EMAN2
Public Member Functions | Private Attributes
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

Detailed Description

Definition at line 10 of file alignoptions.h.


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.

{
    mask3D     = NULL;
    first_ring = 1;
    last_ring  = 0;
    rstep      = 1;
    ri         = 0;
    xrng       = 1.0;
    yrng       = 1.0;
    step       = 1.0;
    dtheta     = 15.0;
    snr        = 1.0;
    symmetry   = "c1";
    CTF        = false;
    have_angles = false;
    ref_angle_type = "P";
    use_sirt = true;
    sirt_tol = 1.0e-1;
    sirt_lam = 1.0e-4;
    sirt_maxit = 100;
    maxit      = 1;
}
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, xrng, and yrng.

{
    int min_dim = (volsize[0] < volsize[1] ? volsize[0] : volsize[1]);
    min_dim = (min_dim < volsize[2] ? min_dim : volsize[2]);
    // min_dim = min(nx,ny,nz)
    mask3D     = NULL;
    first_ring = 1;
    last_ring  = min_dim / 2 - 2;
    rstep      = 1;
    ri         = min_dim / 2 - 2;
    xrng       = 1.0;
    yrng       = 1.0;
    step       = 1.0;
    dtheta     = 15.0;
    snr        = 1.0;
    symmetry   = "c1";
    CTF        = false;
    have_angles = false;
    ref_angle_type = "P";
    use_sirt = true;
    sirt_tol = 1.0e-1;
    sirt_lam = 1.0e-4;
    sirt_maxit = 100;
    maxit      = 1;
}
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.

{
    mask3D     = old_options.mask3D;
    first_ring = old_options.first_ring;
    last_ring  = old_options.last_ring;
    rstep      = old_options.rstep;
    ri         = old_options.ri;
    xrng       = old_options.xrng;
    yrng       = old_options.yrng;
    step       = old_options.step;
    dtheta     = old_options.dtheta;
    snr        = old_options.snr;
    symmetry   = old_options.symmetry;
    CTF        = old_options.CTF;
    have_angles = old_options.have_angles;
    ref_angle_type = old_options.ref_angle_type;
    use_sirt = old_options.use_sirt;
    sirt_tol = old_options.sirt_tol;
    sirt_lam = old_options.sirt_lam;
    sirt_maxit = old_options.sirt_maxit;
    maxit      = old_options.maxit;
}
AlignOptions::~AlignOptions ( ) [virtual]

Definition at line 75 of file alignoptions.cpp.

{
}

Member Function Documentation

bool AlignOptions::get_CTF ( )

Definition at line 170 of file alignoptions.cpp.

References CTF.

Referenced by ali3d_d(), and ParseAlignOptions().

                          {
    return CTF;
}
float AlignOptions::get_dtheta ( )

Definition at line 161 of file alignoptions.cpp.

References dtheta.

Referenced by ali3d_d(), and ParseAlignOptions().

                              {
    return dtheta;
}
int AlignOptions::get_first_ring ( )

Definition at line 140 of file alignoptions.cpp.

References first_ring.

Referenced by ali3d_d(), and ParseAlignOptions().

                                  {
    return first_ring;
}
bool AlignOptions::get_have_angles ( )

Definition at line 173 of file alignoptions.cpp.

References have_angles.

Referenced by ali3d_d().

                                  {
    return have_angles;
}
int AlignOptions::get_last_ring ( )

Definition at line 143 of file alignoptions.cpp.

References last_ring.

Referenced by ali3d_d(), and ParseAlignOptions().

                                 {
    return last_ring;
}
EMData * AlignOptions::get_mask3D ( )

Definition at line 137 of file alignoptions.cpp.

References mask3D.

Referenced by ali3d_d().

                                 {
    return mask3D;
}
int AlignOptions::get_maxit ( )

Definition at line 191 of file alignoptions.cpp.

References maxit.

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

                           {
    return maxit;
}
std::string AlignOptions::get_ref_angle_type ( )

Definition at line 176 of file alignoptions.cpp.

References ref_angle_type.

Referenced by ParseAlignOptions().

                                          {
    return ref_angle_type;
}
int AlignOptions::get_ri ( )

Definition at line 149 of file alignoptions.cpp.

References ri.

Referenced by ali3d_d(), and ParseAlignOptions().

                          {
    return ri;
}
int AlignOptions::get_rstep ( )

Definition at line 146 of file alignoptions.cpp.

References rstep.

Referenced by ali3d_d(), and ParseAlignOptions().

