Documented functions with links to source¶
Program to iteratively refine multiple 3D structures of helical specimens competitively from segment stacks
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class
segmultirefine3d.SegMultiRefine3dPar[source]¶ Class to initiate default dictionary with input parameters including help and range values and status dictionary
Methods
add_custom_refinement_strategy_as_relative
define_input_output_segmentrefine3d
define_parameters_and_their_properties
define_program_states
define_segmentrefine3d_parameters
get_angular_restraint_title
get_restraint_phrase
get_translation_range_phrase
get_translational_range_title
remove_key_from_feature_set
set_3dctf_correction_intensity_option
set_3dctf_correction_option
set_amp_corr_out_of_plane_range
set_bin_cutff_enforce_pitch_even_phi
set_choose_out_of_plane_amp_corr
set_enforce_even_phi_distribution
set_enforce_pitch_even_phi
set_frame_averaging_size
set_frame_motion_correction
set_fsc_based_filter_option
set_halfset_refinement_option
set_halfset_start
set_helical_continuity_option
set_helical_symmetries
set_helical_symmetry_parameters
set_high_resolution_aim
set_high_resolution_angular_restraint
set_high_resolution_trans_range
set_image_size_to_be_aligned
set_inp_refinement_stack
set_iteration_count
set_local_averaging_size
set_low_resolution_aim
set_low_resolution_angular_restraint
set_low_resolution_trans_range
set_max_resolution_trans_range
set_maximum_resolution_aim
set_maximum_resolution_angular_restraint
set_medium_resolution_aim
set_medium_resolution_angular_restraint
set_medium_resolution_trans_range
set_polar_apolar_helix_choices
set_reference_volume
set_reference_volume_option
set_refine_helical_symmetry
set_refinement_strategy
set_refinement_strategy_options
set_relatives_and_level
set_release_cycle_even_phi
set_resolution_aim_choice
set_rotational_symmetries
set_volume_prefix_refined_structure
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class
segmultirefine3d.SegMultiRefine3d(parset=None)[source]¶ Methods
average_shifts_between_frames_along_helix(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
combine_determined_parameters_to_final_five(…)Function to convert (in-plane rotation and shifts) to (shifts and rotation) if mirror parameters have been found, adjust Euler angles
compute_Fourier_radius(res_cutoff, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_alignment_and_reconstruction_size_in_pixels(…)# values for fast boxsizes from http://blake.bcm.edu/emanwiki/EMAN2/BoxSize >>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d >>> s = SegmentRefine3d() >>> s.compute_alignment_and_reconstruction_size_in_pixels(200, 1.408, 100, 1.0) (220, 168) >>> s.compute_alignment_and_reconstruction_size_in_pixels(200, 1.408, 300, 1.0) (352, 352)
compute_corresponding_tilts_from_Fourier_pixel_series(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_optimum_phi_and_index_closest_to_one_of_prj_phis(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_prj_size_from_max_out_of_plane_tilt_and_diameter(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_rec_size_for_helix(helixwidth, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_Euler_angles_from_mirrored_sparx(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_Euler_angles_to_mirrored_sparx(phi, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_Fouier_pixel_to_reciprocal_Angstrom(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_reciprocal_Angstrom_to_Fourier_pixel_position_in_power_spectrum(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
define_series_of_search_steps(pixelsize, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_mean_angle(out_of_plane_angles)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_percent_amplitude_for_Wiener_filter_constant(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_predominant_side_of_angles(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_res_ranges_and_binfactors_to_be_used(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_upper_and_lower_bound_from_central_frame_id(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
distribute_segment_ids_into_two_halves_based_on_helices(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
extrapolate_second_order_to_end_of_box(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
filter_angle_ids_according_to_search_restraint(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
filter_phis_such_that_distribution_remains_even(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
find_inplane_to_match(phiA, thetaA, phiB, thetaB)Find the z rotation such that ZA RA is as close as possible to RB this maximizes trace of ( RB^T ZA RA) = trace(ZA RA RB^T)
generate_Euler_angles_for_projection(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_file_name_with_apix(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_phis_evenly_across_asymmetric_unit_and_distribute_over_360(…)Function contributed by Ambroise Desfosses (May 2012)
generate_refinement_grid_to_be_evaluated(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_refinement_grid_to_be_evaluated_fixed_inc(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_thetas_evenly_dependent_on_cos_of_out_of_plane_angle(thetas)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_aim_dict()>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_and_distribute_total_iteration_count(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_azimuthal_angles_from_prj_params(…[, …])>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_closest_projection_from_projection_list(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_frame_id_from_mic_stack_file(segment_mic)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_maximum_pixel_displacement_by_inplane_rotation_at_edge(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_out_of_plane_angles_from_prj_params(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_resolution_closest_to_value(value, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_sizes_that_increase_by_percent(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_symmetry_views_count_from_stepsize(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
index_coords(data[, origin])Creates x & y coords for the indicies in a numpy array ‘data’.
