Index

A

Aberrations (class in ptyrad.optics.aberrations) AberrationValue (class in ptyrad.optics.aberrations) alpha (ptyrad.params.constraint_params.KzFilter attribute) alpha1 (ptyrad.params.constraint_params.ComplexRatio attribute) alpha2 (ptyrad.params.constraint_params.ComplexRatio attribute) Analyzer (class in ptyrad.analysis) (class in ptyrad.analysis.analyzer) angle (ptyrad.optics.aberrations.AberrationValue attribute) append_params (ptyrad.params.hypertune_params.HypertuneParams attribute) append_shape (ptyrad.params.init_params.MeasExport attribute) apply_complex_ratio() (ptyrad.core.constraints.CombinedConstraint method) apply_fix_probe_int() (ptyrad.core.constraints.CombinedConstraint method) apply_fov() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) apply_kr_filter() (ptyrad.core.constraints.CombinedConstraint method)

apply_kr_thresh() (ptyrad.core.constraints.CombinedConstraint method) apply_kz_filter() (ptyrad.core.constraints.CombinedConstraint method) apply_mirrored_amp() (ptyrad.core.constraints.CombinedConstraint method) apply_obj_rblur() (ptyrad.core.constraints.CombinedConstraint method) apply_obj_z_recenter() (ptyrad.core.constraints.CombinedConstraint method) apply_obj_zblur() (ptyrad.core.constraints.CombinedConstraint method) apply_obja_thresh() (ptyrad.core.constraints.CombinedConstraint method) apply_objp_postiv() (ptyrad.core.constraints.CombinedConstraint method) apply_ortho_pmode() (ptyrad.core.constraints.CombinedConstraint method) apply_pos_recenter() (ptyrad.core.constraints.CombinedConstraint method) apply_probe_mask_k() (ptyrad.core.constraints.CombinedConstraint method) apply_probe_mask_r() (ptyrad.core.constraints.CombinedConstraint method) apply_tilt_smooth() (ptyrad.core.constraints.CombinedConstraint method) approx_torch_quantile() (in module ptyrad.core.functional) asymmetry (ptyrad.params.hypertune_params.TuneParams attribute)

B

backend (ptyrad.params.recon_params.CompilerConfigs attribute) batch_size (ptyrad.params.hypertune_params.TuneParams attribute) BATCH_SIZE (ptyrad.params.recon_params.ReconParams attribute) beam_kev (ptyrad.params.init_params.InitParams attribute)

beta (ptyrad.params.constraint_params.KzFilter attribute) bit (ptyrad.params.recon_params.ResultModes attribute) blur_std (ptyrad.params.loss_params.LossSimlar attribute) build_model() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method)

C

C10 (ptyrad.params.hypertune_params.TuneParams attribute) C12 (ptyrad.params.hypertune_params.TuneParams attribute) C21 (ptyrad.params.hypertune_params.TuneParams attribute) C23 (ptyrad.params.hypertune_params.TuneParams attribute) c3 (ptyrad.params.hypertune_params.TuneParams attribute) C30 (ptyrad.params.hypertune_params.TuneParams attribute) C32 (ptyrad.params.hypertune_params.TuneParams attribute) C34 (ptyrad.params.hypertune_params.TuneParams attribute) C41 (ptyrad.params.hypertune_params.TuneParams attribute) C43 (ptyrad.params.hypertune_params.TuneParams attribute) C45 (ptyrad.params.hypertune_params.TuneParams attribute) c5 (ptyrad.params.hypertune_params.TuneParams attribute) C50 (ptyrad.params.hypertune_params.TuneParams attribute) C52 (ptyrad.params.hypertune_params.TuneParams attribute) C54 (ptyrad.params.hypertune_params.TuneParams attribute) C56 (ptyrad.params.hypertune_params.TuneParams attribute) center_crop() (in module ptyrad.utils.image_proc) check_gpu() (in module ptyrad.cli.commands) check_modes_ortho() (in module ptyrad.utils.dev_tools) clear_cache() (ptyrad.core.models.ptycho.PtychoModel method) close() (ptyrad.runtime.logging.LoggingManager method) collate_results (ptyrad.params.hypertune_params.HypertuneParams attribute) collect_ND_datasets() (in module ptyrad.io.hierarchy) collect_provenance() (in module ptyrad.io.provenance) CombinedConstraint (class in ptyrad.core.constraints) CombinedLoss (class in ptyrad.core.losses)

