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EMAN::ReconstructorVolumeData Class Reference

This is a Mixin class A class object encapsulating the volume data required by Reconstructors It basically stores two (pointers) to EMData objectsd stores the dimensions of the image volume. More...

#include <reconstructor.h>

Inheritance diagram for EMAN::ReconstructorVolumeData:

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Collaboration diagram for EMAN::ReconstructorVolumeData:

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List of all members.

Public Member Functions

 ReconstructorVolumeData ()
 Only constructor All member variables are zeroed.
virtual ~ReconstructorVolumeData ()
 Destructor safely frees memory.
const EMDataget_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

EMDataimage
 Inheriting class allocates this, probably in setup().
EMDatatmp_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.
ReconstructorVolumeDataoperator= (const ReconstructorVolumeData &)
 Disallow assignment.

Detailed Description

This is a Mixin class A class object encapsulating the volume data required by Reconstructors It basically stores two (pointers) to EMData objectsd stores the dimensions of the image volume.

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.


Constructor & Destructor Documentation

EMAN::ReconstructorVolumeData::ReconstructorVolumeData  )  [inline]
 

Only constructor All member variables are zeroed.

Definition at line 212 of file reconstructor.h.

References nx, and ny.

00212 : image(0), tmp_data(0), nx(0), ny(0), nz(0), subnx(0), subny(0), subnz(0), subx0(0), suby0(0), subz0(0) {}

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.


Member Function Documentation

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, and EMAN::FourierPlaneReconstructor.

Definition at line 247 of file reconstructor.h.

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.

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 258 of file reconstructor.cpp.

References EMAN::EMData::get_data(), image, norm(), NullPointerException, nx, ny, nz, rdata, sqrt(), subnx, subny, subx0, tmp_data, and y.

Referenced by EMAN::WienerFourierReconstructor::finish(), EMAN::FourierReconstructor::finish(), and EMAN::FourierReconstructorSimple2D::finish().

00260 {
00261         float* norm = tmp_data->get_data();
00262         float* rdata = image->get_data();
00263 
00264 //      printf("%d %d %d %d %d %d\n",subnx,subny,subnz,image->get_xsize(),image->get_ysize(),image->get_zsize());
00265 
00266         // FIXME should throw a sensible error
00267         if ( 0 == norm ) throw NullPointerException("The normalization volume was null!");
00268         if ( 0 == rdata ) throw NullPointerException("The complex reconstruction volume was null!");
00269 
00270         // The math is a bit tricky to explain. Wiener filter is basically SNR/(1+SNR)
00271         // In this case, data have already been effectively multiplied by SNR (one image at a time),
00272         // so without Wiener filter, we just divide by total SNR. With Wiener filter, we just add
00273         // 1.0 to total SNR, and we're done             --steve
00274         float wfilt=0.0;
00275         if (wiener) wfilt=1.0;          
00276         
00277         for (size_t i = 0; i < (size_t)subnx * subny * subnz; i += 2) {
00278                 float d = norm[i/2];
00279                 if (sqrt_damp) d*=sqrt(d);
00280                 if (d == 0) {
00281                         rdata[i] = 0;
00282                         rdata[i + 1] = 0;
00283                 }
00284                 else {
00285 //                      rdata[i]=1.0/d;
00286 //                      rdata[i+1]=0.0;         // for debugging only
00287                         rdata[i] /= d+wfilt;
00288                         rdata[i + 1] /= d+wfilt;
00289                 }
00290         }
00291 
00292         // enforce complex conj, only works on subvolumes if the complete conjugate plane is in the volume
00293         if (subx0==0 && subnx>1 && subny==ny && subnz==nz) {
00294                 for (int z=0; z<=nz/2; z++) {
00295                         for (int y=1; y<=ny; y++) {
00296                                 if (y==0 && z==0) continue;
00297                                 // x=0
00298                                 size_t i=(size_t)(y%ny)*subnx+(size_t)(z%nz)*subnx*subny;
00299                                 size_t i2=(size_t)(ny-y)*subnx+(size_t)((nz-z)%nz)*subnx*subny;
00300                                 float ar=(rdata[i]+rdata[i2])/2.0f;
00301                                 float ai=(rdata[i+1]-rdata[i2+1])/2.0f;
00302                                 rdata[i]=ar;
00303                                 rdata[i2]=ar;
00304                                 rdata[i+1]=ai;
00305                                 rdata[i2+1]=-ai;
00306                         }
00307                 }
00308         }
00309 
00310         if (subx0+subnx==nx && subnx>1 && subny==ny && subnz==nz) {
00311                 for (int z=0; z<=nz/2; z++) {
00312                         for (int y=1; y<=ny; y++) {
00313                                 if (y==0 && z==0) continue;
00314                                 // x=0
00315                                 size_t i=(size_t)(y%ny)*subnx+(size_t)(z%nz)*subnx*subny+subnx-2;
00316                                 size_t i2=(size_t)(ny-y)*subnx+(size_t)((nz-z)%nz)*subnx*subny+subnx-2;
00317                                 float ar=(rdata[i]+rdata[i2])/2.0f;
00318                                 float ai=(rdata[i+1]-rdata[i2+1])/2.0f;
00319                                 rdata[i]=ar;
00320                                 rdata[i2]=ar;
00321                                 rdata[i+1]=ai;
00322                                 rdata[i2+1]=-ai;
00323                         }
00324                 }
00325         }
00326 }

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 EMAN::EMData::to_zero().

00264                         {
00265                                 if (tmp_data != 0 ) tmp_data->to_zero();
00266                                 if (image != 0 ) image->to_zero();
00267                         }


Member Data Documentation

EMData* EMAN::ReconstructorVolumeData::image [protected]
 

Inheriting class allocates this, probably in setup().

Definition at line 224 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::nx [protected]
 

Definition at line 229 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::nx2 [protected]
 

Definition at line 229 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::ny [protected]
 

Definition at line 230 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::ny2 [protected]
 

Definition at line 230 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::nz [protected]
 

Definition at line 231 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::nz2 [protected]
 

Definition at line 231 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::subnx [protected]
 

Definition at line 233 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::subny [protected]
 

Definition at line 234 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::subnz [protected]
 

Definition at line 235 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::subx0 [protected]
 

Definition at line 237 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::suby0 [protected]
 

Definition at line 238 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::subz0 [protected]
 

Definition at line 239 of file reconstructor.h.

EMData* EMAN::ReconstructorVolumeData::tmp_data [protected]
 

Inheriting class may allocate this, probably in setup().

Definition at line 226 of file reconstructor.h.

Referenced by normalize_threed().


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:49:22 2013 for EMAN2 by  doxygen 1.3.9.1