log_processing_statistics(resolution, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
make_angles_centered_around_phi_and_continuous(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
make_five_xticks_from_all_helix_ids(helix_ids)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
match_each_image_against_all_projections_with_delta_in_plane_restraint(…)Updated Util.multiref_polar_ali_2d_delta(currimg, [polarrefs], [txrng], [tyrng], ringstep, mode, alignrings, halfdim, halfdim, 0.0, delta_psi) 2020-12-11: 1.
normalize_inplane_angles_by_picked_angles(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
plot_polar_image(data[, origin])Plots an image reprojected into polar coordinates with the origin at ‘origin’ (a tuple of (x0, y0), defaults to the center of the image)
randomize_phi_and_corresponding_helix_y_shift_based_to_pitch(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
reduce_y_shifts_and_phis_to_half_stepsize(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
reformat_ticklabels_according_to_image_plot(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
reproject_image_into_polar(data[, origin])Reprojects a 3D numpy array (‘data’) into a polar coordinate system.
rescale_freq_filter_columns(ori_pixelsize, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
select_reference_rings_according_to_angular_restraints(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
sort_data_and_discard_duplicates(x, y)sort_inplane_angles_into_0_360_or_180_degrees(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
update_image_list_after_file_transfer(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
volume_decimate(vol[, decimation, …])Window 3D volume to FFT-friendly size, apply Butterworth low pass filter, and decimate image by integer factor cs: adapted from image_decimate (fundamentals)
add_color_bar_according_to_array
add_iter_id_to_prefix
add_model_id_to_prefix
add_tempdir_directory_to_filename
adjust_volume_dimension_by_padding_or_windowing
apply_inplane_blurring_to_set_of_power_spectra
apply_orientation_parameters_and_reconstruct_imposing_helical_symmetry
apply_square_root_fsc_filter_to_coefficients
assemble_image_plane
assert_at_least_view_count_of_100_for_3dreconstruction
assert_segment_count_on_stack_equals_that_in_database
average_and_summarize_results_of_ang_error_estimation
average_and_summarize_results_of_error_esimation
bin_including_copies_of_frames_if_requested
blur_ideal_power_spectrum_by_even_out_of_plane_variation
build_3d_layer_line_mask_half_as_wide_as_high
build_smooth_mask_with_top_and_bottom_cut
build_structural_mask_from_volume
cart2polar
check_entry_count_for_segmultirefine3d
check_helical_rise_and_segmentation_step
check_sanity_of_input_parameters
check_wether_search_restraints_make_sense_in_multi_model_refinement_and_half_set_refinement
check_whether_adjacent_values_are_closer_to_cutoff_value
check_whether_ref_db_has_fewer_segment_entries_than_requested_in_case_of_continued_refinement
check_whether_search_restraints_and_refinement_option_are_correctly_set
check_whether_search_restraints_are_correctly_set_for_half_set_refinement
choose_reconstruction_stack_based_on_unbending
clean_up_temporary_large_stack
cleanup_of_prj_stacks
collect_prj_params_and_update_reference_info
compute_3dreconstruction_by_Fourier_interpolation
compute_3dreconstruction_by_SIRT
compute_alignment_size_in_pixels
compute_amp_corr_for_different_symmetry_combinations
compute_angular_blur_based_on_Crowther_criterion
compute_bin_count_from_quantity_and_step
compute_cross_fsc_and_write_out_merged_volume
compute_distance
compute_fit_if_more_than_three_datapoints
compute_fitted_parameters
compute_forward_difference_for_selected_segments_and_select
compute_fsc_of_cylinder_masked_reconstruction_halves
compute_fsc_of_layer_line_filtered_reconstruction_halves
compute_fsc_of_raw_reconstruction_halves
compute_fsc_of_structure_masked_reconstruction_halves
compute_fsc_on_volumes_from_half_the_dataset
compute_helical_autocorrelation_map
compute_resolution_ranges_for_binseries
compute_shift_error_from_cc_map
convert_coarse_into_fine_parameters
convert_list_of_projection_parameters_to_prj_tuples
copy_image_stack_to_new_stack
copy_image_stack_to_new_stack_shutil
copy_out_angular_series
copy_ref_db_to_tempdir
copy_spring_db_to_tempdir
define_alignment_parameters
define_all_segmentrefine3d_parameters
define_filter_parameters
define_helical_symmetry_parameters
define_input_output_iteration
define_mpi_parameters
define_original_input_values_before_binning
define_reconstruction_parameters
define_refinement_strategy_options
define_selection_parameters
determine_Fourier_pixel_position_of_highest_resolution_layer_line
determine_angular_error
