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AlignOptions Class Reference

#include <alignoptions.h>

Collaboration diagram for AlignOptions:

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List of all members.

Public Member Functions

 AlignOptions ()
 AlignOptions (Vec3i &volsize)
 AlignOptions (const AlignOptions &old_options)
virtual ~AlignOptions ()
void set_mask3D (EMData *mask3D)
void set_first_ring (int first_ring)
void set_last_ring (int last_ring)
void set_rstep (int rstep)
void set_ri (int ri)
void set_xrng (float xrng)
void set_yrng (float yrng)
void set_step (float step)
void set_dtheta (float dtheta)
void set_snr (float snr)
void set_symmetry (std::string symmetry)
void set_CTF (bool CTF)
void set_have_angles (bool have_angles)
void set_ref_angle_type (std::string ref_angle_type)
void set_use_sirt (bool use_sirt)
void set_sirt_tol (float sirt_tol)
void set_sirt_lam (float sirt_lam)
void set_sirt_maxit (int sirt_maxit)
void set_maxit (int maxit)
EMDataget_mask3D ()
int get_first_ring ()
int get_last_ring ()
int get_rstep ()
int get_ri ()
float get_xrng ()
float get_yrng ()
float get_step ()
float get_dtheta ()
float get_snr ()
std::string get_symmetry ()
bool get_CTF ()
bool get_have_angles ()
std::string get_ref_angle_type ()
bool get_use_sirt ()
float get_sirt_tol ()
float get_sirt_lam ()
int get_sirt_maxit ()
int get_maxit ()

Private Attributes

EMDatamask3D
int first_ring
int last_ring
int rstep
int ri
float xrng
float yrng
float step
float dtheta
float snr
std::string symmetry
bool CTF
bool have_angles
std::string ref_angle_type
bool use_sirt
float sirt_tol
float sirt_lam
int sirt_maxit
int maxit

Constructor & Destructor Documentation

AlignOptions::AlignOptions  ) 
 

Definition at line 3 of file alignoptions.cpp.

References CTF, dtheta, first_ring, have_angles, last_ring, mask3D, maxit, ref_angle_type, ri, rstep, sirt_lam, sirt_maxit, sirt_tol, snr, step, symmetry, use_sirt, xrng, and yrng.

00004 {
00005     mask3D     = NULL;
00006     first_ring = 1;
00007     last_ring  = 0;
00008     rstep      = 1;
00009     ri         = 0;
00010     xrng       = 1.0;
00011     yrng       = 1.0;
00012     step       = 1.0;
00013     dtheta     = 15.0;
00014     snr        = 1.0;
00015     symmetry   = "c1";
00016     CTF        = false;
00017     have_angles = false;
00018     ref_angle_type = "P";
00019     use_sirt = true;
00020     sirt_tol = 1.0e-1;
00021     sirt_lam = 1.0e-4;
00022     sirt_maxit = 100;
00023     maxit      = 1;
00024 }

AlignOptions::AlignOptions Vec3i volsize  ) 
 

Definition at line 26 of file alignoptions.cpp.

References CTF, dtheta, first_ring, have_angles, last_ring, mask3D, maxit, ref_angle_type, ri, rstep, sirt_lam, sirt_maxit, sirt_tol, snr, step, symmetry, use_sirt, EMAN::Vec3i, xrng, and yrng.

00027 {
00028     int min_dim = (volsize[0] < volsize[1] ? volsize[0] : volsize[1]);
00029     min_dim = (min_dim < volsize[2] ? min_dim : volsize[2]);
00030     // min_dim = min(nx,ny,nz)
00031     mask3D     = NULL;
00032     first_ring = 1;
00033     last_ring  = min_dim / 2 - 2;
00034     rstep      = 1;
00035     ri         = min_dim / 2 - 2;
00036     xrng       = 1.0;
00037     yrng       = 1.0;
00038     step       = 1.0;
00039     dtheta     = 15.0;
00040     snr        = 1.0;
00041     symmetry   = "c1";
00042     CTF        = false;
00043     have_angles = false;
00044     ref_angle_type = "P";
00045     use_sirt = true;
00046     sirt_tol = 1.0e-1;
00047     sirt_lam = 1.0e-4;
00048     sirt_maxit = 100;
00049     maxit      = 1;
00050 }

AlignOptions::AlignOptions const AlignOptions old_options  ) 
 

Definition at line 52 of file alignoptions.cpp.

