Index

A

add_dose_noise() (in module epsic_tools.toolbox.sim_utils)

add_to_mask() (in module epsic_tools.toolbox.make_merlin_mask) (in module epsic_tools.toolbox.make_merlin_mask_test)

C

calc_camera_length() (in module epsic_tools.toolbox.sim_utils) calc_pixelSize() (in module epsic_tools.toolbox.sim_utils)

calc_probe_size() (in module epsic_tools.toolbox.sim_utils) compute_transform() (in module epsic_tools.toolbox.warp_3d) crop_recon_obj() (in module epsic_tools.toolbox.ptycho_utils)

D

define_probe_function() (in module epsic_tools.toolbox.define_probe_function)

duplicate_json() (in module epsic_tools.toolbox.ptycho_utils)

E

e_lambda() (in module epsic_tools.toolbox.ptycho_utils) ellipse_angle_of_rotation() (in module epsic_tools.toolbox.warp_3d) ellipse_axis_length() (in module epsic_tools.toolbox.warp_3d) ellipse_center() (in module epsic_tools.toolbox.warp_3d) epsic_tools module epsic_tools.api module epsic_tools.build_params module epsic_tools.ptychography2D module epsic_tools.signals module epsic_tools.toolbox module

epsic_tools.toolbox.define_probe_function module epsic_tools.toolbox.make_merlin_mask module epsic_tools.toolbox.make_merlin_mask_test module epsic_tools.toolbox.ptycho_utils module epsic_tools.toolbox.radial_profile module epsic_tools.toolbox.sim_utils module epsic_tools.toolbox.warp_3d module

F

fft() (in module epsic_tools.toolbox.sim_utils) find_nearest() (in module epsic_tools.toolbox.sim_utils)

fit_ellipse() (in module epsic_tools.toolbox.warp_3d) fitEllipse() (in module epsic_tools.toolbox.warp_3d) FuncAberrUV() (in module epsic_tools.toolbox.define_probe_function)

G

genAp() (in module epsic_tools.toolbox.sim_utils) genStop() (in module epsic_tools.toolbox.sim_utils) get_adf() (in module epsic_tools.toolbox.sim_utils) get_base_dir() (epsic_tools.ptychography2D.Ptychography2D method) get_bf_disc() (in module epsic_tools.toolbox.sim_utils) get_convergence() (epsic_tools.ptychography2D.Ptychography2D method) get_coords_4d() (in module epsic_tools.toolbox.warp_3d) get_data_key() (epsic_tools.ptychography2D.Ptychography2D method) get_data_path() (epsic_tools.ptychography2D.Ptychography2D method) get_dead_px_flag() (epsic_tools.ptychography2D.Ptychography2D method) get_dead_px_path() (epsic_tools.ptychography2D.Ptychography2D method) get_decay() (epsic_tools.ptychography2D.Ptychography2D method) get_defocus() (epsic_tools.ptychography2D.Ptychography2D method) get_detector_bin() (epsic_tools.ptychography2D.Ptychography2D method) get_detector_crop() (epsic_tools.ptychography2D.Ptychography2D method) get_detector_min_max() (epsic_tools.ptychography2D.Ptychography2D method) get_detector_optic_axis() (epsic_tools.ptychography2D.Ptychography2D method) get_detector_pos() (epsic_tools.ptychography2D.Ptychography2D method) get_disc_overlap() (in module epsic_tools.toolbox.sim_utils) get_energy() (epsic_tools.ptychography2D.Ptychography2D method) get_error() (in module epsic_tools.toolbox.ptycho_utils) get_experiment_ID() (epsic_tools.ptychography2D.Ptychography2D method) get_fft() (in module epsic_tools.toolbox.ptycho_utils) get_figs() (in module epsic_tools.toolbox.sim_utils) get_flat_field_flag() (epsic_tools.ptychography2D.Ptychography2D method) get_flat_field_path() (epsic_tools.ptychography2D.Ptychography2D method) get_frc() (in module epsic_tools.toolbox.sim_utils) get_gpu_flag() (epsic_tools.ptychography2D.Ptychography2D method) get_hdf5_complex_probe() (in module epsic_tools.toolbox.ptycho_utils) get_hdf5_error() (in module epsic_tools.toolbox.ptycho_utils) get_hdf5_object_modulus() (in module epsic_tools.toolbox.ptycho_utils) get_hdf5_object_phase() (in module epsic_tools.toolbox.ptycho_utils) get_hdf5_probe_modulus() (in module epsic_tools.toolbox.ptycho_utils) get_hdf5_probe_phase() (in module epsic_tools.toolbox.ptycho_utils) get_interaction() (epsic_tools.ptychography2D.Ptychography2D method)

