#include <reconstructor.h>
Inheritance diagram for EMAN::nn4_ctfReconstructor:
Public Member Functions | |
nn4_ctfReconstructor () | |
nn4_ctfReconstructor (const string &symmetry, int size, int npad, float snr, int sign) | |
virtual | ~nn4_ctfReconstructor () |
virtual void | setup () |
Initialize the reconstructor. | |
virtual int | insert_slice (const EMData *const slice, const Transform &euler, const float weight=1.0) |
Insert a slice into a 3D volume, in a given orientation. | |
virtual EMData * | finish (bool doift=true) |
Finish reconstruction and return the complete model. | |
virtual string | get_name () const |
Get the unique name of this class (especially for factory based instantiation access). | |
virtual string | get_desc () const |
Get a clear, concise description of this class. | |
TypeDict | get_param_types () const |
void | setup (const string &symmetry, int size, int npad, float snr, int sign) |
int | insert_padfft_slice (EMData *padfft, const Transform &trans, int mult=1) |
int | insert_buffed_slice (const EMData *buffer, int mult) |
Static Public Member Functions | |
static Reconstructor * | NEW () |
Static Public Attributes | |
static const string | NAME = "nn4_ctf" |
Private Member Functions | |
void | buildFFTVolume () |
void | buildNormVolume () |
Private Attributes | |
EMData * | m_volume |
EMData * | m_result |
EMData * | m_wptr |
bool | m_delete_volume |
bool | m_delete_weight |
int | m_vnx |
int | m_vny |
int | m_vnz |
int | m_vnzp |
int | m_vnyp |
int | m_vnxp |
int | m_vnxc |
int | m_vnyc |
int | m_vnzc |
int | m_npad |
int | m_sign |
int | m_varsnr |
int | m_weighting |
float | m_wghta |
float | m_wghtb |
float | m_snr |
string | m_symmetry |
int | m_nsym |
Definition at line 1005 of file reconstructor.h.
nn4_ctfReconstructor::nn4_ctfReconstructor | ( | ) |
nn4_ctfReconstructor::nn4_ctfReconstructor | ( | const string & | symmetry, | |
int | size, | |||
int | npad, | |||
float | snr, | |||
int | sign | |||
) |
nn4_ctfReconstructor::~nn4_ctfReconstructor | ( | ) | [virtual] |
Definition at line 3193 of file reconstructor.cpp.
References checked_delete(), m_delete_volume, m_delete_weight, m_result, m_volume, and m_wptr.
03194 { 03195 if( m_delete_volume ) checked_delete(m_volume); 03196 03197 if( m_delete_weight ) checked_delete( m_wptr ); 03198 03199 checked_delete( m_result ); 03200 }
void nn4_ctfReconstructor::buildFFTVolume | ( | ) | [private] |
Definition at line 3255 of file reconstructor.cpp.
References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), m_delete_volume, m_npad, m_vnxp, m_vnyp, m_vnzp, m_volume, EMAN::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_attr(), EMAN::EMData::set_complex(), EMAN::EMData::set_fftpad(), EMAN::EMData::set_nxc(), EMAN::EMData::set_ri(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().
Referenced by setup().
03255 { 03256 int offset = 2 - m_vnxp%2; 03257 if( params.has_key("fftvol") ) { 03258 m_volume = params["fftvol"]; 03259 m_delete_volume = false; 03260 } else { 03261 m_volume = new EMData(); 03262 m_delete_volume = true; 03263 } 03264 03265 if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) { 03266 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp); 03267 m_volume->to_zero(); 03268 } 03269 03270 m_volume->set_nxc(m_vnxp/2); 03271 m_volume->set_complex(true); 03272 m_volume->set_ri(true); 03273 m_volume->set_fftpad(true); 03274 m_volume->set_attr("npad", m_npad); 03275 m_volume->set_array_offsets(0,1,1); 03276 }
void nn4_ctfReconstructor::buildNormVolume | ( | ) | [private] |
Definition at line 3278 of file reconstructor.cpp.