References CTF, dtheta, first_ring, have_angles, last_ring, mask3D, maxit, ref_angle_type, ri, rstep, sirt_lam, sirt_maxit, sirt_tol, snr, step, symmetry, use_sirt, xrng, and yrng.

00053 {
00054     mask3D     = old_options.mask3D;
00055     first_ring = old_options.first_ring;
00056     last_ring  = old_options.last_ring;
00057     rstep      = old_options.rstep;
00058     ri         = old_options.ri;
00059     xrng       = old_options.xrng;
00060     yrng       = old_options.yrng;
00061     step       = old_options.step;
00062     dtheta     = old_options.dtheta;
00063     snr        = old_options.snr;
00064     symmetry   = old_options.symmetry;
00065     CTF        = old_options.CTF;
00066     have_angles = old_options.have_angles;
00067     ref_angle_type = old_options.ref_angle_type;
00068     use_sirt = old_options.use_sirt;
00069     sirt_tol = old_options.sirt_tol;
00070     sirt_lam = old_options.sirt_lam;
00071     sirt_maxit = old_options.sirt_maxit;
00072     maxit      = old_options.maxit;
00073 }

AlignOptions::~AlignOptions  )  [virtual]
 

Definition at line 75 of file alignoptions.cpp.

00076 {
00077 }


Member Function Documentation

bool AlignOptions::get_CTF  ) 
 

Definition at line 170 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00170                           {
00171     return CTF;
00172 }

float AlignOptions::get_dtheta  ) 
 

Definition at line 161 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00161                               {
00162     return dtheta;
00163 }

int AlignOptions::get_first_ring  ) 
 

Definition at line 140 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00140                                   {
00141     return first_ring;
00142 }

bool AlignOptions::get_have_angles  ) 
 

Definition at line 173 of file alignoptions.cpp.

Referenced by ali3d_d().

00173                                   {
00174     return have_angles;
00175 }

int AlignOptions::get_last_ring  ) 
 

Definition at line 143 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00143                                  {
00144     return last_ring;
00145 }

EMData * AlignOptions::get_mask3D  ) 
 

Definition at line 137 of file alignoptions.cpp.

Referenced by ali3d_d().

00137                                  {
00138     return mask3D;
00139 }

int AlignOptions::get_maxit  ) 
 

Definition at line 191 of file alignoptions.cpp.

Referenced by ali3d_d(), main(), and ParseAlignOptions().

00191                            {
00192     return maxit;
00193 }

std::string AlignOptions::get_ref_angle_type  ) 
 

Definition at line 176 of file alignoptions.cpp.

Referenced by ParseAlignOptions().

00176                                           {
00177     return ref_angle_type;
00178 }

int AlignOptions::get_ri  ) 
 

Definition at line 149 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00149                           {
00150     return ri;
00151 }

int AlignOptions::get_rstep  ) 
 

Definition at line 146 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00146                              {
00147     return rstep;
00148 }

float AlignOptions::get_sirt_lam  ) 
 

Definition at line 185 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00185                                 {
00186     return sirt_lam;
00187 }

int AlignOptions::get_sirt_maxit  ) 
 

Definition at line 188 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00188                                 {
00189     return sirt_maxit;
00190 }

float AlignOptions::get_sirt_tol  ) 
 

Definition at line 182 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00182                                 {
00183     return sirt_tol;
00184 }

float AlignOptions::get_snr  ) 
 

Definition at line 164 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00164                            {
00165     return snr;
00166 }

float AlignOptions::get_step  ) 
 

Definition at line 158 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00158                             {
00159     return step;
00160 }

std::string AlignOptions::get_symmetry  ) 
 

Definition at line 167 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00167                                     {
00168     return symmetry;
00169 }

bool AlignOptions::get_use_sirt  ) 
 

Definition at line 179 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00179                                {
00180     return use_sirt;
00181 }

float AlignOptions::get_xrng  ) 
 

Definition at line 152 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00152                             {
00153     return xrng;
00154 }

float AlignOptions::get_yrng  ) 
 

Definition at line 155 of file alignoptions.cpp.

