Documented functions with links to source¶

Program to optimize segmentrefine3d reconstruction by varying refinement parameters systematically on a grid

class segrefine3dgrid.SegRefine3dGridPar[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_parameters_to_be_varied
get_restraint_phrase
get_translation_range_phrase
get_translational_range_title
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_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_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_volume_prefix_refined_structure

define_parameters_and_their_properties()[source]¶

define_program_states()[source]¶

get_parameters_to_be_varied()[source]¶

class segrefine3dgrid.SegRefine3dGridSetup(parset=None)[source]¶

Methods

`add_grid_point_to_parameter_dictionary`(…)	>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
`extrapolate_second_order_to_end_of_box`(…)	>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
`generate_file_name_for_grid_search`(…)	>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
`sort_data_and_discard_duplicates`(x, y)	http://mail.scipy.org/pipermail/scipy-user/2011-February/028341.html

define_alignment_parameters
define_all_segmentrefine3d_parameters
define_filter_parameters
define_helical_symmetry_parameters
define_input_output_iteration
define_mpi_parameters
define_reconstruction_parameters
define_refinement_strategy_options
define_selection_parameters
fill_in_excluded_quantities_by_interpolation
generate_segmentrefine3d_parameters_while_removing_grid_parameters
get_all_helices_from_last_refinement_cycle
get_all_segments_from_refinement_cycle
get_avg_helix_shift_x_and_y_and_avg_inplane_angles
get_cut_coordinates_named_tuple
get_helices_coordinates_required_for_unbending_from_database
get_helix_coordinates_named_tuple
get_picked_segment_coordinates
get_ref_session_and_last_cycle
get_segment_ids_from_helix
get_segments_from_helix
make_unbending_named_tuple
prepare_unique_updated_stack_name
setup_alignment_related_parameters
setup_filter_related_parameters
setup_non_refinement_selection_criteria
setup_parameters_for_each_grid_point
setup_refinement_selection_criteria
setup_symmetry_related_parameters
unbend_window_and_mask_input_stack

generate_segmentrefine3d_parameters_while_removing_grid_parameters(parameters)[source]¶

setup_non_refinement_selection_criteria(each_grid_point, parameters, index, one_of_both_parameters)[source]¶

setup_refinement_selection_criteria(each_grid_point, parameters, index, one_of_both_parameters)[source]¶

setup_symmetry_related_parameters(each_grid_point, parameters, index, one_of_both_parameters)[source]¶

setup_alignment_related_parameters(each_grid_point, parameters, index, one_of_both_parameters)[source]¶

setup_filter_related_parameters(each_grid_point, parameters, index, one_of_both_parameters)[source]¶

add_grid_point_to_parameter_dictionary(first_param, second_param, each_grid_point, parameters)[source]¶

