#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_wptr |
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 1214 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 3169 of file reconstructor.cpp.
03170 { 03171 //if( m_delete_volume ) checked_delete(m_volume); 03172 03173 //if( m_delete_weight ) checked_delete( m_wptr ); 03174 03175 //checked_delete( m_result ); 03176 }
void nn4_ctfReconstructor::buildFFTVolume | ( | ) | [private] |
Definition at line 3231 of file reconstructor.cpp.
References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), 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().
03231 { 03232 int offset = 2 - m_vnxp%2; 03233 03234 m_volume = params["fftvol"]; 03235 03236 if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) { 03237 m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp); 03238 m_volume->to_zero(); 03239 } 03240 03241 m_volume->set_nxc(m_vnxp/2); 03242 m_volume->set_complex(true); 03243 m_volume->set_ri(true); 03244 m_volume->set_fftpad(true); 03245 m_volume->set_attr("npad", m_npad); 03246 m_volume->set_array_offsets(0,1,1); 03247 }
void nn4_ctfReconstructor::buildNormVolume | ( | ) | [private] |
Definition at line 3249 of file reconstructor.cpp.
References EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), 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().
03250 { 03251 m_wptr = params["weight"]; 03252 03253 if( m_wptr->get_xsize() != m_vnxc+1 && m_wptr->get_ysize() != m_vnyp && m_wptr->get_zsize() != m_vnzp ) { 03254 m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp); 03255 m_wptr->to_zero(); 03256 } 03257 03258 m_wptr->set_array_offsets(0,1,1); 03259 03260 }
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 3341 of file reconstructor.cpp.
References abs, circumf(), EMAN::EMData::depad(), EMAN::EMData::do_ift_inplace(), ESTIMATE, EMAN::EMData::get_attr(), 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().
03342 { 03343 m_volume->set_array_offsets(0, 1, 1); 03344 m_wptr->set_array_offsets(0, 1, 1); 03345 m_volume->symplane0_ctf(m_wptr); 03346 03347 int box = 7; 03348 int vol = box*box*box; 03349 int kc = (box-1)/2; 03350 vector< float > pow_a( 3*kc+1, 1.0 ); 03351 for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta); 03352 pow_a[3*kc]=0.0; 03353 03354 03355 float max = max3d( kc, pow_a ); 03356 float alpha = ( 1.0f - 1.0f/(float)vol ) / max; 03357 float osnr = 1.0f/m_snr; 03358 03359 // normalize 03360 int ix,iy,iz; 03361 for (iz = 1; iz <= m_vnzp; iz++) { 03362 for (iy = 1; iy <= m_vnyp; iy++) { 03363 for (ix = 0; ix <= m_vnxc; ix++) { 03364 if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!! 03365 int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1; 03366 int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1; 03367 float tmp=0.0; 03368 if( m_varsnr ) { 03369 float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) ); 03370 tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr)*m_sign; 03371 } else { 03372 tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr)*m_sign; 03373 } 03374 03375 if( m_weighting == ESTIMATE ) { 03376 int cx = ix; 03377 int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp; 03378 int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp; 03379 float sum = 0.0; 03380 for( int ii = -kc; ii <= kc; ++ii ) { 03381 int nbrcx = cx + ii; 03382 if( nbrcx >= m_vnxc ) continue; 03383 for( int jj= -kc; jj <= kc; ++jj ) { 03384 int nbrcy = cy + jj; 03385 if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue; 03386 for( int kk = -kc; kk <= kc; ++kk ) { 03387 int nbrcz = cz + jj; 03388 if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue; 03389 if( nbrcx < 0 ) { 03390 nbrcx = -nbrcx; 03391 nbrcy = -nbrcy; 03392 nbrcz = -nbrcz; 03393 } 03394 03395 int nbrix = nbrcx; 03396 int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp; 03397 int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp; 03398 if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) { 03399 int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk); 03400 sum = sum + pow_a[c]; 03401 // if(ix%20==0 && iy%20==0 && iz%20==0) 03402 // std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl; 03403 } 03404 } 03405 } 03406 } 03407 float wght = 1.0f / ( 1.0f - alpha * sum ); 03408 /* 03409 if(ix%10==0 && iy%10==0) 03410 { 03411 std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz; 03412 std::cout << boost::format( "%10.3f %10.3f %10.3f " ) % tmp % wght % sum; 03413 std:: << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha; 03414 std::cout << std::endl; 03415 } 03416 */ 03417 tmp = tmp * wght; 03418 } 03419 (*m_volume)(2*ix,iy,iz) *= tmp; 03420 (*m_volume)(2*ix+1,iy,iz) *= tmp; 03421 } 03422 } 03423 } 03424 } 03425 03426 // back fft 03427 m_volume->do_ift_inplace(); 03428 int npad = m_volume->get_attr("npad"); 03429 m_volume->depad(); 03430 circumf( m_volume, npad ); 03431 m_volume->set_array_offsets( 0, 0, 0 ); 03432 03433 return 0; 03434 }
virtual string EMAN::nn4_ctfReconstructor::get_desc | ( | ) | const [inline, virtual] |
Get a clear, concise description of this class.
