Xmipp  v3.23.11-Nereus
Classes | Macros | Variables
Parameters and common ART Reconstruction stuff
Collaboration diagram for Parameters and common ART Reconstruction stuff:

Classes

struct  ReconsInfo
 
class  BasicARTParameters
 

Macros

#define TELL_IV   0x100
 
#define TELL_ONLY_SYM   0x80
 
#define TELL_USE_INPUT_BASISVOLUME   0x40
 
#define TELL_SHOW_ERROR   0x20
 
#define TELL_MANUAL_ORDER   0x10
 
#define TELL_SAVE_AT_EACH_STEP   0x8
 
#define TELL_SAVE_INTERMIDIATE   0x4
 
#define TELL_SAVE_BASIS   0x2
 
#define TELL_STATS   0x1
 

Variables

Basis BasicARTParameters::basis
 Basis function. By default, blobs. More...
 
int BasicARTParameters::no_it
 Number of iterations. More...
 
Matrix1D< double > BasicARTParameters::lambda_list
 Relaxation parameter. More...
 
ARTParallelMode BasicARTParameters::parallel_mode
 
int BasicARTParameters::block_size
 Number of projections for each parallel block. More...
 
int BasicARTParameters::eq_mode
 
bool BasicARTParameters::random_sort
 True if random sort of projections. More...
 
bool BasicARTParameters::dont_sort
 True if no sort must be made. More...
 
int BasicARTParameters::sort_last_N
 Sort perpendicular with the last N projections. If -1 with all previous. More...
 
bool BasicARTParameters::WLS
 
Matrix1D< double > BasicARTParameters::kappa_list
 
std::vector< ProjectionBasicARTParameters::residual_imgs
 
double BasicARTParameters::sum_weight
 
double BasicARTParameters::grid_relative_size
 Relative size for the grid. More...
 
int BasicARTParameters::grid_type
 CC, BCC or FCC (in grids.hh) More...
 
int BasicARTParameters::proj_ext
 
double BasicARTParameters::R
 
int BasicARTParameters::Xoutput_volume_size
 
int BasicARTParameters::Youtput_volume_size
 
int BasicARTParameters::Zoutput_volume_size
 
double BasicARTParameters::sampling
 Sampling rate. More...
 
FileName BasicARTParameters::fn_sym
 File containing symmetries. More...
 
int BasicARTParameters::sym_each
 
double BasicARTParameters::max_tilt
 
int BasicARTParameters::ref_trans_after
 Refine the translation alignement after n projection presentations. More...
 
double BasicARTParameters::ref_trans_step
 Refine the translation alignement after n projection presentations. More...
 
double BasicARTParameters::sparseEps
 Sparse reconstruction. More...
 
double BasicARTParameters::diffusionWeight
 Tomographic diffussion. More...
 
int BasicARTParameters::force_sym
 Force the reconstruction to be symmetric this number of times. More...
 
bool BasicARTParameters::do_not_generate_subgroup
 Do not generate symmetry subgroup. More...
 
bool BasicARTParameters::do_not_use_symproj
 Do not use symmetrized projections. More...
 
FileName BasicARTParameters::fn_surface_mask
 File containing surface mask. More...
 
FileName BasicARTParameters::fn_sel
 Selection file with all images to process. More...
 
double BasicARTParameters::goldmask
 Goldmask. More...
 
bool BasicARTParameters::shiftedTomograms
 Shifted tomograms. More...
 
FileName BasicARTParameters::fn_out
 Name of the output volume, also used to set the root of rest output files. More...
 
FileName BasicARTParameters::fn_root
 
FileName BasicARTParameters::fn_start
 Grid volume as initial guess. More...
 
int BasicARTParameters::stop_at
 Stop after this number of images, if 0 then don't use. More...
 
double BasicARTParameters::known_volume
 Known volume. If -1, not applied. More...
 
