#include <reconstructor.h>
Inheritance diagram for EMAN::ReconstructorVolumeData:
Public Member Functions | |
ReconstructorVolumeData () | |
Only constructor All member variables are zeroed. | |
virtual | ~ReconstructorVolumeData () |
Destructor safely frees memory. | |
const EMData * | get_emdata () |
Get the main image pointer, probably redundant (not used). | |
Protected Member Functions | |
void | free_memory () |
Free allocated memorys The inherited class may have allocated image of tmp_data In either case you can safely call this function to delete either of those pointers, even if they bdb:refine_03::threed_00are NULL. | |
virtual void | normalize_threed (const bool sqrt_damp=false, const bool wiener=false) |
Normalize on the assumption that image is a Fourier volume and that tmp_data is a volume of weights corresponding in size to this Fourier volume. | |
virtual void | zero_memory () |
Sends the pixels in tmp_data and image to zero Convenience only. | |
Protected Attributes | |
EMData * | image |
Inheriting class allocates this, probably in setup(). | |
EMData * | tmp_data |
Inheriting class may allocate this, probably in setup(). | |
int | nx |
int | nx2 |
int | ny |
int | ny2 |
int | nz |
int | nz2 |
int | subnx |
int | subny |
int | subnz |
int | subx0 |
int | suby0 |
int | subz0 |
Private Member Functions | |
ReconstructorVolumeData (const ReconstructorVolumeData &that) | |
Disallow copy construction. | |
ReconstructorVolumeData & | operator= (const ReconstructorVolumeData &) |
Disallow assignment. |
One EMData object basically stores the real pixel data, the other is used for storing normalization values. This class was originally added simply to encapsulate the the things common to FourierReconstructor, WienerFourierReconstructor and BackProjectionReconstructor. It was never expected to instantiated on its own, and is intended to be a parent of the Reconstructor class. d.woolford May 2007
Definition at line 206 of file reconstructor.h.
EMAN::ReconstructorVolumeData::ReconstructorVolumeData | ( | ) | [inline] |
virtual EMAN::ReconstructorVolumeData::~ReconstructorVolumeData | ( | ) | [inline, virtual] |
Destructor safely frees memory.
Definition at line 216 of file reconstructor.h.
References free_memory().
00216 { free_memory(); }
EMAN::ReconstructorVolumeData::ReconstructorVolumeData | ( | const ReconstructorVolumeData & | that | ) | [private] |
Disallow copy construction.
void EMAN::ReconstructorVolumeData::free_memory | ( | ) | [inline, protected] |
Free allocated memorys The inherited class may have allocated image of tmp_data In either case you can safely call this function to delete either of those pointers, even if they bdb:refine_03::threed_00are NULL.
Reimplemented in EMAN::FourierReconstructor.
Definition at line 247 of file reconstructor.h.
References image, and tmp_data.
Referenced by ~ReconstructorVolumeData().
00248 { 00249 if (image != 0) {delete image; image = 0;} 00250 if ( tmp_data != 0 ) { delete tmp_data; tmp_data = 0; } 00251 }
const EMData* EMAN::ReconstructorVolumeData::get_emdata | ( | ) | [inline] |
Get the main image pointer, probably redundant (not used).
Definition at line 220 of file reconstructor.h.
References image.
00220 { return image; }
void ReconstructorVolumeData::normalize_threed | ( | const bool | sqrt_damp = false , |
|
const bool | wiener = false | |||
) | [protected, virtual] |
Normalize on the assumption that image is a Fourier volume and that tmp_data is a volume of weights corresponding in size to this Fourier volume.
This means tmp_data is assumed to have have as many x pixels as image.
Definition at line 256 of file reconstructor.cpp.
References EMAN::EMData::get_data(), image, norm(), NullPointerException, nx, ny, nz, rdata, sqrt(), subnx, subny, subnz, subx0, tmp_data, and y.
Referenced by EMAN::WienerFourierReconstructor::finish(), EMAN::FourierReconstructor::finish(), and EMAN::FourierReconstructorSimple2D::finish().
