Documented functions with links to source¶

Program to interactively inspect 3D reconstructions from segmentrefine3d using slice viewer

class segrefine3dinspect.SegRefine3dInspectPar[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_bfactor_and_resolution_cutoff
set_bfactor_option
set_fsc_curve
set_helix_length
set_interactive_vs_batch_mode
set_layer_line_mask_option
set_long_helix_option
set_mask_type
set_processed_reconstruction
set_real_space_mask_option
set_reconstruction_to_be_inspected
set_sn_weighting_option
set_swap_helix

define_parameters_and_their_properties()[source]¶

define_program_states()[source]¶

set_reconstruction_to_be_inspected(feature_set)[source]¶

set_processed_reconstruction(feature_set)[source]¶

set_interactive_vs_batch_mode(feature_set)[source]¶

set_bfactor_option(feature_set)[source]¶

set_bfactor_and_resolution_cutoff(feature_set)[source]¶

set_real_space_mask_option(feature_set)[source]¶

set_mask_type(feature_set)[source]¶

set_layer_line_mask_option(feature_set)[source]¶

set_long_helix_option(feature_set)[source]¶

set_sn_weighting_option(feature_set)[source]¶

set_fsc_curve(feature_set)[source]¶

set_helix_length(feature_set)[source]¶

set_swap_helix(feature_set)[source]¶

class segrefine3dinspect.SegRefine3dInspectPreparation(parset=None)[source]¶

Methods

assemble_volume_from_image_slices(image_slice)

>>> from spring.segment3d.segrefine3dinspect import SegRefine3dInspect

apply_bfactor_if_demanded
apply_cylinder_mask_if_demanded
apply_layerline_filter_if_demanded
apply_structural_mask_if_demanded

apply_bfactor_if_demanded(vol, bfactor, res_cutoff, pixelsize, fsc_line)[source]¶

assemble_volume_from_image_slices(image_slice)[source]¶

>>> from spring.segment3d.segrefine3dinspect import SegRefine3dInspect
>>> SegRefine3dInspect().assemble_volume_from_image_slices(np.ones((3, 3)))
array([[[1., 1., 1.],
        [1., 1., 1.],
        [1., 1., 1.]],

       [[1., 1., 1.],
        [1., 1., 1.],
        [1., 1., 1.]],

       [[1., 1., 1.],
        [1., 1., 1.],
        [1., 1., 1.]]])

apply_cylinder_mask_if_demanded(vol)[source]¶

apply_structural_mask_if_demanded(vol)[source]¶

apply_layerline_filter_if_demanded(vol, pixelsize, helical_symmetry, helixwidth)[source]¶

class segrefine3dinspect.SegRefine3dInspect(parset=None)[source]¶

Methods

assemble_volume_from_image_slices(image_slice)

>>> from spring.segment3d.segrefine3dinspect import SegRefine3dInspect

apply_bfactor_if_demanded
apply_cylinder_mask_if_demanded
apply_layerline_filter_if_demanded
apply_structural_mask_if_demanded
check_whether_pixelsize_set_in_volume
check_whether_volume_is_square_otherwise_pad
choose_correct_volume_for_batch_mode_depending_on_options
launch_inspection_of_reconstruction
launch_interactive_inspect_gui

launch_interactive_inspect_gui(cart_volumes)[source]¶

choose_correct_volume_for_batch_mode_depending_on_options(original_vol, layer_vol, cylinder_vol, cylinder_layer_vol, structural_vol, structural_layer_vol)[source]¶

check_whether_pixelsize_set_in_volume(original_vol)[source]¶

check_whether_volume_is_square_otherwise_pad()[source]¶

launch_inspection_of_reconstruction()[source]¶

segrefine3dinspect.main()[source]¶