get_iterations() (epsic_tools.ptychography2D.Ptychography2D method) get_json_params() (in module epsic_tools.toolbox.ptycho_utils) get_json_pixelSize() (in module epsic_tools.toolbox.ptycho_utils) get_load_data_flag() (epsic_tools.ptychography2D.Ptychography2D method) get_load_object_flag() (epsic_tools.ptychography2D.Ptychography2D method) get_load_object_path() (epsic_tools.ptychography2D.Ptychography2D method) get_load_probe_flag() (epsic_tools.ptychography2D.Ptychography2D method) get_load_probe_path() (epsic_tools.ptychography2D.Ptychography2D method) get_n_cores() (epsic_tools.ptychography2D.Ptychography2D method) get_obj_array() (in module epsic_tools.toolbox.ptycho_utils) get_overlap() (in module epsic_tools.toolbox.sim_utils) get_potential() (in module epsic_tools.toolbox.sim_utils) get_probe_alpha() (epsic_tools.ptychography2D.Ptychography2D method) get_probe_array() (in module epsic_tools.toolbox.ptycho_utils) get_probe_start() (epsic_tools.ptychography2D.Ptychography2D method) get_ptyREX_ready() (in module epsic_tools.toolbox.sim_utils) get_ptyREX_recon_list() (in module epsic_tools.toolbox.sim_utils) get_px_pitch() (epsic_tools.ptychography2D.Ptychography2D method) get_raw_dir_list() (in module epsic_tools.toolbox.sim_utils) get_RMSE() (in module epsic_tools.toolbox.ptycho_utils) get_sampling_factor() (in module epsic_tools.toolbox.ptycho_utils) get_save_dir() (epsic_tools.ptychography2D.Ptychography2D method) get_save_interval() (epsic_tools.ptychography2D.Ptychography2D method) get_save_prefix() (epsic_tools.ptychography2D.Ptychography2D method) get_scan_refine_start() (epsic_tools.ptychography2D.Ptychography2D method) get_scan_region() (epsic_tools.ptychography2D.Ptychography2D method) get_scan_rotation() (epsic_tools.ptychography2D.Ptychography2D method) get_scan_size() (epsic_tools.ptychography2D.Ptychography2D method) get_scan_step() (epsic_tools.ptychography2D.Ptychography2D method) get_sim_data() (in module epsic_tools.toolbox.sim_utils) get_sim_params() (in module epsic_tools.toolbox.sim_utils) get_sim_probe() (in module epsic_tools.toolbox.sim_utils) get_sim_probe_for_ptyrex() (in module epsic_tools.toolbox.sim_utils) get_source_modes() (epsic_tools.ptychography2D.Ptychography2D method) get_step_size() (in module epsic_tools.toolbox.sim_utils)

I

ifft() (in module epsic_tools.toolbox.sim_utils)

init_ptyrex() (in module epsic_tools.build_params) is_number() (in module epsic_tools.ptychography2D)

J

json_to_dict() (in module epsic_tools.toolbox.ptycho_utils)

json_to_dict_sim() (in module epsic_tools.toolbox.sim_utils)

K

kdtree_NN() (in module epsic_tools.toolbox.ptycho_utils)

L

load_dict_from_hdf5() (in module epsic_tools.toolbox.ptycho_utils) load_recon() (epsic_tools.ptychography2D.Ptychography2D method) (in module epsic_tools.toolbox.ptycho_utils)

load_series() (epsic_tools.ptychography2D.Ptychography2D method) (in module epsic_tools.toolbox.ptycho_utils)

M

make_mask() (in module epsic_tools.toolbox.make_merlin_mask) (in module epsic_tools.toolbox.make_merlin_mask_test) makeFourierCoordinates() (in module epsic_tools.toolbox.sim_utils) max_defocus() (in module epsic_tools.toolbox.sim_utils) module epsic_tools epsic_tools.api epsic_tools.build_params epsic_tools.ptychography2D epsic_tools.signals epsic_tools.toolbox epsic_tools.toolbox.define_probe_function epsic_tools.toolbox.make_merlin_mask epsic_tools.toolbox.make_merlin_mask_test epsic_tools.toolbox.ptycho_utils epsic_tools.toolbox.radial_profile epsic_tools.toolbox.sim_utils epsic_tools.toolbox.warp_3d