References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), m_delete_weight, m_vnxc, m_vnyp, m_vnzp, m_wptr, EMAN::FactoryBase::params, EMAN::EMData::set_array_offsets(), EMAN::EMData::set_size(), and EMAN::EMData::to_zero().
Referenced by setup().
03279 { 03280 if( params.has_key("weight") ) { 03281 m_wptr = params["weight"]; 03282 m_delete_weight = false; 03283 } else { 03284 m_wptr = new EMData(); 03285 m_delete_weight = true; 03286 } 03287 03288 if( m_wptr->get_xsize() != m_vnxc+1 && m_wptr->get_ysize() != m_vnyp && m_wptr->get_zsize() != m_vnzp ) { 03289 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03290 m_wptr->to_zero(); 03291 } 03292 03293 m_wptr->set_array_offsets(0,1,1); 03294 03295 }
EMData * nn4_ctfReconstructor::finish | ( | bool | doift = true |
) | [virtual] |
Finish reconstruction and return the complete model.
doift | A flag indicating whether the returned object should be guaranteed to be in real-space (true) or should be left in whatever space the reconstructor generated |
Reimplemented from EMAN::Reconstructor.
Definition at line 3376 of file reconstructor.cpp.
References abs, circumf(), EMAN::EMData::copy(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), ESTIMATE, EMAN::EMData::get_attr(), m_result, m_sign, m_snr, m_varsnr, m_vnxc, m_vnyc, m_vnyp, m_vnzc, m_vnzp, m_volume, m_weighting, m_wghta, m_wptr, max, max3d(), EMAN::EMData::set_array_offsets(), sqrt(), and EMAN::EMData::symplane0_ctf().
03377 { 03378 m_volume->set_array_offsets(0, 1, 1); 03379 m_wptr->set_array_offsets(0, 1, 1); 03380 m_volume->symplane0_ctf(m_wptr); 03381 03382 int box = 7; 03383 int vol = box*box*box; 03384 int kc = (box-1)/2; 03385 vector< float > pow_a( 3*kc+1, 1.0 ); 03386 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 03387 pow_a[3*kc]=0.0; 03388 03389 03390 float max = max3d( kc, pow_a ); 03391 float alpha = ( 1.0f - 1.0f/(float)vol ) / max; 03392 float osnr = 1.0f/m_snr; 03393 03394 // normalize 03395 int ix,iy,iz; 03396 for (iz = 1; iz <= m_vnzp; iz++) { 03397 for (iy = 1; iy <= m_vnyp; iy++) { 03398 for (ix = 0; ix <= m_vnxc; ix++) { 03399 if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!! 03400 int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1; 03401 int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1; 03402 float tmp=0.0; 03403 if( m_varsnr ) 03404 { 03405 float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) ); 03406 tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr)*m_sign; 03407 } 03408 else 03409 { 03410 tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr)*m_sign; 03411 } 03412 03413 if( m_weighting == ESTIMATE ) { 03414 int cx = ix; 03415 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 03416 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 03417 float sum = 0.0; 03418 for( int ii = -kc; ii <= kc; ++ii ) { 03419 int nbrcx = cx + ii; 03420 if( nbrcx >= m_vnxc ) continue; 03421 for( int jj= -kc; jj <= kc; ++jj ) { 03422 int nbrcy = cy + jj; 03423 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 03424 for( int kk = -kc; kk <= kc; ++kk ) { 03425 int nbrcz = cz + jj; 03426 if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 03427 if( nbrcx < 0 ) { 03428 nbrcx = -nbrcx; 03429 nbrcy = -nbrcy; 03430 nbrcz = -nbrcz; 03431 } 03432 03433 int nbrix = nbrcx; 03434 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 03435 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 03436 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) { 03437 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 03438 sum = sum + pow_a[c]; 03439 // if(ix%20==0 && iy%20==0 && iz%20==0) 03440 // std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl; 03441 } 03442 } 03443 } 03444 } 03445 float wght = 1.0f / ( 1.0f - alpha * sum ); 03446 /* 03447 if(ix%10==0 && iy%10==0) 03448 { 03449 std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz; 03450 std::cout << boost::format( "%10.3f %10.3f %10.3f " ) % tmp % wght % sum; 03451 std:: << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha; 03452 std::cout << std::endl; 03453 } 03454 */ 03455 tmp = tmp * wght; 03456 } 03457 (*m_volume)(2*ix,iy,iz) *= tmp; 03458 (*m_volume)(2*ix+1,iy,iz) *= tmp; 03459 } 03460 } 03461 } 03462 } 03463 03464 // back fft 03465 m_volume->do_ift_inplace(); 03466 int npad = m_volume->get_attr("npad"); 03467 m_volume->depad(); 03468 circumf( m_volume, npad ); 03469 m_volume->set_array_offsets( 0, 0, 0 ); 03470 m_result = m_volume->copy(); 03471 return m_result; 03472 }
virtual string EMAN::nn4_ctfReconstructor::get_desc | ( | ) | const [inline, virtual] |
Get a clear, concise description of this class.
