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emdata_sparx.cpp File Reference

#include <stack>
#include "ctf.h"
#include "emdata.h"
#include <iostream>
#include <cmath>
#include <cstring>
#include <gsl/gsl_sf_bessel.h>
#include <gsl/gsl_errno.h>
#include <vector>
#include <boost/shared_ptr.hpp>

Include dependency graph for emdata_sparx.cpp:

Go to the source code of this file.

Classes

class  ctf_store

Defines

#define rdata(i, j, k)   rdata[(i-1)+((j-1)+(k-1)*ny)*nx]
#define square(x)   ((x)*(x))
#define proj(ix, iy, iz)   proj[ix-1+(iy-1+(iz-1)*ny)*nx]
#define pnewimg(ix, iy, iz)   pnewimg[ix-1+(iy-1+(iz-1)*ny)*nx]
#define in(i, j, k)   in[i+(j+(k*ny))*nx]
#define in(i, j, k)   in[i+(j+(k*ny))*nx]
#define QUADPI   3.141592653589793238462643383279502884197
#define DGR_TO_RAD   QUADPI/180
#define rdata(i, j, k)   rdata[(i-1)+((j-1)+(k-1)*ny)*nx]
#define X(i)   X[i-1]
#define Y(j)   Y[j-1]
#define Z(k)   Z[k-1]
#define avagadro   (6.023*(double)pow(10.0,23.0))
#define density_protein   (1.36)
#define R   (0.61803399f)
#define C   (1.f-R)
#define QUADPI   3.141592653589793238462643383279502884197
#define DGR_TO_RAD   QUADPI/180
#define fint(i, j, k)   fint[(i-1) + ((j-1) + (k-1)*ny)*lsd]
#define fout(i, j, k)   fout[(i-1) + ((j-1) + (k-1)*nyn)*lsdn]
#define fint(jx, jy, jz)   fint[jx + (jy + jz*ny)*nox]
#define fint(jx, jy, jz)   fint[jx + (jy + jz*ny)*nx]
#define fout(jx, jy, jz)   fout[jx + (jy + jz*ny)*nx]

Functions

float dist (int lnlen, const float *line_1, const float *line_2)
float dist_r (int lnlen, const float *line_1, const float *line_2)
void swapx (float *a, float *b, float *temp, size_t nbytes)
 Helper function for EMData::fft_shuffle, below.
ostream & operator<< (ostream &os, const Pixel &peak)
float circumference (EMData *emdata, int npixel)


Define Documentation

#define avagadro   (6.023*(double)pow(10.0,23.0))
 

Definition at line 4639 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::find_3d_threshold().

#define C   (1.f-R)
 

Definition at line 4642 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::find_3d_threshold(), EMAN::EMData::phase_cog(), and EMAN::Util::TwoDTestFunc().

#define density_protein   (1.36)
 

Definition at line 4640 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::find_3d_threshold().

#define DGR_TO_RAD   QUADPI/180
 

Definition at line 4936 of file emdata_sparx.cpp.

#define DGR_TO_RAD   QUADPI/180
 

Definition at line 4936 of file emdata_sparx.cpp.

Referenced by EMAN::Util::CANG(), EMAN::EMData::fouriergridrot2d(), EMAN::EMData::fouriergridrot_shift2d(), and EMAN::EMData::helicise().

#define fint jx,
jy,
jz   )     fint[jx + (jy + jz*ny)*nx]
 

Definition at line 5898 of file emdata_sparx.cpp.

#define fint jx,
jy,
jz   )     fint[jx + (jy + jz*ny)*nox]
 

Definition at line 5898 of file emdata_sparx.cpp.

#define fint i,
j,
 )     fint[(i-1) + ((j-1) + (k-1)*ny)*lsd]
 

Definition at line 5898 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::filter_by_image(), EMAN::EMData::Four_ds(), EMAN::EMData::Four_shuf_ds_cen_us(), EMAN::EMData::FourInterpol(), EMAN::EMData::FourTruncate(), and EMAN::EMData::replace_amplitudes().

