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:

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Classes

class  ctf_store
class  ctf_store_new

Defines

#define rdata(i, j, k)   rdata[(i-1)+((j-1)+(k-1)*ny)*(size_t)nx]
#define square(x)   ((x)*(x))
#define proj(ix, iy, iz)   proj[ix-1+(iy-1+(iz-1)*ny)*(size_t)nx]
#define pnewimg(ix, iy, iz)   pnewimg[ix-1+(iy-1+(iz-1)*ny)*(size_t)nx]
#define in(i, j, k)   in[i+(j+(k*ny))*(size_t)nx]
#define in(i, j, k)   in[i+(j+(k*ny))*(size_t)nx]
#define QUADPI   3.141592653589793238462643383279502884197
#define DGR_TO_RAD   QUADPI/180
#define rdata(i, j, k)   rdata[(i-1)+((j-1)+(k-1)*ny)*(size_t)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)*(size_t)lsd]
#define fout(i, j, k)   fout[(i-1) + ((j-1) + (k-1)*nyn)*(size_t)lsdn]
#define fint(jx, jy, jz)   fint[jx + (jy + jz*ny)*(size_t)nox]
#define fint(jx, jy, jz)   fint[jx + (jy + jz*ny)*(size_t)nx]
#define fout(jx, jy, jz)   fout[jx + (jy + jz*ny)*(size_t)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 5971 of file emdata_sparx.cpp.

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

#define C   (1.f-R)

Definition at line 5974 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 5972 of file emdata_sparx.cpp.

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

#define DGR_TO_RAD   QUADPI/180

Definition at line 6268 of file emdata_sparx.cpp.

#define DGR_TO_RAD   QUADPI/180

Definition at line 6268 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)*(size_t)nx]

Definition at line 7216 of file emdata_sparx.cpp.

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

Definition at line 7216 of file emdata_sparx.cpp.

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

Definition at line 7216 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)*(size_t)nx]

Definition at line 7217 of file emdata_sparx.cpp.

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

Definition at line 7217 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))*(size_t)nx]

Definition at line 2779 of file emdata_sparx.cpp.

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

Definition at line 2779 of file emdata_sparx.cpp.

Referenced by EMAN::Log::begin(), EMAN::Util::cl1(), EMAN::EMData::conjg(), frm_2d_Align(), EMAN::newfile_store::get_image(), EMAN::EMUtil::get_image_type(), EMAN::EMData::get_pow(), EMAN::ImagicIO2::init_test(), EMAN::EMData::oneDfftPolar(), EMAN::Wiener2DFourierProcessor::process(), EMAN::ApplyPolynomialProfileToHelix::process_inplace(), EMAN::ModelEMCylinderProcessor::process_inplace(), 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)*(size_t)nx]

Definition at line 1005 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)*(size_t)nx]

Definition at line 1004 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(), EMAN::PointArray::replace_by_summation(), and EMAN::Util::twoD_to_3D_ali().

#define QUADPI   3.141592653589793238462643383279502884197

Definition at line 6267 of file emdata_sparx.cpp.

#define QUADPI   3.141592653589793238462643383279502884197

Definition at line 6267 of file emdata_sparx.cpp.

#define R   (0.61803399f)

Definition at line 5973 of file emdata_sparx.cpp.

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

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

Definition at line 5836 of file emdata_sparx.cpp.

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

Definition at line 5836 of file emdata_sparx.cpp.

#define square (  )     ((x)*(x))

Definition at line 721 of file emdata_sparx.cpp.

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

#define X (  )     X[i-1]

Definition at line 5837 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 5838 of file emdata_sparx.cpp.

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

#define Z (  )     Z[k-1]

Definition at line 5839 of file emdata_sparx.cpp.

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


Function Documentation

float circumference ( EMData emdata,
int  npixel 
)

Definition at line 6465 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.

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

06466 {
06467         int nx = emdata->get_xsize();
06468         int ny = emdata->get_ysize();
06469         int nz = emdata->get_zsize();
06470 
06471         float* data = emdata->get_data();
06472         if( ny==1 && nz==1 ) {
06473                 // 1d case
06474                 float sumf=0.0;
06475                 int   sumn=0;
06476                 for( int i=0; i < npixel; ++i ) {
06477                         sumf += data[i];
06478                         sumf += data[nx-1-i];
06479                         sumn += 2;
06480                 }
06481                 return sumf/sumn;
06482         }
06483 
06484         if( nz==1 ) {
06485                 float sumf=0.0;
06486                 int   sumn=0;
06487                 int   id=0;
06488                 for( int iy=0; iy < ny; ++iy ) {
06489                         for( int ix=0; ix < nx; ++ix ) {
06490                                 if( iy<npixel || iy>ny-1-npixel || ix<npixel || ix>nx-1-npixel ) {
06491                                     sumf += data[id];
06492                                     sumn += 1;
06493                                 }
06494                                 id++;
06495                         }
06496                 }
06497 
06498                 Assert( id==nx*ny  );
06499                 Assert( sumn == nx*ny - (nx-2*npixel)*(ny-2*npixel) );
06500                 return sumf/sumn;
06501         }
06502 
06503         // 3d cases;
06504 
06505         float sumf = 0.0;
06506         size_t   sumn = 0;
06507         size_t   id = 0;
06508         for( int iz=0; iz < nz; ++iz) {
06509                 for( int iy=0; iy < ny; ++iy) {
06510                         for( int ix=0; ix < nx; ++ix ) {
06511                                 if( iz<npixel||iz>nz-1-npixel||iy<npixel||iy>ny-1-npixel||ix<npixel||ix>nx-1-npixel) {
06512                                         sumf += data[id];
06513                                         sumn += 1;
06514                                 }
06515                                 id++;
06516                         }
06517                 }
06518         }
06519 
06520 
06521         Assert( id==(size_t)nx*ny*nz);
06522         Assert( sumn==(size_t)nx*ny*nz-(size_t)(nx-2*npixel)*(ny-2*npixel)*(nz-2*npixel) );
06523         return sumf/sumn;
06524 }

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

Definition at line 474 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().

00475 {
00476         float dis2=0.0;
00477         for( int i=0; i < lnlen; ++i) {
00478                 float tmp = line_1[i] - line_2[i];
00479                 dis2 += tmp*tmp;
00480         }
00481         //return static_cast<float>(std::sqrt(dis2));
00482         return dis2;
00483 }

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

Definition at line 485 of file emdata_sparx.cpp.

References sqrt().

00486 {
00487         double dis2 = 0.0;
00488         for( int i=0; i < lnlen; ++i ) {
00489                 float tmp = line_1[lnlen-1-i] - line_2[i];
00490                 dis2 += tmp*tmp;
00491         }
00492         return static_cast<float>(std::sqrt(dis2));
00493 }

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

Definition at line 4998 of file emdata_sparx.cpp.

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

04998                                                      {
04999     os <<  peak.x <<  peak.y << peak.z  << peak.value;
05000     return os;
05001 }

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

Helper function for EMData::fft_shuffle, below.

Definition at line 4034 of file emdata_sparx.cpp.

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

04034                                                                   {
04035         memcpy(temp, a, nbytes);
04036         memcpy(a, b, nbytes);
04037         memcpy(b, temp, nbytes);
04038 }


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