>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
>>> s = SegRefine3dGrid()
>>> r_p = 'helical_rise_or_pitch'
>>> params = SegRefine3dGridPar().parameters
>>> s.add_grid_point_to_parameter_dictionary('b-factor', r_p, [-111, 1.111], params) 
OrderedDict([('Image input stack refinement', 'protein_stack.hdf'), 
('Output volume name', 'recvol.hdf'), 
('First parameter', 'helical_rise_or_pitch'), ('Second parameter', 
'helical_rotation_or_number_of_units_per_turn'), 
('Lower and upper limit first parameter', (1.4, 1.9)), 
('Lower and upper limit second parameter', (22.0, 24.0)), 
('First and second parameter increment', (0.1, 0.3)), 
('Subgrid option', False), ('Part and number of subgrids', (1, 3)), 
('Grid continue option', False), ('Grid database', 'grid.db'), 
('Diagnostic plot prefix', 'diagnostic_plot.pdf'), 
('Number of iterations', 20), ('Reference structure option', False), 
('Reference volume', 'reference_vol.hdf'), ('spring.db file', 
'spring.db'), ('Continue refinement option', False), 
('refinement.db file', 'refinement.db'), ('Assemble refinement strategy', 
True), ('LR - Low resolution aim', True), 
('LR - azimuthal and out-of-plane search restraint in degrees', 
(180.0, 180.0)), ('LR - X and Y translation range in Angstrom', 
(50, 23)), ('MR - Medium resolution aim', True), 
('MR - azimuthal and out-of-plane search restraint in degrees', 
(180.0, 180.0)), ('MR - X and Y translation range in Angstrom', 
(21, 10)), ('HR - High resolution aim', True), 
('HR - azimuthal and out-of-plane search restraint in degrees', 
(20.0, 20.0)), ('HR - X and Y translation range in Angstrom', 
(14, 7)), ('MaxR - Maximum resolution aim', True), 
('MaxR - azimuthal and out-of-plane search restraint in degrees', 
(2.0, 2.0)), ('MaxR - X and Y translation range in Angstrom', 
(7, 3.5)), ('Absolute X and Y translation limit in Angstrom', 
(100, 100)), ('Frame motion correction', False), 
('Frame average window size', 3),  ('Frame local averaging distance', 700), 
('Independent half-set refinement', False), 
('Half-set refinement start', 'medium'), ('High-pass filter option', False), 
('Low-pass filter option', True), 
('High and low-pass filter cutoffs in 1/Angstrom', 
(0.001, 0.09)), ('B-Factor', -111), ('Custom filter option', 
False), ('Custom-built filter file', 'filter_function.dat'), 
('Automatic FSC filter', True), ('Filter layer-lines option', False), 
('Micrographs select option', False), ('Include or exclude micrographs', 
'include'), ('Micrographs list', '1-9, 11, 13'), ('Helices select option', 
False), ('Include or exclude helices', 'include'), ('Helices list', 
'1-9, 11, 13'), ('Segments select option', False), 
('Include or exclude segments', 'include'), ('Segment file', 
'stackid_file.dat'), ('Classes select option', False), 
('Include or exclude classes', 'include'), ('Class type', 'class_id'), 
('Classes list', '1-9, 11, 13'),  ('Persistence class option', False), 
('Persistence class length in Angstrom', 700), 
('Class occupancy threshold', 0.5), ('Straightness select option', False), 
('Include or exclude straight helices', 'include'), ('Persistence length range', 
(80, 100)), ('Layer line correlation select option', False), 
('Include or exclude segments based on layer-line correlation', 
'include'), ('Correlation layer line range', (60, 100)), 
('Defocus select option', False), ('Include or exclude defocus range', 
'include'), ('Defocus range', (10000, 40000)), 
('Astigmatism select option', False), 
('Include or exclude astigmatic segments', 'include'), 
('Astigmatism range', (0, 4000)), 
('Projection correlation select option', False), 
('Include or exclude segments based on projection correlation', 
'include'), ('Correlation projection range', (60, 100)), 
('Out-of-plane tilt select option', False), 
('Include or exclude out-of-plane tilted segments', 'include'), 
('Out-of-plane tilt range', (-5, 5)), 
('Shift normal to helix select option', False), 
('Include or exclude segments with shift normal to helix', 'include'), 
('Shift normal to helix in Angstrom', 5.0), ('Keep intermediate files', 
False), ('Estimated helix inner and outer diameter in Angstrom', (0, 190)), 
('Pixel size in Angstrom', 1.163), ('Symmetrize helix', True), 
('Helical rise/rotation or pitch/number of units per turn choice', 
'rise/rotation'), ('Enforce even phi option', False), 
('Release cycle even phi', 8), ('Pitch enforce even phi', 8.0), 
('Bin cutoff of phi angles', 100), 
('Helical symmetry in Angstrom or degrees', (1.111, 22.03)), 
('Rotational symmetry', 1), ('Helix polarity', 'polar'), 
('Unbending option', False), ('Force helical continuity', True), 
('Limit in-plane rotation', True), ('Delta in-plane rotation angle', 
10.0), ('Out-of-plane tilt angle range', (-12, 12)), 
('Number of projections azimuthal/out-of-plane angle', 
(90, 7)), ('Image alignment size in Angstrom', 700), 
('Step size of segmentation in Angstrom', 70), 
('Choose out-of-plane tilt amplitude correlation', False), 
('Amplitude correlation out-of-plane tilt range', (-12, 12)), 
('3D CTF correction', True), ('3D CTF correction intensity', 'low'), 
('MPI option', True), ('Number of CPUs', 8), ('Temporary directory', '/tmp')])

generate_file_name_for_grid_search(first_param, second_param, each_grid_point)[source]¶

