template <bool align> void BgrToYuv422p(const uint8_t * bgr, size_t width, size_t height, size_t bgrStride, uint8_t * y, size_t yStride,
uint8_t * u, size_t uStride, uint8_t * v, size_t vStride)
{
assert((width % 2 == 0) && (width >= DA));
if (align)
{
assert(Aligned(y) && Aligned(yStride) && Aligned(u) && Aligned(uStride));
assert(Aligned(v) && Aligned(vStride) && Aligned(bgr) && Aligned(bgrStride));
}
size_t alignedWidth = AlignLo(width, DA);
const size_t A6 = A * 6;
for (size_t row = 0; row < height; ++row)
{
Storer<align> _y(y), _u(u), _v(v);
BgrToYuv422p<align, true>(bgr, _y, _u, _v);
for (size_t col = DA, colBgr = A6; col < alignedWidth; col += DA, colBgr += A6)
BgrToYuv422p<align, false>(bgr + colBgr, _y, _u, _v);
Flush(_y, _u, _v);
if (width != alignedWidth)
{
size_t offset = width - DA;
Storer<false> _y(y + offset), _u(u + offset / 2), _v(v + offset / 2);
BgrToYuv422p<false, true>(bgr + offset * 3, _y, _u, _v);
Flush(_y, _u, _v);
}
y += yStride;
u += uStride;
v += vStride;
bgr += bgrStride;
}
}
template <bool align> void BgrToYuv444p(const uint8_t * bgr, size_t width, size_t height, size_t bgrStride, uint8_t * y, size_t yStride,
uint8_t * u, size_t uStride, uint8_t * v, size_t vStride)
{
assert(width >= A);
if (align)
{
assert(Aligned(y) && Aligned(yStride) && Aligned(u) && Aligned(uStride));
assert(Aligned(v) && Aligned(vStride) && Aligned(bgr) && Aligned(bgrStride));
}
size_t alignedWidth = AlignLo(width, A);
const size_t A3 = A * 3;
for (size_t row = 0; row < height; ++row)
{
Storer<align> _y(y), _u(u), _v(v);
BgrToYuv444p<align, true>(bgr, _y, _u, _v);
for (size_t col = A, colBgr = A3; col < alignedWidth; col += A, colBgr += A3)
BgrToYuv444p<align, false>(bgr + colBgr, _y, _u, _v);
Flush(_y, _u, _v);
if (width != alignedWidth)
{
size_t col = width - A;
Storer<false> _y(y + col), _u(u + col), _v(v + col);
BgrToYuv444p<false, true>(bgr + col * 3, _y, _u, _v);
Flush(_y, _u, _v);
}
y += yStride;
u += uStride;
v += vStride;
bgr += bgrStride;
}
}
Real SphericalBesselGenerator::y(const UnsignedInteger n, const Real z) const
{
if(n <= 2)
{
return _y_smalln(n, z);
}
if(n > getMaxNY())
{
return _y(n, z);
}
const sb_table::Table* table(getSYTable(n));
assert(table != 0);
const Real minz(table->x_start + table->delta_x * 3);
const Real maxz(table->x_start + table->delta_x * (table->N-3));
if(z >= minz && z < maxz)
{
return _y_table(n, z);
}
else
{
return _y(n, z);
}
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
resize_array()
{
int nf = _number_of_frames() ;
Eigen::Array<float,Eigen::Dynamic,Eigen::Dynamic> temp_x(_natoms(),nf) ;
Eigen::Array<float,Eigen::Dynamic,Eigen::Dynamic> temp_y(_natoms(),nf) ;
Eigen::Array<float,Eigen::Dynamic,Eigen::Dynamic> temp_z(_natoms(),nf) ;
temp_x = _x() ;
temp_y = _y() ;
temp_z = _z() ;
_x().resize(_natoms(),_number_of_frames()+1) ;
_y().resize(_natoms(),_number_of_frames()+1) ;
_z().resize(_natoms(),_number_of_frames()+1) ;
// see: slice.cpp in retired_ideas/play_with_eigen/
// mat1.block(i,j,rows,cols)
// a.block(0, 0, 3, 1) = b.block(0,0,3,1) ;
_x().block(0, 0, _natoms(), nf) = temp_x.block(0,0,_natoms(),nf) ;
_y().block(0, 0, _natoms(), nf) = temp_y.block(0,0,_natoms(),nf) ;
_z().block(0, 0, _natoms(), nf) = temp_z.block(0,0,_natoms(),nf) ;
return ;
}
wkt_generator<OutputIterator, Geometry>::wkt_generator(bool single)
: wkt_generator::base_type(wkt)
{
boost::spirit::karma::uint_type uint_;
boost::spirit::karma::_val_type _val;
boost::spirit::karma::_1_type _1;
boost::spirit::karma::lit_type lit;
boost::spirit::karma::_a_type _a;
boost::spirit::karma::_b_type _b;
boost::spirit::karma::_c_type _c;
boost::spirit::karma::_r1_type _r1;
boost::spirit::karma::eps_type eps;
boost::spirit::karma::string_type kstring;