#define fout jx,
jy,
jz   )     fout[jx + (jy + jz*ny)*nx]
 

Definition at line 5899 of file emdata_sparx.cpp.

#define fout i,
j,
 )     fout[(i-1) + ((j-1) + (k-1)*nyn)*lsdn]
 

Definition at line 5899 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::Four_ds(), EMAN::EMData::Four_shuf_ds_cen_us(), EMAN::EMData::FourInterpol(), EMAN::EMData::FourTruncate(), and EMAN::EMData::replace_amplitudes().

#define in i,
j,
 )     in[i+(j+(k*ny))*nx]
 

Definition at line 2123 of file emdata_sparx.cpp.

#define in i,
j,
 )     in[i+(j+(k*ny))*nx]
 

Definition at line 2123 of file emdata_sparx.cpp.

Referenced by EMAN::Log::begin(), EMAN::Util::cl1(), EMAN::EMData::conjg(), EMAN::newfile_store::get_image(), EMAN::EMUtil::get_image_type(), EMAN::EMData::get_pow(), EMAN::FileFourierProcessor::process_inplace(), EMAN::newfile_store::read(), EMAN::XYData::read_file(), EMAN::file_store::restart(), EMAN::newfile_store::restart(), EMAN::EMData::rot_scale_trans(), and EMAN::EMData::rot_scale_trans_background().

#define pnewimg ix,
iy,
iz   )     pnewimg[ix-1+(iy-1+(iz-1)*ny)*nx]
 

Definition at line 965 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::average_circ_sub().

#define proj ix,
iy,
iz   )     proj[ix-1+(iy-1+(iz-1)*ny)*nx]
 

Definition at line 964 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::average_circ_sub(), EMAN::FourierGriddingProjector::project3d(), EMAN::StandardProjector::project3d(), EMAN::PointArray::projection_by_summation(), recons3d_4nn(), and EMAN::Util::twoD_to_3D_ali().

#define QUADPI   3.141592653589793238462643383279502884197
 

Definition at line 4935 of file emdata_sparx.cpp.

#define QUADPI   3.141592653589793238462643383279502884197
 

Definition at line 4935 of file emdata_sparx.cpp.

#define R   (0.61803399f)
 

Definition at line 4641 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::find_3d_threshold(), and EMAN::Transform::orthogonalize().

#define rdata i,
j,
 )     rdata[(i-1)+((j-1)+(k-1)*ny)*nx]
 

Definition at line 4504 of file emdata_sparx.cpp.

#define rdata i,
j,
 )     rdata[(i-1)+((j-1)+(k-1)*ny)*nx]
 

Definition at line 4504 of file emdata_sparx.cpp.

#define square  )     ((x)*(x))
 

Definition at line 671 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::calc_dist(), EMAN::EMData::calc_mutual_correlation(), EMAN::EMData::calc_sigma_diff(), EMAN::OptVarianceCmp::cmp(), EMAN::EMData::cog(), EMAN::WienerFourierReconstructor::insert_slice(), EMAN::EMData::little_big_dot(), main(), and EMAN::BilateralProcessor::process_inplace().

#define X  )     X[i-1]
 

Definition at line 4505 of file emdata_sparx.cpp.

Referenced by EMAN::SVDAnalyzer::analyze(), EMAN::EMData::phase_cog(), and EMAN::Util::svdcmp().

#define Y  )     Y[j-1]
 

Definition at line 4506 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::phase_cog(), and EMAN::Util::WTF().

#define Z  )     Z[k-1]
 

Definition at line 4507 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::phase_cog().


Function Documentation

float circumference EMData emdata,
int  npixel
 

Definition at line 5133 of file emdata_sparx.cpp.

References Assert, data, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), nx, and ny.