FileName BasicARTParameters::fn_ctf
 Selection file with all images to process. More...
 
bool BasicARTParameters::unmatched
 Apply unmatched projectors to correct for the CTF. More...
 
double BasicARTParameters::ray_length
 
bool BasicARTParameters::apply_shifts
 Apply shifts stored in the headers of the 2D-images. More...
 
bool BasicARTParameters::positivity
 Apply positivity constraint. More...
 
bool BasicARTParameters::print_system_matrix
 Print system matrix. More...
 
bool BasicARTParameters::is_crystal
 Is this a crystal 0 means NO 1 YES. More...
 
bool BasicARTParameters::variability_analysis
 Variability analysis. More...
 
bool BasicARTParameters::refine
 Refine experimental projection before backprojecting. More...
 
bool BasicARTParameters::noisy_reconstruction
 Noisy reconstruction. More...
 
bool BasicARTParameters::using_MPI
 Only for internal purposes, MUST be set when running MPI. More...
 
int BasicARTParameters::threads
 Number of threads to use. Can not be different than 1 when using MPI. More...
 
int BasicARTParameters::tell
 
int BasicARTParameters::save_intermidiate_every
 Frequency for saving intermidiate. More...
 
int BasicARTParameters::verbose
 Verbose level. More...
 
FileName BasicARTParameters::fn_control
 Name of file for improved control in parallel jobs. More...
 
SymList BasicARTParameters::SL
 A list with the symmetry matrices. More...
 
size_t BasicARTParameters::projXdim
 Projection X dimension. More...
 
size_t BasicARTParameters::projYdim
 Projection Y dimension. More...
 
std::ofstream * BasicARTParameters::fh_hist =nullptr
 File handler for the history file. More...
 
ReconsInfoBasicARTParameters::IMG_Inf =nullptr
 Array with all the sorting information for each projection. More...
 
MultidimArray< int > BasicARTParameters::ordered_list
 Order in which projections will be presented to algorithm. More...
 
int BasicARTParameters::numIMG
 Total number of images to process (taking symmetries into account) More...
 
int BasicARTParameters::trueIMG
 Number of different images (without symmetries) More...
 
Matrix2D< double > * BasicARTParameters::D =nullptr
 
Matrix2D< double > * BasicARTParameters::Dinv =nullptr
 Just the inverse of D. More...
 
Image< double > * BasicARTParameters::surface_mask =nullptr
 
int BasicARTParameters::POCS_freq
 
GridVolumeT< int > * BasicARTParameters::GVNeq =nullptr
 

Detailed Description

The main difference between ART applied to different cases (single particles, crystals, ...) is the single step applied to each case. Most of the tasks in the ART are common to all ART processes. All these common tasks as well as the common parameters are comprised in the ARTReconsBase class. These common tasks are based on the existence of a BasicARTParameters class containing all the specific information for the ART process.

Macro Definition Documentation

◆ TELL_IV

#define TELL_IV   0x100

Definition at line 269 of file basic_art.h.

◆ TELL_MANUAL_ORDER

#define TELL_MANUAL_ORDER   0x10

Definition at line 273 of file basic_art.h.

◆ TELL_ONLY_SYM

#define TELL_ONLY_SYM   0x80

Definition at line 270 of file basic_art.h.

◆ TELL_SAVE_AT_EACH_STEP

#define TELL_SAVE_AT_EACH_STEP   0x8

Definition at line 274 of file basic_art.h.

◆ TELL_SAVE_BASIS

#define TELL_SAVE_BASIS   0x2

Definition at line 276 of file basic_art.h.

◆ TELL_SAVE_INTERMIDIATE

#define TELL_SAVE_INTERMIDIATE   0x4

Definition at line 275 of file basic_art.h.

◆ TELL_SHOW_ERROR

#define TELL_SHOW_ERROR   0x20

Definition at line 272 of file basic_art.h.

◆ TELL_STATS

#define TELL_STATS   0x1

Definition at line 277 of file basic_art.h.

◆ TELL_USE_INPUT_BASISVOLUME

#define TELL_USE_INPUT_BASISVOLUME   0x40

Definition at line 271 of file basic_art.h.

Variable Documentation

◆ apply_shifts

bool BasicARTParameters::apply_shifts

Apply shifts stored in the headers of the 2D-images.

Definition at line 243 of file basic_art.h.

◆ basis

Basis BasicARTParameters::basis

Basis function. By default, blobs.

Definition at line 97 of file basic_art.h.

◆ block_size

int BasicARTParameters::block_size

Number of projections for each parallel block.

Definition at line 112 of file basic_art.h.

