Index

_

__init__() (ptyrad.constraints.CombinedConstraint method) (ptyrad.initialization.Initializer method) (ptyrad.losses.CombinedLoss method) (ptyrad.models.PtychoAD method) (ptyrad.reconstruction.IndicesDataset method) (ptyrad.reconstruction.PtyRADSolver method) (ptyrad.utils.common.CustomLogger method)

A

approx_torch_quantile() (in module ptyrad.utils.math_ops)

C

center_crop() (in module ptyrad.utils.image_proc) check_gpu() (in module ptyrad.cli) check_modes_ortho() (in module ptyrad.utils.dev_tools) collect_ND_datasets() (in module ptyrad.load) CombinedConstraint (class in ptyrad.constraints) CombinedLoss (class in ptyrad.losses) complex_object_interp3d() (in module ptyrad.utils.physics) complex_object_z_resample_torch() (in module ptyrad.utils.physics) complex_ratio_constraint() (in module ptyrad.constraints)

compose_affine_matrix() (in module ptyrad.utils.math_ops) compute_loss() (in module ptyrad.reconstruction) compute_optuna_error() (in module ptyrad.reconstruction) copy_params_to_dir() (in module ptyrad.save) create_one_hot_mask() (in module ptyrad.utils.image_proc) create_optimizer() (in module ptyrad.reconstruction) create_optuna_pruner() (in module ptyrad.reconstruction) create_optuna_sampler() (in module ptyrad.reconstruction) crop_pos (ptyrad.models.PtychoAD attribute) CustomLogger (class in ptyrad.utils.common)

D

decompose_affine_matrix() (in module ptyrad.utils.math_ops) detector_blur_std (ptyrad.models.PtychoAD attribute) device (ptyrad.models.PtychoAD attribute) (ptyrad.reconstruction.PtyRADSolver attribute)

dk (ptyrad.models.PtychoAD attribute) dx (ptyrad.models.PtychoAD attribute)

E

expand_presets() (in module ptyrad.utils.common)

exponential_decay() (in module ptyrad.utils.math_ops) export_meas_init() (in module ptyrad.cli)

F

fftshift2() (in module ptyrad.utils.math_ops)

fit_background() (in module ptyrad.utils.image_proc) fit_cbed_pattern() (in module ptyrad.utils.image_proc)

G

gaussian_blur_1d() (in module ptyrad.utils.image_proc) get_blob_size() (in module ptyrad.utils.image_proc) get_center_of_mass() (in module ptyrad.utils.image_proc) get_decomposed_affine_matrix_from_bases() (in module ptyrad.utils.math_ops) get_default_probe_simu_params() (in module ptyrad.utils.physics) get_EM_constants() (in module ptyrad.utils.physics) get_gaussian1d() (in module ptyrad.utils.image_proc) get_local_obj_tilts() (in module ptyrad.utils.image_proc)

get_nested() (in module ptyrad.utils.common) get_obj_z_shift() (in module ptyrad.constraints) get_objp_contrast() (in module ptyrad.losses) get_optuna_suggest() (in module ptyrad.reconstruction) get_size_bytes() (in module ptyrad.utils.dev_tools) get_time() (in module ptyrad.utils.common) guess_radius_of_bright_field_disk() (in module ptyrad.utils.image_proc) gui() (in module ptyrad.cli)

H

H (ptyrad.models.PtychoAD attribute) handle_hdf5_types() (in module ptyrad.utils.common)

has_nan_or_inf() (in module ptyrad.utils.dev_tools) hermite_like() (in module ptyrad.utils.physics)

I

if_hypertune (ptyrad.reconstruction.PtyRADSolver attribute) ifftshift2() (in module ptyrad.utils.math_ops) imshift_batch() (in module ptyrad.utils.image_proc)

IndicesDataset (class in ptyrad.reconstruction) infer_dx_from_params() (in module ptyrad.utils.physics) Initializer (class in ptyrad.initialization) is_mig_enabled() (in module ptyrad.utils.common)

K

kr_filter() (in module ptyrad.constraints)

kz_filter() (in module ptyrad.constraints)

L

list_nested_keys() (in module ptyrad.utils.common) load_array_from_file() (in module ptyrad.load) load_hdf5() (in module ptyrad.load) load_json_params() (in module ptyrad.load) load_mat() (in module ptyrad.load) load_ND_with_key() (in module ptyrad.load) load_npy() (in module ptyrad.load) load_params() (in module ptyrad.load)

load_pt() (in module ptyrad.load) load_ptyrad() (in module ptyrad.load) load_py_params() (in module ptyrad.load) load_raw() (in module ptyrad.load) load_tif() (in module ptyrad.load) load_toml_params() (in module ptyrad.load) load_yml_params() (in module ptyrad.load) loss_logger() (in module ptyrad.reconstruction) lr_params (ptyrad.models.PtychoAD attribute)

M

main() (in module ptyrad.cli) make_batches() (in module ptyrad.reconstruction) make_fzp_probe() (in module ptyrad.utils.physics) make_gaussian_mask() (in module ptyrad.utils.math_ops) make_mixed_probe() (in module ptyrad.utils.physics) make_output_folder() (in module ptyrad.save) make_save_dict() (in module ptyrad.save) make_sigmoid_mask() (in module ptyrad.utils.math_ops) make_stem_probe() (in module ptyrad.utils.physics) measurements (ptyrad.models.PtychoAD attribute) mfft2() (in module ptyrad.utils.math_ops) module ptyrad.cli ptyrad.constraints ptyrad.forward ptyrad.initialization ptyrad.load ptyrad.losses ptyrad.models ptyrad.reconstruction ptyrad.save ptyrad.utils ptyrad.utils.common ptyrad.utils.dev_tools ptyrad.utils.image_proc ptyrad.utils.math_ops ptyrad.utils.physics ptyrad.visualization

multislice_forward_model_vec_all() (in module ptyrad.forward)

