- a -

• alpha : PSF_model_density , PSF_model
• alt_d : Alternaria
• alternaria : Sampler_move_parameters
• alternaria_proposal : Sampler_move_parameters
• anaglyph : Alternaria_viewer_modes , Alternaria_gen_modes
• apical : Printed_structure , Structure
• apical_hypha_d : Alternaria
• apical_hypha_p : Alternaria_density

- b -

• base_level : Alternaria
• base_psi : Structure , Printed_structure
• base_theta : Structure , Printed_structure
• begin_pt : Structure
• beta : PSF_model_density , PSF_model
• bg : Imaging_model_density , Imaging_model

- c -

• c_1 : Alternaria_density , Alternaria
• c_2 : Imaging_model , Imaging_model_density
• capture_view : Alternaria_gen_modes , Alternaria_viewer_modes
• centroid : Structure
• centroid_x : Structure_density , Printed_structure
• centroid_y : Structure_density , Printed_structure
• centroid_z : Printed_structure , Structure_density
• clip_near : Alternaria_viewer_modes
• col : Imaging_window
• conv : PSF_padding

- d -

• data : Sampler_move_parameters
• data_avg : Sampler_move_parameters
• dd_spores : Spore_density
• density : Spore , Lateral_hypha , Printed_apical_hypha , Apical_hypha , Imaging_model , Apical_structure , Structure , PSF_model , Lateral_structure , Printed_spore
• dwidth : Apical_hypha_density

- e -

• end_pt : Structure

- f -

• fft : PSF_padding
• focal_prp : Alternaria_gen_modes , Alternaria_viewer_modes
• focal_vrp : Alternaria_gen_modes , Alternaria_viewer_modes

- g -

• gamma : PSF_model_density , PSF_model
• growth_dir : Structure

- h -

• h : PSF

- i -

• id : Structure , Printed_structure
• imaging : Sampler_move_parameters
• imaging_proposal : Sampler_move_parameters
• img : Imaging_window
• info : Sampler_move

- l -

• lat_dist : Lateral_structure , Lateral_structure_density , Printed_lateral_structure
• lateral_hypha_1_d : Alternaria
• lateral_hypha_1_p : Alternaria_density
• lateral_hypha_n_d : Alternaria
• lateral_hypha_n_p : Alternaria_density
• laterals : Structure , Printed_structure
• length : Structure , Structure_density , Printed_structure
• level : Structure , Printed_structure
• level_1_density : Printed_lateral_hypha
• level_apical_hypha : Alternaria
• level_lateral_hypha : Alternaria
• level_n_density : Printed_lateral_hypha
• level_spores : Alternaria
• level_structs : Alternaria
• level_terminals : Alternaria
• ll : Sampler_move_parameters
• ll_proposal : Sampler_move_parameters
• log_prob : Printed_structure , PSF_model , Imaging_model , Structure , Alternaria
• log_prob_descend : Structure

- m -

• max : Density::Uniform_params , Density::Gaussian_params
• min : Density::Gaussian_params , Density::Uniform_params
• modify_structure : Alternaria_gen_modes
• moves : Sampler
• mu : Density::Gaussian_params

- n -

• name : Sampler_move
• name_1 : Sampler_jump_move
• name_2 : Sampler_jump_move
• num_accepted : Sampler_diffusion_move
• num_accepted_1 : Sampler_jump_move
• num_accepted_2 : Sampler_jump_move
• num_attempts : Sampler_diffusion_move
• num_attempts_1 : Sampler_jump_move
• num_attempts_2 : Sampler_jump_move
• num_cols : Imaging_window
• num_imgs : Imaging_window
• num_levels_p : Alternaria_density
• num_rows : Imaging_window

- o -

• opacity : Structure , Printed_structure , Structure_density

- p -

• padding : PSF
• parent : Structure , Printed_structure
• prob : Sampler_diffusion_move
• prob_1 : Sampler_jump_move
• prob_2 : Sampler_jump_move
• proposal_info : Sampler_move
• psf : Sampler_move_parameters
• psf_proposal : Sampler_move_parameters
• psi : Structure_density , Structure , Alternaria , Printed_structure

- r -

• R : Structure
• render_focal_plane : Alternaria_gen_modes , Alternaria_viewer_modes
• render_world_axis : Alternaria_gen_modes , Alternaria_viewer_modes
• root : Alternaria
• rotate_camera : Alternaria_viewer_modes , Alternaria_gen_modes
• row : Imaging_window

- s -

• scale : Imaging_model
• sigma : Density::Gaussian_params , PSF_gauss_model
• spore_d : Alternaria
• spore_p : Alternaria_density

- t -

• theta : Structure , Structure_density , Alternaria , Printed_structure
• translate_camera : Alternaria_viewer_modes , Alternaria_gen_modes

- w -

• width : Structure , Structure_density , Printed_structure
• window : Imaging_model

- x -

• x : Imaging_scale

- y -

• y : Imaging_scale

- z -

• z : Imaging_scale