determine_forward_difference_and_set_ref_segments
determine_whether_is_last_cycle
distribute_x_and_y_ticks_evenly_along_montage
enforce_even_phi_distribution
enter_additional_ref_parameters_in_database
enter_asymmetric_unit_parameters_in_database
enter_cycle_criteria_in_database
enter_excluded_refinement_counts_in_database
enter_final_ids_into_database
enter_fsc_values_in_database
enter_helix_inplane_parameters_in_database
enter_orientation_parameters
enter_refinement_parameters_in_database
enter_results_to_segments
enter_selected_information
estimate_required_tmp_disk_space
evaluate_alignment_parameters_and_summarize_in_plot
evaluate_azimuthal_angles
evaluate_in_plane_rotation_angles
evaluate_out_of_plane_tilt_angles
evaluate_shifts_perpendicular_to_helix_axis
exclude_inplane_angles_outside_delta_psi
fill_in_excluded_quantities_by_interpolation
filter_and_mask_reference_volume
filter_layer_lines_if_demanded
filter_projections_using_provided_layer_line_filters
filter_refined_segments_by_property
filter_segments_by_ccc_against_projections
filter_segments_by_out_of_plane_tilt
filter_segments_when_located_at_end_of_helix
filter_volume_by_fourier_filter_while_padding
finalize_figure_with_gallery
find_maximum_cross_correlation_for_local_in_plane_angle
finish_Fourier_interpolation_reconstruction
generate_and_apply_layerline_filter
generate_binary_layer_line_filter_for_different_out_of_plane_tilt_angles
generate_binary_layer_line_filters_including_angular_blur
generate_cc_maps_and_aligned_segments
generate_diagnostics_reprojection_file_name
generate_diagnostics_statistics_file_name
generate_experimental_sum_of_powerspectra
generate_histogram_of_angular_distribution
generate_long_helix_volume
generate_nice_gallery_of_ten_images_corresponding_projections
generate_power_spectrum_average_by_inplane_angle_blurring
generate_projection_stack
generate_reconstruction_name_with_Angstrom_per_pixel_and_set_header
generate_sim_power_from_reconstruction
generate_simulated_power_from_latest_reconstruction
generate_structure_with_phases_randomized
get_all_distances_and_selection_mask_from_ref_segments
get_all_helices_from_last_refinement_cycle
get_all_segments_from_refinement_cycle
get_all_selected_stack_ids
get_avg_helix_shift_x_and_y_and_avg_inplane_angles
get_azimuthal_angles_from_projection_parameters
get_closest_binfactors
get_cut_coordinates_named_tuple
get_distances_from_segment_ids
get_error_estimates_for_inplane_rotation
get_error_estimates_from_angles
get_error_estimates_from_cc_maps
get_excluded_refinement_count
get_exluded_ref_count_named_tuple
get_frame_stack_path
get_fsc_cutoff_and_mask
get_helically_related_parameters_for_first_refinement_cycle
get_helices_coordinates_required_for_unbending_from_database
get_helices_from_corresponding_frames
get_helix_coordinates_named_tuple
get_inplane_angles_per_segment_and_interpolate_two_oposite_angles
get_inplane_rotation_and_x_and_y_shifts_from_segment_entry
get_last_cycle_from_refinement_database
get_last_cycle_id_from_refinement_database
get_masking_parameters
get_maximum_correlation_symmetry_pair
get_mean_out_of_plane_angle
get_original_image_list
get_padsize_and_unique_tilts
get_picked_segment_coordinates
get_plot_parameters_from_last_cycle
get_polarity_ratios_per_helix
get_prj_named_tuple
get_prj_params_named_tuple
get_prj_stack_name_with_ending
get_ref_file_name
get_ref_session_and_last_cycle
get_refined_parameters_for_advanced_stages_of_refinement
get_restraint_tuple
get_segment_closest_to_given_phi
get_segment_helix_count_and_length_from_spring_db
get_segment_ids_from_helix
get_segment_size
get_segments_from_helix
get_selected_alignment_parameters_from_last_cycle
get_selected_segments_from_last_cycle
get_selected_segments_from_last_refinement_cycle
get_x_and_y_shifts_perpendicular_to_helix_from_penultimate_cycle
get_zero_parameters_for_initial_stages_of_refinement
give_name_and_write_out_reference
if_no_selected_images_left_abort_refinement
launch_3dreconstruction_by_SIRT
log_helical_error
make_experimental_and_simulated_power_spectra_figure
make_fsc_line_named_tuple
make_named_tuple_of_masking_parameters
make_named_tuple_of_orientation_parameters
make_pixel_info_named_tuple
make_reference_info_named_tuple
make_series_info_named_tuple
make_unbending_named_tuple
map_new_coordinates
mask_and_window_and_unbend_if_required
measure_inplane_angle_and_decide_for_predominant_angle
merge_list_of_helical_errors
merge_model_ids_into_presplit_state
merge_prj_ref_stacks_into_single_prj_stack
montage_reprojections_to_image_according_to_given_shape
move_ticks_to_correct_location
normalize_and_scale_volumes_including_mask_and_compute_fsc
package_parameters_and_stack_name_into_prj_info