wkt = point | linestring | polygon
;
point = &uint_(mapnik::geometry_type::types::Point)[_1 = _type(_val)]
<< kstring[ phoenix::if_ (single) [_1 = "Point("]
.else_[_1 = "("]]
<< point_coord [_1 = _first(_val)] << lit(')')
;
linestring = &uint_(mapnik::geometry_type::types::LineString)[_1 = _type(_val)]
<< kstring[ phoenix::if_ (single) [_1 = "LineString("]
.else_[_1 = "("]]
<< coords
<< lit(')')
;
polygon = &uint_(mapnik::geometry_type::types::Polygon)[_1 = _type(_val)]
<< kstring[ phoenix::if_ (single) [_1 = "Polygon("]
.else_[_1 = "("]]
<< coords2
<< lit("))")
;
point_coord = &uint_ << coordinate << lit(' ') << coordinate
;
polygon_coord %= ( &uint_(mapnik::SEG_MOVETO)
<< eps[_r1 += 1][_a = _x(_val)][ _b = _y(_val)]
<< kstring[ if_ (_r1 > 1) [_1 = "),("]
.else_[_1 = "("]]
|
&uint_(mapnik::SEG_LINETO)
<< lit(',') << eps[_a = _x(_val)][_b = _y(_val)]
)
<< coordinate[_1 = _a]
<< lit(' ')
<< coordinate[_1 = _b]
;
coords2 %= *polygon_coord(_a,_b,_c)
;
coords = point_coord % lit(',')
;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
int
sascalc::Prop::
self_overlap(float &cutoff, int &frame){
int check = 0 ; // overlapped == 1
// default == no overlap will return == 0
float dist ;
float this_x , that_x ;
float this_y , that_y ;
float this_z , that_z ;
float dx2, dy2, dz2 ;
int count = 1 ;
for(int i = 0 ; i != _natoms()-1 ; ++i)
{
this_x = _x()(i,frame) ;
this_y = _y()(i,frame) ;
this_z = _z()(i,frame) ;
for(int j = i+1 ; j != _natoms() ; ++j)
{
that_x = _x()(j,frame) ;
that_y = _y()(j,frame) ;
that_z = _z()(j,frame) ;
dx2 = (this_x - that_x)*(this_x - that_x) ;
dy2 = (this_y - that_y)*(this_y - that_y) ;
dz2 = (this_z - that_z)*(this_z - that_z) ;
dist = sqrt(dx2+dy2+dz2) ;
if(dist < cutoff)
{
std::cout << "count = " << count << std::endl ;
std::cout << "this_atom = " << _atom_name()[count-1] << std::endl ;
std::cout << "that_atom = " << _atom_name()[count] << std::endl ;
std::cout << "dist = " << dist << std::endl ;
std::cout << "this_x = " << this_x << std::endl ;
std::cout << "this_y = " << this_y << std::endl ;
std::cout << "this_z = " << this_z << std::endl ;
std::cout << "that_x = " << that_x << std::endl ;
std::cout << "that_y = " << that_y << std::endl ;
std::cout << "that_z = " << that_z << std::endl ;
check = 1 ;
return check ;
}
}
// std::cout << count << " " ;
count++ ;
}
std::cout << std::endl ;
return check ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sascalc::Prop::
calc_pmi(int &frame)
{
std::vector<float> com = calc_com(frame) ;
_x().col(frame) -= com[0] ;
_y().col(frame) -= com[1] ;
_z().col(frame) -= com[2] ;
float Ixx = (_atom_mass()*(_y().col(frame)*_y().col(frame) + _z().col(frame)*_z().col(frame))).sum() ;
float Iyy = (_atom_mass()*(_x().col(frame)*_x().col(frame) + _z().col(frame)*_z().col(frame))).sum() ;
float Izz = (_atom_mass()*(_x().col(frame)*_x().col(frame) + _y().col(frame)*_y().col(frame))).sum() ;
float Ixy = (-_atom_mass()*(_x().col(frame)*_y().col(frame))).sum() ;
float Ixz = (-_atom_mass()*(_x().col(frame)*_z().col(frame))).sum() ;
float Iyz = (-_atom_mass()*(_y().col(frame)*_z().col(frame))).sum() ;
float Iyx = (-_atom_mass()*(_y().col(frame)*_x().col(frame))).sum() ;
float Izx = (-_atom_mass()*(_z().col(frame)*_x().col(frame))).sum() ;
float Izy = (-_atom_mass()*(_z().col(frame)*_y().col(frame))).sum() ;
Eigen::Matrix3f I ;
I << Ixx, Ixy, Ixz,
Iyx, Iyy, Iyz,
Izx, Izy, Izz;
Eigen::SelfAdjointEigenSolver<Eigen::Matrix3f> eigensolver(I);
if (eigensolver.info() != Eigen::Success)
{
std::cout << "PMI calculation failed" << std::endl ;
return ;
}
_uk() = eigensolver.eigenvalues() ; // .col(0) ;
_ak() = eigensolver.eigenvectors() ;
