void ANCFBeamBE2D::GetH(Matrix& H)
{
if (Hmatrix.Getrows() == SOS())
{
H = Hmatrix;
return;
}
else
{
double A = this->GetMaterial().BeamRhoA() / this->GetMaterial().Density();
H.SetSize(SOS(), Dim());
H.SetAll(0);
for (IntegrationPointsIterator ip(integrationRuleLoad); !ip.IsEnd(); ++ip)
{
double x = ip.Point2D().X();
// jacobi determinant
//Vector2D rx0 = GetRefPosx2D(x);
double det = 0.5*GetLx(); //*rx0.Norm();
double d = A * det * ip.Weight();
for (int i = 1; i <= NS(); i++)
{
double s = GetS0(x, i);
H(2*i-1, 1) += d * s;
H(2*i, 2) += d * s; //H(2*i-1, 1);
}
}
Hmatrix = H;
}
};
void ANCFBeamBE2D::EvalM(Matrix& m, double t)
{
if (this->massmatrix.Getrows() != 0) // mass matrix already computed
{
m = massmatrix;
return;
}
Matrix H(Dim(), SOS());
massmatrix.SetSize(SOS(), SOS());
massmatrix.SetAll(0.);
double rhoA = GetBeamRhoA();
for (IntegrationPointsIterator ip(integrationRuleMass); !ip.IsEnd(); ++ip)
{
for (int i = 1; i <= NS(); i++)
{
H(1, 2*i-1) = GetS0(ip.Point2D().X(), i);
H(2, 2*i) = H(1, 2*i-1);
}
H = (0.5*GetLx()*rhoA*ip.Weight()) * (H.GetTp() * H);
massmatrix += H;
}
m = massmatrix;
};
void testSnappyStream()
{
libmaus::autoarray::AutoArray<char> A = ::libmaus::aio::SynchronousGenericInput<char>::readArray("configure");
std::string const message(A.begin(),A.end()) ;
std::ostringstream ostr;
::libmaus::lz::SnappyOutputStream<std::ostringstream> SOS(ostr,64*1024);
SOS.write(A.begin(),A.size());
SOS.flush();
ostr.flush();
std::string const & streamdata = ostr.str();
::libmaus::lz::SnappyStringInputStream SIS(streamdata);
std::ostringstream comp;
int c = -1;
while ( (c = SIS.get()) != -1 )
comp.put(c);
::libmaus::lz::SnappyStringInputStream SISB(streamdata);
libmaus::autoarray::AutoArray<char> B(A.size(),false);
char * p = B.begin();
uint64_t d;
while ( (d = SISB.read(p,64*1024)) != 0 )
p += d;
assert ( std::string(B.begin(),B.end()) == message );
std::cerr << "block stream test " << ((comp.str()==message)?"ok":"FAILED") << std::endl;
}
void Constraint::LinkToElementsPenalty()
{
if (IS()!=0 && SOS()!=0)
{
UO(UO_LVL_err) << "Error: Constraint::LinkToElementsPenalty() is not possible for mixed penalty/Lagrange elements\n";
}
LTGreset();
// add all SOS dofs from the elements
//Position(first SOS)
for (int k=1; k <= NE(); k++)
{
for (int i=1; i <= GetElem(k).SOS(); i++)
{
AddLTG(GetElem(k).LTG(i));
}
}
//and Velocity (second SOS):
for (int k=1; k <= NE(); k++)
{
for (int i=1; i <= GetElem(k).SOS(); i++)
{
AddLTG(GetElem(k).LTG(i+GetElem(k).SOS()));
}
}
}
void ANCFBeamBE2D::GetdPosdqT(const Vector2D& p_loc, Matrix& dpdqi)
{
//p = S(p.x,p.y,p.z)*q; d(p)/dq
dpdqi.SetSize(SOS(),Dim());
dpdqi.FillWithZeros();
//d = S + ...