Implements EMAN::FactoryBase.
Definition at line 1243 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 1238 of file reconstructor.h.
References NAME.
01239 { 01240 return NAME; 01241 }
TypeDict EMAN::nn4_ctfReconstructor::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::FactoryBase.
Definition at line 1254 of file reconstructor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRING.
01255 { 01256 TypeDict d; 01257 d.put("size", EMObject::INT); 01258 d.put("npad", EMObject::INT); 01259 d.put("sign", EMObject::INT); 01260 d.put("symmetry", EMObject::STRING); 01261 d.put("snr", EMObject::FLOAT); 01262 d.put("fftvol", EMObject::EMDATA); 01263 d.put("weight", EMObject::EMDATA); 01264 d.put("weighting", EMObject::INT); 01265 d.put("varsnr", EMObject::INT); 01266 return d; 01267 }
int nn4_ctfReconstructor::insert_buffed_slice | ( | const EMData * | buffer, | |
int | mult | |||
) |
Definition at line 3300 of file reconstructor.cpp.
References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), m_volume, and m_wptr.
Referenced by insert_slice().
03301 { 03302 const float* bufdata = buffed->get_data(); 03303 float* cdata = m_volume->get_data(); 03304 float* wdata = m_wptr->get_data(); 03305 03306 int npoint = buffed->get_xsize()/4; 03307 for( int i=0; i < npoint; ++i ) { 03308 03309 int pos2 = int( bufdata[4*i] ); 03310 int pos1 = pos2 * 2; 03311 cdata[pos1 ] += bufdata[4*i+1]*mult; 03312 cdata[pos1+1] += bufdata[4*i+2]*mult; 03313 wdata[pos2 ] += bufdata[4*i+3]*mult; 03314 /* 03315 std::cout << "pos1, pos2, ctfv1, ctfv2, ctf2: "; 03316 std::cout << pos1 << " " << bufdata[5*i+1] << " " << bufdata[5*i+2] << " "; 03317 std::cout << pos2 << " " << bufdata[5*i+4] << std::endl; 03318 */ 03319 } 03320 return 0; 03321 }
int nn4_ctfReconstructor::insert_padfft_slice | ( | EMData * | padfft, | |
const Transform & | trans, | |||
int | mult = 1 | |||
) |
Definition at line 3323 of file reconstructor.cpp.
References Assert, EMAN::EMData::get_attr(), m_symmetry, m_volume, m_wptr, EMAN::EMData::nn_ctf(), EMAN::EMData::nn_ctf_applied(), and t.
Referenced by insert_slice().
03324 { 03325 Assert( padfft != NULL ); 03326 float tmp = padfft->get_attr("ctf_applied"); 03327 int ctf_applied = (int) tmp; 03328 03329 vector<Transform> tsym = t.get_sym_proj(m_symmetry); 03330 for (unsigned int isym=0; isym < tsym.size(); isym++) { 03331 if(ctf_applied) m_volume->nn_ctf_applied(m_wptr, padfft, tsym[isym], mult); 03332 else m_volume->nn_ctf(m_wptr, padfft, tsym[isym], mult); 03333 } 03334 03335 03336 return 0; 03337 03338 }
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 3262 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.