05134 {
05135         int nx = emdata->get_xsize();
05136         int ny = emdata->get_ysize();
05137         int nz = emdata->get_zsize();
05138 
05139         float* data = emdata->get_data();
05140         if( ny==1 && nz==1 )
05141         {
05142             // 1d case
05143             float sumf=0.0;
05144             int   sumn=0;
05145             for( int i=0; i < npixel; ++i )
05146             {
05147                 sumf += data[i];
05148                 sumf += data[nx-1-i];
05149                 sumn += 2;
05150             }
05151             return sumf/sumn;
05152         }
05153 
05154         if( nz==1 )
05155         {
05156             float sumf=0.0;
05157             int   sumn=0;
05158             int   id=0;
05159             for( int iy=0; iy < ny; ++iy )
05160             {
05161                 for( int ix=0; ix < nx; ++ix )
05162                 {
05163                     if( iy<npixel || iy>ny-1-npixel || ix<npixel || ix>nx-1-npixel )
05164                     {
05165                         sumf += data[id];
05166                         sumn += 1;
05167                     }
05168                     id++;
05169                 }
05170             }
05171 
05172             Assert( id==nx*ny  );
05173             Assert( sumn == nx*ny - (nx-2*npixel)*(ny-2*npixel) );
05174             return sumf/sumn;
05175         }
05176 
05177         // 3d cases;
05178 
05179         float sumf = 0.0;
05180         int   sumn = 0;
05181         int   id = 0;
05182         for( int iz=0; iz < nz; ++iz)
05183         {
05184             for( int iy=0; iy < ny; ++iy)
05185             {
05186                 for( int ix=0; ix < nx; ++ix )
05187                 {
05188                     if( iz<npixel||iz>nz-1-npixel||iy<npixel||iy>ny-1-npixel||ix<npixel||ix>nx-1-npixel)
05189                     {
05190                         sumf += data[id];
05191                         sumn += 1;
05192                     }
05193                     id++;
05194                 }
05195             }
05196         }
05197 
05198 
05199         Assert( id==nx*ny*nz);
05200         Assert( sumn==nx*ny*nz-(nx-2*npixel)*(ny-2*npixel)*(nz-2*npixel) );
05201         return sumf/sumn;
05202 }

float dist int  lnlen,
const float *  line_1,
const float *  line_2
 

Definition at line 452 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::cm_euc(), EMAN::Quaternion::normalize(), EMAN::RotationalSubstractProcessor::process_inplace(), EMAN::RotationalAverageProcessor::process_inplace(), EMAN::MaskGaussNonuniformProcessor::process_pixel(), EMAN::CircularMaskProcessor::process_pixel(), and EMAN::PointArray::set_from_density_map().

00453 {
00454         float dis2=0.0;
00455         for( int i=0; i < lnlen; ++i) {
00456                 float tmp = line_1[i] - line_2[i];
00457                 dis2 += tmp*tmp;
00458         }
00459         //return static_cast<float>(std::sqrt(dis2));
00460         return dis2;
00461 }

float dist_r int  lnlen,
const float *  line_1,
const float *  line_2
 

Definition at line 463 of file emdata_sparx.cpp.

References sqrt().

00464 {
00465         double dis2 = 0.0;
00466         for( int i=0; i < lnlen; ++i ) {
00467                 float tmp = line_1[lnlen-1-i] - line_2[i];
00468                 dis2 += tmp*tmp;
00469         }
00470         return static_cast<float>(std::sqrt(dis2));
00471 }

ostream& operator<< ostream &  os,
const Pixel peak
 

Definition at line 3666 of file emdata_sparx.cpp.

References EMAN::Pixel::value, EMAN::Pixel::x, EMAN::Pixel::y, and EMAN::Pixel::z.

03666                                                      {
03667     os <<  peak.x <<  peak.y << peak.z  << peak.value;
03668     return os;
03669 }

void swapx float *  a,
float *  b,
float *  temp,
size_t  nbytes
[inline]
 

Helper function for EMData::fft_shuffle, below.

Definition at line 3226 of file emdata_sparx.cpp.

Referenced by EMAN::EMData::fft_shuffle().

03226                                                                   {
03227         memcpy(temp, a, nbytes);
03228         memcpy(a, b, nbytes);
03229         memcpy(b, temp, nbytes);
03230 }


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