for (int i = 1; i <= NS(); i++)
{
double s = GetS0(p_loc.X(), i);
dpdqi((i-1)*Dim()+1,1) = s;
dpdqi((i-1)*Dim()+2,2) = s;
}
if (p_loc.Y() != 0)
{
double y = p_loc.Y();
Vector2D rx = GetPosx2D(p_loc.X());
Vector2D n(-rx.X(), rx.Y());
n /= rx.Norm();
for (int i = 1; i <= NS(); i++)
{
double sx = GetS0x(p_loc.X(), i) * 2./GetLx();
//y/|n|*dn/dq
dpdqi((i-1)*Dim()+1,2) += y*sx;
dpdqi((i-1)*Dim()+2,1) += -y*sx;
//y*n/|n|*(r_x1*S_x1 + r_x2*S_x2)
dpdqi((i-1)*Dim()+1,1) += y*n.X()*(rx.X()*sx);
dpdqi((i-1)*Dim()+1,2) += y*n.Y()*(rx.X()*sx);
dpdqi((i-1)*Dim()+2,1) += y*n.X()*(rx.Y()*sx);
dpdqi((i-1)*Dim()+2,2) += y*n.Y()*(rx.Y()*sx);
}
}
};
void ImageFilter<T>::SOS(ImageSize reconSize)
{
SOS(m_associatedData, reconSize);
for (auto &data : *m_associatedData.getChannelImage(0))
{
data = std::sqrt(data);
}
}
//this function assigns default values to the element variables
void Mass1D::ElementDefaultConstructorInitialization()
{
type = TBody;
drawres = 8;
x_init = Vector(2*SOS()); //zero initialized
elementname = GetElementSpec();
radius = 0.1; // DR just some default value
pref3D = Vector3D(0.);
rotref3D = Matrix3D(1.);
}
void _jn516_custom_exception_bus_error(uint32* pu32Stack, int type) {
unsigned char TX_BUFFER[100];
LED_INIT();
UART_INIT(TX_BUFFER);
while (TRUE) {
SOS();
BLINK(1);
vDebug("Bus Error\n");
PRINT_ADDRESSES(pu32Stack);
LONG_OFF();
}
}
void _jn516_custom_exception_stack_overflow(uint32* pu32Stack, int type) {
unsigned char TX_BUFFER[100];
LED_INIT();
UART_INIT(TX_BUFFER);
while (TRUE) {
SOS();
BLINK(7);
vDebug("Stack Overflow\n");
PRINT_ADDRESSES(pu32Stack);
LONG_OFF();
}
}
void _jn516_custom_exception_illegal_instruction(uint32* pu32Stack, int type) {
unsigned char TX_BUFFER[100];
LED_INIT();
UART_INIT(TX_BUFFER);
while (TRUE) {
SOS();
BLINK(3);
vDebug("Illegal Instruction\n");
PRINT_ADDRESSES(pu32Stack);
LONG_OFF();
}
}
void _jn516_custom_exception_unaligned_access(uint32* pu32Stack, int type) {
unsigned char TX_BUFFER[100];
LED_INIT();
UART_INIT(TX_BUFFER);
while (TRUE) {
SOS();
BLINK(2);
vDebug("Unaligned Access\n");
PRINT_ADDRESSES(pu32Stack);
LONG_OFF();
}
}
#define KMZ_CREATEZONE ((void *)-2)
#define KMZ_LOOKUPZONE ((void *)-1)
#define KMZ_MALLOC ((void *)0)
#define KMZ_SHAREZONE ((void *)1)
struct kmzones {
size_t kz_elemsize;
void *kz_zalloczone;
boolean_t kz_noencrypt;
} kmzones[M_LAST] = {
#define SOS(sname) sizeof (struct sname)
#define SOX(sname) -1
{ -1, 0, FALSE }, /* 0 M_FREE */
{ MSIZE, KMZ_CREATEZONE, FALSE }, /* 1 M_MBUF */
{ 0, KMZ_MALLOC, FALSE }, /* 2 M_DEVBUF */
{ SOS(socket), KMZ_CREATEZONE, TRUE }, /* 3 M_SOCKET */
{ SOS(inpcb), KMZ_LOOKUPZONE, TRUE }, /* 4 M_PCB */
{ M_MBUF, KMZ_SHAREZONE, FALSE }, /* 5 M_RTABLE */
{ M_MBUF, KMZ_SHAREZONE, FALSE }, /* 6 M_HTABLE */
{ M_MBUF, KMZ_SHAREZONE, FALSE }, /* 7 M_FTABLE */
{ SOS(rusage), KMZ_CREATEZONE, TRUE }, /* 8 M_ZOMBIE */
{ 0, KMZ_MALLOC, FALSE }, /* 9 M_IFADDR */
{ M_MBUF, KMZ_SHAREZONE, FALSE }, /* 10 M_SOOPTS */
{ 0, KMZ_MALLOC, FALSE }, /* 11 M_SONAME */
{ MAXPATHLEN, KMZ_CREATEZONE, FALSE }, /* 12 M_NAMEI */
{ 0, KMZ_MALLOC, FALSE }, /* 13 M_GPROF */
{ 0, KMZ_MALLOC, FALSE }, /* 14 M_IOCTLOPS */
{ 0, KMZ_MALLOC, FALSE }, /* 15 M_MAPMEM */
{ SOS(ucred), KMZ_CREATEZONE, FALSE }, /* 16 M_CRED */
{ SOS(pgrp), KMZ_CREATEZONE, FALSE }, /* 17 M_PGRP */
{ SOS(session), KMZ_CREATEZONE, FALSE }, /* 18 M_SESSION */
int main(int argc, char *argv[])
{
ProgramOptions options(argc, argv);
options.showParameters();
ReconParameters params = options.getReconParameters();
// -------------- Load multi-channel data -----------------
auto reconData = ReconData<float>::Create(params.samples, params.projections, options.isGPU());
loadReconData(params, reconData.get());
