, double) ;
if (p != NULL)
copyarr(p,pp,n) ;
else
vclear(pp, 1.0, n) ;
y1 = asum(pp,n) ;
y2 = asum(a,n) ;
if ( (y1==0.0) || (y2==0.0) ) {
free(pp) ;
return 0.0 ;
}
ZALLOC(x,n,double) ;
ZALLOC(b,n,double) ;
vst (x, pp, y2/y1, n) ; /* expected */
vsp (x, x, .0001, n) ;
vvm (b, a, x, n) ;
vvt (b, b, b, n) ;
vvd (b, b, x, n) ;
y1 = asum(b,n) ;
free(x) ;
free(b) ;
return y1 ;
}
/** this is the code to parallelize */
void
domult(double *tvecs, double *tblock, int numrow, int len)
{
int i ;
double ycheck ;
vzero(tvecs, len*len) ;
for (i=0; i<numrow; i++) {
ycheck = asum(tblock+i*len, len) ;
if (fabs(ycheck)>.00001) fatalx("bad ycheck\n") ;
addoutersym(tvecs, tblock+i*len, len) ;
}
}
void bal(double *a, double *b, int n)
/**
normalize mean 0 s.d 1
*/
{
double t ;
t = asum(b,n)/ (double) n ;
vsp (a, b, -t, n) ;
t = asum2(a,n)/ (double) n ;
vst (a, a, 1.0/sqrt(t), n) ;
}
double twestxx(double *lam, int m, double *pzn, double *pzvar)
{
double tw, y ;
if (twl2mode == NO) return oldtwestxx(lam, m, pzn, pzvar) ;
(void) doeig2(lam, m, pzn, &tw) ;
y = (*pzn) * (double) m ;
*pzvar = asum(lam, m) / y ;
return tw ;
}
double binlogtail(int n, int t, double p, char c)
{
double *bindis ;
double val, base ;
ZALLOC(bindis, n+1, double) ;
genlogbin(bindis, n, p) ;
base = bindis[t] ;
vsp(bindis, bindis, -base, n+1) ;
if (c=='+') {
vexp(bindis+t, bindis+t, n-t+1) ;
val = asum(bindis+t, n-t+1) ;
}
else {
vexp(bindis, bindis, t) ;
val = asum(bindis, t) ;
}
free(bindis) ;
return (log(val) + base) ;
}
void ransamp(int *samp, int nsamp, double *p, int plen)
/**
pick nsamp elements from random distribution
uses randis but array is at least sorted optimally
*/
{
double *px ;
int *indx ;
double y ;
int i, j, k ;
if (plen<=1) {
ivzero(samp, nsamp) ;
return ;
}
ZALLOC(px, plen, double) ;
ZALLOC(indx, plen, int) ;
y = asum(p, plen) ;
vst(px, p, -1.0/y, plen) ;
sortit(px, indx, plen) ;
vst(px, px, -1.0, plen) ;
for (i=0; i<nsamp; i++) {
/**
really need binary chop picker
*/
j = randis(px, plen) ;
if (j<0) {
for (k=0; k<plen; k++) {
printf("zz %d %d %12.6f %12.6f\n",k, indx[k], p[k], px[k]) ;
}
fatalx("bad ransamp\n") ;
}
k = indx[j] ;
samp[i] = k ;
}
free (px) ;
free (indx) ;
}
double
dotwcalc(double *lambda, int m, double *ptw, double *pzn, double *pzvar, int minm)
{
double nv, mv, tzn, tm ;
double *evals ;
double y, top, bot, zn, tw, ystat ;
double tail, lsum ;
if (m<minm) {
*pzn = *pzvar = *ptw = -1 ;
return -1.0 ;
}
lsum = asum(lambda, m) ;
if (lsum<=0.0) {
*pzn = *pzvar = *ptw = -1 ;
return -1.0 ;
}
tzn = *pzn ;
tm = (double) m ;
y = (double) m / lsum ;
ystat = lambda[0] * y * tzn ;
if (tzn>0.0) {
tw = twnorm(ystat, tm, tzn) ;
*pzn = tzn ;
*ptw = tw ;
tail = twtail(tw) ;
return tail ;
}
ZALLOC(evals, m, double) ;
vst(evals, lambda, y, m) ;
top = (double) (m*(m+2)) ;
bot = asum2(evals, m) - (double) m ;
zn = top/bot ; // see appendix to eigenpaper NJP
y = evals[0]*zn ;
tw = twnorm(y, tm, zn) ;
*pzn = zn ;
*ptw = tw ;
tail = twtail(tw) ;
free(evals) ;
return tail ;
}
double
anova1 (double *vec, int len, int *xtypes, int numeg)
{
int i, k;
double y1, y2, ylike;
double *w0, *w1, *popsize, *wmean;
ZALLOC(w0, len, double);
ZALLOC(w1, len, double);
