Xmipp
v3.23.11-Nereus
|
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 |
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.
#define TELL_IV 0x100 |
Definition at line 269 of file basic_art.h.
#define TELL_MANUAL_ORDER 0x10 |
Definition at line 273 of file basic_art.h.
#define TELL_ONLY_SYM 0x80 |
Definition at line 270 of file basic_art.h.
#define TELL_SAVE_AT_EACH_STEP 0x8 |
Definition at line 274 of file basic_art.h.
#define TELL_SAVE_BASIS 0x2 |
Definition at line 276 of file basic_art.h.
#define TELL_SAVE_INTERMIDIATE 0x4 |
Definition at line 275 of file basic_art.h.
#define TELL_SHOW_ERROR 0x20 |
Definition at line 272 of file basic_art.h.
#define TELL_STATS 0x1 |
Definition at line 277 of file basic_art.h.
#define TELL_USE_INPUT_BASISVOLUME 0x40 |
Definition at line 271 of file basic_art.h.
bool BasicARTParameters::apply_shifts |
Apply shifts stored in the headers of the 2D-images.
Definition at line 243 of file basic_art.h.
Basis BasicARTParameters::basis |
Basis function. By default, blobs.
Definition at line 97 of file basic_art.h.
int BasicARTParameters::block_size |
Number of projections for each parallel block.
Definition at line 112 of file basic_art.h.
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.
Definition at line 365 of file basic_art.h.
double BasicARTParameters::diffusionWeight |
Tomographic diffussion.
Definition at line 193 of file basic_art.h.
Matrix2D<double>* BasicARTParameters::Dinv =nullptr |
Just the inverse of D.
Definition at line 367 of file basic_art.h.
bool BasicARTParameters::do_not_generate_subgroup |
Do not generate symmetry subgroup.
Definition at line 199 of file basic_art.h.
bool BasicARTParameters::do_not_use_symproj |
Do not use symmetrized projections.
Definition at line 202 of file basic_art.h.
bool BasicARTParameters::dont_sort |
True if no sort must be made.
Definition at line 123 of file basic_art.h.
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.
std::ofstream* BasicARTParameters::fh_hist =nullptr |
File handler for the history file.
Definition at line 339 of file basic_art.h.
FileName BasicARTParameters::fn_control |
Name of file for improved control in parallel jobs.
Definition at line 320 of file basic_art.h.
FileName BasicARTParameters::fn_ctf |
Selection file with all images to process.
Definition at line 229 of file basic_art.h.
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.
FileName BasicARTParameters::fn_root |
Definition at line 217 of file basic_art.h.
FileName BasicARTParameters::fn_sel |
Selection file with all images to process.
Definition at line 208 of file basic_art.h.
FileName BasicARTParameters::fn_start |
Grid volume as initial guess.
Definition at line 220 of file basic_art.h.
FileName BasicARTParameters::fn_surface_mask |
File containing surface mask.
Definition at line 205 of file basic_art.h.
FileName BasicARTParameters::fn_sym |
File containing symmetries.
Definition at line 173 of file basic_art.h.
int BasicARTParameters::force_sym |
Force the reconstruction to be symmetric this number of times.
Definition at line 196 of file basic_art.h.
double BasicARTParameters::goldmask |
Goldmask.
Definition at line 211 of file basic_art.h.
double BasicARTParameters::grid_relative_size |
Relative size for the grid.
Definition at line 141 of file basic_art.h.
int BasicARTParameters::grid_type |
CC, BCC or FCC (in grids.hh)
Definition at line 144 of file basic_art.h.
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.
ReconsInfo* BasicARTParameters::IMG_Inf =nullptr |
Array with all the sorting information for each projection.
Definition at line 342 of file basic_art.h.
bool BasicARTParameters::is_crystal |
Is this a crystal 0 means NO 1 YES.
Definition at line 252 of file basic_art.h.
Matrix1D<double> BasicARTParameters::kappa_list |
Relaxation parameter for WLS residual volume
Definition at line 132 of file basic_art.h.
double BasicARTParameters::known_volume |
Known volume. If -1, not applied.
Definition at line 226 of file basic_art.h.
Matrix1D<double> BasicARTParameters::lambda_list |
Relaxation parameter.
Definition at line 103 of file basic_art.h.
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.
int BasicARTParameters::no_it |
Number of iterations.
Definition at line 100 of file basic_art.h.
bool BasicARTParameters::noisy_reconstruction |
Noisy reconstruction.
Definition at line 261 of file basic_art.h.
int BasicARTParameters::numIMG |
Total number of images to process (taking symmetries into account)
Definition at line 348 of file basic_art.h.
MultidimArray<int> BasicARTParameters::ordered_list |
Order in which projections will be presented to algorithm.
Definition at line 345 of file basic_art.h.
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.
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.
bool BasicARTParameters::positivity |
Apply positivity constraint.
Definition at line 246 of file basic_art.h.
bool BasicARTParameters::print_system_matrix |
Print system matrix.
Definition at line 249 of file basic_art.h.
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.
size_t BasicARTParameters::projXdim |
Projection X dimension.
Definition at line 333 of file basic_art.h.
size_t BasicARTParameters::projYdim |
Projection Y dimension.
Definition at line 336 of file basic_art.h.
double BasicARTParameters::R |
Interest sphere. If -1 not considered.
Definition at line 155 of file basic_art.h.
bool BasicARTParameters::random_sort |
True if random sort of projections.
Definition at line 120 of file basic_art.h.
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.
int BasicARTParameters::ref_trans_after |
Refine the translation alignement after n projection presentations.
Definition at line 184 of file basic_art.h.
double BasicARTParameters::ref_trans_step |
Refine the translation alignement after n projection presentations.
Definition at line 187 of file basic_art.h.
bool BasicARTParameters::refine |
Refine experimental projection before backprojecting.
Definition at line 258 of file basic_art.h.
std::vector<Projection> BasicARTParameters::residual_imgs |
Vector containing all residual images for wlsART
Definition at line 135 of file basic_art.h.
double BasicARTParameters::sampling |
Sampling rate.
Definition at line 170 of file basic_art.h.
int BasicARTParameters::save_intermidiate_every |
Frequency for saving intermidiate.
Definition at line 314 of file basic_art.h.
bool BasicARTParameters::shiftedTomograms |
Shifted tomograms.
Definition at line 214 of file basic_art.h.
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.
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.
double BasicARTParameters::sparseEps |
Sparse reconstruction.
Definition at line 190 of file basic_art.h.
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.
double BasicARTParameters::sum_weight |
Sum ML-weight of all projections
Definition at line 138 of file basic_art.h.
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.
int BasicARTParameters::sym_each |
Inpose simetry each sym_each iterations (iteration=projection) deafult is 0
Definition at line 177 of file basic_art.h.
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
\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.
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.
int BasicARTParameters::trueIMG |
Number of different images (without symmetries)
Definition at line 351 of file basic_art.h.
bool BasicARTParameters::unmatched |
Apply unmatched projectors to correct for the CTF.
Definition at line 232 of file basic_art.h.
bool BasicARTParameters::using_MPI |
Only for internal purposes, MUST be set when running MPI.
Definition at line 264 of file basic_art.h.
bool BasicARTParameters::variability_analysis |
Variability analysis.
Definition at line 255 of file basic_art.h.
int BasicARTParameters::verbose |
Verbose level.
Definition at line 317 of file basic_art.h.
bool BasicARTParameters::WLS |
Flag for weighted least squares reconstruction (for maximum-likelihood)
Definition at line 129 of file basic_art.h.
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.
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.
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.