00258 { 00259 float* norm = tmp_data->get_data(); 00260 float* rdata = image->get_data(); 00261 00262 // printf("%d %d %d %d %d %d\n",subnx,subny,subnz,image->get_xsize(),image->get_ysize(),image->get_zsize()); 00263 00264 // FIXME should throw a sensible error 00265 if ( 0 == norm ) throw NullPointerException("The normalization volume was null!"); 00266 if ( 0 == rdata ) throw NullPointerException("The complex reconstruction volume was null!"); 00267 00268 // The math is a bit tricky to explain. Wiener filter is basically SNR/(1+SNR) 00269 // In this case, data have already been effectively multiplied by SNR (one image at a time), 00270 // so without Wiener filter, we just divide by total SNR. With Wiener filter, we just add 00271 // 1.0 to total SNR, and we're done --steve 00272 float wfilt=0.0; 00273 if (wiener) wfilt=1.0; 00274 00275 for (size_t i = 0; i < (size_t)subnx * subny * subnz; i += 2) { 00276 float d = norm[i/2]; 00277 if (sqrt_damp) d*=sqrt(d); 00278 if (d == 0) { 00279 rdata[i] = 0; 00280 rdata[i + 1] = 0; 00281 } 00282 else { 00283 // rdata[i]=1.0/d; 00284 // rdata[i+1]=0.0; // for debugging only 00285 rdata[i] /= d+wfilt; 00286 rdata[i + 1] /= d+wfilt; 00287 } 00288 } 00289 00290 // enforce complex conj, only works on subvolumes if the complete conjugate plane is in the volume 00291 if (subx0==0 && subnx>1 && subny==ny && subnz==nz) { 00292 for (int z=0; z<=nz/2; z++) { 00293 for (int y=1; y<=ny; y++) { 00294 if (y==0 && z==0) continue; 00295 // x=0 00296 size_t i=(size_t)(y%ny)*subnx+(size_t)(z%nz)*subnx*subny; 00297 size_t i2=(size_t)(ny-y)*subnx+(size_t)((nz-z)%nz)*subnx*subny; 00298 float ar=(rdata[i]+rdata[i2])/2.0f; 00299 float ai=(rdata[i+1]-rdata[i2+1])/2.0f; 00300 rdata[i]=ar; 00301 rdata[i2]=ar; 00302 rdata[i+1]=ai; 00303 rdata[i2+1]=-ai; 00304 } 00305 } 00306 } 00307 00308 if (subx0+subnx==nx && subnx>1 && subny==ny && subnz==nz) { 00309 for (int z=0; z<=nz/2; z++) { 00310 for (int y=1; y<=ny; y++) { 00311 if (y==0 && z==0) continue; 00312 // x=0 00313 size_t i=(size_t)(y%ny)*subnx+(size_t)(z%nz)*subnx*subny+subnx-2; 00314 size_t i2=(size_t)(ny-y)*subnx+(size_t)((nz-z)%nz)*subnx*subny+subnx-2; 00315 float ar=(rdata[i]+rdata[i2])/2.0f; 00316 float ai=(rdata[i+1]-rdata[i2+1])/2.0f; 00317 rdata[i]=ar; 00318 rdata[i2]=ar; 00319 rdata[i+1]=ai; 00320 rdata[i2+1]=-ai; 00321 } 00322 } 00323 } 00324 }
ReconstructorVolumeData& EMAN::ReconstructorVolumeData::operator= | ( | const ReconstructorVolumeData & | ) | [private] |
Disallow assignment.
virtual void EMAN::ReconstructorVolumeData::zero_memory | ( | ) | [inline, protected, virtual] |
Sends the pixels in tmp_data and image to zero Convenience only.
Definition at line 263 of file reconstructor.h.
References image, tmp_data, and EMAN::EMData::to_zero().
00264 { 00265 if (tmp_data != 0 ) tmp_data->to_zero(); 00266 if (image != 0 ) image->to_zero(); 00267 }
EMData* EMAN::ReconstructorVolumeData::image [protected] |
Inheriting class allocates this, probably in setup().
