├── .clang-format ├── .github └── workflows │ ├── build.yml │ └── release.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .sonarcloud.properties ├── CHANGELOG.md ├── CMakeLists.txt ├── LICENSE ├── README.md ├── cmake ├── fetch_cifpp.cmake ├── fetch_ctpl.cmake ├── fetch_cuFFTAdvisor.cmake ├── fetch_googletest.cmake ├── fetch_libsvm.cmake ├── link_to_scipion.cmake ├── write_bashrc.cmake └── xmipp.bashrc.in ├── scripts ├── API.py ├── __init__.py ├── config.py ├── environment.py ├── tar.py └── utils.py ├── src └── xmipp │ ├── CMakeLists.txt │ ├── applications │ ├── CMakeLists.txt │ ├── programs │ │ ├── CMakeLists.txt │ │ ├── angular_accuracy_pca │ │ │ └── angular_accuracy_pca_main.cpp │ │ ├── angular_assignment_mag │ │ │ └── angular_assignment_mag_main.cpp │ │ ├── angular_break_symmetry │ │ │ └── angular_break_symmetry_main.cpp │ │ ├── angular_commonline │ │ │ └── angular_commonline_main.cpp │ │ ├── angular_continuous_assign │ │ │ └── angular_continuous_assign_main.cpp │ │ ├── angular_continuous_assign2 │ │ │ └── angular_continuous_assign_main2.cpp │ │ ├── angular_discrete_assign │ │ │ └── angular_discrete_assign_main.cpp │ │ ├── angular_distance │ │ │ └── angular_distance_main.cpp │ │ ├── angular_distribution_show │ │ │ └── angular_distribution_show_main.cpp │ │ ├── angular_estimate_tilt_axis │ │ │ └── angular_estimate_tilt_axis_main.cpp │ │ ├── angular_neighbourhood │ │ │ └── angular_neighbourhood_main.cpp │ │ ├── angular_project_library │ │ │ └── angular_project_library_main.cpp │ │ ├── angular_projection_matching │ │ │ └── angular_projection_matching_main.cpp │ │ ├── angular_rotate │ │ │ └── angular_rotate_main.cpp │ │ ├── angular_sph_alignment │ │ │ └── angular_sph_alignment_main.cpp │ │ ├── art_zernike3d │ │ │ └── art_zernike3d_main.cpp │ │ ├── classify_analyze_cluster │ │ │ └── classify_analyze_cluster_main.cpp │ │ ├── classify_compare_classes │ │ │ └── classify_compare_classes_main.cpp │ │ ├── classify_evaluate_classes │ │ │ └── classify_evaluate_classes_main.cpp │ │ ├── classify_extract_features │ │ │ └── classify_extract_features_main.cpp │ │ ├── classify_first_split │ │ │ └── classify_first_split_main.cpp │ │ ├── classify_first_split3 │ │ │ └── classify_first_split3_main.cpp │ │ ├── classify_kerdensom │ │ │ └── classify_kerdensom_main.cpp │ │ ├── compare_density │ │ │ └── compare_density_main.cpp │ │ ├── compare_views │ │ │ └── compare_views_main.cpp │ │ ├── continuous_create_residuals │ │ │ └── continuous_create_residuals_main.cpp │ │ ├── coordinates_noisy_zones_filter │ │ │ └── coordinates_noisy_zones_filter_main.cpp │ │ ├── ctf_correct_phase │ │ │ └── ctf_correct_phase_main.cpp │ │ ├── ctf_correct_wiener2d │ │ │ └── ctf_correct_wiener2d_main.cpp │ │ ├── ctf_correct_wiener3d │ │ │ └── ctf_correct_wiener3d_main.cpp │ │ ├── ctf_enhance_psd │ │ │ └── ctf_enhance_psd_main.cpp │ │ ├── ctf_estimate_from_micrograph │ │ │ └── ctf_estimate_from_micrograph_main.cpp │ │ ├── ctf_estimate_from_psd │ │ │ └── ctf_estimate_from_psd_main.cpp │ │ ├── ctf_estimate_from_psd_fast │ │ │ └── ctf_estimate_from_psd_fast_main.cpp │ │ ├── ctf_group │ │ │ └── ctf_group_main.cpp │ │ ├── ctf_phase_flip │ │ │ └── ctf_phase_flip_main.cpp │ │ ├── ctf_sort_psds │ │ │ └── ctf_sort_psds_main.cpp │ │ ├── cuda11_forward_art_zernike3d │ │ │ └── cuda_forward_art_zernike3d_main.cpp │ │ ├── cuda_align_significant │ │ │ └── cuda_align_significant.cpp │ │ ├── cuda_angular_continuous_assign2 │ │ │ └── cuda_angular_continuous_assign2_main.cpp │ │ ├── cuda_angular_sph_alignment │ │ │ └── cuda_angular_sph_alignment_main.cpp │ │ ├── cuda_movie_alignment_correlation │ │ │ └── cuda_movie_alignment_correlation.cpp │ │ ├── cuda_reconstruct_fourier │ │ │ └── cuda_reconstruct_fourier_main.cpp │ │ ├── cuda_volume_deform_sph │ │ │ └── cuda_volume_deform_sph_main.cpp │ │ ├── cuda_volume_halves_restoration │ │ │ └── cuda_volume_halves_restoration.cpp │ │ ├── flexible_alignment │ │ │ └── flexible_alignment_main.cpp │ │ ├── forward_art_zernike3d_subtomos │ │ │ └── forward_art_zernike3d_subtomos.cpp │ │ ├── forward_zernike_images │ │ │ └── forward_zernike_images_main.cpp │ │ ├── forward_zernike_images_priors │ │ │ └── forward_zernike_images_priors_main.cpp │ │ ├── forward_zernike_subtomos │ │ │ └── forward_zernike_subtomos.cpp │ │ ├── forward_zernike_volume │ │ │ └── forward_zernike_volume.cpp │ │ ├── image_align │ │ │ └── image_align_main.cpp │ │ ├── image_align_tilt_pairs │ │ │ └── image_align_tilt_pairs.cpp │ │ ├── image_assignment_tilt_pair │ │ │ └── assignment_tilt_pair_main.cpp │ │ ├── image_convert │ │ │ └── image_convert_main.cpp │ │ ├── image_eliminate_byEnergy │ │ │ └── image_eliminate_byEnergy_main.cpp │ │ ├── image_eliminate_empty_particles │ │ │ └── image_eliminate_empty_particles_main.cpp │ │ ├── image_find_center │ │ │ └── image_find_center_main.cpp │ │ ├── image_header │ │ │ └── image_header_main.cpp │ │ ├── image_histogram │ │ │ └── image_histogram_main.cpp │ │ ├── image_odd_even │ │ │ └── image_odd_even_main.cpp │ │ ├── image_operate │ │ │ └── image_operate_main.cpp │ │ ├── image_peak_high_contrast │ │ │ └── image_peak_high_contrast.cpp │ │ ├── image_residuals │ │ │ └── image_residuals_main.cpp │ │ ├── image_resize │ │ │ └── image_resize.cpp │ │ ├── image_rotational_pca │ │ │ └── image_rotational_pca_main.cpp │ │ ├── image_sort_by_statistics │ │ │ └── image_sort_by_statistics_main.cpp │ │ ├── image_ssnr │ │ │ └── image_ssnr_main.cpp │ │ ├── image_statistics │ │ │ └── image_statistics_main.cpp │ │ ├── image_vectorize │ │ │ └── image_vectorize_main.cpp │ │ ├── local_volume_adjust │ │ │ └── local_volume_adjust_main.cpp │ │ ├── matrix_dimred │ │ │ └── matrix_dimred_main.cpp │ │ ├── metadata_histogram │ │ │ └── metadata_histogram_main.cpp │ │ ├── metadata_import │ │ │ └── metadata_import_main.cpp │ │ ├── metadata_split │ │ │ └── metadata_split_main.cpp │ │ ├── metadata_split_3D │ │ │ └── metadata_split_3D_main.cpp │ │ ├── metadata_utilities │ │ │ └── metadata_utilities_main.cpp │ │ ├── metadata_xml │ │ │ └── metadata_xml_main.cpp │ │ ├── micrograph_automatic_picking │ │ │ └── micrograph_automatic_picking_main.cpp │ │ ├── micrograph_scissor │ │ │ └── micrograph_scissor_main.cpp │ │ ├── ml_align2d │ │ │ └── ml_align2d_main.cpp │ │ ├── mlf_align2d │ │ │ └── mlf_align2d_main.cpp │ │ ├── movie_alignment_correlation │ │ │ └── movie_alignment_correlation.cpp │ │ ├── movie_estimate_gain │ │ │ └── movie_estimate_gain_main.cpp │ │ ├── movie_filter_dose │ │ │ └── movie_filter_dose.cpp │ │ ├── mpi_angular_accuracy_pca │ │ │ └── mpi_angular_accuracy_pca_main.cpp │ │ ├── mpi_angular_assignment_mag │ │ │ └── mpi_angular_assignment_mag_main.cpp │ │ ├── mpi_angular_class_average │ │ │ └── mpi_angular_class_average_main.cpp │ │ ├── mpi_angular_continuous_assign │ │ │ └── mpi_angular_continuous_assign_main.cpp │ │ ├── mpi_angular_continuous_assign2 │ │ │ └── mpi_angular_continuous_assign_main2.cpp │ │ ├── mpi_angular_discrete_assign │ │ │ └── mpi_angular_discrete_assign_main.cpp │ │ ├── mpi_angular_project_library │ │ │ └── mpi_angular_project_library_main.cpp │ │ ├── mpi_angular_projection_matching │ │ │ └── mpi_angular_projection_matching_main.cpp │ │ ├── mpi_angular_sph_alignment │ │ │ └── mpi_angular_sph_alignment_main.cpp │ │ ├── mpi_classify_CL2D │ │ │ └── mpi_classify_CL2D_main.cpp │ │ ├── mpi_classify_CL2D_core_analysis │ │ │ └── mpi_classify_CL2D_core_analysis_main.cpp │ │ ├── mpi_classify_CLTomo_prog │ │ │ └── mpi_classify_CLTomo_prog_main.cpp │ │ ├── mpi_classify_FTTRI │ │ │ └── mpi_classify_FTTRI_main.cpp │ │ ├── mpi_continuous_create_residuals │ │ │ └── mpi_continuous_create_residuals_main.cpp │ │ ├── mpi_ctf_correct_phase │ │ │ └── mpi_ctf_correct_phase_main.cpp │ │ ├── mpi_ctf_correct_wiener2d │ │ │ └── mpi_ctf_correct_wiener2d_main.cpp │ │ ├── mpi_ctf_sort_psds │ │ │ └── mpi_ctf_sort_psds_main.cpp │ │ ├── mpi_cuda_reconstruct_fourier │ │ │ └── mpi_cuda_reconstruct_fourier_main.cpp │ │ ├── mpi_forward_zernike_images │ │ │ └── mpi_forward_zernike_images_main.cpp │ │ ├── mpi_forward_zernike_images_priors │ │ │ └── mpi_forward_zernike_images_priors_main.cpp │ │ ├── mpi_forward_zernike_subtomos │ │ │ └── mpi_forward_zernike_subtomos.cpp │ │ ├── mpi_image_eliminate_byEnergy │ │ │ └── mpi_image_eliminate_byEnergy_main.cpp │ │ ├── mpi_image_operate │ │ │ └── mpi_image_operate_main.cpp │ │ ├── mpi_image_resize │ │ │ └── mpi_image_resize_main.cpp │ │ ├── mpi_image_rotational_pca │ │ │ └── mpi_image_rotational_pca_main.cpp │ │ ├── mpi_image_sort │ │ │ └── mpi_image_sort_main.cpp │ │ ├── mpi_image_ssnr │ │ │ └── mpi_image_ssnr_main.cpp │ │ ├── mpi_ml_align2d │ │ │ └── mpi_ml_align2d_main.cpp │ │ ├── mpi_mlf_align2d │ │ │ └── mpi_mlf_align2d_main.cpp │ │ ├── mpi_multireference_aligneability │ │ │ └── mpi_multireference_aligneability_main.cpp │ │ ├── mpi_nma_alignment │ │ │ └── mpi_nma_alignment_main.cpp │ │ ├── mpi_nma_alignment_vol │ │ │ └── mpi_nma_alignment_vol_main.cpp │ │ ├── mpi_performance_test │ │ │ └── mpi_performance_test_main.cpp │ │ ├── mpi_reconstruct_art │ │ │ └── mpi_reconstruct_art_main.cpp │ │ ├── mpi_reconstruct_fourier │ │ │ └── mpi_reconstruct_fourier_main.cpp │ │ ├── mpi_reconstruct_fourier_accel │ │ │ └── mpi_reconstruct_fourier_accel_main.cpp │ │ ├── mpi_reconstruct_significant │ │ │ └── mpi_reconstruct_significant_main.cpp │ │ ├── mpi_reconstruct_wbp │ │ │ └── mpi_reconstruct_wbp_main.cpp │ │ ├── mpi_run │ │ │ └── mpi_run_main.cpp │ │ ├── mpi_subtomo_subtraction │ │ │ └── mpi_subtomo_subtraction.cpp │ │ ├── mpi_subtract_projection │ │ │ └── mpi_subtract_projection_main.cpp │ │ ├── mpi_transform_adjust_image_grey_levels │ │ │ └── mpi_transform_adjust_image_grey_levels_main.cpp │ │ ├── mpi_transform_filter │ │ │ └── mpi_transform_filter_main.cpp │ │ ├── mpi_transform_geometry │ │ │ └── mpi_transform_geometry_main.cpp │ │ ├── mpi_transform_mask │ │ │ └── mpi_transform_mask_main.cpp │ │ ├── mpi_transform_normalize │ │ │ └── mpi_transform_normalize_main.cpp │ │ ├── mpi_transform_symmetrize │ │ │ └── mpi_transform_symmetrize.cpp │ │ ├── mpi_transform_threshold │ │ │ └── mpi_transform_threshold_main.cpp │ │ ├── mpi_validation_nontilt │ │ │ └── mpi_validation_nontilt_main.cpp │ │ ├── mpi_volumeset_align │ │ │ └── mpi_volumeset_align_main.cpp │ │ ├── mpi_write_test │ │ │ └── mpi_write_test.cpp │ │ ├── multireference_aligneability │ │ │ └── multireference_aligneabililty_main.cpp │ │ ├── nma_alignment │ │ │ └── nma_alignment_main.cpp │ │ ├── nma_alignment_vol │ │ │ └── nma_alignment_vol_main.cpp │ │ ├── pdb_analysis │ │ │ └── pdb_analysis_main.cpp │ │ ├── pdb_label_from_volume │ │ │ └── pdb_label_from_volume_main.cpp │ │ ├── pdb_nma_deform │ │ │ └── pdb_nma_deform_main.cpp │ │ ├── pdb_reduce_pseudoatoms │ │ │ └── pdb_reduce_pseudoatoms_main.cpp │ │ ├── pdb_sph_deform │ │ │ └── pdb_sph_deform_main.cpp │ │ ├── phantom_create │ │ │ └── phantom_create_main.cpp │ │ ├── phantom_movie │ │ │ └── phantom_movie_main.cpp │ │ ├── phantom_project │ │ │ └── phantom_project_main.cpp │ │ ├── phantom_simulate_microscope │ │ │ └── phantom_simulate_microscope_main.cpp │ │ ├── phantom_transform │ │ │ └── phantom_transform_main.cpp │ │ ├── psd_estimate │ │ │ └── psd_estimate_main.cpp │ │ ├── reconstruct_art │ │ │ └── reconstruct_art_main.cpp │ │ ├── reconstruct_fourier │ │ │ └── reconstruct_fourier_main.cpp │ │ ├── reconstruct_fourier_accel │ │ │ └── reconstruct_fourier_accel_main.cpp │ │ ├── reconstruct_significant │ │ │ └── reconstruct_significant_main.cpp │ │ ├── reconstruct_wbp │ │ │ └── reconstruct_wbp_main.cpp │ │ ├── resolution_directional │ │ │ └── resolution_directional_main.cpp │ │ ├── resolution_fsc │ │ │ └── resolution_fsc_main.cpp │ │ ├── resolution_fso │ │ │ └── resolution_fso.cpp │ │ ├── resolution_localfilter │ │ │ └── resolution_localfilter_main.cpp │ │ ├── resolution_monogenic_signal │ │ │ └── resolution_monogenic_signal_main.cpp │ │ ├── resolution_monotomo │ │ │ └── resolution_monotomo_main.cpp │ │ ├── resolution_pdb_bfactor │ │ │ └── resolution_pdb_bfactor_main.cpp │ │ ├── subtomo_subtraction │ │ │ └── subtomo_subtraction_main.cpp │ │ ├── subtract_projection │ │ │ └── subtract_projection_main.cpp │ │ ├── tomo_average_subtomos │ │ │ └── tomo_average_subtomos.cpp │ │ ├── tomo_calculate_landmark_residuals │ │ │ └── tomo_calculate_landmark_residuals.cpp │ │ ├── tomo_detect_landmarks │ │ │ └── tomo_detect_landmarks.cpp │ │ ├── tomo_detect_missing_wedge │ │ │ └── tomo_detect_missing_wedge_main.cpp │ │ ├── tomo_extract_particlestacks │ │ │ └── tomo_extract_particlestacks_main.cpp │ │ ├── tomo_extract_subtomograms │ │ │ └── tomo_extract_subtomograms_main.cpp │ │ ├── tomo_filter_coordinates │ │ │ └── tomo_filter_coordinates.cpp │ │ ├── tomo_map_back │ │ │ └── tomo_map_back_main.cpp │ │ ├── tomo_project │ │ │ └── tomo_project_main.cpp │ │ ├── tomo_simulate_tilt_series │ │ │ └── tomo_simulate_tilt_series_main.cpp │ │ ├── tomo_tiltseries_dose_filter │ │ │ └── tomo_tiltseries_dose_filter_main.cpp │ │ ├── transform_add_noise │ │ │ └── transform_add_noise_main.cpp │ │ ├── transform_adjust_image_grey_levels │ │ │ └── transform_adjust_image_grey_levels_main.cpp │ │ ├── transform_adjust_volume_grey_levels │ │ │ └── transform_adjust_volume_grey_levels_main.cpp │ │ ├── transform_center_image │ │ │ └── transform_center_image_main.cpp │ │ ├── transform_dimred │ │ │ └── transform_dimred_main.cpp │ │ ├── transform_downsample │ │ │ └── transform_downsample_main.cpp │ │ ├── transform_filter │ │ │ └── transform_filter_main.cpp │ │ ├── transform_geometry │ │ │ └── transform_geometry_main.cpp │ │ ├── transform_mask │ │ │ └── transform_mask_main.cpp │ │ ├── transform_mirror │ │ │ └── transform_mirror_main.cpp │ │ ├── transform_morphology │ │ │ └── transform_morphology_main.cpp │ │ ├── transform_normalize │ │ │ └── transform_normalize_main.cpp │ │ ├── transform_randomize_phases │ │ │ └── transform_randomize_phases_main.cpp │ │ ├── transform_symmetrize │ │ │ └── transform_symmetrize_main.cpp │ │ ├── transform_threshold │ │ │ └── transform_threshold_main.cpp │ │ ├── transform_window │ │ │ └── transform_window_main.cpp │ │ ├── validation_nontilt │ │ │ └── validation_nontilt_main.cpp │ │ ├── volume_align │ │ │ └── volume_align_main.cpp │ │ ├── volume_apply_coefficient_zernike3d │ │ │ └── volume_apply_coefficient_zernike3d.cpp │ │ ├── volume_apply_deform_sph │ │ │ └── volume_apply_deform_sph.cpp │ │ ├── volume_center │ │ │ └── volume_center_main.cpp │ │ ├── volume_correct_bfactor │ │ │ └── volume_correct_bfactor_main.cpp │ │ ├── volume_deform_sph │ │ │ └── volume_deform_sph_main.cpp │ │ ├── volume_find_symmetry │ │ │ └── volume_find_symmetry_main.cpp │ │ ├── volume_from_pdb │ │ │ └── volume_from_pdb_main.cpp │ │ ├── volume_halves_restoration │ │ │ └── volume_halves_restoration_main.cpp │ │ ├── volume_initial_simulated_annealing │ │ │ └── volume_initial_simulated_annealing_main.cpp │ │ ├── volume_local_sharpening │ │ │ └── volume_local_sharpening_main.cpp │ │ ├── volume_segment │ │ │ └── volume_segment_main.cpp │ │ ├── volume_structure_factor │ │ │ └── volume_structure_factor_main.cpp │ │ ├── volume_subtraction │ │ │ └── volume_subtraction_main.cpp │ │ ├── volume_to_pseudoatoms │ │ │ └── volume_to_pseudoatoms_main.cpp │ │ ├── volume_to_web │ │ │ └── volume_to_web_main.cpp │ │ └── volumeset_align │ │ │ └── volumeset_align_main.cpp │ ├── scripts │ │ ├── CMakeLists.txt │ │ ├── cl2d_clustering │ │ │ └── cl2d_clustering.py │ │ ├── classify_pca │ │ │ └── batch_classify_pca.py │ │ ├── classify_pca_train │ │ │ └── batch_classify_pca_train.py │ │ ├── compile │ │ │ └── batch_compile.py │ │ ├── coordinates_consensus │ │ │ └── coordinates_consensus.py │ │ ├── deepRes_resolution │ │ │ └── batch_deepRes_resolution.py │ │ ├── deep_center │ │ │ └── batch_deep_center.py │ │ ├── deep_center_predict │ │ │ └── batch_deep_center_predict.py │ │ ├── deep_consensus │ │ │ ├── deep_consensus.py │ │ │ └── helpers │ │ │ │ ├── howToPretrainDeepConsensus.txt │ │ │ │ └── protocol_prepare_deepConsensus.py │ │ ├── deep_global_assignment │ │ │ └── batch_deep_global_assignment.py │ │ ├── deep_global_assignment_predict │ │ │ └── batch_deep_global_assignment_predict.py │ │ ├── deep_hand │ │ │ └── batch_deep_hand.py │ │ ├── deep_micrograph_cleaner │ │ │ └── deep_micrograph_cleaner.py │ │ ├── deep_misalignment_detection │ │ │ └── batch_deep_misalignment_detection.py │ │ ├── deep_volume_postprocessing │ │ │ └── deep_volume_postprocessing.py │ │ ├── denoising_tv │ │ │ └── denoising_tv.py │ │ ├── extract_particles │ │ │ └── extract_particles.py │ │ ├── graph_max_cut │ │ │ └── graph_max_cut.py │ │ ├── metadata_selfile_create │ │ │ └── batch_metadata_selfile_create.py │ │ ├── mpi_classify_CLTomo │ │ │ └── batch_mpi_classify_CLTomo.sh │ │ ├── pdb_center │ │ │ └── batch_pdb_center.py │ │ ├── pdb_select │ │ │ └── batch_pdb_select.py │ │ ├── pick_noise │ │ │ └── pick_noise.py │ │ ├── preprocess_mics │ │ │ └── preprocess_mics.py │ │ ├── swiftalign_aligned_2d_classification │ │ │ └── swiftalign_aligned_2d_classfication.py │ │ ├── swiftalign_wiener_2d │ │ │ └── swiftalign_wiener_2d.py │ │ ├── sync_data │ │ │ └── batch_sync_data.py │ │ ├── test_script_importing_module │ │ │ └── batch_test_script_importing_module.py │ │ ├── tomo_misalignment_resid_statistics │ │ │ └── batch_tomo_misalignment_resid_statistics.py │ │ ├── tomogram_reconstruction │ │ │ └── tomogram_reconstruction.py │ │ └── volume_consensus │ │ │ └── volume_consensus.py │ └── tests │ │ ├── CMakeLists.txt │ │ └── function_tests │ │ ├── aft_tests.h │ │ ├── aiterative_alignment_tests.h │ │ ├── alignment_test_utils.h │ │ ├── arotation_estimator_tests.h │ │ ├── ashift_corr_estimator_tests.h │ │ ├── ashift_estimator_tests.h │ │ ├── asingle_extrema_finder_tests.h │ │ ├── test_cif_main.cpp │ │ ├── test_ctf_main.cpp │ │ ├── test_cuda_fft.cpp │ │ ├── test_cuda_flexalign_correlate.cpp │ │ ├── test_cuda_geo_transformer_apply_bspline_transform.cpp │ │ ├── test_cuda_geo_transformer_produce_and_load_coeffs.cpp │ │ ├── test_cuda_iterative_alignment_estimator.cpp │ │ ├── test_cuda_polar_rotation_estimator.cpp │ │ ├── test_cuda_shift_corr_estimator.cpp │ │ ├── test_cuda_single_extrema_finder.cpp │ │ ├── test_cuda_volume_halves_restoration.cpp │ │ ├── test_dimred_main.cpp │ │ ├── test_euler_main.cpp │ │ ├── test_fftw_main.cpp │ │ ├── test_fftwt.cpp │ │ ├── test_filename_main.cpp │ │ ├── test_filters_main.cpp │ │ ├── test_fringe_processing_main.cpp │ │ ├── test_funcs_main.cpp │ │ ├── test_geometry_main.cpp │ │ ├── test_image_generic_main.cpp │ │ ├── test_image_main.cpp │ │ ├── test_iterative_alignment_estimator.cpp │ │ ├── test_matrix_main.cpp │ │ ├── test_metadata_db_main.cpp │ │ ├── test_metadata_vec_main.cpp │ │ ├── test_movie_filter_dose.cpp │ │ ├── test_multidim_main.cpp │ │ ├── test_pocs_main.cpp │ │ ├── test_polar_main.cpp │ │ ├── test_polar_rotation_estimator.cpp │ │ ├── test_polynomials_main.cpp │ │ ├── test_psd_estimator.cpp │ │ ├── test_radAvgNonCubic_main.cpp │ │ ├── test_resolution_frc.cpp │ │ ├── test_sampling_main.cpp │ │ ├── test_shift_corr_estimator.cpp │ │ ├── test_single_extrema_finder.cpp │ │ ├── test_symmetries_main.cpp │ │ ├── test_transform_window.cpp │ │ ├── test_transformation_main.cpp │ │ ├── test_volume_subtraction_main.cpp │ │ └── test_wavelets_main.cpp │ ├── bindings │ ├── matlab │ │ ├── README │ │ ├── mirt3D_mexinterp.cpp │ │ ├── mirt3D_mexinterp.m │ │ ├── tom_calc_periodogram.m │ │ ├── tom_xmipp_adjust_ctf.cpp │ │ ├── tom_xmipp_adjust_ctf.m │ │ ├── tom_xmipp_align2d.cpp │ │ ├── tom_xmipp_align2d.m │ │ ├── tom_xmipp_align2d_stack.m │ │ ├── tom_xmipp_ctf_correct_phase.cpp │ │ ├── tom_xmipp_ctf_correct_phase.m │ │ ├── tom_xmipp_helpers.h │ │ ├── tom_xmipp_mask.cpp │ │ ├── tom_xmipp_mask.m │ │ ├── tom_xmipp_mirror.cpp │ │ ├── tom_xmipp_mirror.m │ │ ├── tom_xmipp_morphology.cpp │ │ ├── tom_xmipp_morphology.m │ │ ├── tom_xmipp_normalize.cpp │ │ ├── tom_xmipp_normalize.m │ │ ├── tom_xmipp_psd_enhance.cpp │ │ ├── tom_xmipp_psd_enhance.m │ │ ├── tom_xmipp_resolution.cpp │ │ ├── tom_xmipp_resolution.m │ │ ├── tom_xmipp_rotate.cpp │ │ ├── tom_xmipp_rotate.m │ │ ├── tom_xmipp_scale.cpp │ │ ├── tom_xmipp_scale.m │ │ ├── tom_xmipp_scale_pyramid.cpp │ │ ├── tom_xmipp_scale_pyramid.m │ │ ├── tom_xmipp_volume_segment.cpp │ │ ├── tom_xmipp_volume_segment.m │ │ ├── xmipp_calculate_strain.m │ │ ├── xmipp_ctf_for_metadata_row.m │ │ ├── xmipp_ctf_generate_filter.cpp │ │ ├── xmipp_nma_read_alignment.cpp │ │ ├── xmipp_nma_read_alignment.m │ │ ├── xmipp_nma_save_cluster.cpp │ │ ├── xmipp_nma_save_cluster.m │ │ ├── xmipp_nma_selection_tool.m │ │ ├── xmipp_nma_selection_tool_gui.fig │ │ ├── xmipp_nma_selection_tool_gui.m │ │ ├── xmipp_read.cpp │ │ ├── xmipp_read.m │ │ ├── xmipp_read_metadata.m │ │ ├── xmipp_read_structure_factor.cpp │ │ ├── xmipp_show_structure_factor.m │ │ ├── xmipp_write.cpp │ │ └── xmipp_write.m │ └── python │ │ ├── envs_DLTK │ │ ├── condaVersionRestriction.md │ │ ├── xmipp_DLTK_v0.3-gpu.yml │ │ ├── xmipp_DLTK_v0.3.yml │ │ ├── xmipp_DLTK_v1.0-gpu.yml │ │ ├── xmipp_DLTK_v1.0.yml │ │ ├── xmipp_MicCleaner.yml │ │ ├── xmipp_deepEMhancer.yml │ │ ├── xmipp_pyTorch-gpu.yml │ │ ├── xmipp_pyTorch.yml │ │ └── xtomo_tigre.yml │ │ ├── python_constants.cpp │ │ ├── python_filename.cpp │ │ ├── python_filename.h │ │ ├── python_fourierprojector.cpp │ │ ├── python_fourierprojector.h │ │ ├── python_image.cpp │ │ ├── python_image.h │ │ ├── python_metadata.cpp │ │ ├── python_metadata.h │ │ ├── python_program.cpp │ │ ├── python_program.h │ │ ├── python_symmetry.cpp │ │ ├── python_symmetry.h │ │ ├── xmipp.py │ │ ├── xmipp_base.py │ │ ├── xmipp_conda_envs.py │ │ ├── xmippmodule.cpp │ │ └── xmippmodule.h │ ├── external │ ├── condor │ │ ├── CNLSolver.cpp │ │ ├── CTRSSolver.cpp │ │ ├── IntPoly.cpp │ │ ├── IntPoly.h │ │ ├── KeepBests.cpp │ │ ├── KeepBests.h │ │ ├── MSSolver.cpp │ │ ├── Matrix.cpp │ │ ├── Matrix.h │ │ ├── MatrixTriangle.cpp │ │ ├── MatrixTriangle.h │ │ ├── MultInd.cpp │ │ ├── MultInd.h │ │ ├── ObjectiveFunction.cpp │ │ ├── ObjectiveFunction.h │ │ ├── Poly.cpp │ │ ├── Poly.h │ │ ├── QPSolver.cpp │ │ ├── Solver.h │ │ ├── UTRSSolver.cpp │ │ ├── Vector.cpp │ │ ├── Vector.h │ │ ├── VectorChar.cpp │ │ ├── VectorChar.h │ │ ├── VectorInt.cpp │ │ ├── VectorInt.h │ │ ├── parallel.cpp │ │ ├── parallel.h │ │ ├── tools.cpp │ │ └── tools.h │ ├── delaunay │ │ ├── dcel.cpp │ │ ├── dcel.h │ │ ├── defines.h │ │ ├── delaunay.cpp │ │ ├── delaunay.h │ │ ├── graph.cpp │ │ ├── graph.h │ │ ├── point.cpp │ │ ├── point.h │ │ ├── polygon.cpp │ │ ├── polygon.h │ │ ├── sorting.cpp │ │ ├── sorting.h │ │ ├── stack.cpp │ │ ├── stack.h │ │ ├── triangulation.cpp │ │ ├── triangulation.h │ │ ├── voronoi.cpp │ │ └── voronoi.h │ └── sh_alignment │ │ ├── README │ │ ├── SpharmonicKit27 │ │ ├── BACKGROUND │ │ ├── FFTcode.cpp │ │ ├── FFTcode.h │ │ ├── FST_semi_memo.cpp │ │ ├── FST_semi_memo.h │ │ ├── LICENSE │ │ ├── MathFace.cpp │ │ ├── MathFace.h │ │ ├── OURmods.cpp │ │ ├── OURmods.h │ │ ├── OURperms.cpp │ │ ├── OURperms.h │ │ ├── README │ │ ├── config.h │ │ ├── cospmls.cpp │ │ ├── cospmls.h │ │ ├── csecond.cpp │ │ ├── csecond.h │ │ ├── fft_grids.cpp │ │ ├── fft_grids.h │ │ ├── fftpack.h │ │ ├── indextables.cpp │ │ ├── indextables.h │ │ ├── naive_synthesis.cpp │ │ ├── naive_synthesis.h │ │ ├── newFCT.cpp │ │ ├── newFCT.h │ │ ├── oddweights.cpp │ │ ├── oddweights.h │ │ ├── permroots.h │ │ ├── primitive.cpp │ │ ├── primitive.h │ │ ├── primitive_FST.cpp │ │ ├── primitive_FST.h │ │ ├── seminaive.cpp │ │ ├── seminaive.h │ │ ├── weights.cpp │ │ └── weights.h │ │ ├── frm.cpp │ │ ├── frm.i │ │ ├── frm_wrap.cpp │ │ ├── lib_err.cpp │ │ ├── lib_err.h │ │ ├── lib_eul.cpp │ │ ├── lib_eul.h │ │ ├── lib_pio.cpp │ │ ├── lib_pio.h │ │ ├── lib_pwk.cpp │ │ ├── lib_pwk.h │ │ ├── lib_std.cpp │ │ ├── lib_std.h │ │ ├── lib_tim.cpp │ │ ├── lib_tim.h │ │ ├── lib_vec.cpp │ │ ├── lib_vec.h │ │ ├── lib_vio.cpp │ │ ├── lib_vio.h │ │ ├── lib_vwk.cpp │ │ ├── lib_vwk.h │ │ ├── numpy.i │ │ ├── python │ │ ├── __init__.py │ │ ├── constrained_frm.py │ │ ├── frm.py │ │ ├── tompy │ │ │ ├── __init__.py │ │ │ ├── filter.py │ │ │ ├── io.py │ │ │ ├── plot.py │ │ │ ├── score.py │ │ │ ├── tools.py │ │ │ └── transform.py │ │ └── vol2sf.py │ │ ├── situs.h │ │ └── swig_frm.py │ ├── legacy │ ├── .travis.yml │ ├── applications │ │ ├── programs │ │ │ ├── angular_resolution_alignment │ │ │ │ └── angular_resolution_alignment_main.cpp │ │ │ ├── classify_kmeans_2d │ │ │ │ └── classify_kmeans_2d_main.cpp │ │ │ ├── classify_significant │ │ │ │ └── classify_significant_main.cpp │ │ │ ├── ctf_correct_idr │ │ │ │ └── ctf_correct_idr_main.cpp │ │ │ ├── ctf_create_ctfdat │ │ │ │ └── ctf_create_ctfdat_main.cpp │ │ │ ├── ctf_show │ │ │ │ └── ctf_show_main.cpp │ │ │ ├── cuda_correlation │ │ │ │ └── cuda_correlation_main.cpp │ │ │ ├── evaluate_coordinates │ │ │ │ └── evaluate_coordinates_main.cpp │ │ │ ├── extract_subset │ │ │ │ ├── prog_extract_subset_main.cpp │ │ │ │ └── prog_extract_subset_main.h │ │ │ ├── forward_art_zernike3d │ │ │ │ └── forward_art_zernike3d_main.cpp │ │ │ ├── idr_xray_tomo │ │ │ │ └── idr_xray_tomo_main.cpp │ │ │ ├── image_common_lines │ │ │ │ └── image_common_lines_main.cpp │ │ │ ├── image_rotational_spectra │ │ │ │ └── image_rotational_spectra_main.cpp │ │ │ ├── image_separate_objects │ │ │ │ └── image_separate_objects_main.cpp │ │ │ ├── metadata_convert_to_spider │ │ │ │ └── metadata_convert_to_spider_main.cpp │ │ │ ├── ml_refine3d │ │ │ │ └── ml_refine3d_main.cpp │ │ │ ├── ml_tomo │ │ │ │ └── ml_tomo_main.cpp │ │ │ ├── mlf_refine3d │ │ │ │ └── mlf_refine3d_main.cpp │ │ │ ├── mpi_ctf_correct_idr │ │ │ │ └── mpi_ctf_correct_idr_main.cpp │ │ │ ├── mpi_ml_refine3d │ │ │ │ └── mpi_ml_refine3d_main.cpp │ │ │ ├── mpi_ml_tomo │ │ │ │ └── mpi_ml_tomo_main.cpp │ │ │ ├── mpi_mlf_refine3d │ │ │ │ └── mpi_mlf_refine3d_main.cpp │ │ │ ├── mpi_reconstruct_admm │ │ │ │ └── mpi_reconstruct_admm_main.cpp │ │ │ ├── mpi_tomo_extract_subvolume │ │ │ │ └── mpi_tomo_extract_subvolume.cpp │ │ │ ├── mpi_xray_project │ │ │ │ └── mpi_xray_project_main.cpp │ │ │ ├── mrc_create_metadata │ │ │ │ └── mrc_create_metadata_main.cpp │ │ │ ├── parallel_forward_art_zernike3d │ │ │ │ └── parallel_forward_art_zernike3d_main.cpp │ │ │ ├── parallel_forward_art_zernike3d_float │ │ │ │ └── parallel_forward_art_zernike3d_float_main.cpp │ │ │ ├── pdb_construct_dictionary │ │ │ │ └── pdb_construct_dictionary_main.cpp │ │ │ ├── pdb_restore_with_dictionary │ │ │ │ └── pdb_restore_with_dictionary_main.cpp │ │ │ ├── reconstruct_admm │ │ │ │ └── reconstruct_admm_main.cpp │ │ │ ├── reconstruct_art_pseudo │ │ │ │ └── reconstruct_art_pseudo_main.cpp │ │ │ ├── reconstruct_art_xray │ │ │ │ └── reconstruct_art_xray_main.cpp │ │ │ ├── resolution_ibw │ │ │ │ └── resolution_ibw_main.cpp │ │ │ ├── resolution_ssnr │ │ │ │ └── resolution_ssnr_main.cpp │ │ │ ├── score_micrograph │ │ │ │ └── score_micrograph_main.cpp │ │ │ ├── starpu_reconstruct_fourier │ │ │ │ └── starpu_reconstruct_fourier_main.cpp │ │ │ ├── tomo_align_dual_tilt_series │ │ │ │ └── tomo_align_dual_tilt_series_main.cpp │ │ │ ├── tomo_align_refinement │ │ │ │ └── tomo_align_refinement_main.cpp │ │ │ ├── tomo_align_tilt_series │ │ │ │ └── tomo_align_tilt_series_main.cpp │ │ │ ├── tomo_extract_subvolume │ │ │ │ └── tomo_extract_volume_main.cpp │ │ │ ├── tomo_remove_fluctuations │ │ │ │ └── tomo_remove_fluctuations_main.cpp │ │ │ ├── transform_range_adjust │ │ │ │ └── transform_range_adjust_main.cpp │ │ │ ├── validation_tilt_pairs │ │ │ │ └── validation_tilt_pairs_main.cpp │ │ │ ├── volume_enhance_contrast │ │ │ │ └── volume_enhance_contrast_main.cpp │ │ │ ├── volume_pca │ │ │ │ └── volume_pca_main.cpp │ │ │ ├── volume_reslice │ │ │ │ └── volume_reslice_main.cpp │ │ │ ├── volume_validate_pca │ │ │ │ └── volume_validate_pca_main.cpp │ │ │ ├── work_test │ │ │ │ └── work_test.cpp │ │ │ ├── xray_import │ │ │ │ └── xray_import_main.cpp │ │ │ ├── xray_project │ │ │ │ └── xray_project_main.cpp │ │ │ └── xray_psf_create │ │ │ │ └── xray_psf_create_main.cpp │ │ └── scripts │ │ │ ├── apropos │ │ │ └── batch_apropos.py │ │ │ ├── cone_deepalign │ │ │ └── batch_cone_deepalign.py │ │ │ ├── cone_deepalign_predict │ │ │ └── batch_cone_deepalign_predict.py │ │ │ ├── deep_denoising │ │ │ └── batch_deep_denoising.py │ │ │ └── particle_boxsize │ │ │ └── batch_particle_boxsize.py │ ├── install_cuda_github.sh │ ├── install_cuda_travis.sh │ └── libraries │ │ ├── data │ │ ├── psf_xr.cpp │ │ └── psf_xr.h │ │ ├── parallel │ │ ├── mpi_project_XR.cpp │ │ ├── mpi_project_XR.h │ │ ├── mpi_reconstruct_admm.cpp │ │ └── mpi_reconstruct_admm.h │ │ ├── reconstruction │ │ ├── angular_resolution_alignment.cpp │ │ ├── angular_resolution_alignment.h │ │ ├── art_xray.cpp │ │ ├── art_xray.h │ │ ├── classify_kmeans_2d.cpp │ │ ├── classify_kmeans_2d.h │ │ ├── classify_significant.cpp │ │ ├── classify_significant.h │ │ ├── common_lines.cpp │ │ ├── common_lines.h │ │ ├── ctf_correct_idr.cpp │ │ ├── ctf_correct_idr.h │ │ ├── ctf_create_ctfdat.cpp │ │ ├── ctf_show.cpp │ │ ├── ctf_show.h │ │ ├── evaluate_coordinates.cpp │ │ ├── evaluate_coordinates.h │ │ ├── extract_subset.cpp │ │ ├── extract_subset.h │ │ ├── forward_art_zernike3d.cpp │ │ ├── forward_art_zernike3d.h │ │ ├── idr_xray_tomo.cpp │ │ ├── idr_xray_tomo.h │ │ ├── image_rotational_spectra.cpp │ │ ├── image_rotational_spectra.h │ │ ├── image_separate_objects.cpp │ │ ├── metadata_convert_to_spider.cpp │ │ ├── ml_refine3d.cpp │ │ ├── ml_refine3d.h │ │ ├── ml_tomo.cpp │ │ ├── ml_tomo.h │ │ ├── parallel_forward_art_zernike3d.cpp │ │ ├── parallel_forward_art_zernike3d.h │ │ ├── parallel_forward_art_zernike3d_floats.cpp │ │ ├── parallel_forward_art_zernike3d_floats.h │ │ ├── pdb_construct_dictionary.cpp │ │ ├── pdb_construct_dictionary.h │ │ ├── pdb_restore_with_dictionary.cpp │ │ ├── pdb_restore_with_dictionary.h │ │ ├── project_xray.cpp │ │ ├── project_xray.h │ │ ├── reconstruct_ADMM.cpp │ │ ├── reconstruct_ADMM.h │ │ ├── reconstruct_art_pseudo.cpp │ │ ├── reconstruct_art_pseudo.h │ │ ├── reconstruct_art_xray.cpp │ │ ├── reconstruct_art_xray.h │ │ ├── resolution_ibw.cpp │ │ ├── resolution_ibw.h │ │ ├── resolution_ssnr.cpp │ │ ├── resolution_ssnr.h │ │ ├── score_micrograph.cpp │ │ ├── score_micrograph.h │ │ ├── tomo_align_dual_tilt_series.cpp │ │ ├── tomo_align_dual_tilt_series.h │ │ ├── tomo_align_refinement.cpp │ │ ├── tomo_align_refinement.h │ │ ├── tomo_align_tilt_series.cpp │ │ ├── tomo_align_tilt_series.h │ │ ├── tomo_extract_subvolume.cpp │ │ ├── tomo_extract_subvolume.h │ │ ├── tomo_remove_fluctuations.cpp │ │ ├── tomo_remove_fluctuations.h │ │ ├── transform_range_adjust.cpp │ │ ├── validation_tilt_pairs.cpp │ │ ├── validation_tilt_pairs.h │ │ ├── volume_enhance_contrast.cpp │ │ ├── volume_enhance_contrast.h │ │ ├── volume_pca.cpp │ │ ├── volume_pca.h │ │ ├── volume_reslice.cpp │ │ ├── volume_validate_pca.cpp │ │ ├── volume_validate_pca.h │ │ ├── xray_import.cpp │ │ ├── xray_import.h │ │ └── xray_psf_create.cpp │ │ ├── reconstruction_adapt_cuda │ │ ├── xmipp_gpu_correlation.cpp │ │ ├── xmipp_gpu_correlation.h │ │ ├── xmipp_gpu_utils.cpp │ │ └── xmipp_gpu_utils.h │ │ ├── reconstruction_starpu │ │ ├── mpi │ │ │ ├── mpi_reconstruct_fourier_starpu.cpp │ │ │ └── mpi_reconstruct_fourier_starpu.h │ │ ├── reconstruct_fourier_codelet_load_projections.cpp │ │ ├── reconstruct_fourier_codelet_padded_image_to_fft.cpp │ │ ├── reconstruct_fourier_codelet_reconstruct.cpp │ │ ├── reconstruct_fourier_codelet_redux.cpp │ │ ├── reconstruct_fourier_codelets.cpp │ │ ├── reconstruct_fourier_codelets.h │ │ ├── reconstruct_fourier_defines.h │ │ ├── reconstruct_fourier_scheduler.cpp │ │ ├── reconstruct_fourier_scheduler.h │ │ ├── reconstruct_fourier_timing.cpp │ │ ├── reconstruct_fourier_timing.h │ │ ├── reconstruct_fourier_util.h │ │ └── util │ │ │ └── queue_bag.h │ │ └── tomo │ │ ├── resolution_monotomo.cpp │ │ ├── resolution_monotomo.h │ │ ├── tomo_tiltseries_detect_misalignment_corr.cpp │ │ └── tomo_tiltseries_detect_misalignment_corr.h │ ├── libraries │ ├── classification │ │ ├── ahc_classifier.cpp │ │ ├── ahc_classifier.h │ │ ├── analyze_cluster.cpp │ │ ├── analyze_cluster.h │ │ ├── base_algorithm.h │ │ ├── batch_som.cpp │ │ ├── batch_som.h │ │ ├── code_book.cpp │ │ ├── code_book.h │ │ ├── data_set.h │ │ ├── data_types.h │ │ ├── fcmeans.cpp │ │ ├── fcmeans.h │ │ ├── fkcn.cpp │ │ ├── fkcn.h │ │ ├── fuzzy_code_book.cpp │ │ ├── fuzzy_code_book.h │ │ ├── fuzzy_som.cpp │ │ ├── fuzzy_som.h │ │ ├── gaussian_kerdensom.cpp │ │ ├── gaussian_kerdensom.h │ │ ├── kSVD.cpp │ │ ├── kSVD.h │ │ ├── kerdensom.cpp │ │ ├── kerdensom.h │ │ ├── knn_classifier.cpp │ │ ├── knn_classifier.h │ │ ├── map.cpp │ │ ├── map.h │ │ ├── naive_bayes.cpp │ │ ├── naive_bayes.h │ │ ├── pca.cpp │ │ ├── pca.h │ │ ├── sammon.cpp │ │ ├── sammon.h │ │ ├── som.cpp │ │ ├── som.h │ │ ├── svm.cpp │ │ ├── svm_classifier.cpp │ │ ├── svm_classifier.h │ │ ├── training_set.h │ │ ├── training_vector.cpp │ │ ├── training_vector.h │ │ └── vector_ops.h │ ├── data │ │ ├── aft.h │ │ ├── alignment_estimation.h │ │ ├── alignment_result.h │ │ ├── array_2D.h │ │ ├── basic_pca.cpp │ │ ├── basic_pca.h │ │ ├── basis.cpp │ │ ├── basis.h │ │ ├── blobs.cpp │ │ ├── blobs.h │ │ ├── bspline_grid.h │ │ ├── chimeraTesterC.txt │ │ ├── chimeraTesterD.txt │ │ ├── chimeraTesterI2.txt │ │ ├── chimeraTesterO.txt │ │ ├── chimeraTesterT.txt │ │ ├── cpu.cpp │ │ ├── cpu.h │ │ ├── ctf.cpp │ │ ├── ctf.h │ │ ├── cuda_compatibility.h │ │ ├── dimensions.h │ │ ├── euler.cpp │ │ ├── euler.h │ │ ├── fft_settings.cpp │ │ ├── fft_settings.h │ │ ├── fftwT.cpp │ │ ├── fftwT.h │ │ ├── filters.cpp │ │ ├── filters.h │ │ ├── fourier_filter.cpp │ │ ├── fourier_filter.h │ │ ├── fourier_projection.cpp │ │ ├── fourier_projection.h │ │ ├── grids.cpp │ │ ├── grids.h │ │ ├── hw.h │ │ ├── image_operate.cpp │ │ ├── image_operate.h │ │ ├── image_resize.cpp │ │ ├── image_resize.h │ │ ├── integration.cpp │ │ ├── integration.h │ │ ├── local_alignment_result.h │ │ ├── mask.cpp │ │ ├── mask.h │ │ ├── micrograph.cpp │ │ ├── micrograph.h │ │ ├── monogenic_signal.cpp │ │ ├── monogenic_signal.h │ │ ├── morphology.cpp │ │ ├── morphology.h │ │ ├── normalize.cpp │ │ ├── normalize.h │ │ ├── numerical_tools.cpp │ │ ├── numerical_tools.h │ │ ├── pdb.cpp │ │ ├── pdb.h │ │ ├── phantom.cpp │ │ ├── phantom.h │ │ ├── point.h │ │ ├── point2D.h │ │ ├── point3D.h │ │ ├── polar.cpp │ │ ├── polar.h │ │ ├── projection.cpp │ │ ├── projection.h │ │ ├── rectangle.h │ │ ├── rotational_spectrum.cpp │ │ ├── rotational_spectrum.h │ │ ├── sampling.cpp │ │ ├── sampling.h │ │ ├── sparse_matrix2d.cpp │ │ ├── sparse_matrix2d.h │ │ ├── spherical_harmonics.cpp │ │ ├── spherical_harmonics.h │ │ ├── splines.cpp │ │ ├── splines.h │ │ ├── steerable.cpp │ │ ├── steerable.h │ │ ├── symmetries.cpp │ │ ├── symmetries.h │ │ ├── transform_downsample.cpp │ │ ├── transform_downsample.h │ │ ├── transform_geometry.cpp │ │ ├── transform_geometry.h │ │ ├── unitCell.cpp │ │ ├── unitCell.h │ │ ├── vectorial.h │ │ ├── wavelet.cpp │ │ ├── wavelet.h │ │ ├── wiener2d.cpp │ │ ├── wiener2d.h │ │ ├── xmipp_image_convert.cpp │ │ ├── xmipp_image_convert.h │ │ ├── xmipp_image_over.cpp │ │ ├── xmipp_image_over.h │ │ ├── xmipp_polynomials.cpp │ │ └── xmipp_polynomials.h │ ├── dimred │ │ ├── diffusionMaps.cpp │ │ ├── diffusionMaps.h │ │ ├── dimred_tools.cpp │ │ ├── dimred_tools.h │ │ ├── gplvm.cpp │ │ ├── gplvm.h │ │ ├── hessianLLE.cpp │ │ ├── hessianLLE.h │ │ ├── kernelPCA.cpp │ │ ├── kernelPCA.h │ │ ├── laplacianEigenmaps.cpp │ │ ├── laplacianEigenmaps.h │ │ ├── lltsa.cpp │ │ ├── lltsa.h │ │ ├── lpp.cpp │ │ ├── lpp.h │ │ ├── ltsa.cpp │ │ ├── ltsa.h │ │ ├── matrix_dimred.cpp │ │ ├── matrix_dimred.h │ │ ├── nca.cpp │ │ ├── nca.h │ │ ├── npe.cpp │ │ ├── npe.h │ │ ├── pca.cpp │ │ ├── pca.h │ │ ├── probabilisticPCA.cpp │ │ ├── probabilisticPCA.h │ │ ├── spe.cpp │ │ ├── spe.h │ │ ├── transform_dimred.cpp │ │ └── transform_dimred.h │ ├── interface │ │ ├── docfile.cpp │ │ ├── docfile.h │ │ ├── frm.cpp │ │ ├── frm.h │ │ ├── python_utils.cpp │ │ ├── python_utils.h │ │ ├── selfile.cpp │ │ ├── selfile.h │ │ ├── spider.cpp │ │ ├── spider.h │ │ └── virus.h │ ├── parallel │ │ ├── mpi_angular_accuracy_pca.cpp │ │ ├── mpi_angular_accuracy_pca.h │ │ ├── mpi_angular_assignment_mag.cpp │ │ ├── mpi_angular_assignment_mag.h │ │ ├── mpi_angular_class_average.cpp │ │ ├── mpi_angular_class_average.h │ │ ├── mpi_angular_continuous_assign.cpp │ │ ├── mpi_angular_project_library.cpp │ │ ├── mpi_angular_projection_matching.cpp │ │ ├── mpi_angular_projection_matching.h │ │ ├── mpi_angular_sph_alignment.cpp │ │ ├── mpi_classify_CL2D.cpp │ │ ├── mpi_classify_CL2D.h │ │ ├── mpi_classify_CL2D_core_analysis.cpp │ │ ├── mpi_classify_CL2D_core_analysis.h │ │ ├── mpi_classify_CLTomo.h │ │ ├── mpi_classify_CLTomo_prog.cpp │ │ ├── mpi_classify_FTTRI.cpp │ │ ├── mpi_classify_FTTRI.h │ │ ├── mpi_continuous_create_residuals.cpp │ │ ├── mpi_forward_zernike_images.cpp │ │ ├── mpi_forward_zernike_images_priors.cpp │ │ ├── mpi_forward_zernike_subtomos.cpp │ │ ├── mpi_image_rotational_pca.cpp │ │ ├── mpi_image_rotational_pca.h │ │ ├── mpi_image_sort.cpp │ │ ├── mpi_ml_align2d.cpp │ │ ├── mpi_ml_align2d.h │ │ ├── mpi_multireference_aligneability.cpp │ │ ├── mpi_multireference_aligneability.h │ │ ├── mpi_nma_alignment.cpp │ │ ├── mpi_nma_alignment_vol.cpp │ │ ├── mpi_nma_alignment_vol.h │ │ ├── mpi_performance_test.cpp │ │ ├── mpi_performance_test.h │ │ ├── mpi_reconstruct_art.cpp │ │ ├── mpi_reconstruct_art.h │ │ ├── mpi_reconstruct_fourier.cpp │ │ ├── mpi_reconstruct_fourier.h │ │ ├── mpi_reconstruct_fourier_accel.cpp │ │ ├── mpi_reconstruct_fourier_accel.h │ │ ├── mpi_reconstruct_significant.cpp │ │ ├── mpi_reconstruct_significant.h │ │ ├── mpi_reconstruct_wbp.cpp │ │ ├── mpi_reconstruct_wbp.h │ │ ├── mpi_run.cpp │ │ ├── mpi_subtomo_subtraction.cpp │ │ ├── mpi_subtomo_subtraction.h │ │ ├── mpi_subtract_projection.cpp │ │ ├── mpi_subtract_projection.h │ │ ├── mpi_transform_adjust_image_grey_levels.cpp │ │ ├── mpi_validation_nontilt.cpp │ │ ├── mpi_validation_nontilt.h │ │ ├── mpi_volumeset_align.cpp │ │ ├── mpi_volumeset_align.h │ │ ├── xmipp_mpi.cpp │ │ └── xmipp_mpi.h │ ├── parallel_adapt_cuda │ │ ├── mpi_reconstruct_fourier_gpu.cpp │ │ └── mpi_reconstruct_fourier_gpu.h │ ├── parallel_adapt_cuda11 │ │ └── .gitkeep │ ├── py_xmipp │ │ ├── classifyPcaFuntion │ │ │ ├── __init__.py │ │ │ ├── assessment.py │ │ │ ├── bnb_gpu.py │ │ │ └── pca_gpu.py │ │ ├── coordinatesTools │ │ │ ├── __init__.py │ │ │ └── coordinatesTools.py │ │ ├── deepConsensusWorkers │ │ │ ├── __init__.py │ │ │ ├── deepConsensus_deepLearning1.py │ │ │ ├── deepConsensus_networkDef.py │ │ │ └── updateModels.py │ │ ├── deepDenoising │ │ │ ├── DeepLearningGeneric.py │ │ │ ├── __init__.py │ │ │ ├── augmentators.py │ │ │ ├── dataGenerator.py │ │ │ ├── gan.py │ │ │ └── unet.py │ │ ├── deepLearningToolkitUtils │ │ │ ├── __init__.py │ │ │ └── utils.py │ │ ├── deepResLearner │ │ │ ├── __init__.py │ │ │ ├── cnn_deepRes_1_7.py │ │ │ └── cnn_deepRes_2_13.py │ │ ├── example_module.py │ │ ├── example_module2 │ │ │ ├── __init__.py │ │ │ └── example_inmodule2.py │ │ └── swiftalign │ │ │ ├── __init__.py │ │ │ ├── alignment │ │ │ ├── InPlaneTransformCorrector.py │ │ │ └── __init__.py │ │ │ ├── classification │ │ │ ├── __init__.py │ │ │ └── aligned_2d_classficiation.py │ │ │ ├── ctf │ │ │ ├── __init__.py │ │ │ ├── compute_ctf_image_2d.py │ │ │ └── wiener.py │ │ │ ├── fourier │ │ │ ├── __init__.py │ │ │ ├── rfftnfreq.py │ │ │ └── zero_pad.py │ │ │ ├── image │ │ │ ├── Path.py │ │ │ ├── __init__.py │ │ │ ├── read.py │ │ │ ├── torch_utils │ │ │ │ ├── Dataset.py │ │ │ │ └── __init__.py │ │ │ ├── utils.py │ │ │ └── write.py │ │ │ ├── metadata │ │ │ ├── __init__.py │ │ │ ├── labels.py │ │ │ ├── read.py │ │ │ ├── utils.py │ │ │ └── write.py │ │ │ ├── operators │ │ │ ├── MaskFlattener.py │ │ │ └── __init__.py │ │ │ ├── transform │ │ │ ├── __init__.py │ │ │ ├── affine_2d.py │ │ │ ├── affine_matrix_2d.py │ │ │ ├── euler_to_matrix.py │ │ │ ├── euler_to_quaternion.py │ │ │ ├── matrix_to_euler.py │ │ │ ├── quaternion_arithmetic.py │ │ │ ├── quaternion_to_matrix.py │ │ │ ├── rotation_matrix_2d.py │ │ │ └── twist_swing_decomposition.py │ │ │ └── utils │ │ │ ├── LruCache.py │ │ │ ├── __init__.py │ │ │ └── progress_bar.py │ ├── reconstruction │ │ ├── aalign_significant.cpp │ │ ├── aalign_significant.h │ │ ├── adjust_volume_grey_levels.cpp │ │ ├── adjust_volume_grey_levels.h │ │ ├── aextrema_finder.cpp │ │ ├── aextrema_finder.h │ │ ├── ageo_transformer.h │ │ ├── align2d.cpp │ │ ├── align2d.h │ │ ├── align_tilt_pairs.cpp │ │ ├── align_tilt_pairs.h │ │ ├── align_type.h │ │ ├── amerit_computer.h │ │ ├── angular_accuracy_pca.cpp │ │ ├── angular_accuracy_pca.h │ │ ├── angular_assignment_mag.cpp │ │ ├── angular_assignment_mag.h │ │ ├── angular_break_symmetry.cpp │ │ ├── angular_break_symmetry.h │ │ ├── angular_commonline.cpp │ │ ├── angular_commonline.h │ │ ├── angular_continuous_assign.cpp │ │ ├── angular_continuous_assign.h │ │ ├── angular_continuous_assign2.cpp │ │ ├── angular_continuous_assign2.h │ │ ├── angular_discrete_assign.cpp │ │ ├── angular_discrete_assign.h │ │ ├── angular_distance.cpp │ │ ├── angular_distance.h │ │ ├── angular_distribution_show.cpp │ │ ├── angular_estimate_tilt_axis.cpp │ │ ├── angular_estimate_tilt_axis.h │ │ ├── angular_neighbourhood.cpp │ │ ├── angular_neighbourhood.h │ │ ├── angular_project_library.cpp │ │ ├── angular_project_library.h │ │ ├── angular_projection_matching.cpp │ │ ├── angular_projection_matching.h │ │ ├── angular_rotate.cpp │ │ ├── angular_sph_alignment.cpp │ │ ├── angular_sph_alignment.h │ │ ├── arotation_estimator.cpp │ │ ├── arotation_estimator.h │ │ ├── art_crystal.cpp │ │ ├── art_crystal.h │ │ ├── art_zernike3d.cpp │ │ ├── art_zernike3d.h │ │ ├── ashift_corr_estimator.cpp │ │ ├── ashift_corr_estimator.h │ │ ├── ashift_estimator.cpp │ │ ├── ashift_estimator.h │ │ ├── base_art_recons.cpp │ │ ├── base_art_recons.h │ │ ├── basic_art.cpp │ │ ├── basic_art.h │ │ ├── bspline_geo_transformer.cpp │ │ ├── bspline_geo_transformer.h │ │ ├── bspline_helper.cpp │ │ ├── bspline_helper.h │ │ ├── classify_compare_classes.cpp │ │ ├── classify_compare_classes.h │ │ ├── classify_evaluate_classes.cpp │ │ ├── classify_evaluate_classes.h │ │ ├── classify_extract_features.cpp │ │ ├── classify_extract_features.h │ │ ├── classify_first_split.cpp │ │ ├── classify_first_split.h │ │ ├── classify_first_split3.cpp │ │ ├── classify_first_split3.h │ │ ├── classify_kerdensom.cpp │ │ ├── compare_density.cpp │ │ ├── compare_density.h │ │ ├── compare_views.cpp │ │ ├── compare_views.h │ │ ├── continuous_create_residuals.cpp │ │ ├── continuous_create_residuals.h │ │ ├── coordinates_noisy_zones_filter.cpp │ │ ├── coordinates_noisy_zones_filter.h │ │ ├── correlation_computer.cpp │ │ ├── correlation_computer.h │ │ ├── ctf_correct_phase.cpp │ │ ├── ctf_correct_phase.h │ │ ├── ctf_correct_wiener2d.cpp │ │ ├── ctf_correct_wiener2d.h │ │ ├── ctf_correct_wiener3d.cpp │ │ ├── ctf_correct_wiener3d.h │ │ ├── ctf_enhance_psd.cpp │ │ ├── ctf_enhance_psd.h │ │ ├── ctf_estimate_from_micrograph.cpp │ │ ├── ctf_estimate_from_micrograph.h │ │ ├── ctf_estimate_from_psd.cpp │ │ ├── ctf_estimate_from_psd.h │ │ ├── ctf_estimate_from_psd_base.cpp │ │ ├── ctf_estimate_from_psd_base.h │ │ ├── ctf_estimate_from_psd_fast.cpp │ │ ├── ctf_estimate_from_psd_fast.h │ │ ├── ctf_estimate_psd_with_arma.cpp │ │ ├── ctf_estimate_psd_with_arma.h │ │ ├── ctf_group.cpp │ │ ├── ctf_group.h │ │ ├── ctf_phase_flip.cpp │ │ ├── ctf_phase_flip.h │ │ ├── ctf_sort_psds.cpp │ │ ├── ctf_sort_psds.h │ │ ├── denoise.cpp │ │ ├── denoise.h │ │ ├── directions.cpp │ │ ├── directions.h │ │ ├── eq_system_solver.cpp │ │ ├── eq_system_solver.h │ │ ├── flexible_alignment.cpp │ │ ├── flexible_alignment.h │ │ ├── forward_art_zernike3d_subtomos.cpp │ │ ├── forward_art_zernike3d_subtomos.h │ │ ├── forward_zernike_images.cpp │ │ ├── forward_zernike_images.h │ │ ├── forward_zernike_images_priors.cpp │ │ ├── forward_zernike_images_priors.h │ │ ├── forward_zernike_subtomos.cpp │ │ ├── forward_zernike_subtomos.h │ │ ├── forward_zernike_volume.cpp │ │ ├── forward_zernike_volume.h │ │ ├── fringe_processing.cpp │ │ ├── fringe_processing.h │ │ ├── gpu_geo_transformer_defines.h │ │ ├── image_assignment_tilt_pair.cpp │ │ ├── image_assignment_tilt_pair.h │ │ ├── image_eliminate_byEnergy.cpp │ │ ├── image_eliminate_byEnergy.h │ │ ├── image_eliminate_empty_particles.cpp │ │ ├── image_eliminate_empty_particles.h │ │ ├── image_find_center.cpp │ │ ├── image_header.cpp │ │ ├── image_histogram.cpp │ │ ├── image_odd_even.cpp │ │ ├── image_odd_even.h │ │ ├── image_peak_high_contrast.cpp │ │ ├── image_peak_high_contrast.h │ │ ├── image_rotational_pca.cpp │ │ ├── image_rotational_pca.h │ │ ├── image_sort_by_statistics.cpp │ │ ├── image_sort_by_statistics.h │ │ ├── image_statistics.cpp │ │ ├── image_vectorize.cpp │ │ ├── iterative_alignment_estimator.cpp │ │ ├── iterative_alignment_estimator.h │ │ ├── local_volume_adjust.cpp │ │ ├── local_volume_adjust.h │ │ ├── mean_shift.cpp │ │ ├── mean_shift.h │ │ ├── metadata_histogram.cpp │ │ ├── metadata_split.cpp │ │ ├── metadata_split_3D.cpp │ │ ├── metadata_split_3D.h │ │ ├── metadata_utilities.cpp │ │ ├── metadata_xml.cpp │ │ ├── micrograph_automatic_picking2.cpp │ │ ├── micrograph_automatic_picking2.h │ │ ├── micrograph_scissor.cpp │ │ ├── ml2d.cpp │ │ ├── ml2d.h │ │ ├── ml_align2d.cpp │ │ ├── ml_align2d.h │ │ ├── mlf_align2d.cpp │ │ ├── mlf_align2d.h │ │ ├── movie_alignment_correlation.cpp │ │ ├── movie_alignment_correlation.h │ │ ├── movie_alignment_correlation_base.cpp │ │ ├── movie_alignment_correlation_base.h │ │ ├── movie_alignment_gpu_defines.h │ │ ├── movie_estimate_gain.cpp │ │ ├── movie_estimate_gain.h │ │ ├── movie_filter_dose.cpp │ │ ├── movie_filter_dose.h │ │ ├── multireference_aligneability.cpp │ │ ├── multireference_aligneability.h │ │ ├── nma_alignment.cpp │ │ ├── nma_alignment.h │ │ ├── nma_alignment_vol.cpp │ │ ├── nma_alignment_vol.h │ │ ├── pdb_analysis.cpp │ │ ├── pdb_analysis.h │ │ ├── pdb_label_from_volume.cpp │ │ ├── pdb_label_from_volume.h │ │ ├── pdb_nma_deform.cpp │ │ ├── pdb_nma_deform.h │ │ ├── pdb_reduce_pseudoatoms.cpp │ │ ├── pdb_reduce_pseudoatoms.h │ │ ├── pdb_sph_deform.cpp │ │ ├── pdb_sph_deform.h │ │ ├── phantom_movie.cpp │ │ ├── phantom_movie.h │ │ ├── phantom_movie_param_estimator.m │ │ ├── phantom_simulate_microscope.cpp │ │ ├── phantom_simulate_microscope.h │ │ ├── phantom_transform.cpp │ │ ├── polar_rotation_estimator.cpp │ │ ├── polar_rotation_estimator.h │ │ ├── precompute_sampling.cpp │ │ ├── precompute_sampling.h │ │ ├── program_extension.cpp │ │ ├── program_extension.h │ │ ├── program_filter.cpp │ │ ├── program_filter.h │ │ ├── program_image_residuals.cpp │ │ ├── program_image_residuals.h │ │ ├── program_image_ssnr.cpp │ │ ├── program_image_ssnr.h │ │ ├── project.cpp │ │ ├── project.h │ │ ├── project_crystal.cpp │ │ ├── project_crystal.h │ │ ├── project_real_shears.cpp │ │ ├── project_real_shears.h │ │ ├── project_tomography.cpp │ │ ├── project_tomography.h │ │ ├── psd_estimator.cpp │ │ ├── psd_estimator.h │ │ ├── radon.cpp │ │ ├── radon.h │ │ ├── recons.h │ │ ├── recons_misc.cpp │ │ ├── recons_misc.h │ │ ├── reconstruct_art.cpp │ │ ├── reconstruct_art.h │ │ ├── reconstruct_fourier.cpp │ │ ├── reconstruct_fourier.h │ │ ├── reconstruct_fourier_accel.cpp │ │ ├── reconstruct_fourier_accel.h │ │ ├── reconstruct_fourier_buffer_data.h │ │ ├── reconstruct_fourier_defines.h │ │ ├── reconstruct_fourier_projection_traverse_space.h │ │ ├── reconstruct_significant.cpp │ │ ├── reconstruct_significant.h │ │ ├── reconstruct_wbp.cpp │ │ ├── reconstruct_wbp.h │ │ ├── refinement.cpp │ │ ├── refinement.h │ │ ├── resolution_directional.cpp │ │ ├── resolution_directional.h │ │ ├── resolution_fsc.cpp │ │ ├── resolution_fsc.h │ │ ├── resolution_fso.cpp │ │ ├── resolution_fso.h │ │ ├── resolution_localfilter.cpp │ │ ├── resolution_localfilter.h │ │ ├── resolution_monogenic_signal.cpp │ │ ├── resolution_monogenic_signal.h │ │ ├── resolution_pdb_bfactor.cpp │ │ ├── resolution_pdb_bfactor.h │ │ ├── shift_corr_estimator.cpp │ │ ├── shift_corr_estimator.h │ │ ├── single_extrema_finder.cpp │ │ ├── single_extrema_finder.h │ │ ├── subtomo_subtraction.cpp │ │ ├── subtomo_subtraction.h │ │ ├── subtract_projection.cpp │ │ ├── subtract_projection.h │ │ ├── symmetrize.cpp │ │ ├── symmetrize.h │ │ ├── threshold.cpp │ │ ├── threshold.h │ │ ├── transform_add_noise.cpp │ │ ├── transform_adjust_image_grey_levels.cpp │ │ ├── transform_adjust_image_grey_levels.h │ │ ├── transform_center_image.cpp │ │ ├── transform_morphology.cpp │ │ ├── transform_window.cpp │ │ ├── validation_nontilt.cpp │ │ ├── validation_nontilt.h │ │ ├── volume_align_prog.cpp │ │ ├── volume_apply_coefficient_zernike3d.cpp │ │ ├── volume_apply_coefficient_zernike3d.h │ │ ├── volume_apply_deform_sph.cpp │ │ ├── volume_apply_deform_sph.h │ │ ├── volume_correct_bfactor.cpp │ │ ├── volume_correct_bfactor.h │ │ ├── volume_deform_sph.cpp │ │ ├── volume_deform_sph.h │ │ ├── volume_find_symmetry.cpp │ │ ├── volume_from_pdb.cpp │ │ ├── volume_from_pdb.h │ │ ├── volume_halves_restoration.cpp │ │ ├── volume_halves_restoration.h │ │ ├── volume_initial_simulated_annealing.cpp │ │ ├── volume_initial_simulated_annealing.h │ │ ├── volume_local_sharpening.cpp │ │ ├── volume_local_sharpening.h │ │ ├── volume_segment.cpp │ │ ├── volume_segment.h │ │ ├── volume_structure_factor.cpp │ │ ├── volume_subtraction.cpp │ │ ├── volume_subtraction.h │ │ ├── volume_to_pseudoatoms.cpp │ │ ├── volume_to_pseudoatoms.h │ │ ├── volume_to_web.cpp │ │ ├── volumeset_align.cpp │ │ └── volumeset_align.h │ ├── reconstruction_adapt_cuda │ │ ├── align_significant_gpu.cpp │ │ ├── align_significant_gpu.h │ │ ├── angular_continuous_assign2_gpu.cpp │ │ ├── angular_continuous_assign2_gpu.h │ │ ├── angular_sph_alignment_gpu.cpp │ │ ├── angular_sph_alignment_gpu.h │ │ ├── basic_mem_manager.h │ │ ├── movie_alignment_correlation_gpu.cpp │ │ ├── movie_alignment_correlation_gpu.h │ │ ├── reconstruct_fourier_gpu.cpp │ │ ├── reconstruct_fourier_gpu.h │ │ ├── volume_deform_sph_gpu.cpp │ │ ├── volume_deform_sph_gpu.h │ │ ├── volume_halves_restoration_gpu.cpp │ │ └── volume_halves_restoration_gpu.h │ ├── reconstruction_adapt_cuda11 │ │ ├── .gitkeep │ │ ├── forward_art_zernike3d_gpu.cpp │ │ └── forward_art_zernike3d_gpu.h │ ├── reconstruction_cuda │ │ ├── basic_mem_manager.cpp │ │ ├── cuda_all.cpp │ │ ├── cuda_angular_sph_alignment.cpp │ │ ├── cuda_angular_sph_alignment.cu │ │ ├── cuda_angular_sph_alignment.h │ │ ├── cuda_asserts.h │ │ ├── cuda_basic_math.h │ │ ├── cuda_bspline_geo_transformer.cpp │ │ ├── cuda_bspline_geo_transformer.h │ │ ├── cuda_cdf.cpp │ │ ├── cuda_cdf.cu │ │ ├── cuda_cdf.h │ │ ├── cuda_compatibility.cu │ │ ├── cuda_compatibility.h │ │ ├── cuda_correlation.cu │ │ ├── cuda_correlation_computer.cpp │ │ ├── cuda_correlation_computer.h │ │ ├── cuda_fft.cpp │ │ ├── cuda_fft.h │ │ ├── cuda_flexalign_correlate.cpp │ │ ├── cuda_flexalign_correlate.h │ │ ├── cuda_flexalign_scale.cpp │ │ ├── cuda_flexalign_scale.h │ │ ├── cuda_fourier_projection.cpp │ │ ├── cuda_fourier_projection.cu │ │ ├── cuda_fourier_projection.h │ │ ├── cuda_geo_linear_interpolator.cu │ │ ├── cuda_gpu_bilib.cu │ │ ├── cuda_gpu_correlation.cpp │ │ ├── cuda_gpu_correlation.h │ │ ├── cuda_gpu_geo_shift_transformer.cpp │ │ ├── cuda_gpu_geo_shift_transformer.cu │ │ ├── cuda_gpu_geo_shift_transformer.h │ │ ├── cuda_gpu_geo_transformer.cpp │ │ ├── cuda_gpu_geo_transformer.cu │ │ ├── cuda_gpu_geo_transformer.h │ │ ├── cuda_gpu_iirconvolve.cu │ │ ├── cuda_gpu_movie_alignment_correlation_kernels.cu │ │ ├── cuda_gpu_multidim_array.cu │ │ ├── cuda_gpu_polar.cu │ │ ├── cuda_gpu_reconstruct_fourier.cpp │ │ ├── cuda_gpu_reconstruct_fourier.h │ │ ├── cuda_rot_polar_estimator.cpp │ │ ├── cuda_rot_polar_estimator.h │ │ ├── cuda_scaleFFT.h │ │ ├── cuda_scaleFFT_kernels.cu │ │ ├── cuda_shift_corr_estimator.cpp │ │ ├── cuda_shift_corr_estimator.h │ │ ├── cuda_single_extrema_finder.cpp │ │ ├── cuda_single_extrema_finder.cu │ │ ├── cuda_single_extrema_finder.h │ │ ├── cuda_vec2.h │ │ ├── cuda_volume_deform_sph.cpp │ │ ├── cuda_volume_deform_sph.cu │ │ ├── cuda_volume_deform_sph.h │ │ ├── cuda_volume_deform_sph_defines.h │ │ ├── cuda_volume_halves_restorator.cpp │ │ ├── cuda_volume_halves_restorator.h │ │ ├── cuda_volume_restoration_kernels.cpp │ │ ├── cuda_volume_restoration_kernels.cu │ │ ├── cuda_volume_restoration_kernels.h │ │ ├── cuda_xmipp_utils.cpp │ │ ├── cuda_xmipp_utils.h │ │ ├── gpu.cpp │ │ └── gpu.h │ ├── reconstruction_cuda11 │ │ ├── .gitkeep │ │ ├── cuda_forward_art_zernike3d.cpp │ │ ├── cuda_forward_art_zernike3d.cu │ │ ├── cuda_forward_art_zernike3d.h │ │ └── cuda_forward_art_zernike3d_defines.h │ └── tomo │ │ ├── resolution_monotomo.cpp │ │ ├── resolution_monotomo.h │ │ ├── tomo_average_subtomos.cpp │ │ ├── tomo_average_subtomos.h │ │ ├── tomo_calculate_landmark_residuals.cpp │ │ ├── tomo_calculate_landmark_residuals.h │ │ ├── tomo_ctf_wiener2d_correction.cpp │ │ ├── tomo_ctf_wiener2d_correction.h │ │ ├── tomo_detect_landmarks.cpp │ │ ├── tomo_detect_landmarks.h │ │ ├── tomo_detect_misalignment_residuals.cpp │ │ ├── tomo_detect_misalignment_residuals.h │ │ ├── tomo_detect_missing_wedge.cpp │ │ ├── tomo_detect_missing_wedge.h │ │ ├── tomo_extract_particlestacks.cpp │ │ ├── tomo_extract_particlestacks.h │ │ ├── tomo_extract_subtomograms.cpp │ │ ├── tomo_extract_subtomograms.h │ │ ├── tomo_filter_coordinates.cpp │ │ ├── tomo_filter_coordinates.h │ │ ├── tomo_map_back.cpp │ │ ├── tomo_map_back.h │ │ ├── tomo_simulate_tilt_series.cpp │ │ ├── tomo_simulate_tilt_series.h │ │ ├── tomo_tiltseries_dose_filter.cpp │ │ └── tomo_tiltseries_dose_filter.h │ ├── resources │ └── test │ │ ├── EMX │ │ ├── EMXread.emx │ │ ├── EMXwrite.emx │ │ ├── EMXwrite_badly_formed.emx │ │ ├── EMXwrite_badly_formed_assert.emx │ │ └── emx.xsd │ │ ├── dimred │ │ ├── clusters.txt │ │ ├── diffusionMaps.txt │ │ ├── gplvm.txt │ │ ├── helix.txt │ │ ├── hessianlle.txt │ │ ├── intersect.txt │ │ ├── kernelPCA.txt │ │ ├── laplacianEigenmap.txt │ │ ├── lltsa.txt │ │ ├── lltsaSCG.txt │ │ ├── lpp.txt │ │ ├── ltsa.txt │ │ ├── nca.txt │ │ ├── npe.txt │ │ ├── probabilisticPCA.txt │ │ ├── spe.txt │ │ ├── swiss.txt │ │ └── twinpeaks.txt │ │ ├── filters │ │ ├── KLH.tif │ │ └── test2.spi │ │ ├── funcs │ │ ├── singleImage.mrc │ │ └── singleImage.spi │ │ ├── image │ │ ├── mappedFile.vol │ │ ├── progVol.vol │ │ ├── singleImage.hed │ │ ├── singleImage.img │ │ ├── singleImage.inf │ │ ├── singleImage.mrc │ │ ├── singleImage.raw │ │ ├── singleImage.raw.inf │ │ ├── singleImage.spi │ │ ├── singleImage.tif │ │ ├── singleImage_swap.spi │ │ ├── smallStack.hed │ │ ├── smallStack.img │ │ ├── smallStack.mrcs │ │ ├── smallStack.stk │ │ ├── smallVolume.vol │ │ ├── smallVolumeStack.stk │ │ ├── smallVolumeStackCorrupted.stk │ │ ├── sum.spi │ │ ├── test2.spi │ │ ├── test2_wrap_false.spi │ │ └── test2_wrap_true.spi │ │ ├── metadata │ │ ├── ReadWriteAppendBlock.xmd │ │ ├── WriteIntermediateBlock.xmd │ │ ├── WriteIntermediateBlock2.xmd │ │ ├── mDsource.sqlite │ │ ├── mDsource.xmd │ │ ├── mDsource.xml │ │ ├── noXmipp.xmd │ │ ├── smallStack.stk │ │ └── symop.star │ │ ├── polynomials │ │ └── down1_42_Periodogramavg.psd │ │ ├── pythoninterface │ │ ├── Bsoft │ │ │ └── symop.star │ │ ├── importObject.xmd │ │ ├── progVol.vol │ │ ├── singleImage.spi │ │ ├── smallStack.stk │ │ ├── sum.spi │ │ ├── test.xmd │ │ ├── testBlock.xmd │ │ ├── test_row.xmd │ │ ├── tinyImage.spi │ │ └── tinyRotated.spi │ │ └── sampling │ │ ├── experimental_images.xmd │ │ ├── neigh_ref_c1_exp_sampling.xmd │ │ ├── neigh_ref_i3h_exp_sampling.xmd │ │ ├── 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