                             {
    return rstep;
}
float AlignOptions::get_sirt_lam ( )

Definition at line 185 of file alignoptions.cpp.

References sirt_lam.

Referenced by ali3d_d(), and ParseAlignOptions().

                                {
    return sirt_lam;
}
int AlignOptions::get_sirt_maxit ( )

Definition at line 188 of file alignoptions.cpp.

References sirt_maxit.

Referenced by ali3d_d(), and ParseAlignOptions().

                                {
    return sirt_maxit;
}
float AlignOptions::get_sirt_tol ( )

Definition at line 182 of file alignoptions.cpp.

References sirt_tol.

Referenced by ali3d_d(), and ParseAlignOptions().

                                {
    return sirt_tol;
}
float AlignOptions::get_snr ( )

Definition at line 164 of file alignoptions.cpp.

References snr.

Referenced by ali3d_d(), and ParseAlignOptions().

                           {
    return snr;
}
float AlignOptions::get_step ( )

Definition at line 158 of file alignoptions.cpp.

References step.

Referenced by ali3d_d(), and ParseAlignOptions().

                            {
    return step;
}
std::string AlignOptions::get_symmetry ( )

Definition at line 167 of file alignoptions.cpp.

References symmetry.

Referenced by ali3d_d(), and ParseAlignOptions().

                                    {
    return symmetry;
}
bool AlignOptions::get_use_sirt ( )

Definition at line 179 of file alignoptions.cpp.

References use_sirt.

Referenced by ali3d_d(), and ParseAlignOptions().

                               {
    return use_sirt;
}
float AlignOptions::get_xrng ( )

Definition at line 152 of file alignoptions.cpp.

References xrng.

Referenced by ali3d_d(), and ParseAlignOptions().

                            {
    return xrng;
}
float AlignOptions::get_yrng ( )

Definition at line 155 of file alignoptions.cpp.

References yrng.

Referenced by ali3d_d(), and ParseAlignOptions().

                            {
    return yrng;
}
void AlignOptions::set_CTF ( bool  CTF)

Definition at line 112 of file alignoptions.cpp.

References CTF.

Referenced by ParseAlignOptions().

                                     {
    CTF = in_CTF;
}
void AlignOptions::set_dtheta ( float  dtheta)

Definition at line 103 of file alignoptions.cpp.

References dtheta.

Referenced by ParseAlignOptions().

                                            {
    dtheta = in_dtheta;
}
void AlignOptions::set_first_ring ( int  first_ring)

Definition at line 82 of file alignoptions.cpp.

References first_ring.

Referenced by ParseAlignOptions().

                                                  {
    first_ring = in_first_ring;
}
void AlignOptions::set_have_angles ( bool  have_angles)

Definition at line 115 of file alignoptions.cpp.

References have_angles.

Referenced by main().

                                                     {
    have_angles = in_have_angles;
}
void AlignOptions::set_last_ring ( int  last_ring)

Definition at line 85 of file alignoptions.cpp.

References last_ring.

Referenced by ParseAlignOptions().

                                                {
    last_ring = in_last_ring;
}
void AlignOptions::set_mask3D ( EMData mask3D)

Definition at line 79 of file alignoptions.cpp.

References mask3D.

Referenced by ParseAlignOptions().

                                               {
    mask3D = in_mask3D;
}
void AlignOptions::set_maxit ( int  maxit)

Definition at line 133 of file alignoptions.cpp.

References maxit.

Referenced by main(), and ParseAlignOptions().

                                        {
    maxit = in_maxit;
}
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().

                                                                {
    ref_angle_type = in_ref_angle_type;
}
void AlignOptions::set_ri ( int  ri)

Definition at line 91 of file alignoptions.cpp.

References ri.

Referenced by ParseAlignOptions().

                                  {
    ri = in_ri;
}
void AlignOptions::set_rstep ( int  rstep)

Definition at line 88 of file alignoptions.cpp.

References rstep.

Referenced by ParseAlignOptions().

                                        {
    rstep = in_rstep;
}
void AlignOptions::set_sirt_lam ( float  sirt_lam)

Definition at line 127 of file alignoptions.cpp.

References sirt_lam.

Referenced by ParseAlignOptions().

                                                {
    sirt_lam = in_sirt_lam;
}
void AlignOptions::set_sirt_maxit ( int  sirt_maxit)

Definition at line 130 of file alignoptions.cpp.

References sirt_maxit.

Referenced by ParseAlignOptions().

                                                  {
    sirt_maxit = in_sirt_maxit;
}
void AlignOptions::set_sirt_tol ( float  sirt_tol)

Definition at line 124 of file alignoptions.cpp.