>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
>>> s = SegRefine3dGrid()
>>> s.generate_file_name_for_grid_search('b-factor', None, [-200, 3])
'b-factor_-200'
>>> sec_par = 'helical_rise_or_pitch'
>>> s.generate_file_name_for_grid_search('b-factor', sec_par, [-200, 3.344])
'b-factor_-200_helical_rise_or_pitch_3344'

setup_parameters_for_each_grid_point(first_param, second_param, each_grid_point, parameters)[source]¶

class segrefine3dgrid.SegRefine3dGrid(parset=None)[source]¶

Methods

`add_grid_point_to_parameter_dictionary`(…)	>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
`extrapolate_second_order_to_end_of_box`(…)	>>> from spring.segment3d.refine.sr3d_main import SegmentRefine3d
`generate_cmdline_for_each_grid_point`(…)	>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
`generate_file_name_for_grid_search`(…)	>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
`sort_data_and_discard_duplicates`(x, y)	http://mail.scipy.org/pipermail/scipy-user/2011-February/028341.html
`split_grid_if_demanded`(subgrid_option, …)	>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid

define_alignment_parameters
define_all_segmentrefine3d_parameters
define_filter_parameters
define_helical_symmetry_parameters
define_input_output_iteration
define_mpi_parameters
define_reconstruction_parameters
define_refinement_strategy_options
define_selection_parameters
enter_parameters_in_grid_database
enter_variables_into_grid_database
fill_in_excluded_quantities_by_interpolation
generate_segmentrefine3d_parameters_while_removing_grid_parameters
get_all_helices_from_last_refinement_cycle
get_all_segments_from_refinement_cycle
get_avg_helix_shift_x_and_y_and_avg_inplane_angles
get_cut_coordinates_named_tuple
get_grid_database_name
get_grid_parameters_and_final_grid_entry
get_helices_coordinates_required_for_unbending_from_database
get_helix_coordinates_named_tuple
get_picked_segment_coordinates
get_ref_session_and_last_cycle
get_segment_ids_from_helix
get_segments_from_helix
get_variables_ranges_and_increments
launch_segmentrefine3d_jobs
make_database_entries
make_unbending_named_tuple
prepare_grid_database
prepare_unique_updated_stack_name
setup_alignment_related_parameters
setup_filter_related_parameters
setup_grid_sequence
setup_non_refinement_selection_criteria
setup_parameters_for_each_grid_point
setup_refinement_selection_criteria
setup_symmetry_related_parameters
unbend_window_and_mask_input_stack

split_grid_if_demanded(subgrid_option, subgrid, grid_sequence)[source]¶

>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
>>> from spring.segment3d.segclassreconstruct import SegClassReconstruct
>>> s = SegClassReconstruct()
>>> grid = s.generate_rise_rotation_or_pitch_unitnumber_pairs_for_symmetry_grid((275.0, 305.0), 5.0, (3.8, 4.2), 0.1)
>>> SegRefine3dGrid().split_grid_if_demanded(True, (1, 6), grid.ravel())
array([(275.0, 3.8), (275.0, 3.9), (275.0, 4.0), (275.0, 4.1),
       (275.0, 4.2), (280.0, 3.8)], dtype=object)
>>> SegRefine3dGrid().split_grid_if_demanded(True, (7, 6), grid.ravel())
Traceback (most recent call last):
  File '/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/doctest.py', line 1254, in __run
    compileflags, 1) in test.globs
  File '<doctest segrefine3dgrid.SegRefine3dGrid.split_grid_if_demanded[5]>', line 1, in <module>
    SegRefine3dGrid().split_grid_if_demanded(True, (7, 6), grid.ravel())
  File 'spring/segment3d/segrefine3dgrid.py', line 430, in split_grid_if_demanded
    raise ValueError(msg)
ValueError: Part of subgrids must not be larger than entire number of subgrids. Enter part of subgrids < number of subgrids.

get_grid_parameters_and_final_grid_entry(grid_database, grid_name)[source]¶

get_grid_database_name(subgrid_option)[source]¶

get_variables_ranges_and_increments(grid_name)[source]¶

setup_grid_sequence()[source]¶

generate_cmdline_for_each_grid_point(parameter_file)[source]¶

>>> from spring.segment3d.segrefine3dgrid import SegRefine3dGrid
>>> s = SegRefine3dGrid()
>>> s.generate_cmdline_for_each_grid_point('rot_23432_rise_4224.par')
'segmentrefine3d --d rot_23432_rise_4224 --f rot_23432_rise_4224.par'

make_database_entries(run_name, each_grid_point, grid_session, last_cycle, stat_file, reproj_file, latest_reconstruction)[source]¶

enter_parameters_in_grid_database(primary_variable, secondary_variable, run_name, each_grid_point, grid_name, target_cycle_id)[source]¶

enter_variables_into_grid_database(primary_variable, secondary_variable, primary_range, secondary_range, primary_inc, second_inc, rise_rot_or_pitch_unit_choice)[source]¶

prepare_grid_database(primary_variable, secondary_variable, primary_range, secondary_range, primary_inc, second_inc, grid_name)[source]¶

launch_segmentrefine3d_jobs()[source]¶

segrefine3dgrid.main()[source]¶