ZALLOC(wmean, numeg, double);
ZALLOC(popsize, numeg, double);
y1 = asum (vec, len) / (double) len; // mean
vsp (w0, vec, -y1, len);
for (i = 0; i < len; i++)
{
k = xtypes[i];
++popsize[k];
wmean[k] += w0[i];
}
vsp (popsize, popsize, 1.0e-12, numeg);
vvd (wmean, wmean, popsize, numeg);
for (i = 0; i < len; i++)
{
k = xtypes[i];
w1[i] = w0[i] - wmean[k];
}
y1 = asum2 (w0, len) / (double) len;
y2 = asum2 (w1, len) / (double) len;
ylike = 0.5 * ((double) len) * log (y1 / y2);
free (w0);
free (w1);
free (popsize);
free (wmean);
return ylike;
}
static Point_2 centroid(const Polygon_2& poly)
{
assert(poly.size() >= 3);
Polygon_2::Vertex_circulator vcir = poly.vertices_circulator();
Polygon_2::Vertex_circulator vend = vcir;
Polygon_2::Vertex_circulator vnext = vcir; ++vnext;
Vector_2 centre(0, 0);
NT a(0), asum(0);
do {
a = (vcir->x() * vnext->y()) - (vnext->x() * vcir->y());
centre = centre + a * ((*vcir - CGAL::ORIGIN) + (*vnext - CGAL::ORIGIN)); // slow...
asum += a;
vcir = vnext;
++vnext;
} while(vcir != vend);
centre = centre / (asum * 3);
return CGAL::ORIGIN + centre;
}
double hwstat(double *x)
/** Hardy-Weinberg equilibrium test
returns standard normal in null case.
+sign is excess heterozygosity
x[0] [1] [2] are counts for homozm hetero h**o (alt allele)
*/
{
double p, q, ysum, s1, y1, y2, ychi, sig ;
double a1[3], a2[3] ;
ysum = asum(x,3) ;
if (ysum < 0.001) return 0.0 ;
s1 = 2*x[2]+x[1] ;
p = 0.5*s1/ysum;
q = 1.0-p ;
a1 [0] = q*q ;
a1 [1] = 2*p*q ;
a1 [2] = p*p ;
vsp(a1, a1, 1.0e-8, 3) ;
vst(a2, x, 1.0/ysum, 3) ;
vsp(a2, a2, 1.0e-8, 3) ;
y2 = vldot(x, a2, 3) ;
y1 = vldot(x, a1, 3) ;
ychi = 2.0*(y2-y1) ;
sig = sqrt(ychi+1.0e-8) ;
if (a2[1]<a1[1]) sig = -sig ;
/* negative => hets lo */
return sig ;
}
double doeig2(double *vals, int m, double *pzn, double *ptw)
{
static int ncall = 0 ;
double y, tw, tail ;
double zn, top, bot ;
double *evals ;
++ncall ;
ZALLOC(evals, m, double) ;
copyarr(vals, evals, m) ;
y = (double) m / asum(evals, m) ;
vst(evals, evals, y, m) ;
top = (double) (m*(m+2)) ;
bot = asum2(evals, m) - (double) m ;
zn = top/bot ;
y = evals[0]*zn ;
tw = twnorm(y, (double) m, zn) ;
tail = twtail(tw) ;
free(evals) ;
*pzn = zn ;
*ptw = tw ;
return tail ;
}
int
ridoutlier (double *evecs, int n, int neigs, double thresh, int *badlist,
OUTLINFO **outinfo)
{
/* badlist contains list of outliers */
double *ww, *w2, y1, y2, yy, zz;
int *vbad;
int i, j;
int nbad = 0;
OUTLINFO *outpt;
if (outliermode > 1)
return 0;
if (n < 3)
return 0;
ZALLOC(ww, n, double);
ZALLOC(vbad, n, int);
for (j = 0; j < n; j++)
{
outpt = outinfo[j];
outpt->vecno = -1;
}
for (i = 0; i < neigs; ++i)
{
copyarr (evecs + i * n, ww, n);
if (outliermode == 0)
{
y1 = asum (ww, n) / (double) n;
vsp (ww, ww, -y1, n);
y2 = asum2 (ww, n) / (double) n;
y2 = sqrt (y2);
vst (ww, ww, 1.0 / y2, n);
for (j = 0; j < n; j++)
{
if (fabs (ww[j]) > thresh)
{
vbad[j] = 1;
outpt = outinfo[j];
if (outpt->vecno < 0)
{
outpt->vecno = i;
outpt->score = ww[j];
}
}
}
}
if (outliermode == 1)
{
ZALLOC(w2, n, double);
for (j = 0; j < n; j++)
{
yy = ww[j];
ww[j] = 0;
y1 = asum (ww, n) / (double) (n - 1);
vsp (w2, ww, -y1, n);
w2[j] = 0;
y2 = asum2 (w2, n) / (double) n;