// std::cout << "The eigenvalues of I are:\n" << eigensolver.eigenvalues() << std::endl;
// std::cout << "Here's a matrix whose columns are eigenvectors of I \n"
// << "corresponding to these eigenvalues:\n"
// << eigensolver.eigenvectors() << std::endl;
_x().col(frame) += com[0] ;
_y().col(frame) += com[1] ;
_z().col(frame) += com[2] ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
std::vector<float>
sascalc::Prop::
calc_com(int &frame)
{
if(_total_mass() <= 0.0) {
calc_mass() ;
std::cout << "com tot mass = " << _total_mass() << std::endl ;
}
float comx = 0.0, comy = 0.0, comz = 0.0 ;
try
{
comx = (_atom_mass()*_x().col(frame)).sum() / _total_mass() ;
comy = (_atom_mass()*_y().col(frame)).sum() / _total_mass() ;
comz = (_atom_mass()*_z().col(frame)).sum() / _total_mass() ;
}
catch(std::overflow_error e) {
std::cout << "failed in calc_com" << std::endl ;
std::cout << "total_mass = " << _total_mass() << std::endl ;
std::cout << e.what() << " -> ";
std::vector<float> com = {comx, comy, comz} ;
return com ;
}
std::vector<float> com = {comx, comy, comz} ;
return com ;
}
/* Find and execute hook. */
int tracy_execute_hook(struct tracy *t, char *syscall, struct tracy_event *e) {
struct tracy_ll_item *item;
int hash;
union {
void *pvoid;
tracy_hook_func pfunc;
} _hax;
if (TRACY_PRINT_SYSCALLS(t))
printf(_y("%04d System call: %s (%ld) Pre: %d")"\n",
e->child->pid, get_syscall_name_abi(e->syscall_num, e->abi),
e->syscall_num, e->child->pre_syscall);
hash = hash_syscall(syscall, e->abi);
item = ll_find(t->hooks, hash);
if (item) {
/* printf("Executing hook for: %s\n", syscall); */
/* ANSI C has some disadvantages too ... */
_hax.pvoid = item->data;
return _hax.pfunc(e);
}
if (t->defhook)
return t->defhook(e);
return TRACY_HOOK_NOHOOK;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_dcd(std::string &dcd_input_file_name)
{
int input_natoms, input_nset, input_reverseEndian ;
FILE *dcd_file_pointer ;
dcd_file_pointer = sasio::open_dcd_read(dcd_input_file_name, input_natoms, input_nset, input_reverseEndian) ;
int input_frame = 0 ;
_number_of_frames() = 0 ;
_x().setZero(_natoms(), input_nset);
_y().setZero(_natoms(), input_nset);
_z().setZero(_natoms(), input_nset);
std::cout << "_x().cols() = " << _x().cols() << std::endl ;
std::cout << "input_nset = " << input_nset << std::endl ;
for(int i = 0 ; i < input_nset ; ++i)
{
std::cout << "." ;
read_dcd_step(dcd_file_pointer, i, input_natoms, input_reverseEndian) ;
}
int result = close_dcd_read(dcd_file_pointer) ;
std::cout << std::endl ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_dcd_step(FILE *dcd_infile, int &frame, int &natoms, int &reverseEndian)
{
int charmm = 0 ;
int num_fixed = 0 ;
int result ;
std::vector<float> vector_x(natoms) ;
std::vector<float> vector_y(natoms) ;
std::vector<float> vector_z(natoms) ;
result = read_dcdstep(dcd_infile,natoms,&vector_x[0],&vector_y[0],&vector_z[0],num_fixed,frame,reverseEndian,charmm) ;
if(_x().cols() < frame)
{
std::cout << "resizing array: cols() = " << _x().cols() << " frame = " << frame << std::endl ;
resize_array() ;
}
for(int i = 0 ; i < _natoms() ; ++i)
{
_x()(i,frame) = vector_x[i] ;
_y()(i,frame) = vector_y[i] ;
_z()(i,frame) = vector_z[i] ;
}
_number_of_frames()++ ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
write_dcd_step(FILE *outfile, int &frame, int &step)
{
int step_result = 0 ;
step_result = write_dcdstep(outfile,_natoms(),&_x()(0,frame),&_y()(0,frame),&_z()(0,frame),step+1) ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
std::vector<std::vector<float >>
sascalc::Prop::
calc_minmax(int &frame){
float min_x = _x().col(frame).minCoeff() ; float max_x = _x().col(frame).maxCoeff() ;
float min_y = _y().col(frame).minCoeff() ; float max_y = _y().col(frame).maxCoeff() ;