◆ D

Matrix2D<double>* BasicARTParameters::D =nullptr

Volume deformation matrix. Samples stored in the basis volume really relate to real space using this matrix. This means that a sample which is at index (0,1,0) can be placed at a space position given by D*(0,1,0)*grid_size, which could be for example (0,1.05,0)*grid_size. This is really useful for crystals. If you don't use it, set it to NULL. This matrix passes from a to aint, and from b to bint.

aint = Dinv*a; a=D*aint;
bint = Dinv*b; b=D*bint;

Definition at line 365 of file basic_art.h.

◆ diffusionWeight

double BasicARTParameters::diffusionWeight

Tomographic diffussion.

Definition at line 193 of file basic_art.h.

◆ Dinv

Matrix2D<double>* BasicARTParameters::Dinv =nullptr

Just the inverse of D.

Definition at line 367 of file basic_art.h.

◆ do_not_generate_subgroup

bool BasicARTParameters::do_not_generate_subgroup

Do not generate symmetry subgroup.

Definition at line 199 of file basic_art.h.

◆ do_not_use_symproj

bool BasicARTParameters::do_not_use_symproj

Do not use symmetrized projections.

Definition at line 202 of file basic_art.h.

◆ dont_sort

bool BasicARTParameters::dont_sort

True if no sort must be made.

Definition at line 123 of file basic_art.h.

◆ eq_mode

int BasicARTParameters::eq_mode

Valid modes are ARTK, CAVK and CAV. This is the mode of updating a single projection, it has nothing to do with the global ART or SIRT mode

Definition at line 117 of file basic_art.h.

◆ fh_hist

std::ofstream* BasicARTParameters::fh_hist =nullptr

File handler for the history file.

Definition at line 339 of file basic_art.h.

◆ fn_control

FileName BasicARTParameters::fn_control

Name of file for improved control in parallel jobs.

Definition at line 320 of file basic_art.h.

◆ fn_ctf

FileName BasicARTParameters::fn_ctf

Selection file with all images to process.

Definition at line 229 of file basic_art.h.

◆ fn_out

FileName BasicARTParameters::fn_out

Name of the output volume, also used to set the root of rest output files.

Definition at line 217 of file basic_art.h.

◆ fn_root

FileName BasicARTParameters::fn_root

Definition at line 217 of file basic_art.h.

◆ fn_sel

FileName BasicARTParameters::fn_sel

Selection file with all images to process.

Definition at line 208 of file basic_art.h.

◆ fn_start

FileName BasicARTParameters::fn_start

Grid volume as initial guess.

Definition at line 220 of file basic_art.h.

◆ fn_surface_mask

FileName BasicARTParameters::fn_surface_mask

File containing surface mask.

Definition at line 205 of file basic_art.h.

◆ fn_sym

FileName BasicARTParameters::fn_sym

File containing symmetries.

Definition at line 173 of file basic_art.h.

◆ force_sym

int BasicARTParameters::force_sym

Force the reconstruction to be symmetric this number of times.

Definition at line 196 of file basic_art.h.

◆ goldmask

double BasicARTParameters::goldmask

Goldmask.

Definition at line 211 of file basic_art.h.

◆ grid_relative_size

double BasicARTParameters::grid_relative_size

Relative size for the grid.

Definition at line 141 of file basic_art.h.

◆ grid_type

int BasicARTParameters::grid_type

CC, BCC or FCC (in grids.hh)

Definition at line 144 of file basic_art.h.

◆ GVNeq

GridVolumeT<int>* BasicARTParameters::GVNeq =nullptr

CAV equation count. This volume contains the number of equations at which each basis is involved

Definition at line 381 of file basic_art.h.

◆ IMG_Inf

ReconsInfo* BasicARTParameters::IMG_Inf =nullptr

Array with all the sorting information for each projection.

Definition at line 342 of file basic_art.h.

◆ is_crystal

bool BasicARTParameters::is_crystal

Is this a crystal 0 means NO 1 YES.

Definition at line 252 of file basic_art.h.

◆ kappa_list

Matrix1D<double> BasicARTParameters::kappa_list

Relaxation parameter for WLS residual volume

Definition at line 132 of file basic_art.h.

◆ known_volume

double BasicARTParameters::known_volume

Known volume. If -1, not applied.