N

N_scan_fast (ptyrad.models.PtychoAD attribute) N_scan_slow (ptyrad.models.PtychoAD attribute) ndarrays_to_tensors() (in module ptyrad.utils.common) near_field_evolution() (in module ptyrad.utils.physics)

near_field_evolution_torch() (in module ptyrad.utils.physics) normalize_by_bit_depth() (in module ptyrad.utils.image_proc) normalize_constraint_params() (in module ptyrad.utils.common) normalize_from_zero_to_one() (in module ptyrad.utils.image_proc)

O

obj_preblur_std (ptyrad.models.PtychoAD attribute) omode_occu (ptyrad.models.PtychoAD attribute) opt_obj_tilts (ptyrad.models.PtychoAD attribute) opt_obja (ptyrad.models.PtychoAD attribute) opt_objp (ptyrad.models.PtychoAD attribute)

opt_probe (ptyrad.models.PtychoAD attribute) opt_probe_pos_shifts (ptyrad.models.PtychoAD attribute) optimizable_tensors (ptyrad.models.PtychoAD attribute) optuna_objective() (in module ptyrad.reconstruction) orthogonalize_modes_vec() (in module ptyrad.constraints) orthogonalize_modes_vec_np() (in module ptyrad.utils.physics)

P

params (ptyrad.reconstruction.PtyRADSolver attribute) parse_hypertune_params_to_str() (in module ptyrad.utils.common) parse_sec_to_time_str() (in module ptyrad.utils.common) parse_torch_compile_configs() (in module ptyrad.reconstruction) plot_affine_transformation() (in module ptyrad.visualization) plot_forward_pass() (in module ptyrad.visualization) plot_loss_curves() (in module ptyrad.visualization) plot_obj_tilts() (in module ptyrad.visualization) plot_obj_tilts_avg() (in module ptyrad.visualization) plot_pos_grouping() (in module ptyrad.visualization) plot_probe_modes() (in module ptyrad.visualization) plot_scan_positions() (in module ptyrad.visualization) plot_sigmoid_mask() (in module ptyrad.visualization) plot_slice_thickness() (in module ptyrad.visualization) plot_summary() (in module ptyrad.visualization) power_law() (in module ptyrad.utils.math_ops) prepare_recon() (in module ptyrad.reconstruction) print_gpu_info() (in module ptyrad.utils.common) print_info() (in module ptyrad.cli) print_package_tree() (in module ptyrad.utils.dev_tools) print_packages_info() (in module ptyrad.utils.common) print_system_info() (in module ptyrad.utils.common) probe_int_sum (ptyrad.models.PtychoAD attribute) PtychoAD (class in ptyrad.models) ptyrad.cli module ptyrad.constraints module

ptyrad.forward module ptyrad.initialization module ptyrad.load module ptyrad.losses module ptyrad.models module ptyrad.reconstruction module ptyrad.save module ptyrad.utils module ptyrad.utils.common module ptyrad.utils.dev_tools module ptyrad.utils.image_proc module ptyrad.utils.math_ops module ptyrad.utils.physics module ptyrad.visualization module PtyRADSolver (class in ptyrad.reconstruction)

R

recon_loop() (in module ptyrad.reconstruction) recon_step() (in module ptyrad.reconstruction)

resolve_seed_priority() (in module ptyrad.utils.common) run() (in module ptyrad.cli)

S

safe_filename() (in module ptyrad.utils.common) save_array() (in module ptyrad.save) save_dict_to_hdf5() (in module ptyrad.save) save_results() (in module ptyrad.save) scan_affine (ptyrad.models.PtychoAD attribute) select_scan_indices() (in module ptyrad.reconstruction) set_accelerator() (in module ptyrad.utils.common)

set_gpu_device() (in module ptyrad.utils.common) set_random_seed() (in module ptyrad.utils.common) shift_obj_along_z() (in module ptyrad.constraints) shift_probes (ptyrad.models.PtychoAD attribute) slice_thickness (ptyrad.models.PtychoAD attribute) sort_by_mode_int() (in module ptyrad.constraints) sort_by_mode_int_np() (in module ptyrad.utils.physics)

T

tensors_to_ndarrays() (in module ptyrad.utils.common) test_constraint_fn() (in module ptyrad.utils.dev_tools) test_loss_fn() (in module ptyrad.utils.dev_tools)

tilt_obj (ptyrad.models.PtychoAD attribute) time_sync() (in module ptyrad.utils.common) toggle_grad_requires() (in module ptyrad.reconstruction) torch_phasor() (in module ptyrad.utils.math_ops)

V

validate_params() (in module ptyrad.cli) verbose (ptyrad.models.PtychoAD attribute) (ptyrad.reconstruction.PtyRADSolver attribute)

vprint() (in module ptyrad.utils.common) vprint_nested_dict() (in module ptyrad.utils.common)

W

write_hdf5() (in module ptyrad.save)

write_npy() (in module ptyrad.save) write_tif() (in module ptyrad.save)

Y

yaml2json() (in module ptyrad.utils.dev_tools)