float min_z = _z().col(frame).minCoeff() ; float max_z = _z().col(frame).maxCoeff() ;
std::vector<float> min_vector ;
std::vector<float> max_vector ;
min_vector.push_back(min_x) ; min_vector.push_back(min_y) ; min_vector.push_back(min_z) ;
max_vector.push_back(max_x) ; max_vector.push_back(max_y) ; max_vector.push_back(max_z) ;
std::vector<std::vector<float >> minmax ;
minmax.push_back(min_vector) ; minmax.push_back(max_vector) ;
return minmax ;
}
/* Handle SIGINT in tracy_main and shutdown smoothly */
static void _main_interrupt_handler(int sig)
{
if (kill(global_fpid, SIGINT) < 0) {
if (errno == ESRCH)
fprintf(stderr, _y("\ntracy: Received %s, foreground PID "
"does not exists, killing all."), get_signal_name(sig));
else
fprintf(stderr, _y("\ntracy: Received %s, kill(%i, SIGINT) failed: %s"),
get_signal_name(sig), global_fpid, strerror(errno));
/* Reset to default so tracy can be killed */
signal(sig, SIG_DFL);
/* Cancel main loop */
main_loop_go_on = 0;
}
return;
}
static void _tracer_fork_signal_handler(int sig, siginfo_t *info, void *uctx)
{
/* Context useable by setcontext, not of any use for us */
(void)uctx;
fprintf(stderr, _y("tracy: Received %s would attach to child %d")"\n",
get_signal_name(sig),
info->si_pid);
/*PTRACE_CHECK_NORETURN(PTRACE_ATTACH, info->si_pid, 0, 0); */
}
BlockLowPass::BlockLowPass(AP_Var_group * group, uint8_t groupStart, float fCut,
const prog_char_t * fCutLabel) :
AP_ControllerBlock(group, groupStart, 1),
_fCut(group, groupStart, fCut, fCutLabel ? : PSTR("fCut")),
_y(0) {
}
float BlockLowPass::update(const float & input, const float & dt) {
float RC = 1 / (2 * M_PI * _fCut); // low pass filter
_y = _y + (input - _y) * (dt / (dt + RC));
return _y;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
float
sascalc::Prop::
calc_rmsd(sasmol::SasMol &mol, int &frame){
float dx = (_x().col(frame)-mol._x().col(frame)).pow(2.0).sum() ;
float dy = (_y().col(frame)-mol._y().col(frame)).pow(2.0).sum() ;
float dz = (_z().col(frame)-mol._z().col(frame)).pow(2.0).sum() ;
float rmsd = sqrt((dx + dy + dz)/_natoms()) ;
return rmsd ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
float
sascalc::Prop::
calc_rg(int &frame){
std::vector<float> com = calc_com(frame) ;
float rgx = ((_x().col(frame) - com[0]).pow(2.0)).sum() ;
float rgy = ((_y().col(frame) - com[1]).pow(2.0)).sum() ;
float rgz = ((_z().col(frame) - com[2]).pow(2.0)).sum() ;
float rg = sqrt((rgx + rgy + rgz) / _natoms()) ;
return rg ;
}
bool gcta::check_case_control(double &ncase)
{
double case_num=0.0;
vector<double> value(_n);
for(int i=0; i<_n; i++) value[i]=_y(i);
stable_sort(value.begin(), value.end());
value.erase(unique(value.begin(), value.end()), value.end());
if(value.size()==2){
if(CommFunc::FloatEqual(value[0],0.0) && CommFunc::FloatEqual(value[1],1.0)) case_num=_y.sum();
else if(CommFunc::FloatEqual(value[0],1.0) && CommFunc::FloatEqual(value[1],2.0)) case_num=(_y.sum()-_n);
cout<<"Assuming a disease phenotype for a case-control study ";
cout<<"("<<(int)case_num<<" cases and "<<(int)(_n-case_num)<<" controls)."<<endl;
ncase=case_num/_n;
return true;
}
else if(value.size()<2) throw("Error: invalid phenotype. Please check the phenotype file.");
return false;
}
int usermult(Mat A, Vec x, Vec y)
{
// Wrap PETSc Vec as dolfin::PETScVector
boost::shared_ptr<Vec> _x(&x, NoDeleter());
boost::shared_ptr<Vec> _y(&y, NoDeleter());
PETScVector __x(_x);
PETScVector __y(_y);
// Extract pointer to PETScLinearOperator
void* ctx = 0;
MatShellGetContext(A, &ctx);
PETScLinearOperator* _A = ((PETScLinearOperator*) ctx);
// Call user-defined mult function through wrapper
dolfin_assert(_A);
GenericLinearOperator* wrapper = _A->wrapper();
dolfin_assert(wrapper);