03263 { 03264 // sanity checks 03265 if (!slice) { 03266 LOGERR("try to insert NULL slice"); 03267 return 1; 03268 } 03269 03270 int buffed = slice->get_attr_default( "buffed", 0 ); 03271 if( buffed > 0 ) { 03272 int mult = slice->get_attr_default( "mult", 1 ); 03273 insert_buffed_slice( slice, mult ); 03274 return 0; 03275 } 03276 03277 int padffted= slice->get_attr_default("padffted", 0); 03278 if( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx) ) 03279 { 03280 // FIXME: Why doesn't this throw an exception? 03281 LOGERR("Tried to insert a slice that is the wrong size."); 03282 return 1; 03283 } 03284 03285 EMData* padfft = NULL; 03286 03287 if( padffted != 0 ) padfft = new EMData(*slice); 03288 else padfft = padfft_slice( slice, t, m_npad ); 03289 03290 int mult= slice->get_attr_default("mult", 1); 03291 03292 Assert( mult > 0 ); 03293 insert_padfft_slice( padfft, t, mult ); 03294 03295 checked_delete( padfft ); 03296 03297 return 0; 03298 }
static Reconstructor* EMAN::nn4_ctfReconstructor::NEW | ( | ) | [inline, static] |
Definition at line 1248 of file reconstructor.h.
References nn4_ctfReconstructor().
01249 { 01250 return new nn4_ctfReconstructor(); 01251 }
void nn4_ctfReconstructor::setup | ( | const string & | symmetry, | |
int | size, | |||
int | npad, | |||
float | snr, | |||
int | sign | |||
) |
Definition at line 3195 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.
03196 { 03197 m_weighting = ESTIMATE; 03198 if( params.has_key("weighting") ) { 03199 int tmp = int( params["weighting"] ); 03200 if( tmp==0 ) m_weighting = NONE; 03201 } 03202 03203 03204 03205 m_wghta = 0.2f; 03206 m_wghtb = 0.004f; 03207 03208 m_symmetry = symmetry; 03209 m_npad = npad; 03210 m_sign = sign; 03211 m_nsym = Transform::get_nsym(m_symmetry); 03212 03213 m_snr = snr; 03214 03215 m_vnx = size; 03216 m_vny = size; 03217 m_vnz = size; 03218 03219 m_vnxp = size*npad; 03220 m_vnyp = size*npad; 03221 m_vnzp = size*npad; 03222 03223 m_vnxc = m_vnxp/2; 03224 m_vnyc = m_vnyp/2; 03225 m_vnzc = m_vnzp/2; 03226 03227 buildFFTVolume(); 03228 buildNormVolume(); 03229 }
void nn4_ctfReconstructor::setup | ( | ) | [virtual] |
Initialize the reconstructor.
Implements EMAN::Reconstructor.
Definition at line 3178 of file reconstructor.cpp.
References EMAN::Dict::has_key(), m_varsnr, EMAN::FactoryBase::params, and sign.
Referenced by nn4_ctfReconstructor().
03179 { 03180 if( ! params.has_key("size") ) throw std::logic_error("Error: image size is not given"); 03181 03182 int size = params["size"]; 03183 int npad = params.has_key("npad") ? int(params["npad"]) : 4; 03184 // int sign = params.has_key("sign") ? int(params["sign"]) : 1; 03185 int sign = 1; 03186 string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1"; 03187 03188 float snr = params["snr"]; 03189 03190 m_varsnr = params.has_key("varsnr") ? int(params["varsnr"]) : 0; 03191 setup( symmetry, size, npad, snr, sign ); 03192 03193 }
int EMAN::nn4_ctfReconstructor::m_npad [private] |
Definition at line 1283 of file reconstructor.h.
Referenced by buildFFTVolume(), insert_slice(), and setup().
int EMAN::nn4_ctfReconstructor::m_nsym [private] |
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 1282 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 1281 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 1281 of file reconstructor.h.
Referenced by buildFFTVolume(), buildNormVolume(), finish(), and setup().
EMData* EMAN::nn4_ctfReconstructor::m_volume [private] |
Definition at line 1278 of file reconstructor.h.
Referenced by buildFFTVolume(), finish(), insert_buffed_slice(), insert_padfft_slice(), 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 1279 of file reconstructor.h.
Referenced by buildNormVolume(), finish(), insert_buffed_slice(), insert_padfft_slice(), and nn4_ctfReconstructor().
const string nn4_ctfReconstructor::NAME = "nn4_ctf" [static] |