y2 = sqrt (y2);
zz = yy - y1;
zz /= y2;
if (fabs (zz) > thresh)
{
vbad[j] = 1;
outpt = outinfo[j];
if (outpt->vecno < 0)
{
outpt->vecno = i;
outpt->score = zz;
}
}
ww[j] = yy;
}
free (w2);
}
}
for (j = 0; j < n; j++)
{
if (vbad[j] == 1)
{
badlist[nbad] = j;
++nbad;
}
}
free (ww);
free (vbad);
return nbad;
}
template<class T> void asum(const hoNDArray<T>& x, typename realType<T>::Type& r)
{
asum(x.get_number_of_elements(), x.begin(), r);
}
template<class T> typename realType<T>::Type asum(const hoNDArray<T>& x)
{
typename realType<T>::Type r;
asum(x, r);
return r;
}
int main(){
srand(time(0));
size_t n = 100;
std::complex<double> *A = new std::complex<double>[n*n];
std::complex<double> *Acopy = new std::complex<double>[n*n];
std::complex<double> *w = new std::complex<double>[n];
std::complex<double> *U = new std::complex<double>[n*n];
std::complex<double> *V = new std::complex<double>[n*n];
for(size_t i = 0; i < n; ++i){
for(size_t j = 0; j < n; ++j){
A[i+j*n] = crand();
}
}
//makeid(n,n,A);
/*
A[1+0*n] = frand();
A[2+1*n] = frand();
A[2+0*n] = frand();
makesym(n,n,A);
*/
//print(n,n,A); std::cout << std::endl;
for(size_t i = 0; i < n; ++i){
for(size_t j = 0; j < n; ++j){
Acopy[i+j*n] = A[i+j*n];
}
}
size_t lwork = 2*n;
std::complex<double> *work = new std::complex<double>[lwork];
size_t lrwork = 8*n;
double *rwork = new double[lrwork];
int info;
info = RNP::Eigensystem(n,A,n,w,U,n,V,n, work,rwork);
delete [] work;
delete [] rwork;
//std::cout << "alpha = "; print(n,alpha); std::cout << std::endl;
//std::cout << "beta = "; print(n,beta ); std::cout << std::endl;
std::cout << "Info = " << info << std::endl;
// Verify
std::complex<double> *temp = new std::complex<double>[n*n];
double maxerr = 0;
for(size_t i = 0; i < n; ++i){
// Compute A*V - w*V
for(size_t j = 0; j < n; ++j){
std::complex<double> asum(0);
for(size_t k = 0; k < n; ++k){
asum += Acopy[i+k*n]*V[k+j*n];
}
temp[i+j*n] = asum-w[j]*V[i+j*n];
double curerr = std::abs(temp[i+j*n]);
if(curerr > maxerr){ maxerr = curerr; }
}
}
//print(n,n,temp); std::cout << std::endl;
std::cout << "Max err = " << maxerr << std::endl;
maxerr = 0;
for(size_t i = 0; i < n; ++i){
// Compute beta*U^H*A - alpha*U^H*B
for(size_t j = 0; j < n; ++j){
std::complex<double> asum(0);
for(size_t k = 0; k < n; ++k){
asum += Acopy[k+j*n]*std::conj(U[k+i*n]);
}
temp[i+j*n] = asum-w[i]*std::conj(U[i+j*n]);
double curerr = std::abs(temp[i+j*n]);
if(curerr > maxerr){ maxerr = curerr; }
}
}
//print(n,n,temp); std::cout << std::endl;
std::cout << "Max err = " << maxerr << std::endl;
delete [] temp;
//print(n,evals); std::cout << std::endl;
//print(n,n,evecs); std::cout << std::endl;
delete [] A;
delete [] Acopy;
delete [] w;
delete [] U;
delete [] V;
return 0;
}
int gpuBufferSensePrepGadget::process(
GadgetContainerMessage<IsmrmrdReconData>* m1) {
IsmrmrdReconData* recondata= m1->getObjectPtr();
if (recondata->rbit_.size() != 1){
throw std::runtime_error("gpuBufferSensePrepGadget only support a single encoding space");
}
IsmrmrdReconBit& reconbit = recondata->rbit_[0];
GenericReconJob job;
IsmrmrdDataBuffered* buffer = &reconbit.data_;
//Use reference data if available.