wrapper->mult(__x, __y);
return 0;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_xyz(const std::string &filename)
{
/* NOT CHECKED FOR MULTIPLE FRAMES */
std::string line, word ;
std::ifstream infile(filename) ;
std::string local_natoms ;
infile >> local_natoms ;
_natoms() = stoi(local_natoms) ;
_number_of_frames() = 1 ; // HARDWIRED
// #### need to cleanly read the end of the first line
// #### and the next line
getline(infile,line) ;
std::istringstream record(line) ;
while(record >> word) ;
getline(infile,line) ;
while(record >> word) ;
std::vector<float> vector_x;
std::vector<float> vector_y;
std::vector<float> vector_z;
std::vector<float> coor;
while(getline(infile,line))
{
std::istringstream record(line) ;
record >> word ;
_atom_name().push_back(word) ;
while(record >> word)
{
coor.push_back(stod(word));
}
}
auto begin = coor.begin() ;
auto end = coor.end() ;
std::vector<float>::iterator ii ;
for(ii = begin ; ii != end ; ii+=3)
{
vector_x.push_back(*ii) ;
vector_y.push_back(*(ii+1)) ;
vector_z.push_back(*(ii+2));
}
infile.close() ;
if(_number_of_frames() == 0)
{
_x().setZero(_natoms(), 1);
_y().setZero(_natoms(), 1);
_z().setZero(_natoms(), 1);
}
else
{
resize_array() ;
}
for(int i = 0 ; i < _natoms() ; ++i)
{
_x()(i,_number_of_frames()) = vector_x[i] ;
_y()(i,_number_of_frames()) = vector_y[i] ;
_z()(i,_number_of_frames()) = vector_z[i] ;
}
_number_of_frames()++ ;
return ;
/*
5
test
N -3.259000 -5.011000 -14.360000
*/
} // end of read_xyz
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
Eigen::Matrix3f
sasmath::Math::
find_u(sasmol::SasMol &mol, int &frame)
{
Eigen::Matrix3f r ;
float rxx = (mol._x().col(frame)*_x().col(frame)).sum() ;
float rxy = (mol._x().col(frame)*_y().col(frame)).sum() ;
float rxz = (mol._x().col(frame)*_z().col(frame)).sum() ;
float ryx = (mol._y().col(frame)*_x().col(frame)).sum() ;
float ryy = (mol._y().col(frame)*_y().col(frame)).sum() ;
float ryz = (mol._y().col(frame)*_z().col(frame)).sum() ;
float rzx = (mol._z().col(frame)*_x().col(frame)).sum() ;
float rzy = (mol._z().col(frame)*_y().col(frame)).sum() ;
float rzz = (mol._z().col(frame)*_z().col(frame)).sum() ;
r << rxx,rxy,rxz,
ryx,ryy,ryz,
rzx,rzy,rzz;
Eigen::Matrix3f rtr = r.transpose() * r ;
Eigen::SelfAdjointEigenSolver<Eigen::Matrix3f> eigensolver(rtr);
if (eigensolver.info() != Eigen::Success)
{
std::cout << "find_u calculation failed" << std::endl ;
}
Eigen::Matrix<float,3,1> uk ; // eigenvalues
Eigen::Matrix3f ak ; // eigenvectors
uk = eigensolver.eigenvalues() ;
ak = eigensolver.eigenvectors() ;
Eigen::Matrix3f akt = ak.transpose() ;
Eigen::Matrix3f new_ak ;
new_ak.row(0) = akt.row(2) ; //sort eigenvectors
new_ak.row(1) = akt.row(1) ;
new_ak.row(2) = akt.row(0) ;
// python ak0 --> ak[2] ; ak1 --> ak[1] ; ak2 --> ak[0]
//Eigen::Matrix<float,3,1> ak2 = akt.row(2).cross(akt.row(1)) ;
Eigen::MatrixXf rak0 = (r * (akt.row(2).transpose())) ;
Eigen::MatrixXf rak1 = (r * (akt.row(1).transpose())) ;
Eigen::Matrix<float,3,1> urak0 ;
if(uk[2] == 0.0)
{
urak0 = 1E15 * rak0 ;
}
else
{
urak0 = (1.0/sqrt(fabs(uk[2])))*rak0 ;
}
Eigen::Matrix<float,3,1> urak1 ;
if(uk[1] == 0.0)
{
urak1 = 1E15 * rak1 ;
}
else
{
urak1 = (1.0/sqrt(fabs(uk[1])))*rak1 ;
}
Eigen::Matrix<float,3,1> urak2 = urak0.col(0).cross(urak1.col(0)) ;
Eigen::Matrix3f bk ;
bk << urak0,urak1,urak2;
Eigen::Matrix3f u ;
u = (bk * new_ak).transpose() ;
return u ;
/*
u = array([[-0.94513198, 0.31068658, 0.100992 ],
[-0.3006246 , -0.70612572, -0.64110165],
[-0.12786863, -0.63628635, 0.76078203]])
check:
u =
-0.945133 0.310686 0.100992
-0.300624 -0.706126 -0.641102
-0.127869 -0.636287 0.760782
*/
}
static void
HoughLinesSDiv( const Mat& img,
float rho, float theta, int threshold,