perform_coarse_and_fine_projection_matching
perform_ctf_correction_and_volume_symmetrization
perform_ctf_correction_on_volume
perform_fit_of_gaussian
perform_helix_based_computations_and_selection
perform_iterative_projection_matching_and_3d_reconstruction
perform_local_averaging_across_frames
perform_local_frame_averaging_and_ref_database_update
perform_local_symmetry_refinement_based_on_power_spectra_matching
perform_mean_ccc_evaluation_of_images_with_symmetry_related_projections
perform_volume_operations_ctf_and_symmetrization
plot_excluded_criteria_as_bar_plot
plot_forward_difference_x_shift
plot_fsc_lines
plot_x_and_yshifts_in_scattered
polar2cart
pre_cycle_setup
precycle_setup_before_binning
prepare_3dctf_avg_squared
prepare_average_from_maximum_of_20_images
prepare_binary_layer_line_filters_if_layer_line_filtering_demanded
prepare_databases_for_selection
prepare_empty_helical_error
prepare_gallery_figure
prepare_helical_reconstruction_using_Fourier_interpolation
prepare_local_symmetry_refinement
prepare_previous_parameters_either_from_inplane_angle_or_from_previous_cycle
prepare_projection_images_and_cc_maps_on_diagnostic_stack
prepare_reference_files_for_halfset_refinement
prepare_reference_rings_from_projections
prepare_reference_volumes
prepare_refined_alignment_parameters_from_database
prepare_segment_for_alignment
prepare_unique_updated_stack_name
prepare_upper_part_of_figure
prepare_volume_for_projection_by_masking_and_thresholding
print_fsc_to_diagnostic_plot
project_including_masking_and_filtering
project_through_reference_volume_in_helical_perspectives
randomize_quant_beyond_circle
read_large_segment_average_if_running_avg_frames_requested
reconstruct_volume
refine_each_image_against_projections_including_delta_inplane_restraint
refine_local_inplane_angle
remove_frames_if_running_avg_frames_requested
remove_intermediate_files_if_desired
remove_projection_stacks_and_copy_out_azimuthal_and_out_of_plane_series
reproject_polar_into_image
reproject_volume_into_cylinder
rescale_custom_filter_file
rescale_reference_volume_in_case_vol_pixelsize_differs_from_current_pixelsize
round_grid_value_tuples_to_readable_number_of_digits
select_refinement_parameters_based_on_selection_criteria_hierarchically
select_segments_based_on_in_plane_rotation
select_segments_based_on_out_of_plane_tilt
select_segments_based_on_specified_criteria
set_euler_angles_to_reference_rings
set_res_expectation
setup_dummies_for_iteration
setup_new_refinement_db_for_each_cycle
setup_parameter_containers
setup_statistics_plot_layout
setup_summary_figure
sort_and_enter_averaged_shifts
split_ref_ids_according_to_even_and_odd_helices
summarize_each_bin_round_with_simulated_vs_experimental_images_and_powerspectra
symmetrize_long_volume_in_steps
symmetrize_volume
unbend_window_and_mask_input_stack
update_average_helix_shift_x_per_helix
update_average_in_plane_rotation_angle_per_helix
update_average_out_of_plane_per_helix
update_highest_fsc_database
update_persistence_length_in_spring_db
update_pixelinfo_based_on_different_helical_symmetries
update_reference_info
update_segment_subunits_database_with_final_refinement_parameters
update_total_nonorientation_counts_in_ref_db
visualize_in_plane_rotation_angles
window_and_mask_input_stack
write_out_file_of_fsc_lines
write_out_fsc_line
write_out_reconstruction_and_remove_reference
write_out_reference_and_get_prj_prefix_depending_on_number_of_models
write_out_reference_volume
-
class
segmultirefine3d_mpi.SegMultiRefine3dMpi(parset=None)[source]¶ Methods
average_shifts_between_frames_along_helix(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
combine_determined_parameters_to_final_five(…)Function to convert (in-plane rotation and shifts) to (shifts and rotation) if mirror parameters have been found, adjust Euler angles
compute_Fourier_radius(res_cutoff, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_alignment_and_reconstruction_size_in_pixels(…)# values for fast boxsizes from http://blake.bcm.edu/emanwiki/EMAN2/BoxSize >>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d >>> s = SegmentRefine3d() >>> s.compute_alignment_and_reconstruction_size_in_pixels(200, 1.408, 100, 1.0) (220, 168) >>> s.compute_alignment_and_reconstruction_size_in_pixels(200, 1.408, 300, 1.0) (352, 352)
compute_corresponding_tilts_from_Fourier_pixel_series(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_optimum_phi_and_index_closest_to_one_of_prj_phis(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_prj_size_from_max_out_of_plane_tilt_and_diameter(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