Definition at line 226 of file basic_art.h.

◆ lambda_list

Matrix1D<double> BasicARTParameters::lambda_list

Relaxation parameter.

Definition at line 103 of file basic_art.h.

◆ max_tilt

double BasicARTParameters::max_tilt

Skip projection with absolute tilt angle greater than max_tilt deafult is infinite

Definition at line 181 of file basic_art.h.

◆ no_it

int BasicARTParameters::no_it

Number of iterations.

Definition at line 100 of file basic_art.h.

◆ noisy_reconstruction

bool BasicARTParameters::noisy_reconstruction

Noisy reconstruction.

Definition at line 261 of file basic_art.h.

◆ numIMG

int BasicARTParameters::numIMG

Total number of images to process (taking symmetries into account)

Definition at line 348 of file basic_art.h.

◆ ordered_list

MultidimArray<int> BasicARTParameters::ordered_list

Order in which projections will be presented to algorithm.

Definition at line 345 of file basic_art.h.

◆ parallel_mode

ARTParallelMode BasicARTParameters::parallel_mode

Valid methods are ART, pCAV, pAVSP, pSART, pBiCAV, pSIRT and pfSIRT for parallel computation. This variable establish the way that particles are divided into blocks for parallel processing. If sequential processing is wanted, set it to ART or SIRT. This is the default.

Definition at line 109 of file basic_art.h.

◆ POCS_freq

int BasicARTParameters::POCS_freq

POCS frequency. POCS restrictions are imposed every (this value) projections. By default, 1

Definition at line 376 of file basic_art.h.

◆ positivity

bool BasicARTParameters::positivity

Apply positivity constraint.

Definition at line 246 of file basic_art.h.

◆ print_system_matrix

bool BasicARTParameters::print_system_matrix

Print system matrix.

Definition at line 249 of file basic_art.h.

◆ proj_ext

int BasicARTParameters::proj_ext

Projection extension. Sometimes for avoiding the box effects produced by the ART and SIRT algorithms, projections are extended in size such that the projection is supposed to be larger than it really is. The extended part is set to 0 telling so that no measure has been done in that area. This parameter is measured in pixels, and by default is 0.

Definition at line 152 of file basic_art.h.

◆ projXdim

size_t BasicARTParameters::projXdim

Projection X dimension.

Definition at line 333 of file basic_art.h.

◆ projYdim

size_t BasicARTParameters::projYdim

Projection Y dimension.

Definition at line 336 of file basic_art.h.

◆ R

double BasicARTParameters::R

Interest sphere. If -1 not considered.

Definition at line 155 of file basic_art.h.

◆ random_sort

bool BasicARTParameters::random_sort

True if random sort of projections.

Definition at line 120 of file basic_art.h.

◆ ray_length

double BasicARTParameters::ray_length

Ray length. Basis functions are taken into account only if their distance to the projection plane is smaller than this value. This value is expressed in basis units. Set it to -1 to disable it. Set it to 1 (1 basis away maximum) to interpolate a set of planes).

Definition at line 240 of file basic_art.h.

◆ ref_trans_after

int BasicARTParameters::ref_trans_after

Refine the translation alignement after n projection presentations.

Definition at line 184 of file basic_art.h.

◆ ref_trans_step

double BasicARTParameters::ref_trans_step

Refine the translation alignement after n projection presentations.

Definition at line 187 of file basic_art.h.

◆ refine

bool BasicARTParameters::refine

Refine experimental projection before backprojecting.

Definition at line 258 of file basic_art.h.

◆ residual_imgs

std::vector<Projection> BasicARTParameters::residual_imgs

Vector containing all residual images for wlsART

Definition at line 135 of file basic_art.h.

◆ sampling

double BasicARTParameters::sampling

Sampling rate.

Definition at line 170 of file basic_art.h.

◆ save_intermidiate_every

int BasicARTParameters::save_intermidiate_every

Frequency for saving intermidiate.

Definition at line 314 of file basic_art.h.

◆ shiftedTomograms

bool BasicARTParameters::shiftedTomograms

Shifted tomograms.

Definition at line 214 of file basic_art.h.

◆ SL

SymList BasicARTParameters::SL

A list with the symmetry matrices.