if (reconbit.ref_){
GDEBUG("Using Reference data for CSM estimation\n");
buffer = reconbit.ref_.get_ptr();
}
size_t ncoils = buffer->headers_[0].active_channels;
std::vector<size_t> new_order = {0,1,2,4,5,6,3};
boost::shared_ptr<cuNDArray<float>> dcw;
boost::shared_ptr<cuNDArray<floatd2>> traj;
if (buffer->trajectory_){
auto & trajectory = *buffer->trajectory_;
if (buffer->headers_[0].trajectory_dimensions == 3){
auto traj_dcw = separate_traj_and_dcw(&trajectory);
dcw = boost::make_shared<cuNDArray<float>>(std::get<1>(traj_dcw).get());
traj = boost::make_shared<cuNDArray<floatd2>>(std::get<0>(traj_dcw).get());
} else if (buffer->headers_[0].trajectory_dimensions == 2){
auto old_traj_dims = *trajectory.get_dimensions();
std::vector<size_t> traj_dims (old_traj_dims.begin()+1,old_traj_dims.end()); //Remove first element
hoNDArray<floatd2> tmp_traj(traj_dims,(floatd2*)trajectory.get_data_ptr());
traj = boost::make_shared<cuNDArray<floatd2>>(tmp_traj);
} else {
throw std::runtime_error("Unsupported number of trajectory dimensions");
}
}
{
auto tmpdim = *buffer->data_.get_dimensions();
for (auto dim : tmpdim)
std::cout << dim << " ";
std::cout << std::endl;
auto permuted = permute((hoNDArray<float_complext>*)&buffer->data_,&new_order);
cuNDArray<float_complext> data(*permuted);
if (dcw){
float scale_factor = float(prod(image_dims_recon_os_))/asum(dcw.get());
*dcw *= scale_factor;
}
auto reg_images = reconstruct_regularization(&data,traj.get(),dcw.get(),ncoils);
//reg_images->squeeze();
auto csm = estimate_b1_map<float,2>(reg_images.get());
*reg_images *= *csm;
auto combined = sum(reg_images.get(),reg_images->get_number_of_dimensions()-1);
auto tmp_combined = abs(reg_images.get());
auto tmpcsm = abs(csm.get());
job.csm_host_ = csm->to_host();
job.reg_host_ = combined->to_host();
}
IsmrmrdDataBuffered* mainbuffer = &reconbit.data_;
//Permute as Sensegadgets expect last dimension to be coils. *Sigh*
job.dat_host_ =permute((hoNDArray<float_complext>*)&mainbuffer->data_,&new_order);
if (mainbuffer->trajectory_){
auto & trajectory = *mainbuffer->trajectory_;
if (mainbuffer->headers_[0].trajectory_dimensions >2 ){
auto traj_dcw = separate_traj_and_dcw(&trajectory);
job.tra_host_ = std::get<0>(traj_dcw);
job.dcw_host_ = std::get<1>(traj_dcw);
} else if (mainbuffer->headers_[0].trajectory_dimensions == 2){
auto old_traj_dims = *trajectory.get_dimensions();
std::vector<size_t> traj_dims (old_traj_dims.begin()+1,old_traj_dims.end()); //Remove first element
hoNDArray<floatd2> tmp_traj(traj_dims,(floatd2*)trajectory.get_data_ptr());
job.tra_host_ = boost::make_shared<hoNDArray<floatd2>>(tmp_traj);
auto host_dcw = boost::make_shared<hoNDArray<float>>(traj_dims);
fill(host_dcw.get(),1.0f);
job.dcw_host_ = host_dcw;
} else {
throw std::runtime_error("Unsupported number of trajectory dimensions");
}
}
{
float scale_factor = float(prod(image_dims_recon_os_))/asum(job.dcw_host_.get());
*job.dcw_host_ *= scale_factor;
}
auto data_dims = *job.dat_host_->get_dimensions();
//Sense gadgets expect only 1 dimension for encoding, so collapse the first
size_t elements = std::accumulate(data_dims.begin(),data_dims.end()-1,1,std::multiplies<size_t>());
std::vector<size_t> new_data_dims = {elements,data_dims.back()};
job.dat_host_->reshape(&new_data_dims);
size_t traj_elements = job.tra_host_->get_number_of_elements();
auto traj_dims = *job.tra_host_->get_dimensions();
size_t kpoints_per_frame = traj_dims[0]*profiles_per_frame_;
if (traj_elements%kpoints_per_frame){
std::stringstream ss;
ss << "Profiles per frame (" << profiles_per_frame_ << ") must be a divisor of total number of profiles (" << traj_elements/traj_dims[0] << ")";
throw std::runtime_error(ss.str());
}
std::vector<size_t> new_traj_dims ={kpoints_per_frame,traj_elements/kpoints_per_frame};
job.tra_host_->reshape(&new_traj_dims);
job.dcw_host_->reshape(&new_traj_dims);
//Let's invent some image headers!