Implements EMAN::FactoryBase.
Definition at line 1034 of file reconstructor.h.
virtual string EMAN::nn4_ctfReconstructor::get_name | ( | ) | const [inline, virtual] |
Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase.
Definition at line 1029 of file reconstructor.h.
References NAME.
01030 { 01031 return NAME; 01032 }
TypeDict EMAN::nn4_ctfReconstructor::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::FactoryBase.
Definition at line 1045 of file reconstructor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.
01046 { 01047 TypeDict d; 01048 d.put("size", EMObject::INT); 01049 d.put("npad", EMObject::INT); 01050 d.put("sign", EMObject::INT); 01051 d.put("symmetry", EMObject::STRING); 01052 d.put("snr", EMObject::FLOAT); 01053 d.put("fftvol", EMObject::EMDATA); 01054 d.put("weight", EMObject::EMDATA); 01055 d.put("weighting", EMObject::INT); 01056 d.put("varsnr", EMObject::INT); 01057 return d; 01058 }
int nn4_ctfReconstructor::insert_buffed_slice | ( | const EMData * | buffer, | |
int | mult | |||
) |
Definition at line 3335 of file reconstructor.cpp.
References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), m_volume, and m_wptr.
Referenced by insert_slice().
03336 { 03337 const float* bufdata = buffed->get_data(); 03338 float* cdata = m_volume->get_data(); 03339 float* wdata = m_wptr->get_data(); 03340 03341 int npoint = buffed->get_xsize()/4; 03342 for( int i=0; i < npoint; ++i ) { 03343 03344 int pos2 = int( bufdata[4*i] ); 03345 int pos1 = pos2 * 2; 03346 cdata[pos1 ] += bufdata[4*i+1]*mult; 03347 cdata[pos1+1] += bufdata[4*i+2]*mult; 03348 wdata[pos2 ] += bufdata[4*i+3]*mult; 03349 /* 03350 std::cout << "pos1, pos2, ctfv1, ctfv2, ctf2: "; 03351 std::cout << pos1 << " " << bufdata[5*i+1] << " " << bufdata[5*i+2] << " "; 03352 std::cout << pos2 << " " << bufdata[5*i+4] << std::endl; 03353 */ 03354 } 03355 return 0; 03356 }
int nn4_ctfReconstructor::insert_padfft_slice | ( | EMData * | padfft, | |
const Transform & | trans, | |||
int | mult = 1 | |||
) |
Definition at line 3358 of file reconstructor.cpp.
References Assert, EMAN::EMData::get_attr(), m_nsym, m_symmetry, m_volume, m_wptr, EMAN::EMData::nn_ctf(), EMAN::EMData::nn_ctf_applied(), and t.
Referenced by insert_slice().
