Documented functions with links to source

Program to plot refinement parameters from segmentrefine3d

class segrefine3dplot.SegRefine3dPlotPar

Class to initiate default dictionary with input parameters including help and range values and status dictionary

Methods

define_parameters_and_their_properties
define_program_states
set_inp_spring_path
set_interactive_vs_batch_mode
set_quantities_to_be_plotted
set_ref_quantities_to_be_plotted
set_refinement_cycle
set_set_size

define_parameters_and_their_properties()

define_program_states()

set_refinement_cycle(feature_set)

set_ref_quantities_to_be_plotted(feature_set)

class segrefine3dplot.SegRefine3dPlotPreparation(parset=None)

• Class that holds functions for examining segments from micrographs

• __init__ Function to interpret multi-input parameters

Methods

get_labels_according_to_ref_quantities(…)

>>> from spring.segment3d.segrefine3dplot import SegRefine3dPlot

check_ref_values_and_raise_error
get_refinement_cycle_id

check_ref_values_and_raise_error(quantities, y_plot)

get_labels_according_to_ref_quantities(set_size, quantities)

>>> from spring.segment3d.segrefine3dplot import SegRefine3dPlot
>>> SegRefine3dPlot().get_labels_according_to_ref_quantities('helix', 'coordinates') 
['Stack_id', 'Refined X-Coordinate (Angstrom)', 'Refined Y-Coordinate (Angstrom)', 
'Picked X-Coordinate (Angstrom)', 'Picked Y-Coordinate (Angstrom)', 
'Selected refined X-Coordinate (Angstrom)', 'Selected refined Y-Coordinate (Angstrom)']
>>> SegRefine3dPlot().get_labels_according_to_ref_quantities('helix', 'in-plane_rotation') 
['Stack_id', 'Distance Along Helix (Angstrom)', 'In-Plane Rotation Angle (Degrees)', 
'Selected In-Plane Rotation Angle (Degrees)', 'Local Average In-Plane Rotation Angle (Degrees)']
>>> SegRefine3dPlot().get_labels_according_to_ref_quantities('helix', 'normalized_in-plane_rotation') 
['Stack_id', 'Distance Along Helix (Angstrom)', 'Normalized In-Plane Rotation Angle (Degrees)', 
'Selected Normalized In-Plane Rotation Angle (Degrees)']
>>> SegRefine3dPlot().get_labels_according_to_ref_quantities('helix', 'coordinates_subunit') 
['Stack_id', 'Refined subunit X-Coordinate (Angstrom)', 'Refined subunit Y-Coordinate (Angstrom)', 
'Picked X-Coordinate (Angstrom)', 'Picked Y-Coordinate (Angstrom)', 'Selected refined X-Coordinate (Angstrom)', 
'Selected refined Y-Coordinate (Angstrom)']

get_refinement_cycle_id(infile)

class segrefine3dplot.SegRefine3dPlotDataRetrieval(parset=None)

Methods

get_labels_according_to_ref_quantities(…)

>>> from spring.segment3d.segrefine3dplot import SegRefine3dPlot

add_picked_coordinates_of_exluded_segments
check_ref_values_and_raise_error
get_coordinates_from_refinement
get_ref_quantities_per_set
get_refined_quantities_from_segments
get_refined_subunit_coordinates
get_refinement_cycle_id
get_refinement_parameters
get_refinement_parameters_including_local_averaging
get_refinement_parameters_no_local_averaging
get_specified_ref_quantities
get_x_and_y_coordinates_from_helix_segments
prepare_data_for_table_display

get_x_and_y_coordinates_from_helix_segments(each_helix_segments, each_helix_ref_segments, excluded_segments)

get_refined_quantities_from_segments(quantities, each_helix_ref_segments)

get_refined_subunit_coordinates(session, ref_session, each_helix_ref_segments)

prepare_data_for_table_display(each_helix_stack_ids, x_coord, y_coord, sel_ref_x_coord, sel_ref_y_coord, each_helix_su_stack_ids, sub_xcoord, sub_ycoord)

add_picked_coordinates_of_exluded_segments(each_helix_stack_ids, excluded_segments, x_coord, y_coord, each_helix_su_stack_ids, sub_xcoord, sub_ycoord, filled_x_coord, filled_y_coord, filled_ref_x_coord, filled_ref_y_coord)

get_coordinates_from_refinement(session, ref_session, each_plot_set_string, quantities, xy_quantities, each_helix_stack_ids, each_helix_segments, each_helix_ref_segments, excluded_segments)

get_refinement_parameters_no_local_averaging(each_plot_set_string, set_size, quantities, xy_quantities, each_helix_stack_ids, each_helix_ref_segments, excluded_segments, distances)

get_refinement_parameters_including_local_averaging(each_plot_set_string, set_size, quantities, xy_quantities, each_helix_stack_ids, each_helix_ref_segments, excluded_segments, distances)

get_refinement_parameters(each_plot_set_string, set_size, quantities, xy_quantities, each_helix_stack_ids, each_helix_segments, each_helix_ref_segments, excluded_segments, distances)

get_specified_ref_quantities(session, ref_session, each_plot_set_string, set_size, quantities, xy_quantities, each_helix_stack_ids, each_helix_segments, each_helix_ref_segments)

get_ref_quantities_per_set(spring_path, quantities)

class segrefine3dplot.SegRefine3dPlotVisualize(parset=None)

Methods

get_labels_according_to_ref_quantities(…)

>>> from spring.segment3d.segrefine3dplot import SegRefine3dPlot

add_picked_coordinates_of_exluded_segments
check_ref_values_and_raise_error
get_coordinates_from_refinement
get_ref_quantities_per_set
get_refined_quantities_from_segments
get_refined_subunit_coordinates
get_refinement_cycle_id
get_refinement_parameters
get_refinement_parameters_including_local_averaging
get_refinement_parameters_no_local_averaging
get_specified_ref_quantities
get_x_and_y_coordinates_from_helix_segments
plot_ref_data_on_figure
prepare_data_for_table_display

plot_ref_data_on_figure(xy_quantities, quantities, labels)

class segrefine3dplot.SegRefine3dPlot(parset=None)

Methods

get_labels_according_to_ref_quantities(…)

>>> from spring.segment3d.segrefine3dplot import SegRefine3dPlot

add_picked_coordinates_of_exluded_segments
check_ref_values_and_raise_error
get_coordinates_from_refinement
get_ref_quantities_per_set
get_refined_quantities_from_segments
get_refined_subunit_coordinates
get_refinement_cycle_id
get_refinement_parameters
get_refinement_parameters_including_local_averaging
get_refinement_parameters_no_local_averaging
get_specified_ref_quantities
get_x_and_y_coordinates_from_helix_segments
launch_interactive_plot_gui
plot_desired_ref_quantities
plot_ref_data_on_figure
prepare_data_for_table_display

launch_interactive_plot_gui(figures, tables, labels)

plot_desired_ref_quantities()

segrefine3dplot.main()