size_t total_frames = profiles_per_frame_ > 0 ? mainbuffer->headers_.get_number_of_elements()/profiles_per_frame_ : 1 ;
job.image_headers_ = boost::shared_array<ISMRMRD::ImageHeader>(new ISMRMRD::ImageHeader[total_frames]);
for (size_t i = 0; i < total_frames; i++){
job.image_headers_[i] = create_image_header(mainbuffer->headers_[i*profiles_per_frame_],mainbuffer->sampling_,i,total_frames);
}
m1->release(); //We be done with everything now.
auto header_message = new GadgetContainerMessage<ISMRMRD::ImageHeader>(job.image_headers_[0]);
auto job_message = new GadgetContainerMessage<GenericReconJob>(job);
header_message->cont(job_message);
if (!this->next()->putq(header_message)){
GDEBUG("Failed to put message on que");
return GADGET_FAIL;
} else
return GADGET_OK;
//cuNDArray<float_complext> reg_images = reconstruct_regularization(reconbit.data_);
}
void
dof2score(double *f2score, double *f2scoresig, SNP **xsnplist, int *xindex, int *xtypes,
int nrows, int ncols, int numeg, int nblocks)
{
int t1, t2 ;
int a, b, c, d ;
int c1[2], c2[2], *cc ;
int *rawcol, *popall, *pop0, *pop1 ;
int k, g, i, col, j ;
double ya, yb, y, jest, jsig, mean ;
SNP *cupt ;
double top, bot, *djack, *wjack, gtop, gbot, *wbot, *wtop ;
double *btop, *bbot, wt ;
double ytop, ybot ;
double y1, y2, yscal ;
double *w1, *w2, *ww, m1, m2 ;
int bnum, totnum ;
if (nrows==0) fatalx("badbug\n") ;
ZALLOC(w1, nblocks, double) ;
ZALLOC(w2, nblocks, double) ;
ZALLOC(ww, nblocks, double) ;
ZALLOC(wjack, nblocks, double) ;
ZALLOC(djack, nblocks, double) ;
ZALLOC(btop, nblocks, double) ;
ZALLOC(bbot, nblocks, double) ;
ZALLOC(wtop, nblocks, double) ;
ZALLOC(wbot, nblocks, double) ;
setjquart(NO, YES, -1.0) ;
totnum = 0 ;
for (col=0; col<ncols; ++col) {
cupt = xsnplist[col] ;
if (cupt -> ignore) continue ;
bnum = cupt -> tagnumber ;
if (bnum<0) continue ;
if (bnum>=nblocks) fatalx("logic bug\n") ;
f2sc(&ytop, &ybot, cupt, indivmarkers, xindex, xtypes, nrows, 2, 0, 1) ;
if (isnan(ytop)) fatalx("zznan\n") ;
if (ybot < -0.5) continue ;
btop[bnum] += ytop ;
bbot[bnum] += ybot ;
++wjack[bnum] ;
++totnum ;
}
gtop = asum(btop, nblocks) ;
gbot = asum(bbot, nblocks) ;
*f2score = mean = gtop/gbot ;
for (k=0; k<nblocks; k++) {
top = btop[k] ;
bot = bbot[k] ;
wtop[k] = gtop-top ;
wbot[k] = gbot-bot ;
wbot[k] += 1.0e-10 ;
djack[k] = wtop[k]/wbot[k] ; // delete-block estimate
}
wjackest(&jest, &jsig, mean, djack, wjack, nblocks) ;
*f2scoresig = jsig ;
free(w1) ;
free(w2) ;
free(ww) ;
free(wtop) ;
free(wbot) ;
free(djack) ;
free(wjack) ;
free(btop) ;