int srn, int stn,
std::vector<Vec2f>& lines, int linesMax,
double min_theta, double max_theta )
{
#define _POINT(row, column)\
(image_src[(row)*step+(column)])
int index, i;
int ri, ti, ti1, ti0;
int row, col;
float r, t; /* Current rho and theta */
float rv; /* Some temporary rho value */
int fn = 0;
float xc, yc;
const float d2r = (float)(CV_PI / 180);
int sfn = srn * stn;
int fi;
int count;
int cmax = 0;
std::vector<hough_index> lst;
CV_Assert( img.type() == CV_8UC1 );
CV_Assert( linesMax > 0 );
threshold = MIN( threshold, 255 );
const uchar* image_src = img.ptr();
int step = (int)img.step;
int w = img.cols;
int h = img.rows;
float irho = 1 / rho;
float itheta = 1 / theta;
float srho = rho / srn;
float stheta = theta / stn;
float isrho = 1 / srho;
float istheta = 1 / stheta;
int rn = cvFloor( std::sqrt( (double)w * w + (double)h * h ) * irho );
int tn = cvFloor( 2 * CV_PI * itheta );
lst.push_back(hough_index(threshold, -1.f, 0.f));
// Precalculate sin table
std::vector<float> _sinTable( 5 * tn * stn );
float* sinTable = &_sinTable[0];
for( index = 0; index < 5 * tn * stn; index++ )
sinTable[index] = (float)cos( stheta * index * 0.2f );
std::vector<uchar> _caccum(rn * tn, (uchar)0);
uchar* caccum = &_caccum[0];
// Counting all feature pixels
for( row = 0; row < h; row++ )
for( col = 0; col < w; col++ )
fn += _POINT( row, col ) != 0;
std::vector<int> _x(fn), _y(fn);
int* x = &_x[0], *y = &_y[0];
// Full Hough Transform (it's accumulator update part)
fi = 0;
for( row = 0; row < h; row++ )
{
for( col = 0; col < w; col++ )
{
if( _POINT( row, col ))
{
int halftn;
float r0;
float scale_factor;
int iprev = -1;
float phi, phi1;
float theta_it; // Value of theta for iterating
// Remember the feature point
x[fi] = col;
y[fi] = row;
fi++;
yc = (float) row + 0.5f;
xc = (float) col + 0.5f;
/* Update the accumulator */
t = (float) fabs( cvFastArctan( yc, xc ) * d2r );
r = (float) std::sqrt( (double)xc * xc + (double)yc * yc );
r0 = r * irho;
ti0 = cvFloor( (t + CV_PI*0.5) * itheta );
caccum[ti0]++;
theta_it = rho / r;
theta_it = theta_it < theta ? theta_it : theta;
scale_factor = theta_it * itheta;
halftn = cvFloor( CV_PI / theta_it );
for( ti1 = 1, phi = theta_it - (float)(CV_PI*0.5), phi1 = (theta_it + t) * itheta;
ti1 < halftn; ti1++, phi += theta_it, phi1 += scale_factor )
{
rv = r0 * std::cos( phi );
i = (int)rv * tn;
i += cvFloor( phi1 );
assert( i >= 0 );
assert( i < rn * tn );
caccum[i] = (uchar) (caccum[i] + ((i ^ iprev) != 0));
iprev = i;
if( cmax < caccum[i] )
cmax = caccum[i];
}
}
}
}
// Starting additional analysis
count = 0;
for( ri = 0; ri < rn; ri++ )
{
for( ti = 0; ti < tn; ti++ )
{
if( caccum[ri * tn + ti] > threshold )
count++;
}
}
if( count * 100 > rn * tn )
{
HoughLinesStandard( img, rho, theta, threshold, lines, linesMax, min_theta, max_theta );
return;
}
std::vector<uchar> _buffer(srn * stn + 2);
uchar* buffer = &_buffer[0];
uchar* mcaccum = buffer + 1;
count = 0;
for( ri = 0; ri < rn; ri++ )
{
for( ti = 0; ti < tn; ti++ )
{
if( caccum[ri * tn + ti] > threshold )
{
count++;
memset( mcaccum, 0, sfn * sizeof( uchar ));
for( index = 0; index < fn; index++ )
{
int ti2;
float r0;
yc = (float) y[index] + 0.5f;
xc = (float) x[index] + 0.5f;
// Update the accumulator
t = (float) fabs( cvFastArctan( yc, xc ) * d2r );
r = (float) std::sqrt( (double)xc * xc + (double)yc * yc ) * isrho;
ti0 = cvFloor( (t + CV_PI * 0.5) * istheta );
ti2 = (ti * stn - ti0) * 5;
r0 = (float) ri *srn;
for( ti1 = 0; ti1 < stn; ti1++, ti2 += 5 )
{
rv = r * sinTable[(int) (std::abs( ti2 ))] - r0;
i = cvFloor( rv ) * stn + ti1;
i = CV_IMAX( i, -1 );
i = CV_IMIN( i, sfn );
mcaccum[i]++;
assert( i >= -1 );
assert( i <= sfn );
}
}
// Find peaks in maccum...