compute_rec_size_for_helix(helixwidth, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_Euler_angles_from_mirrored_sparx(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_Euler_angles_to_mirrored_sparx(phi, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_Fouier_pixel_to_reciprocal_Angstrom(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
convert_reciprocal_Angstrom_to_Fourier_pixel_position_in_power_spectrum(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
define_series_of_search_steps(pixelsize, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_mean_angle(out_of_plane_angles)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_percent_amplitude_for_Wiener_filter_constant(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_predominant_side_of_angles(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_res_ranges_and_binfactors_to_be_used(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
determine_upper_and_lower_bound_from_central_frame_id(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
distribute_segment_ids_into_two_halves_based_on_helices(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
extrapolate_second_order_to_end_of_box(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
filter_angle_ids_according_to_search_restraint(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
filter_phis_such_that_distribution_remains_even(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
find_inplane_to_match(phiA, thetaA, phiB, thetaB)Find the z rotation such that ZA RA is as close as possible to RB this maximizes trace of ( RB^T ZA RA) = trace(ZA RA RB^T)
generate_Euler_angles_for_projection(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_file_name_with_apix(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_phis_evenly_across_asymmetric_unit_and_distribute_over_360(…)Function contributed by Ambroise Desfosses (May 2012)
generate_refinement_grid_to_be_evaluated(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_refinement_grid_to_be_evaluated_fixed_inc(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
generate_thetas_evenly_dependent_on_cos_of_out_of_plane_angle(thetas)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_aim_dict()>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_and_distribute_total_iteration_count(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_azimuthal_angles_from_prj_params(…[, …])>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_closest_projection_from_projection_list(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_even_reconstruction_files(rec_files)>>> from spring.segment3d.refine.sr3d_mpi import SegmentRefine3dMpi
get_first_half_reconstruction_files(rec_files)>>> from spring.segment3d.refine.sr3d_mpi import SegmentRefine3dMpi
get_frame_id_from_mic_stack_file(segment_mic)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_maximum_pixel_displacement_by_inplane_rotation_at_edge(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_odd_reconstruction_files(rec_files)>>> from spring.segment3d.refine.sr3d_mpi import SegmentRefine3dMpi
get_out_of_plane_angles_from_prj_params(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_resolution_closest_to_value(value, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_second_half_reconstruction_files(rec_files)>>> from spring.segment3d.refine.sr3d_mpi import SegmentRefine3dMpi
get_sizes_that_increase_by_percent(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
get_symmetry_views_count_from_stepsize(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
index_coords(data[, origin])Creates x & y coords for the indicies in a numpy array ‘data’.
log_processing_statistics(resolution, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
make_angles_centered_around_phi_and_continuous(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
make_five_xticks_from_all_helix_ids(helix_ids)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
match_each_image_against_all_projections_with_delta_in_plane_restraint(…)Updated Util.multiref_polar_ali_2d_delta(currimg, [polarrefs], [txrng], [tyrng], ringstep, mode, alignrings, halfdim, halfdim, 0.0, delta_psi) 2020-12-11: 1.
normalize_inplane_angles_by_picked_angles(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
plot_polar_image(data[, origin])Plots an image reprojected into polar coordinates with the origin at ‘origin’ (a tuple of (x0, y0), defaults to the center of the image)
randomize_phi_and_corresponding_helix_y_shift_based_to_pitch(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
reduce_y_shifts_and_phis_to_half_stepsize(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
reformat_ticklabels_according_to_image_plot(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
reproject_image_into_polar(data[, origin])Reprojects a 3D numpy array (‘data’) into a polar coordinate system.
