#include <reconstructor.h>
Public Member Functions | |
newfile_store (const string &prefix, int npad, bool ctf) | |
virtual | ~newfile_store () |
void | add_image (EMData *data, const Transform &tf) |
void | add_tovol (EMData *fftvol, EMData *wgtvol, const vector< int > &mults, int pbegin, int pend) |
void | get_image (int id, EMData *buf) |
void | read (int nprj) |
void | restart () |
Private Attributes | |
int | m_npad |
bool | m_ctf |
string | m_bin_file |
string | m_txt_file |
shared_ptr< std::ofstream > | m_bin_of |
shared_ptr< std::ofstream > | m_txt_of |
shared_ptr< std::ifstream > | m_bin_if |
vector< std::istream::off_type > | m_offsets |
vector< point_t > | m_points |
Definition at line 1165 of file reconstructor.h.
newfile_store::newfile_store | ( | const string & | prefix, | |
int | npad, | |||
bool | ctf | |||
) |
Definition at line 3397 of file reconstructor.cpp.
03398 : m_bin_file( filename + ".bin" ), 03399 m_txt_file( filename + ".txt" ) 03400 { 03401 m_npad = npad; 03402 m_ctf = ctf; 03403 }
newfile_store::~newfile_store | ( | ) | [virtual] |
Definition at line 3409 of file reconstructor.cpp.
References checked_delete(), EMAN::EMData::cmplx(), EMAN::point_t::ctf2, EMAN::EMData::get_attr(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::point_t::imag, m_bin_file, m_bin_of, m_ctf, m_npad, m_offsets, m_txt_file, m_txt_of, nx, ny, EMAN::padfft_slice(), EMAN::point_t::pos2, EMAN::point_t::real, sqrt(), tf(), and EMAN::Ctf::to_dict().
03410 { 03411 if( m_bin_of == NULL ) 03412 { 03413 m_bin_of = shared_ptr<ofstream>( new ofstream(m_bin_file.c_str(), std::ios::out|std::ios::binary) ); 03414 m_txt_of = shared_ptr<ofstream>( new ofstream(m_txt_file.c_str()) ); 03415 } 03416 03417 03418 EMData* padfft = padfft_slice( emdata, tf, m_npad ); 03419 03420 int nx = padfft->get_xsize(); 03421 int ny = padfft->get_ysize(); 03422 int n2 = ny / 2; 03423 int n = ny; 03424 03425 float voltage=0.0f, pixel=0.0f, Cs=0.0f, ampcont=0.0f, bfactor=0.0f, defocus=0.0f; 03426 03427 if( m_ctf ) 03428 { 03429 Ctf* ctf = emdata->get_attr( "ctf" ); 03430 Dict params = ctf->to_dict(); 03431 voltage = params["voltage"]; 03432 pixel = params["apix"]; 03433 Cs = params["cs"]; 03434 ampcont = params["ampcont"]; 03435 bfactor = params["bfactor"]; 03436 defocus = params["defocus"]; 03437 if(ctf) {delete ctf; ctf=0;} 03438 } 03439 03440 vector<point_t> points; 03441 for( int j=-ny/2+1; j <= ny/2; j++ ) 03442 { 03443 int jp = (j>=0) ? j+1 : ny+j+1; 03444 for( int i=0; i <= n2; ++i ) 03445 { 03446 int r2 = i*i + j*j; 03447 if( (r2<ny*ny/4) && !( (i==0) && (j<0) ) ) 03448 { 03449 float ctf; 03450 if( m_ctf ) 03451 { 03452 float ak = std::sqrt( r2/float(ny*ny) )/pixel; 03453 ctf = Util::tf( defocus, ak, voltage, Cs, ampcont, bfactor, 1); 03454 } 03455 else 03456 { 03457 ctf = 1.0; 03458 } 03459 03460 float xnew = i*tf[0][0] + j*tf[1][0]; 03461 float ynew = i*tf[0][1] + j*tf[1][1]; 03462 float znew = i*tf[0][2] + j*tf[1][2]; 03463 std::complex<float> btq; 03464 if (xnew < 0.) 