Documented functions with links to source

Program to plot refinement parameters from segmentrefine3d

class segrefine3dplot.SegRefine3dPlotPar[source]

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()[source]
define_program_states()[source]
set_refinement_cycle(feature_set)[source]
set_ref_quantities_to_be_plotted(feature_set)[source]
class segrefine3dplot.SegRefine3dPlotPreparation(parset=None)[source]
  • 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)[source]
get_labels_according_to_ref_quantities(set_size, quantities)[source]
>>> 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)[source]
class segrefine3dplot.SegRefine3dPlotDataRetrieval(parset=None)[source]

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)[source]
get_refined_quantities_from_segments(quantities, each_helix_ref_segments)[source]
get_refined_subunit_coordinates(session, ref_session, each_helix_ref_segments)[source]
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)[source]
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)[source]
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)[source]
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)[source]
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)[source]
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)[source]
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)[source]
get_ref_quantities_per_set(spring_path, quantities)[source]
class segrefine3dplot.SegRefine3dPlotVisualize(parset=None)[source]

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)[source]
class segrefine3dplot.SegRefine3dPlot(parset=None)[source]

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)[source]
plot_desired_ref_quantities()[source]
segrefine3dplot.main()[source]