N

NestedDefaultDict (class in epsic_tools.build_params) (class in epsic_tools.toolbox.sim_utils)

P

parse_params_file() (in module epsic_tools.toolbox.sim_utils) plot_ellipse() (in module epsic_tools.toolbox.warp_3d)

plot_ptyr() (in module epsic_tools.toolbox.ptycho_utils) plot_ptyREX_output() (in module epsic_tools.toolbox.ptycho_utils) Ptychography2D (class in epsic_tools.ptychography2D)

R

rad_array() (in module epsic_tools.toolbox.define_probe_function) radial_profile() (in module epsic_tools.toolbox.radial_profile)

radial_profile_stack() (in module epsic_tools.toolbox.radial_profile) remove_cross() (in module epsic_tools.toolbox.warp_3d)

S

save_dict_to_hdf5() (in module epsic_tools.toolbox.ptycho_utils) save_json() (epsic_tools.ptychography2D.Ptychography2D method) sector_mask() (in module epsic_tools.toolbox.radial_profile) set_base_dir() (epsic_tools.ptychography2D.Ptychography2D method) set_convergence() (epsic_tools.ptychography2D.Ptychography2D method) set_data_key() (epsic_tools.ptychography2D.Ptychography2D method) set_data_path() (epsic_tools.ptychography2D.Ptychography2D method) set_dead_px_flag() (epsic_tools.ptychography2D.Ptychography2D method) set_dead_px_path() (epsic_tools.ptychography2D.Ptychography2D method) set_decay() (epsic_tools.ptychography2D.Ptychography2D method) set_defocus() (epsic_tools.ptychography2D.Ptychography2D method) set_detector_bin() (epsic_tools.ptychography2D.Ptychography2D method) set_detector_crop() (epsic_tools.ptychography2D.Ptychography2D method) set_detector_min_max() (epsic_tools.ptychography2D.Ptychography2D method) set_detector_optic_axis() (epsic_tools.ptychography2D.Ptychography2D method) set_detector_pos() (epsic_tools.ptychography2D.Ptychography2D method) set_energy() (epsic_tools.ptychography2D.Ptychography2D method) set_experiment_ID() (epsic_tools.ptychography2D.Ptychography2D method) set_flat_field_flag() (epsic_tools.ptychography2D.Ptychography2D method) set_flat_field_path() (epsic_tools.ptychography2D.Ptychography2D method) set_gpu_flag() (epsic_tools.ptychography2D.Ptychography2D method) set_interaction() (epsic_tools.ptychography2D.Ptychography2D method)

set_iterations() (epsic_tools.ptychography2D.Ptychography2D method) set_load_data_flag() (epsic_tools.ptychography2D.Ptychography2D method) set_load_object_flag() (epsic_tools.ptychography2D.Ptychography2D method) set_load_object_path() (epsic_tools.ptychography2D.Ptychography2D method) set_load_probe_flag() (epsic_tools.ptychography2D.Ptychography2D method) set_load_probe_path() (epsic_tools.ptychography2D.Ptychography2D method) set_n_cores() (epsic_tools.ptychography2D.Ptychography2D method) set_probe_alpha() (epsic_tools.ptychography2D.Ptychography2D method) set_probe_start() (epsic_tools.ptychography2D.Ptychography2D method) set_px_pitch() (epsic_tools.ptychography2D.Ptychography2D method) set_save_dir() (epsic_tools.ptychography2D.Ptychography2D method) set_save_interval() (epsic_tools.ptychography2D.Ptychography2D method) set_save_prefix() (epsic_tools.ptychography2D.Ptychography2D method) set_scan_refine_start() (epsic_tools.ptychography2D.Ptychography2D method) set_scan_region() (epsic_tools.ptychography2D.Ptychography2D method) set_scan_rotation() (epsic_tools.ptychography2D.Ptychography2D method) set_scan_size() (epsic_tools.ptychography2D.Ptychography2D method) set_scan_step() (epsic_tools.ptychography2D.Ptychography2D method) set_source_modes() (epsic_tools.ptychography2D.Ptychography2D method) setPower() (in module epsic_tools.toolbox.sim_utils) shift_probe() (in module epsic_tools.toolbox.sim_utils) sim_to_hs() (in module epsic_tools.toolbox.sim_utils)

W

warp_all() (in module epsic_tools.toolbox.warp_3d)

warp_all_np() (in module epsic_tools.toolbox.warp_3d) write_ptyrex_json() (in module epsic_tools.toolbox.sim_utils)