unsigned threads = std::min(reconData->channels(), omp_get_num_procs());
QElapsedTimer timer0, timer;
timer0.start();
// -------------- Gridding -------------------------------
timer.start();
auto grid = GridLut<float>::Create(*reconData);
#ifdef BUILD_CUDA
if (options.isGPU()) {
dynamic_cast<cuGridLut<float> *>(grid.get())->setNumOfPartitions(25);
}
#endif // BUILD_CUDA
grid->setNumOfThreads(threads);
grid->plan(params.rcxres, params.overgridding_factor, params.kernel_width, 512);
auto imgData = grid->execute();
std::cout << "Gridding total time " << timer.elapsed() << " ms" << std::endl;
ImageData<float> imgMap;
if (params.pils)
imgMap = *imgData;
auto filter = ImageFilter<float>::Create(*imgData);
filter->setNumOfThreads(threads);
// --------------- FFT ----------------------------------
filter->fftPlan();
timer.restart();
filter->fftExecute();
filter->fftShift();
std::cout << "FFT total time " << timer.restart() << " ms" << std::endl;
// -------------- Recon Methods -----------------------------------
timer.restart();
if (params.pils) {
auto filterMap = ImageFilter<float>::Create(imgMap);
std::cout << "\nRecon PILS... " << std::endl;
filterMap->lowFilter(22);
std::cout << "\nLow pass filtering | " << timer.restart() << " ms" << std::endl;
std::cout << "\nFFT low res image... " << std::endl;
filterMap->fftExecute();
filterMap->fftShift();
std::cout << "FFT total time " << timer.restart() << " ms" << std::endl;
filterMap->normalize();
std::cout << "\nSum of Square Field Map..." << std::flush;
filter->SOS(imgMap, {params.rcxres, params.rcyres, params.rczres});
std::cout << " | " << timer.elapsed() << " ms" << std::endl;
}
else
{
std::cout << "\nRecon SOS... " << std::flush;
filter->SOS({params.rcxres, params.rcyres, params.rczres});
std::cout << " | " << timer.elapsed() << " ms" << std::endl;
}
std::cout << "\nProgram total time excluding I/O: " << timer0.elapsed() / 1000.0 << " s" << std::endl;
// -------------------------- Save Data ---------------------------
QFile file(params.path + params.outFile);
file.open(QIODevice::WriteOnly);
for (const auto &data : *imgData->getChannelImage()) {
auto value = std::abs(data);
file.write((const char *)&value, sizeof(decltype(value)));
}
file.close();
// -------------------------- Display Data -----------------------
int n = 0;
if (options.isDisplay())
{
QApplication app(argc, argv);
for (int i = 0; i < imgData->channels(); i++)
{
auto data = imgData->getChannelImage(i);
displayData(*data, imgData->imageSize(), QString("channel ") + QString::number(n++));
}
return app.exec();
}
else
return 0;
}
/* for use with kmzones.kz_zalloczone */
#define KMZ_CREATEZONE ((void *)-2)
#define KMZ_LOOKUPZONE ((void *)-1)
#define KMZ_MALLOC ((void *)0)
#define KMZ_SHAREZONE ((void *)1)
struct kmzones {
size_t kz_elemsize;
void *kz_zalloczone;
} kmzones[M_LAST] = {
#define SOS(sname) sizeof (struct sname)
#define SOX(sname) -1
{ -1, 0 }, /* 0 M_FREE */
{ MSIZE, KMZ_CREATEZONE }, /* 1 M_MBUF */
{ 0, KMZ_MALLOC }, /* 2 M_DEVBUF */
{ SOS(socket), KMZ_CREATEZONE }, /* 3 M_SOCKET */
{ SOS(inpcb), KMZ_LOOKUPZONE }, /* 4 M_PCB */
{ M_MBUF, KMZ_SHAREZONE }, /* 5 M_RTABLE */
{ M_MBUF, KMZ_SHAREZONE }, /* 6 M_HTABLE */
{ M_MBUF, KMZ_SHAREZONE }, /* 7 M_FTABLE */
{ SOS(rusage), KMZ_CREATEZONE }, /* 8 M_ZOMBIE */
{ 0, KMZ_MALLOC }, /* 9 M_IFADDR */
{ M_MBUF, KMZ_SHAREZONE }, /* 10 M_SOOPTS */
{ 0, KMZ_MALLOC }, /* 11 M_SONAME */
{ MAXPATHLEN, KMZ_CREATEZONE }, /* 12 M_NAMEI */
{ 0, KMZ_MALLOC }, /* 13 M_GPROF */
{ 0, KMZ_MALLOC }, /* 14 M_IOCTLOPS */
{ 0, KMZ_MALLOC }, /* 15 M_MAPMEM */
{ SOS(ucred), KMZ_CREATEZONE }, /* 16 M_CRED */
{ SOS(pgrp), KMZ_CREATEZONE }, /* 17 M_PGRP */
{ SOS(session), KMZ_CREATEZONE }, /* 18 M_SESSION */
