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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 EMData *const 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

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 202 of file reconstructor.h.


Constructor & Destructor Documentation

EMAN::ReconstructorVolumeData::ReconstructorVolumeData  )  [inline]
 

Only constructor All member variables are zeroed.

Definition at line 208 of file reconstructor.h.

References nx, and ny.

00208 : 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 212 of file reconstructor.h.

References free_memory().

00212 { 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.

Definition at line 243 of file reconstructor.h.

00244                         {
00245                                 if (image != 0)  {delete image; image = 0;}
00246                                 if ( tmp_data != 0 ) { delete tmp_data; tmp_data = 0; }
00247                         }

const EMData* const EMAN::ReconstructorVolumeData::get_emdata  )  [inline]
 

Get the main image pointer, probably redundant (not used).

Definition at line 216 of file reconstructor.h.

00216 { 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 250 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().

00252 {
00253         float* norm = tmp_data->get_data();
00254         float* rdata = image->get_data();
00255 
00256 //      printf("%d %d %d %d %d %d\n",subnx,subny,subnz,image->get_xsize(),image->get_ysize(),image->get_zsize());
00257 
00258         // FIXME should throw a sensible error
00259         if ( 0 == norm ) throw NullPointerException("The normalization volume was null!");
00260         if ( 0 == rdata ) throw NullPointerException("The complex reconstruction volume was null!");
00261 
00262         // The math is a bit tricky to explain. Wiener filter is basically SNR/(1+SNR)
00263         // In this case, data have already been effectively multiplied by SNR (one image at a time),
00264         // so without Wiener filter, we just divide by total SNR. With Wiener filter, we just add
00265         // 1.0 to total SNR, and we're done             --steve
00266         float wfilt=0.0;
00267         if (wiener) wfilt=1.0;          
00268         
00269         for (int i = 0; i < subnx * subny * subnz; i += 2) {
00270                 float d = norm[i/2];
00271                 if (sqrt_damp) d*=sqrt(d);
00272                 if (d == 0) {
00273                         rdata[i] = 0;
00274                         rdata[i + 1] = 0;
00275                 }
00276                 else {
00277 //                      rdata[i]=1.0/d;
00278 //                      rdata[i+1]=0.0;         // for debugging only
00279                         rdata[i] /= d+wfilt;
00280                         rdata[i + 1] /= d+wfilt;
00281                 }
00282         }
00283 
00284         // enforce complex conj, only works on subvolumes if the complete conjugate plane is in the volume
00285         if (subx0==0 && subnx>1 && subny==ny && subnz==nz) {
00286                 for (int z=0; z<=nz/2; z++) {
00287                         for (int y=1; y<=ny; y++) {
00288                                 if (y==0 && z==0) continue;
00289                                 // x=0
00290                                 int i=(y%ny)*subnx+(z%nz)*subnx*subny;
00291                                 int i2=(ny-y)*subnx+((nz-z)%nz)*subnx*subny;
00292                                 float ar=(rdata[i]+rdata[i2])/2.0f;
00293                                 float ai=(rdata[i+1]-rdata[i2+1])/2.0f;
00294                                 rdata[i]=ar;
00295                                 rdata[i2]=ar;
00296                                 rdata[i+1]=ai;
00297                                 rdata[i2+1]=-ai;
00298                         }
00299                 }
00300         }
00301 
00302         if (subx0+subnx==nx && subnx>1 && subny==ny && subnz==nz) {
00303                 for (int z=0; z<=nz/2; z++) {
00304                         for (int y=1; y<=ny; y++) {
00305                                 if (y==0 && z==0) continue;
00306                                 // x=0
00307                                 int i=(y%ny)*subnx+(z%nz)*subnx*subny+subnx-2;
00308                                 int i2=(ny-y)*subnx+((nz-z)%nz)*subnx*subny+subnx-2;
00309                                 float ar=(rdata[i]+rdata[i2])/2.0f;
00310                                 float ai=(rdata[i+1]-rdata[i2+1])/2.0f;
00311                                 rdata[i]=ar;
00312                                 rdata[i2]=ar;
00313                                 rdata[i+1]=ai;
00314                                 rdata[i2+1]=-ai;
00315                         }
00316                 }
00317         }
00318 }

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 259 of file reconstructor.h.

References EMAN::EMData::to_zero().

00260                         {
00261                                 if (tmp_data != 0 ) tmp_data->to_zero();
00262                                 if (image != 0 ) image->to_zero();
00263                         }


Member Data Documentation

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

Inheriting class allocates this, probably in setup().

Definition at line 220 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::nx [protected]
 

Definition at line 225 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::nx2 [protected]
 

Definition at line 225 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::ny [protected]
 

Definition at line 226 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::ny2 [protected]
 

Definition at line 226 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::nz [protected]
 

Definition at line 227 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::nz2 [protected]
 

Definition at line 227 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::subnx [protected]
 

Definition at line 229 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::subny [protected]
 

Definition at line 230 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::subnz [protected]
 

Definition at line 231 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::subx0 [protected]
 

Definition at line 233 of file reconstructor.h.

Referenced by normalize_threed().

int EMAN::ReconstructorVolumeData::suby0 [protected]
 

Definition at line 234 of file reconstructor.h.

int EMAN::ReconstructorVolumeData::subz0 [protected]
 

Definition at line 235 of file reconstructor.h.

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

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

Definition at line 222 of file reconstructor.h.

Referenced by normalize_threed().


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:32 2010 for EMAN2 by  doxygen 1.3.9.1