for( index = 0; index < sfn; index++ )
{
i = 0;
int pos = (int)(lst.size() - 1);
if( pos < 0 || lst[pos].value < mcaccum[index] )
{
hough_index vi(mcaccum[index],
index / stn * srho + ri * rho,
index % stn * stheta + ti * theta - (float)(CV_PI*0.5));
lst.push_back(vi);
for( ; pos >= 0; pos-- )
{
if( lst[pos].value > vi.value )
break;
lst[pos+1] = lst[pos];
}
lst[pos+1] = vi;
if( (int)lst.size() > linesMax )
lst.pop_back();
}
}
}
}
}
for( size_t idx = 0; idx < lst.size(); idx++ )
{
if( lst[idx].rho < 0 )
continue;
lines.push_back(Vec2f(lst[idx].rho, lst[idx].theta));
}
}
void
sasio::Files::
write_pdb(const std::string &filename, int &frame)
{
std::ofstream outfile(filename) ;
std::string time_and_user_string ;
time_and_user_string = util::time_and_user();
std::string temp_remark = "REMARK PDB FILE WRITTEN ";
temp_remark += time_and_user_string ;
std::string remark(temp_remark,0,80) ;
std::cout << remark << std::endl ;
outfile << remark << std::endl;
//std::string dum1 =" 1 2 3 4 5 6 7 8";
//std::string dum2 ="12345678901234567890123456789012345678901234567890123456789012345678901234567890";
//outfile << dum1 << std::endl;
//outfile << dum2 << std::endl;
std::stringstream line ;
std::stringstream my_stringstream;
for(int i = 0 ; i < _natoms() ; ++i)
{
line.str( std::string() );
line.clear() ;
std::string tmp(_atom_record()[i],0,6) ;
line << std::setfill(' ') << std::setw(6) << tmp ;
if(_atom_index()[i] > 99999)
{
std::string tmp2(std::to_string(99999),0,5) ;
line << std::setfill(' ') << std::setw(5) << std::right << tmp2 ;
}
else if(_atom_index()[i] < -9999)
{
std::string tmp2(std::to_string(-9999),0,5) ;
line << std::setfill(' ') << std::setw(5) << std::right << tmp2 ;
}
else
{
std::string tmp2(std::to_string(_atom_index()[i]),0,5) ;
line << std::setfill(' ') << std::setw(5) << std::right << tmp2 ;
}
std::string tmp0 = " ";
line << tmp0 ;
std::string tmp3(_atom_name()[i],0,4) ;
line << std::setfill(' ') << std::setw(4) << std::left << tmp3 ;
std::string tmp4(_atom_altloc()[i],0,1) ;
line << std::setw(1) << tmp4 ;
std::string tmp5(_atom_resname()[i],0,3) ;
line << std::setfill(' ') << std::setw(4) << std::left << tmp5 ;
std::string tmp6(_atom_chain()[i],0,1) ;
line << std::setfill(' ') << std::setw(1) << std::left << tmp6 ;
if(_atom_resid()[i] > 9999)
{
std::string tmp7(std::to_string(9999),0,4) ;
line << std::setfill(' ') << std::setw(4) << std::right << tmp7 ;
}
else if(_atom_resid()[i] < -999)
{
std::string tmp7(std::to_string(-999),0,4) ;
line << std::setfill(' ') << std::setw(4) << std::right << tmp7 ;
}
else
{
std::string tmp7(std::to_string(_atom_resid()[i]),0,4) ;
line << std::setfill(' ') << std::setw(4) << std::right << tmp7 ;
}
std::string tmp8(_atom_icode()[i],0,1) ;
line << std::setw(4) << std::left << tmp8 ;
//std::string f_str = std::to_string(f);
//here
//
my_stringstream << _x()(i,frame) ;
//my_stringstream << std::to_string(_x()(i,frame)) ;
//line << std::setfill(' ') << std::setw(8) << std::right << my_stringstream.str() ;
line << std::setfill(' ') << std::setw(8) << std::right << my_stringstream.str() ;
my_stringstream << _y()(i,frame) ;
line << my_stringstream.str() ;
my_stringstream << _z()(i,frame) ;
line << my_stringstream.str() ;
std::string tmp12(_atom_occupancy()[i],0,6) ;
line << std::setfill(' ') << std::setw(6) << std::right << tmp12 ;
std::string tmp13(_atom_beta()[i],0,6) ;
line << std::setfill(' ') << std::setw(6) << std::right << tmp13 ;
std::string tmp14(_atom_segname()[i],0,4) ;
line << std::setfill(' ') << std::setw(10) << std::right << tmp14 ;
std::string tmp15(_atom_element()[i],0,2) ;
line << std::setfill(' ') << std::setw(2) << std::right << tmp15 ;
std::string tmp16(_atom_charge()[i],0,2) ;
line << std::setfill(' ') << std::setw(2) << std::right << tmp16 ;
outfile << line.str() << std::endl ;
}
outfile << "END" << std::endl;
outfile.close() ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_pdb(const std::string &filename)
{
std::string line, word ;
std::string element_string ;
std::ifstream infile(filename) ;
int count = 0 ;
int frame = 0 ;
//string s(line, index, number_characters) ;
std::vector<float> vector_x;
std::vector<float> vector_y;
std::vector<float> vector_z;
while(getline(infile,line))
{
std::istringstream record(line) ;
record >> word ;
std::string temp1(word,0,5) ;
if(temp1 != "ATOM" && temp1 != "HETAT")
{
std::cout << "excluding: " << word << std::endl ;
}
else
{
std::string tmp(line,0,6) ;
_atom_record().push_back(tmp) ;
std::string tmp2(line,6,5) ;
_atom_index().push_back(stoi(tmp2)) ;
std::string tmp3(line,12,4) ;
_atom_name().push_back(tmp3) ;