rescale_freq_filter_columns(ori_pixelsize, …)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
select_reference_rings_according_to_angular_restraints(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
sort_data_and_discard_duplicates(x, y)sort_inplane_angles_into_0_360_or_180_degrees(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
update_image_list_after_file_transfer(…)>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
volume_decimate(vol[, decimation, …])Window 3D volume to FFT-friendly size, apply Butterworth low pass filter, and decimate image by integer factor cs: adapted from image_decimate (fundamentals)
add_color_bar_according_to_array
add_iter_id_to_prefix
add_model_id_to_prefix
add_tempdir_directory_to_filename
adjust_volume_dimension_by_padding_or_windowing
apply_inplane_blurring_to_set_of_power_spectra
apply_orientation_parameters_and_reconstruct_imposing_helical_symmetry
apply_square_root_fsc_filter_to_coefficients
assemble_image_plane
assert_at_least_view_count_of_100_for_3dreconstruction
assert_segment_count_on_stack_equals_that_in_database
average_and_summarize_results_of_ang_error_estimation
average_and_summarize_results_of_error_esimation
bin_including_copies_of_frames_if_requested
blur_ideal_power_spectrum_by_even_out_of_plane_variation
build_3d_layer_line_mask_half_as_wide_as_high
build_smooth_mask_with_top_and_bottom_cut
build_structural_mask_from_volume
cart2polar
check_entry_count_for_segmultirefine3d
check_for_each_node_wether_sufficient_temporary_disk_space_available
check_helical_rise_and_segmentation_step
check_sanity_of_input_parameters
check_wether_search_restraints_make_sense_in_multi_model_refinement_and_half_set_refinement
check_whether_adjacent_values_are_closer_to_cutoff_value
check_whether_ref_db_has_fewer_segment_entries_than_requested_in_case_of_continued_refinement
check_whether_search_restraints_and_refinement_option_are_correctly_set
check_whether_search_restraints_are_correctly_set_for_half_set_refinement
choose_reconstruction_stack_based_on_unbending
clean_up_temporary_large_stack
cleanup_of_prj_stacks
collect_and_avearge_helical_error
collect_prj_params_and_update_reference_info
collect_selected_images_from_large_binned_stack_to_common_disk
compute_3dreconstruction_by_Fourier_interpolation
compute_3dreconstruction_by_SIRT
compute_alignment_size_in_pixels
compute_amp_corr_for_different_symmetry_combinations
compute_angular_blur_based_on_Crowther_criterion
compute_bin_count_from_quantity_and_step
compute_cross_fsc_and_write_out_merged_volume
compute_distance
compute_fit_if_more_than_three_datapoints
compute_fitted_parameters
compute_forward_difference_for_selected_segments_and_select
compute_fsc_of_cylinder_masked_reconstruction_halves
compute_fsc_of_layer_line_filtered_reconstruction_halves
compute_fsc_of_raw_reconstruction_halves
compute_fsc_of_structure_masked_reconstruction_halves
compute_fsc_on_volumes_from_half_the_dataset
compute_helical_autocorrelation_map
compute_resolution_ranges_for_binseries
compute_shift_error_from_cc_map
convert_coarse_into_fine_parameters
convert_list_of_projection_parameters_to_prj_tuples
copy_image_stack_to_new_stack
copy_image_stack_to_new_stack_shutil
copy_one_entry_from_one_session_to_local_session_by_id
copy_out_angular_series
copy_ref_db_to_tempdir
copy_spring_db_to_tempdir
copy_stack_from_to
create_new_spring_db_with_specified_ids
define_alignment_parameters
define_all_segmentrefine3d_parameters
define_filter_parameters
define_helical_symmetry_parameters
define_input_output_iteration
define_mpi_parameters
define_original_input_values_before_binning
define_reconstruction_parameters
define_refinement_strategy_options
define_selection_parameters
determine_Fourier_pixel_position_of_highest_resolution_layer_line
determine_angular_error
determine_forward_difference_and_set_ref_segments
determine_whether_is_last_cycle
distribute_x_and_y_ticks_evenly_along_montage
enforce_even_phi_distribution
enter_additional_ref_parameters_in_database
enter_asymmetric_unit_parameters_in_database
enter_cycle_criteria_in_database
enter_excluded_refinement_counts_in_database
enter_final_ids_into_database
enter_fsc_values_in_database
enter_helix_inplane_parameters_in_database
enter_orientation_parameters
enter_refinement_parameters_in_database
enter_results_to_segments
enter_selected_information
estimate_required_tmp_disk_space