compiler_configs (ptyrad.params.recon_params.ReconParams attribute) complex_object_z_resample_torch() (in module ptyrad.core.functional) complex_ratio (ptyrad.params.constraint_params.ConstraintParams attribute) complex_ratio_constraint() (in module ptyrad.core.constraints) compose_affine_matrix() (in module ptyrad.utils.affine) compute_loss() (in module ptyrad.solver.reconstruction) compute_optuna_error() (in module ptyrad.solver.hypertune) configs (ptyrad.params.hypertune_params.PrunerParams attribute) (ptyrad.params.hypertune_params.SamplerParams attribute) (ptyrad.params.model_params.OptimizerParams attribute) (ptyrad.params.model_params.SchedulerParams attribute) constraint_params (ptyrad.params.ptyrad_params.PtyRADParams attribute) conv_angle (ptyrad.params.hypertune_params.TuneParams attribute) convergence_monitor (ptyrad.params.recon_params.ReconParams attribute) ConvergenceMonitor (class in ptyrad.runtime.convergence) copy_params (ptyrad.params.recon_params.ReconParams attribute) copy_params_to_dir() (in module ptyrad.params.parser) create_convergence_monitor() (in module ptyrad.runtime.convergence) create_grids() (ptyrad.core.models.ptycho.PtychoModel method) create_one_hot_mask() (in module ptyrad.utils.image_proc) create_optimizable_params_dict() (ptyrad.core.models.ptycho.PtychoModel method) create_optimizer() (in module ptyrad.solver.reconstruction) create_optuna_pruner() (in module ptyrad.solver.hypertune) create_optuna_sampler() (in module ptyrad.solver.hypertune) create_scheduler() (in module ptyrad.solver.reconstruction) create_starter_project() (in module ptyrad.cli.templates) crop_pos (ptyrad.core.models.ptycho.PtychoModel attribute)

D

data (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) dct_2d() (in module ptyrad.core.functional) dct_threshold_filter() (in module ptyrad.core.constraints) decompose_affine_matrix() (in module ptyrad.utils.affine) default() (ptyrad.io.provenance.SafeJSONEncoder method) defocus (ptyrad.params.hypertune_params.TuneParams attribute) detector_blur_std (ptyrad.core.models.ptycho.PtychoModel attribute) (ptyrad.params.model_params.ModelParams attribute) device (ptyrad.core.models.ptycho.PtychoModel attribute) (ptyrad.solver.ptyrad_solver.PtyRADSolver attribute) dk (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) (ptyrad.core.models.ptycho.PtychoModel attribute)

dp_pow (ptyrad.params.loss_params.LossPacbed attribute) (ptyrad.params.loss_params.LossPoissn attribute) (ptyrad.params.loss_params.LossSingle attribute) dx (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) (ptyrad.core.models.ptycho.PtychoModel attribute) (ptyrad.params.hypertune_params.TuneParams attribute) dynamic (ptyrad.params.recon_params.CompilerConfigs attribute) dz (ptyrad.params.hypertune_params.TuneParams attribute) dzlr (ptyrad.params.hypertune_params.TuneParams attribute)

E

enable (ptyrad.params.recon_params.CompilerConfigs attribute) end_iter (ptyrad.params.constraint_params.ComplexRatio attribute) (ptyrad.params.constraint_params.FixProbeInt attribute) (ptyrad.params.constraint_params.KrFilter attribute) (ptyrad.params.constraint_params.KrThresh attribute) (ptyrad.params.constraint_params.KzFilter attribute) (ptyrad.params.constraint_params.MirroredAmp attribute) (ptyrad.params.constraint_params.ObjaThresh attribute) (ptyrad.params.constraint_params.ObjpPostiv attribute) (ptyrad.params.constraint_params.ObjRblur attribute) (ptyrad.params.constraint_params.ObjZblur attribute) (ptyrad.params.constraint_params.ObjZRecenter attribute) (ptyrad.params.constraint_params.OrthoPmode attribute) (ptyrad.params.constraint_params.PosRecenter attribute) (ptyrad.params.constraint_params.ProbeMaskK attribute) (ptyrad.params.constraint_params.TiltSmooth attribute) eps (ptyrad.params.loss_params.LossPoissn attribute) error_metric (ptyrad.params.hypertune_params.HypertuneParams attribute) every_n_iters (ptyrad.params.recon_params.ConvergenceMonitorParams attribute) expand_presets() (in module ptyrad.io.save) exponential_decay() (in module ptyrad.utils.image_proc) export() (ptyrad.optics.aberrations.Aberrations method)

export_examples() (in module ptyrad.cli.templates) export_hdf5_provenance_to_json() (in module ptyrad.io.provenance) export_meas() (in module ptyrad.cli.commands) export_params() (in module ptyrad.cli.templates) export_templates() (in module ptyrad.cli.templates) export_walkthrough() (in module ptyrad.cli.templates) extract_keys() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) extract_loss_curves() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) extract_object() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) extract_object_amplitude() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) extract_object_phase() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) extract_probe() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) extract_probe_positions() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) extract_provenance() (in module ptyrad.analysis) (in module ptyrad.analysis.extract)