03359 { 03360 Assert( padfft != NULL ); 03361 float tmp = padfft->get_attr("ctf_applied"); 03362 int ctf_applied = (int) tmp; 03363 for( int isym=0; isym < m_nsym; isym++) { 03364 Transform tsym = t.get_sym( m_symmetry, isym ); 03365 03366 if(ctf_applied) m_volume->nn_ctf_applied(m_wptr, padfft, tsym, mult); 03367 03368 else m_volume->nn_ctf(m_wptr, padfft, tsym, mult); 03369 } 03370 03371 return 0; 03372 03373 }
int nn4_ctfReconstructor::insert_slice | ( | const EMData *const | slice, | |
const Transform & | euler, | |||
const float | weight = 1.0 | |||
) | [virtual] |
Insert a slice into a 3D volume, in a given orientation.
slice | the image slice to be inserted into the 3D volume | |
euler | Euler angle of this image slice. | |
weight | A weighting factor for this slice, generally the number of particles in a class-average. May be ignored by some reconstructors |
NullPointerException | if the input EMData pointer is null | |
ImageFormatException | if the image is complex as opposed to real |
Reimplemented from EMAN::Reconstructor.
Definition at line 3297 of file reconstructor.cpp.
References Assert, checked_delete(), EMAN::EMData::get_attr_default(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), insert_buffed_slice(), insert_padfft_slice(), LOGERR, m_npad, m_vnx, mult(), EMAN::padfft_slice(), and t.
03298 { 03299 // sanity checks 03300 if (!slice) { 03301 LOGERR("try to insert NULL slice"); 03302 return 1; 03303 } 03304 03305 int buffed = slice->get_attr_default( "buffed", 0 ); 03306 if( buffed > 0 ) { 03307 int mult = slice->get_attr_default( "mult", 1 ); 03308 insert_buffed_slice( slice, mult ); 03309 return 0; 03310 } 03311 03312 int padffted= slice->get_attr_default("padffted", 0); 03313 if( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) 03314 { 03315 // FIXME: Why doesn't this throw an exception? 03316 LOGERR("Tried to insert a slice that is the wrong size."); 03317 return 1; 03318 } 03319 03320 EMData* padfft = NULL; 03321 03322 if( padffted != 0 ) padfft = new EMData(*slice); 03323 else padfft = padfft_slice( slice, t, m_npad ); 03324 03325 int mult= slice->get_attr_default("mult", 1); 03326 03327 Assert( mult > 0 ); 03328 insert_padfft_slice( padfft, t, mult ); 03329 03330 checked_delete( padfft ); 03331 03332 return 0; 03333 }
static Reconstructor* EMAN::nn4_ctfReconstructor::NEW | ( | ) | [inline, static] |
Definition at line 1039 of file reconstructor.h.
References nn4_ctfReconstructor().
01040 { 01041 return new nn4_ctfReconstructor(); 01042 }
void nn4_ctfReconstructor::setup | ( | const string & | symmetry, | |
int | size, | |||
int | npad, | |||
float | snr, | |||
int | sign | |||
) |
Definition at line 3219 of file reconstructor.cpp.
References buildFFTVolume(), buildNormVolume(), ESTIMATE, EMAN::Transform::get_nsym(), EMAN::Dict::has_key(), m_npad, m_nsym, m_sign, m_snr, m_symmetry, m_vnx, m_vnxc, m_vnxp, m_vny, m_vnyc, m_vnyp, m_vnz, m_vnzc, m_vnzp, m_weighting, m_wghta, m_wghtb, NONE, and EMAN::FactoryBase::params.
03220 { 03221 m_weighting = ESTIMATE; 03222 if( params.has_key("weighting") ) { 03223 int tmp = int( params["weighting"] ); 03224 if( tmp==0 ) m_weighting = NONE; 03225 } 03226 03227 03228 03229 m_wghta = 0.2f; 03230 m_wghtb = 0.004f; 03231 03232 m_symmetry = symmetry; 03233 m_npad = npad; 03234 m_sign = sign; 03235 m_nsym = Transform::get_nsym(m_symmetry); 03236 03237 m_snr = snr; 03238 03239 m_vnx = size; 03240 m_vny = size; 03241 m_vnz = size; 03242 03243 m_vnxp = size*npad; 03244 m_vnyp = size*npad; 03245 m_vnzp = size*npad; 03246 03247 m_vnxc = m_vnxp/2; 03248 m_vnyc = m_vnyp/2; 03249 m_vnzc = m_vnzp/2; 03250 03251 buildFFTVolume(); 03252 buildNormVolume(); 03253 }
void nn4_ctfReconstructor::setup | ( | ) | [virtual] |
Initialize the reconstructor.