free(bbot) ;
}
void
dof3score(double *f3score, double *f3scoresig, SNP **xsnplist, int *xindex, int *xtypes,
int nrows, int ncols, int numeg, int nblocks)
{
int t1, t2 ;
int a, b, c, d ;
int c1[2], c2[2], *cc ;
int *rawcol, *popall, *pop0, *pop1 ;
int k, g, i, col, j ;
double ya, yb, y, jest, jsig, mean ;
SNP *cupt ;
double top, bot, *djack, *wjack, gtop, gbot, *wbot, *wtop ;
double *btop, *bbot, wt ;
double ytop, ybot ;
double y1, y2, yscal ;
double *w1, *w2, *ww, m1, m2 ;
int bnum, totnum ;
FILE *fff ;
double xn[3], xmean[3], xh[3] ;
if (snpdetailsname != NULL) openit(snpdetailsname, &fff, "w") ;
if (nrows==0) fatalx("badbug\n") ;
ZALLOC(w1, nblocks, double) ;
ZALLOC(w2, nblocks, double) ;
ZALLOC(ww, nblocks, double) ;
ZALLOC(wjack, nblocks, double) ;
ZALLOC(djack, nblocks, double) ;
ZALLOC(btop, nblocks, double) ;
ZALLOC(bbot, nblocks, double) ;
ZALLOC(wtop, nblocks, double) ;
ZALLOC(wbot, nblocks, double) ;
setjquart(pubjack, jackweight, jackquart) ;
totnum = 0 ;
for (col=0; col<ncols; ++col) {
cupt = xsnplist[col] ;
if (cupt -> ignore) continue ;
bnum = cupt -> tagnumber ;
if (bnum<0) continue ;
if (bnum>=nblocks) fatalx("logic bug\n") ;
f3sc(&ytop, &ybot, cupt, indivmarkers, xindex, xtypes, nrows, 2, 0, 1) ;
if (isnan(ytop)) fatalx("zznan\n") ;
if (ybot < -0.5) continue ;
if ((dzeromode == NO) && (ybot<=0.001)) continue ;
if (snpdetailsname != NULL) {
finfo(xn+0, xmean+0, xh+0, 0) ;
finfo(xn+1, xmean+1, xh+1, 1) ;
finfo(xn+2, xmean+2, xh+2, 2) ; // Sardin Karit CEU
fprintf(fff, "%20s ", cupt -> ID) ;
for (a=0; a<=2; ++a) {
fprintf(fff, " %6.0f", xn[a]) ;
fprintf(fff, " %9.3f", xmean[a]) ;
fprintf(fff, " %9.3f", xh[a]) ;
}
fprintf(fff, " %9.3f ", ytop) ;
// fprintf(fff, "%9.3f ", ybot/2.0) ;
fprintf(fff, " %c ", cupt -> alleles[0]) ;
fprintf(fff, "%c", cupt -> alleles[1]) ;
fprintf(fff, "\n") ;
}
btop[bnum] += ytop ;
bbot[bnum] += ybot ;
++wjack[bnum] ;
++totnum ;
}
if (totnum <= 1) fatalx("no data...\n") ;
/**
printf("totnum: %d ", totnum) ;
printmat(wjack, 1, 10) ;
*/
gtop = asum(btop, nblocks) ;
gbot = asum(bbot, nblocks) ;
*f3score = mean = gtop/gbot ;
for (k=0; k<nblocks; k++) {
top = btop[k] ;
bot = bbot[k] ;
wtop[k] = gtop-top ;
wbot[k] = gbot-bot ;
wbot[k] += 1.0e-10 ;
djack[k] = wtop[k]/wbot[k] ; // delete-block estimate
}
estjackq(&jest, &jsig, btop, bbot, wjack, nblocks) ;
*f3score = jest ;
*f3scoresig = jsig ;
free(w1) ;
free(w2) ;
free(ww) ;
free(wtop) ;
free(wbot) ;
free(djack) ;
free(wjack) ;
free(btop) ;
free(bbot) ;
if (snpdetailsname != NULL) fclose(fff) ;
}