std::string tmp4(line,16,1) ;
_atom_altloc().push_back(tmp4) ;
std::string tmp5(line,17,3) ;
_atom_resname().push_back(tmp5) ;
std::string tmp6(line,21,1) ;
_atom_chain().push_back(tmp6) ;
std::string tmp7(line,22,4) ;
_atom_resid().push_back(stoi(tmp7)) ;
std::string tmp8(line,26,1) ;
_atom_icode().push_back(tmp8) ;
std::string tmp9(line,30,8) ;
vector_x.push_back(stof(tmp9)) ;
std::string tmp10(line,38,8) ;
vector_y.push_back(stof(tmp10)) ;
std::string tmp11(line,46,8) ;
vector_z.push_back(stof(tmp11)) ;
try
{
std::string tmp12(line,54,6) ;
if(util::has_only_spaces(tmp12))
{
_atom_occupancy().push_back("0.00") ;
}
else
{
_atom_occupancy().push_back(tmp12) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_occupancy().push_back("0.00") ;
std::cerr<<"Occupancy: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp13(line,60,6) ;
if(util::has_only_spaces(tmp13))
{
_atom_beta().push_back("0.00") ;
}
else
{
_atom_beta().push_back(tmp13) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_beta().push_back("0.00") ;
std::cerr<<"Beta: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp14(line,72,4) ;
if(util::has_only_spaces(tmp14))
{
_atom_segname().push_back("SEGN") ;
}
else
{
_atom_segname().push_back(tmp14) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_segname().push_back("SEGN") ;
std::cerr<<"Segname: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp15(line,76,2) ;
if(util::has_only_spaces(tmp15))
{
std::cout << "Element not found" << std::endl;
element_string = element_from_name(tmp3) ;
_atom_element().push_back(element_string) ;
}
else
{
_atom_element().push_back(tmp15) ;
}
}
catch(const std::out_of_range& oor)
{
element_string = element_from_name(tmp3) ;
_atom_element().push_back(element_string) ;
std::cerr<<"Element: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp16(line,78,2) ;
if(util::has_only_spaces(tmp16))
{
_atom_charge().push_back(" ") ;
}
else
{
_atom_charge().push_back(tmp16) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_charge().push_back(" ") ;
std::cerr<<"Charge: Out of range error: "<< oor.what() <<std::endl ;
}
count++ ;
}
}
_natoms() = count ;
infile.close() ;
int nf = _number_of_frames() ;
if(_number_of_frames() == 0)
{
_x().setZero(_natoms(), 1);
_y().setZero(_natoms(), 1);
_z().setZero(_natoms(), 1);
}
else
{
resize_array() ;
}
for(int i = 0 ; i < _natoms() ; ++i)
{
_x()(i,_number_of_frames()) = vector_x[i] ;
_y()(i,_number_of_frames()) = vector_y[i] ;
_z()(i,_number_of_frames()) = vector_z[i] ;
}
std::vector<std::string> s_element ;
s_element = util::strip_white_space(_atom_element()) ;
_atom_selement() = s_element ;
dynamic_cast<sasmol::SasMol*>(this)->calc_mass() ;
_atom_com() = dynamic_cast<sasmol::SasMol*>(this)->calc_com(frame) ;
_number_of_frames() += 1 ;
_set_unique_attributes();
/*
1 2 3 4 5 6 7 8
012345678901234567890123456789012345678901234567890123456789012345678901234567890
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
0 6 1 2 7
ATOM 1 N GLY X 1 -21.525 -67.562 86.759 1.00 0.00 GAG N
ATOM 2 HT1 GLY X 1 -22.003 -68.460 86.892 1.00 0.00 GAG H
ATOM 3 HT2 GLY X 1 -21.905 -66.929 87.525 1.00 0.00 GAG H
*/
}
/* Main function for simple tracy based applications */
int tracy_main(struct tracy *tracy) {
struct tracy_event *e;
/* Setup interrupt handler */
main_loop_go_on = 1;
signal(SIGINT, _main_interrupt_handler);
while (main_loop_go_on) {
e = tracy_wait_event(tracy, -1);
if (!e) {
fprintf(stderr, "tracy_main: tracy_wait_Event returned NULL\n");
continue;
}
if (e->type == TRACY_EVENT_NONE) {
break;
} else if (e->type == TRACY_EVENT_INTERNAL) {
/*
printf("Internal event for syscall: %s\n",
get_syscall_name(e->syscall_num));
*/
}
if (e->type == TRACY_EVENT_SIGNAL) {
if (TRACY_PRINT_SIGNALS(tracy)) {
fprintf(stderr, _y("Signal %s (%ld) for child %d")"\n",
get_signal_name(e->signal_num), e->signal_num, e->child->pid);
}
} else
if (e->type == TRACY_EVENT_SYSCALL) {
/*
if (TRACY_PRINT_SYSCALLS(tracy)) {
printf(_y("%04d System call: %s (%ld) Pre: %d")"\n",
e->child->pid, get_syscall_name(e->syscall_num),
e->syscall_num, e->child->pre_syscall);
}
*/
} else
if (e->type == TRACY_EVENT_QUIT) {
if (tracy->opt & TRACY_VERBOSE)
printf(_b("EVENT_QUIT from %d with signal %s (%ld)\n"),
e->child->pid, get_signal_name(e->signal_num),
e->signal_num);
if (e->child->pid == tracy->fpid) {
if (tracy->opt & TRACY_VERBOSE)
printf(_g("Our first child died.\n"));
}
tracy_remove_child(e->child);
continue;
}
if (!tracy_children_count(tracy)) {
break;
}
tracy_continue(e, 0);
}
/* Tear down interrupt handler */
signal(SIGINT, SIG_DFL);
return 0;
}