Referenced by ali3d_d(), and ParseAlignOptions().

00155                             {
00156     return yrng;
00157 }

void AlignOptions::set_CTF bool  CTF  ) 
 

Definition at line 112 of file alignoptions.cpp.

References CTF.

Referenced by ParseAlignOptions().

00112                                      {
00113     CTF = in_CTF;
00114 }

void AlignOptions::set_dtheta float  dtheta  ) 
 

Definition at line 103 of file alignoptions.cpp.

References dtheta.

Referenced by ParseAlignOptions().

00103                                             {
00104     dtheta = in_dtheta;
00105 }

void AlignOptions::set_first_ring int  first_ring  ) 
 

Definition at line 82 of file alignoptions.cpp.

References first_ring.

Referenced by ParseAlignOptions().

00082                                                   {
00083     first_ring = in_first_ring;
00084 }

void AlignOptions::set_have_angles bool  have_angles  ) 
 

Definition at line 115 of file alignoptions.cpp.

References have_angles.

Referenced by main().

00115                                                      {
00116     have_angles = in_have_angles;
00117 }

void AlignOptions::set_last_ring int  last_ring  ) 
 

Definition at line 85 of file alignoptions.cpp.

References last_ring.

Referenced by ParseAlignOptions().

00085                                                 {
00086     last_ring = in_last_ring;
00087 }

void AlignOptions::set_mask3D EMData mask3D  ) 
 

Definition at line 79 of file alignoptions.cpp.

References mask3D.

Referenced by ParseAlignOptions().

00079                                                {
00080     mask3D = in_mask3D;
00081 }

void AlignOptions::set_maxit int  maxit  ) 
 

Definition at line 133 of file alignoptions.cpp.

References maxit.

Referenced by main(), and ParseAlignOptions().

00133                                         {
00134     maxit = in_maxit;
00135 }

void AlignOptions::set_ref_angle_type std::string  ref_angle_type  ) 
 

Definition at line 118 of file alignoptions.cpp.

References ref_angle_type.

Referenced by ParseAlignOptions().

00118                                                                 {
00119     ref_angle_type = in_ref_angle_type;
00120 }

void AlignOptions::set_ri int  ri  ) 
 

Definition at line 91 of file alignoptions.cpp.

References ri.

Referenced by ParseAlignOptions().

00091                                   {
00092     ri = in_ri;
00093 }

void AlignOptions::set_rstep int  rstep  ) 
 

Definition at line 88 of file alignoptions.cpp.

References rstep.

Referenced by ParseAlignOptions().

00088                                         {
00089     rstep = in_rstep;
00090 }

void AlignOptions::set_sirt_lam float  sirt_lam  ) 
 

Definition at line 127 of file alignoptions.cpp.

References sirt_lam.

Referenced by ParseAlignOptions().

00127                                                 {
00128     sirt_lam = in_sirt_lam;
00129 }

void AlignOptions::set_sirt_maxit int  sirt_maxit  ) 
 

Definition at line 130 of file alignoptions.cpp.

References sirt_maxit.

Referenced by ParseAlignOptions().

00130                                                   {
00131     sirt_maxit = in_sirt_maxit;
00132 }

void AlignOptions::set_sirt_tol float  sirt_tol  ) 
 

Definition at line 124 of file alignoptions.cpp.

References sirt_tol.

Referenced by ParseAlignOptions().

00124                                                 {
00125     sirt_tol = in_sirt_tol;
00126 }

void AlignOptions::set_snr float  snr  ) 
 

Definition at line 106 of file alignoptions.cpp.

References snr.

Referenced by ParseAlignOptions().

00106                                       {
00107     snr = in_snr;
00108 }

void AlignOptions::set_step float  step  ) 
 

Definition at line 100 of file alignoptions.cpp.