evaluate_alignment_parameters_and_summarize_in_plot
evaluate_azimuthal_angles
evaluate_in_plane_rotation_angles
evaluate_out_of_plane_tilt_angles
evaluate_shifts_perpendicular_to_helix_axis
exclude_inplane_angles_outside_delta_psi
fill_in_excluded_quantities_by_interpolation
filter_and_mask_reference_volume
filter_layer_lines_if_demanded
filter_projections_using_provided_layer_line_filters
filter_refined_segments_by_property
filter_segments_by_ccc_against_projections
filter_segments_by_out_of_plane_tilt
filter_segments_when_located_at_end_of_helix
filter_volume_by_fourier_filter_while_padding
finalize_figure_with_gallery
find_maximum_cross_correlation_for_local_in_plane_angle
finish_Fourier_interpolation_reconstruction
gather_images_from_distributed_stacks_or_add_blank
gather_reconstructions_from_nodes_compute_fsc_lines
generate_and_apply_layerline_filter
generate_binary_layer_line_filter_for_different_out_of_plane_tilt_angles
generate_binary_layer_line_filters_including_angular_blur
generate_cc_maps_and_aligned_segments
generate_diagnostics_reprojection_file_name
generate_diagnostics_statistics_file_name
generate_experimental_sum_of_powerspectra
generate_experimental_sum_of_powerspectra_mpi
generate_histogram_of_angular_distribution
generate_long_helix_volume
generate_nice_gallery_of_ten_images_corresponding_projections
generate_power_spectrum_average_by_inplane_angle_blurring
generate_projection_stack
generate_projection_stack_mpi
generate_reconstruction_name_with_Angstrom_per_pixel_and_set_header
generate_sim_power_from_reconstruction
generate_simulated_power_from_latest_reconstruction
generate_structure_with_phases_randomized
get_all_distances_and_selection_mask_from_ref_segments
get_all_helices_from_last_refinement_cycle
get_all_segments_from_refinement_cycle
get_all_selected_stack_ids
get_avg_helix_shift_x_and_y_and_avg_inplane_angles
get_azimuthal_angles_from_projection_parameters
get_closest_binfactors
get_cut_coordinates_named_tuple
get_distances_from_segment_ids
get_error_estimates_for_inplane_rotation
get_error_estimates_from_angles
get_error_estimates_from_cc_maps
get_excluded_refinement_count
get_exluded_ref_count_named_tuple
get_frame_stack_path
get_fsc_cutoff_and_mask
get_helically_related_parameters_for_first_refinement_cycle
get_helices_coordinates_required_for_unbending_from_database
get_helices_from_corresponding_frames
get_helix_coordinates_named_tuple
get_inplane_angles_per_segment_and_interpolate_two_oposite_angles
get_inplane_rotation_and_x_and_y_shifts_from_segment_entry
get_last_cycle_from_refinement_database
get_last_cycle_id_from_refinement_database
get_masking_parameters
get_maximum_correlation_symmetry_pair
get_mean_out_of_plane_angle
get_mean_out_of_plane_angle_mpi
get_original_image_list
get_padsize_and_unique_tilts
get_picked_segment_coordinates
get_plot_parameters_from_last_cycle
get_polarity_ratios_per_helix
get_prj_named_tuple
get_prj_params_named_tuple
get_prj_stack_name_with_ending
get_ref_file_name
get_ref_session_and_last_cycle
get_refined_parameters_for_advanced_stages_of_refinement
get_restraint_tuple
get_segment_closest_to_given_phi
get_segment_entries_closest_to_phi_on_rank0_and_broadcast_results
get_segment_helix_count_and_length_from_spring_db
get_segment_ids_from_helix
get_segment_size
get_segments_from_helix
get_selected_alignment_parameters_from_last_cycle
get_selected_segments_from_last_cycle
get_selected_segments_from_last_refinement_cycle
get_x_and_y_shifts_perpendicular_to_helix_from_penultimate_cycle
get_zero_parameters_for_initial_stages_of_refinement
give_name_and_write_out_reference
if_no_selected_images_left_abort_refinement
launch_3dreconstruction_by_SIRT
log_helical_error
make_experimental_and_simulated_power_spectra_figure
make_fsc_line_named_tuple
make_named_tuple_of_masking_parameters
make_named_tuple_of_orientation_parameters
make_pixel_info_named_tuple
make_reference_info_named_tuple
make_series_info_named_tuple
make_unbending_named_tuple
map_new_coordinates
mask_and_window_and_unbend_if_required
mask_and_window_and_unbend_if_required_mpi
measure_inplane_angle_and_decide_for_predominant_angle
merge_and_reduce_local_entries_from_refinement_cycle_table
merge_list_of_helical_errors
merge_local_db_into_global_databases
merge_local_db_table_entries_to_single_db
merge_local_entries_from_refinement_segment_and_refinement_helix_table
merge_local_entries_from_spring_db