03465 { 03466 xnew = -xnew; 03467 ynew = -ynew; 03468 znew = -znew; 03469 btq = conj(padfft->cmplx(i,jp-1)); 03470 } 03471 else 03472 { 03473 btq = padfft->cmplx(i,jp-1); 03474 } 03475 03476 int ixn = int(xnew + 0.5 + n) - n; 03477 int iyn = int(ynew + 0.5 + n) - n; 03478 int izn = int(znew + 0.5 + n) - n; 03479 if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) 03480 { 03481 int ixf, iyf, izf; 03482 if (ixn >= 0) 03483 { 03484 int iza, iya; 03485 if (izn >= 0) 03486 iza = izn + 1; 03487 else 03488 iza = n + izn + 1; 03489 03490 if (iyn >= 0) 03491 iya = iyn + 1; 03492 else 03493 iya = n + iyn + 1; 03494 03495 ixf = ixn; 03496 iyf = iya; 03497 izf = iza; 03498 } 03499 else 03500 { 03501 int izt, iyt; 03502 if (izn > 0) 03503 izt = n - izn + 1; 03504 else 03505 izt = -izn + 1; 03506 03507 if (iyn > 0) 03508 iyt = n - iyn + 1; 03509 else 03510 iyt = -iyn + 1; 03511 03512 ixf = -ixn; 03513 iyf = iyt; 03514 izf = izt; 03515 } 03516 03517 03518 int pos2 = ixf + (iyf-1)*nx/2 + (izf-1)*ny*nx/2; 03519 float ctfv1 = btq.real() * ctf; 03520 float ctfv2 = btq.imag() * ctf; 03521 float ctf2 = ctf*ctf; 03522 03523 point_t p; 03524 p.pos2 = pos2; 03525 p.real = ctfv1; 03526 p.imag = ctfv2; 03527 p.ctf2 = ctf2; 03528 03529 points.push_back( p ); 03530 } 03531 } 03532 } 03533 } 03534 03535 03536 int npoint = points.size(); 03537 std::istream::off_type offset = (m_offsets.size()==0) ? 0 : m_offsets.back(); 03538 offset += npoint*sizeof(point_t); 03539 m_offsets.push_back( offset ); 03540 03541 *m_txt_of << m_offsets.back() << std::endl; 03542 m_bin_of->write( (char*)(&points[0]), sizeof(point_t)*npoint ); 03543 checked_delete( padfft ); 03544 }
void newfile_store::add_tovol | ( | EMData * | fftvol, | |
EMData * | wgtvol, | |||
const vector< int > & | mults, | |||
int | pbegin, | |||
int | pend | |||
) |
Definition at line 3627 of file reconstructor.cpp.
References Assert, EMAN::EMData::get_data(), m_offsets, and m_points.
03628 { 03629 float* vdata = fftvol->get_data(); 03630 float* wdata = wgtvol->get_data(); 03631 03632 int npoint = m_offsets[0]/sizeof(point_t); 03633 // Assert( int(mults.size())==nprj ); 03634 Assert( int(m_points.size())== (pend - pbegin)*npoint ); 03635 03636 for( int iprj=pbegin; iprj < pend; ++iprj ) 03637 { 03638 int m = mults[iprj]; 03639 if( m==0 ) continue; 03640 03641 int ipt = (iprj-pbegin)*npoint; 03642 for( int i=0; i < npoint; ++i ) 03643 { 03644 int pos2 = m_points[ipt].pos2; 03645 int pos1 = pos2*2; 03646 03647 wdata[pos2] += m_points[ipt].ctf2*m; 03648 vdata[pos1] += m_points[ipt].real*m; 03649 vdata[pos1+1]+= m_points[ipt].imag*m; 03650 ++ipt; 03651 } 03652 } 03653 }
void newfile_store::get_image | ( | int | id, | |
EMData * | buf | |||
) |
Definition at line 3546 of file reconstructor.cpp.