Implements EMAN::Reconstructor.
Definition at line 3202 of file reconstructor.cpp.
References EMAN::Dict::has_key(), m_varsnr, EMAN::FactoryBase::params, and sign.
Referenced by nn4_ctfReconstructor().
03203 { 03204 if( ! params.has_key("size") ) throw std::logic_error("Error: image size is not given"); 03205 03206 int size = params["size"]; 03207 int npad = params.has_key("npad") ? int(params["npad"]) : 4; 03208 // int sign = params.has_key("sign") ? int(params["sign"]) : 1; 03209 int sign = 1; 03210 string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1"; 03211 03212 float snr = params["snr"]; 03213 03214 m_varsnr = params.has_key("varsnr") ? int(params["varsnr"]) : 0; 03215 setup( symmetry, size, npad, snr, sign ); 03216 03217 }
bool EMAN::nn4_ctfReconstructor::m_delete_volume [private] |
Definition at line 1072 of file reconstructor.h.
Referenced by buildFFTVolume(), and ~nn4_ctfReconstructor().
bool EMAN::nn4_ctfReconstructor::m_delete_weight [private] |
Definition at line 1073 of file reconstructor.h.
Referenced by buildNormVolume(), and ~nn4_ctfReconstructor().
int EMAN::nn4_ctfReconstructor::m_npad [private] |
Definition at line 1077 of file reconstructor.h.
Referenced by buildFFTVolume(), insert_slice(), and setup().
int EMAN::nn4_ctfReconstructor::m_nsym [private] |
EMData* EMAN::nn4_ctfReconstructor::m_result [private] |
Definition at line 1070 of file reconstructor.h.
Referenced by finish(), nn4_ctfReconstructor(), and ~nn4_ctfReconstructor().
int EMAN::nn4_ctfReconstructor::m_sign [private] |
float EMAN::nn4_ctfReconstructor::m_snr [private] |
string EMAN::nn4_ctfReconstructor::m_symmetry [private] |
int EMAN::nn4_ctfReconstructor::m_varsnr [private] |
int EMAN::nn4_ctfReconstructor::m_vnx [private] |
int EMAN::nn4_ctfReconstructor::m_vnxc [private] |
Definition at line 1076 of file reconstructor.h.
Referenced by buildNormVolume(), finish(), and setup().
int EMAN::nn4_ctfReconstructor::m_vnxp [private] |
int EMAN::nn4_ctfReconstructor::m_vny [private] |
int EMAN::nn4_ctfReconstructor::m_vnyc [private] |
int EMAN::nn4_ctfReconstructor::m_vnyp [private] |
Definition at line 1075 of file reconstructor.h.
Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().
int EMAN::nn4_ctfReconstructor::m_vnz [private] |
int EMAN::nn4_ctfReconstructor::m_vnzc [private] |
int EMAN::nn4_ctfReconstructor::m_vnzp [private] |
Definition at line 1075 of file reconstructor.h.
Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().
EMData* EMAN::nn4_ctfReconstructor::m_volume [private] |
Definition at line 1069 of file reconstructor.h.
Referenced by buildFFTVolume(), finish(), insert_buffed_slice(), insert_padfft_slice(), nn4_ctfReconstructor(), and ~nn4_ctfReconstructor().
int EMAN::nn4_ctfReconstructor::m_weighting [private] |
float EMAN::nn4_ctfReconstructor::m_wghta [private] |
float EMAN::nn4_ctfReconstructor::m_wghtb [private] |
EMData* EMAN::nn4_ctfReconstructor::m_wptr [private] |
Definition at line 1071 of file reconstructor.h.
Referenced by buildNormVolume(), finish(), insert_buffed_slice(), insert_padfft_slice(), nn4_ctfReconstructor(), and ~nn4_ctfReconstructor().
const string nn4_ctfReconstructor::NAME = "nn4_ctf" [static] |