merge_model_ids_into_presplit_state
merge_prj_ref_stacks_into_single_prj_stack
montage_reprojections_to_image_according_to_given_shape
move_ticks_to_correct_location
normalize_and_scale_volumes_including_mask_and_compute_fsc
package_parameters_and_stack_name_into_prj_info
perform_binning_mpi
perform_coarse_and_fine_projection_matching
perform_ctf_correction_and_volume_symmetrization
perform_ctf_correction_on_volume
perform_fit_of_gaussian
perform_helix_based_computations_and_selection
perform_iterative_projection_matching_and_3d_reconstruction
perform_local_averaging_across_frames
perform_local_frame_averaging_and_ref_database_update
perform_local_frame_averaging_and_ref_database_update_mpi
perform_local_symmetry_refinement_based_on_power_spectra_matching
perform_local_symmetry_refinement_based_on_power_spectra_matching_mpi
perform_mean_ccc_evaluation_of_images_with_symmetry_related_projections
perform_volume_operations_ctf_and_symmetrization
plot_excluded_criteria_as_bar_plot
plot_forward_difference_x_shift
plot_fsc_lines
plot_x_and_yshifts_in_scattered
polar2cart
post_processing_of_reconstruct_mpi
pre_cycle_setup
precycle_setup_before_binning
prepare_3dctf_avg_squared
prepare_average_from_maximum_of_20_images
prepare_binary_layer_line_filters_if_layer_line_filtering_demanded
prepare_databases_for_selection
prepare_empty_helical_error
prepare_gallery_figure
prepare_helical_reconstruction_using_Fourier_interpolation
prepare_local_symmetry_refinement
prepare_pre_cycle_setup_mpi
prepare_previous_parameters_either_from_inplane_angle_or_from_previous_cycle
prepare_projection_images_and_cc_maps_on_diagnostic_stack
prepare_reference_files_for_halfset_refinement
prepare_reference_rings_from_projections
prepare_reference_volumes
prepare_refined_alignment_parameters_from_database
prepare_segment_for_alignment
prepare_unique_updated_stack_name
prepare_upper_part_of_figure
prepare_volume_for_projection_by_masking_and_thresholding
print_fsc_to_diagnostic_plot
project_including_masking_and_filtering
project_including_masking_and_filtering_mpi
project_through_reference_volume_in_helical_perspectives
randomize_quant_beyond_circle
read_large_segment_average_if_running_avg_frames_requested
reconstruct_partial_volumes_on_distributed_nodes
reconstruct_volume
reconstruct_volume_mpi
refine_each_image_against_projections_including_delta_inplane_restraint
refine_local_inplane_angle
remove_frames_if_running_avg_frames_requested
remove_intermediate_files_if_desired
remove_projection_stacks_and_copy_out_azimuthal_and_out_of_plane_series
reproject_polar_into_image
reproject_volume_into_cylinder
rescale_custom_filter_file
rescale_reference_volume_in_case_vol_pixelsize_differs_from_current_pixelsize
round_grid_value_tuples_to_readable_number_of_digits
select_refinement_parameters_based_on_selection_criteria_hierarchically
select_segment_ids_and_corresponding_helices_from_spring_db
select_segments_based_on_in_plane_rotation
select_segments_based_on_out_of_plane_tilt
select_segments_based_on_specified_criteria
select_segments_based_on_specified_criteria_mpi
set_euler_angles_to_reference_rings
set_res_expectation
setup_dummies_for_iteration
setup_new_refinement_db_for_each_cycle
setup_parameter_containers
setup_statistics_plot_layout
setup_summary_figure
sort_and_enter_averaged_shifts
split_ref_ids_according_to_even_and_odd_helices
split_refinement_db_according_to_seg_ids
split_spring_db_according_to_helix_entities_to_local_db
summarize_each_bin_round_with_simulated_vs_experimental_images_and_powerspectra
summarize_each_bin_round_with_simulated_vs_experimental_images_and_powerspectra_mpi
symmetrize_long_volume_in_steps
symmetrize_volume
transfer_records_from_local_table_to_global
unbend_window_and_mask_input_stack
update_average_helix_shift_x_per_helix
update_average_in_plane_rotation_angle_per_helix
update_average_out_of_plane_per_helix
update_highest_fsc_database
update_persistence_length_in_spring_db
update_pixelinfo_based_on_different_helical_symmetries
update_reference_info
update_segment_subunits_database_with_final_refinement_parameters
update_total_nonorientation_counts_in_ref_db
visualize_in_plane_rotation_angles
window_and_mask_input_stack
write_out_file_of_fsc_lines
write_out_fsc_line
write_out_reconstruction_and_remove_reference
write_out_reconstruction_on_rank0
write_out_reference_and_get_prj_prefix_depending_on_number_of_models
write_out_reference_volume