References Assert, data, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), in, m_bin_file, m_bin_if, m_offsets, m_txt_file, EMAN::EMData::set_size(), and EMAN::EMData::update().
03547 { 03548 if( m_offsets.size()==0 ) 03549 { 03550 ifstream is( m_txt_file.c_str() ); 03551 std::istream::off_type off; 03552 while( is >> off ) 03553 { 03554 m_offsets.push_back( off ); 03555 } 03556 03557 m_bin_if = shared_ptr<std::ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) ); 03558 } 03559 03560 Assert( m_bin_if != NULL ); 03561 03562 std::istream::off_type offset = (id==0) ? 0 : m_offsets[id-1]; 03563 Assert( offset >= 0 ); 03564 m_bin_if->seekg( offset, std::ios::beg ); 03565 03566 03567 if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() ) 03568 { 03569 std::cout << "bad or fail or eof while fetching id, offset: " << id << " " << offset << std::endl; 03570 throw std::logic_error( "bad happen" ); 03571 } 03572 03573 int bufsize = (m_offsets[id] - offset)/sizeof(float); 03574 if( buf->get_xsize() != bufsize ) 03575 { 03576 buf->set_size( bufsize, 1, 1 ); 03577 } 03578 03579 char* data = (char*)(buf->get_data()); 03580 m_bin_if->read( data, sizeof(float)*bufsize ); 03581 buf->update(); 03582 }
void newfile_store::read | ( | int | nprj | ) |
Definition at line 3584 of file reconstructor.cpp.
References in, m_bin_file, m_bin_if, m_offsets, m_points, and m_txt_file.
03585 { 03586 if( m_offsets.size()==0 ) 03587 { 03588 ifstream is( m_txt_file.c_str() ); 03589 std::istream::off_type off; 03590 while( is >> off ) 03591 { 03592 m_offsets.push_back( off ); 03593 } 03594 } 03595 03596 if( m_bin_if==NULL ) 03597 { 03598 m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) ); 03599 } 03600 03601 03602 int npoint = m_offsets[0]/sizeof(point_t); 03603 std::ios::off_type prjsize = m_offsets[0]; 03604 03605 try 03606 { 03607 m_points.resize(nprj * npoint); 03608 } 03609 catch( std::exception& e ) 03610 { 03611 std::cout << "Error: " << e.what() << std::endl; 03612 } 03613 03614 int ip = 0; 03615 for( int i=0; i < nprj; ++i ) 03616 { 03617 m_bin_if->read( (char*)(&m_points[ip]), prjsize ); 03618 if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() ) 03619 { 03620 std::cout << "Error: file hander bad or fail or eof" << std::endl; 03621 return; 03622 } 03623 ip += npoint; 03624 } 03625 }
void newfile_store::restart | ( | ) |
Definition at line 3655 of file reconstructor.cpp.
References in, m_bin_file, and m_bin_if.
03656 { 03657 m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) ); 03658 }
string EMAN::newfile_store::m_bin_file [private] |
Definition at line 1187 of file reconstructor.h.
Referenced by add_image(), get_image(), read(), and restart().
shared_ptr<std::ifstream> EMAN::newfile_store::m_bin_if [private] |
shared_ptr<std::ofstream> EMAN::newfile_store::m_bin_of [private] |
bool EMAN::newfile_store::m_ctf [private] |
int EMAN::newfile_store::m_npad [private] |
vector< std::istream::off_type > EMAN::newfile_store::m_offsets [private] |
Definition at line 1193 of file reconstructor.h.
Referenced by add_image(), add_tovol(), get_image(), and read().
vector< point_t > EMAN::newfile_store::m_points [private] |
string EMAN::newfile_store::m_txt_file [private] |
Definition at line 1188 of file reconstructor.h.
Referenced by add_image(), get_image(), and read().
shared_ptr<std::ofstream> EMAN::newfile_store::m_txt_of [private] |