References sirt_tol.

Referenced by ParseAlignOptions().

                                                {
    sirt_tol = in_sirt_tol;
}
void AlignOptions::set_snr ( float  snr)

Definition at line 106 of file alignoptions.cpp.

References snr.

Referenced by ParseAlignOptions().

                                      {
    snr = in_snr;
}
void AlignOptions::set_step ( float  step)

Definition at line 100 of file alignoptions.cpp.

References step.

Referenced by ParseAlignOptions().

                                        {
    step = in_step;
}
void AlignOptions::set_symmetry ( std::string  symmetry)

Definition at line 109 of file alignoptions.cpp.

References symmetry.

Referenced by ParseAlignOptions().

                                                    {
    symmetry = in_symmetry;
}
void AlignOptions::set_use_sirt ( bool  use_sirt)

Definition at line 121 of file alignoptions.cpp.

References use_sirt.

Referenced by ParseAlignOptions().

                                               {
    use_sirt = in_use_sirt;
}
void AlignOptions::set_xrng ( float  xrng)

Definition at line 94 of file alignoptions.cpp.

References xrng.

Referenced by ParseAlignOptions().

                                        {
    xrng = in_xrng;
}
void AlignOptions::set_yrng ( float  yrng)

Definition at line 97 of file alignoptions.cpp.

References yrng.

Referenced by ParseAlignOptions().

                                        {
    yrng = in_yrng;
}

Member Data Documentation

bool AlignOptions::CTF [private]

Definition at line 69 of file alignoptions.h.

Referenced by AlignOptions(), get_CTF(), and set_CTF().

float AlignOptions::dtheta [private]

Definition at line 66 of file alignoptions.h.

Referenced by AlignOptions(), get_dtheta(), and set_dtheta().

int AlignOptions::first_ring [private]

Definition at line 59 of file alignoptions.h.

Referenced by AlignOptions(), get_first_ring(), and set_first_ring().

bool AlignOptions::have_angles [private]

Definition at line 70 of file alignoptions.h.

Referenced by AlignOptions(), get_have_angles(), and set_have_angles().

int AlignOptions::last_ring [private]

Definition at line 60 of file alignoptions.h.

Referenced by AlignOptions(), get_last_ring(), and set_last_ring().

Definition at line 58 of file alignoptions.h.

Referenced by AlignOptions(), get_mask3D(), and set_mask3D().

int AlignOptions::maxit [private]

Definition at line 76 of file alignoptions.h.

Referenced by AlignOptions(), get_maxit(), and set_maxit().

std::string AlignOptions::ref_angle_type [private]

Definition at line 71 of file alignoptions.h.

Referenced by AlignOptions(), get_ref_angle_type(), and set_ref_angle_type().

int AlignOptions::ri [private]

Definition at line 62 of file alignoptions.h.

Referenced by AlignOptions(), get_ri(), and set_ri().

int AlignOptions::rstep [private]

Definition at line 61 of file alignoptions.h.

Referenced by AlignOptions(), get_rstep(), and set_rstep().

float AlignOptions::sirt_lam [private]

Definition at line 74 of file alignoptions.h.

Referenced by AlignOptions(), get_sirt_lam(), and set_sirt_lam().

int AlignOptions::sirt_maxit [private]

Definition at line 75 of file alignoptions.h.

Referenced by AlignOptions(), get_sirt_maxit(), and set_sirt_maxit().

float AlignOptions::sirt_tol [private]

Definition at line 73 of file alignoptions.h.

Referenced by AlignOptions(), get_sirt_tol(), and set_sirt_tol().

float AlignOptions::snr [private]

Definition at line 67 of file alignoptions.h.

Referenced by AlignOptions(), get_snr(), and set_snr().

float AlignOptions::step [private]

Definition at line 65 of file alignoptions.h.

Referenced by AlignOptions(), get_step(), and set_step().

std::string AlignOptions::symmetry [private]

Definition at line 68 of file alignoptions.h.

Referenced by AlignOptions(), get_symmetry(), and set_symmetry().

bool AlignOptions::use_sirt [private]

Definition at line 72 of file alignoptions.h.

Referenced by AlignOptions(), get_use_sirt(), and set_use_sirt().

float AlignOptions::xrng [private]

Definition at line 63 of file alignoptions.h.

Referenced by AlignOptions(), get_xrng(), and set_xrng().

float AlignOptions::yrng [private]

Definition at line 64 of file alignoptions.h.

Referenced by AlignOptions(), get_yrng(), and set_yrng().


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