References step.

Referenced by ParseAlignOptions().

00100                                         {
00101     step = in_step;
00102 }

void AlignOptions::set_symmetry std::string  symmetry  ) 
 

Definition at line 109 of file alignoptions.cpp.

References symmetry.

Referenced by ParseAlignOptions().

00109                                                     {
00110     symmetry = in_symmetry;
00111 }

void AlignOptions::set_use_sirt bool  use_sirt  ) 
 

Definition at line 121 of file alignoptions.cpp.

References use_sirt.

Referenced by ParseAlignOptions().

00121                                                {
00122     use_sirt = in_use_sirt;
00123 }

void AlignOptions::set_xrng float  xrng  ) 
 

Definition at line 94 of file alignoptions.cpp.

References xrng.

Referenced by ParseAlignOptions().

00094                                         {
00095     xrng = in_xrng;
00096 }

void AlignOptions::set_yrng float  yrng  ) 
 

Definition at line 97 of file alignoptions.cpp.

References yrng.

Referenced by ParseAlignOptions().

00097                                         {
00098     yrng = in_yrng;
00099 }


Member Data Documentation

bool AlignOptions::CTF [private]
 

Definition at line 69 of file alignoptions.h.

Referenced by AlignOptions(), and set_CTF().

float AlignOptions::dtheta [private]
 

Definition at line 66 of file alignoptions.h.

Referenced by AlignOptions(), and set_dtheta().

int AlignOptions::first_ring [private]
 

Definition at line 59 of file alignoptions.h.

Referenced by AlignOptions(), and set_first_ring().

bool AlignOptions::have_angles [private]
 

Definition at line 70 of file alignoptions.h.

Referenced by AlignOptions(), and set_have_angles().

int AlignOptions::last_ring [private]
 

Definition at line 60 of file alignoptions.h.

Referenced by AlignOptions(), and set_last_ring().

EMData* AlignOptions::mask3D [private]
 

Definition at line 58 of file alignoptions.h.

Referenced by AlignOptions(), and set_mask3D().

int AlignOptions::maxit [private]
 

Definition at line 76 of file alignoptions.h.

Referenced by AlignOptions(), and set_maxit().

std::string AlignOptions::ref_angle_type [private]
 

Definition at line 71 of file alignoptions.h.

Referenced by AlignOptions(), and set_ref_angle_type().

int AlignOptions::ri [private]
 

Definition at line 62 of file alignoptions.h.

Referenced by AlignOptions(), and set_ri().

int AlignOptions::rstep [private]
 

Definition at line 61 of file alignoptions.h.

Referenced by AlignOptions(), and set_rstep().

float AlignOptions::sirt_lam [private]
 

Definition at line 74 of file alignoptions.h.

Referenced by AlignOptions(), and set_sirt_lam().

int AlignOptions::sirt_maxit [private]
 

Definition at line 75 of file alignoptions.h.

Referenced by AlignOptions(), and set_sirt_maxit().

float AlignOptions::sirt_tol [private]
 

Definition at line 73 of file alignoptions.h.

Referenced by AlignOptions(), and set_sirt_tol().

float AlignOptions::snr [private]
 

Definition at line 67 of file alignoptions.h.

Referenced by AlignOptions(), and set_snr().

float AlignOptions::step [private]
 

Definition at line 65 of file alignoptions.h.

Referenced by AlignOptions(), and set_step().

std::string AlignOptions::symmetry [private]
 

Definition at line 68 of file alignoptions.h.

Referenced by AlignOptions(), and set_symmetry().

bool AlignOptions::use_sirt [private]
 

Definition at line 72 of file alignoptions.h.

Referenced by AlignOptions(), and set_use_sirt().

float AlignOptions::xrng [private]
 

Definition at line 63 of file alignoptions.h.

Referenced by AlignOptions(), and set_xrng().

float AlignOptions::yrng [private]
 

Definition at line 64 of file alignoptions.h.

Referenced by AlignOptions(), and set_yrng().


The documentation for this class was generated from the following files:
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