ART Side Information The Side information is useful information that needn't be computed more than once at the beginning from the ART parameters and that is used all over the program.

Definition at line 330 of file basic_art.h.

◆ sort_last_N

int BasicARTParameters::sort_last_N

Sort perpendicular with the last N projections. If -1 with all previous.

Definition at line 126 of file basic_art.h.

◆ sparseEps

double BasicARTParameters::sparseEps

Sparse reconstruction.

Definition at line 190 of file basic_art.h.

◆ stop_at

int BasicARTParameters::stop_at

Stop after this number of images, if 0 then don't use.

Definition at line 223 of file basic_art.h.

◆ sum_weight

double BasicARTParameters::sum_weight

Sum ML-weight of all projections

Definition at line 138 of file basic_art.h.

◆ surface_mask

Image<double>* BasicARTParameters::surface_mask =nullptr

Surface mask. The volume is supposed to be 0 where the mask is 1.

Definition at line 371 of file basic_art.h.

◆ sym_each

int BasicARTParameters::sym_each

Inpose simetry each sym_each iterations (iteration=projection) deafult is 0

Definition at line 177 of file basic_art.h.

◆ tell

int BasicARTParameters::tell

Debugging level. This is a bit valued field, you can set the following bits \TELL_IV: Show intermediate images if saved, \ Show the reconstructed volume each time the progress bar is updated. \TELL_ONLY_SYM: Skip all the extra projections created using the sample symmetry \TELL_USE_INPUT_BASISVOLUME: This flag causes the program to not resizing the gridvolume. The same as the input one is used as starting point for the algorithm \TELL_SHOW_ERROR: The program will show the error for each projection \TELL_MANUAL_ORDER: The program will ask the number of the following projection to process instead of using the default perpendicular order \TELL_SAVE_AT_EACH_STEP: At each step (an iteration is compound of several steps) the following files are written to disk

PPPdiff --> Difference between theoretical and real projections
PPPtheo --> Theoretical projection
PPPread --> Real projection
PPPcorr --> Correction image applied
PPPbasis.basis --> Reconstructed volume in the used basis
PPPvol.vol --> Reconstructed volume in voxels

\TELL_SAVE_INTERMIDIATE: At each iteration a voxel (and possibly a basis volume (if the TELL_SAVE_BASIS flag is set) is stored with the names fn_root"it"it.vol and .basis (for instance, w0001it00.vol and w0001it00.basis). \TELL_SAVE_BASIS: Save basis volume at the end and in the intermidiate iterations (if TELL_SAVE_INTERMIDIATE is set). \TELL_STATS: Show image and volume (only of the first grid, of the 1, 2 or 4 possible subgrids) statistics.

Definition at line 311 of file basic_art.h.

◆ threads

int BasicARTParameters::threads

Number of threads to use. Can not be different than 1 when using MPI.

Definition at line 267 of file basic_art.h.

◆ trueIMG

int BasicARTParameters::trueIMG

Number of different images (without symmetries)

Definition at line 351 of file basic_art.h.

◆ unmatched

bool BasicARTParameters::unmatched

Apply unmatched projectors to correct for the CTF.

Definition at line 232 of file basic_art.h.

◆ using_MPI

bool BasicARTParameters::using_MPI

Only for internal purposes, MUST be set when running MPI.

Definition at line 264 of file basic_art.h.

◆ variability_analysis

bool BasicARTParameters::variability_analysis

Variability analysis.

Definition at line 255 of file basic_art.h.

◆ verbose

int BasicARTParameters::verbose

Verbose level.

Definition at line 317 of file basic_art.h.

◆ WLS

bool BasicARTParameters::WLS

Flag for weighted least squares reconstruction (for maximum-likelihood)

Definition at line 129 of file basic_art.h.

◆ Xoutput_volume_size

int BasicARTParameters::Xoutput_volume_size

Output X size. If not given, the input images size is assumed.

Definition at line 159 of file basic_art.h.

◆ Youtput_volume_size

int BasicARTParameters::Youtput_volume_size

Output Y size. If not given, the input images size is assumed.

Definition at line 163 of file basic_art.h.

◆ Zoutput_volume_size

int BasicARTParameters::Zoutput_volume_size

Output Z size. If not given, the input images size is assumed.

Definition at line 167 of file basic_art.h.