Definition at line 224 of file reconstructor.h.
Referenced by EMAN::FourierReconstructor::clear(), EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_insert_slice_work(), EMAN::BackProjectionReconstructor::finish(), EMAN::WienerFourierReconstructor::finish(), EMAN::FourierReconstructor::finish(), EMAN::FourierReconstructorSimple2D::finish(), free_memory(), EMAN::FourierReconstructor::free_memory(), get_emdata(), EMAN::BackProjectionReconstructor::insert_slice(), EMAN::FourierReconstructorSimple2D::insert_slice(), EMAN::FourierReconstructor::load_default_settings(), EMAN::FourierReconstructor::load_inserter(), normalize_threed(), EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::BackProjectionReconstructor::setup(), EMAN::FourierReconstructor::setup(), EMAN::FourierReconstructorSimple2D::setup(), EMAN::FourierReconstructor::setup_seed(), and zero_memory().
int EMAN::ReconstructorVolumeData::nx [protected] |
Definition at line 229 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::WienerFourierReconstructor::do_insert_slice_work(), EMAN::FourierReconstructor::do_insert_slice_work(), EMAN::BackProjectionReconstructor::insert_slice(), EMAN::FourierReconstructorSimple2D::insert_slice(), normalize_threed(), EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::BackProjectionReconstructor::setup(), EMAN::FourierReconstructor::setup(), EMAN::FourierReconstructorSimple2D::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::nx2 [protected] |
Definition at line 229 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::ny [protected] |
Definition at line 230 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::WienerFourierReconstructor::do_insert_slice_work(), EMAN::FourierReconstructor::do_insert_slice_work(), EMAN::BackProjectionReconstructor::insert_slice(), EMAN::FourierReconstructorSimple2D::insert_slice(), normalize_threed(), EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::BackProjectionReconstructor::setup(), EMAN::FourierReconstructor::setup(), EMAN::FourierReconstructorSimple2D::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::ny2 [protected] |
Definition at line 230 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::nz [protected] |
Definition at line 231 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::WienerFourierReconstructor::do_insert_slice_work(), EMAN::FourierReconstructor::do_insert_slice_work(), EMAN::BackProjectionReconstructor::insert_slice(), normalize_threed(), EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::BackProjectionReconstructor::setup(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::nz2 [protected] |
Definition at line 231 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::subnx [protected] |
Definition at line 233 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_compare_slice_work(), normalize_threed(), EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::subny [protected] |
Definition at line 234 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_compare_slice_work(), normalize_threed(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::subnz [protected] |
Definition at line 235 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_compare_slice_work(), normalize_threed(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::subx0 [protected] |
Definition at line 237 of file reconstructor.h.
Referenced by normalize_threed(), EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::suby0 [protected] |
Definition at line 238 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
int EMAN::ReconstructorVolumeData::subz0 [protected] |
Definition at line 239 of file reconstructor.h.
Referenced by EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), and EMAN::FourierReconstructor::setup_seed().
EMData* EMAN::ReconstructorVolumeData::tmp_data [protected] |
Inheriting class may allocate this, probably in setup().
Definition at line 226 of file reconstructor.h.
Referenced by EMAN::FourierReconstructor::clear(), EMAN::FourierReconstructor::do_compare_slice_work(), EMAN::FourierReconstructor::do_insert_slice_work(), EMAN::WienerFourierReconstructor::finish(), EMAN::FourierReconstructor::finish(), free_memory(), EMAN::FourierReconstructor::free_memory(), EMAN::BackProjectionReconstructor::insert_slice(), EMAN::FourierReconstructorSimple2D::insert_slice(), EMAN::FourierReconstructor::load_default_settings(), EMAN::FourierReconstructor::load_inserter(), normalize_threed(), EMAN::WienerFourierReconstructor::pixel_at(), EMAN::FourierReconstructor::pixel_at(), EMAN::FourierReconstructor::setup(), EMAN::FourierReconstructorSimple2D::setup(), EMAN::FourierReconstructor::setup_seed(), and zero_memory().