F

fftshift2() (in module ptyrad.core.functional) file_dir (ptyrad.params.init_params.MeasExport attribute) file_format (ptyrad.params.init_params.MeasExport attribute) file_name (ptyrad.params.init_params.MeasExport attribute) filter() (ptyrad.runtime.logging.RankZeroFilter method) find_probe_focus_dz() (in module ptyrad.core.functional) fit_background() (in module ptyrad.utils.image_proc) fit_cbed_pattern() (in module ptyrad.utils.image_proc) fix_probe_int (ptyrad.params.constraint_params.ConstraintParams attribute)

flush_to_file() (ptyrad.runtime.logging.LoggingManager method) force (ptyrad.params.init_params.MeasRemoveNegValues attribute) forward() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) (ptyrad.core.constraints.CombinedConstraint method) (ptyrad.core.losses.CombinedLoss method) (ptyrad.core.models.ptycho.PtychoModel method) FOV (ptyrad.params.recon_params.ResultModes attribute) fullgraph (ptyrad.params.recon_params.CompilerConfigs attribute)

G

gap (ptyrad.params.init_params.FilePathWithKey attribute) gaussian_blur_1d() (in module ptyrad.core.functional) generate_provenance_json() (in module ptyrad.io.provenance) get_blob_size() (in module ptyrad.utils.image_proc) get_center_of_mass() (in module ptyrad.core.functional) get_coefficients() (ptyrad.optics.aberrations.Aberrations method) get_complex_probe_view() (ptyrad.core.models.ptycho.PtychoModel method) get_decomposed_affine_matrix_from_bases() (in module ptyrad.utils.affine) get_detector_pattern() (ptyrad.core.models.ptycho.PtychoModel method) get_EM_constants() (in module ptyrad.optics.constants) get_examples() (in module ptyrad.cli.commands) get_forward_pattern() (ptyrad.core.models.ptycho.PtychoModel method) get_fov_bbox() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_gaussian1d() (in module ptyrad.core.functional) get_haider() (ptyrad.optics.aberrations.Aberrations method) get_hilbert_key() (in module ptyrad.solver.grouping) get_interaction_parameter_sigma() (in module ptyrad.optics.constants) get_keys() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_krivanek_cartesian() (ptyrad.optics.aberrations.Aberrations method) get_krivanek_polar() (ptyrad.optics.aberrations.Aberrations method) get_logging_manager() (in module ptyrad.runtime.logging) get_lorentz_factor_gamma() (in module ptyrad.optics.constants) get_loss_curves() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_loss_pacbed() (ptyrad.core.losses.CombinedLoss method) get_loss_poissn() (ptyrad.core.losses.CombinedLoss method) get_loss_simlar() (ptyrad.core.losses.CombinedLoss method) get_loss_single() (ptyrad.core.losses.CombinedLoss method) get_loss_sparse() (ptyrad.core.losses.CombinedLoss method) get_measurements() (ptyrad.core.models.ptycho.PtychoModel method)

get_nested() (in module ptyrad.analysis.extract) (in module ptyrad.io.hierarchy) get_obj_patches() (ptyrad.core.models.ptycho.PtychoModel method) get_obj_z_shift() (in module ptyrad.core.constraints) get_object() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_object_amplitude() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_object_phase() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_objp_contrast() (in module ptyrad.core.losses) get_optuna_suggest() (in module ptyrad.solver.hypertune) get_params() (in module ptyrad.cli.commands) get_probe() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_probe_center_positions() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) get_probe_positions() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) get_probes() (ptyrad.core.models.ptycho.PtychoModel method) get_propagated_probe() (ptyrad.core.models.ptycho.PtychoModel method) get_propagators() (ptyrad.core.models.ptycho.PtychoModel method) get_scanned_fov_bbox() (in module ptyrad.analysis) (in module ptyrad.analysis.extract) get_size_bytes() (in module ptyrad.utils.dev_tools) get_templates() (in module ptyrad.cli.commands) get_time() (in module ptyrad.utils.time) get_walkthrough() (in module ptyrad.cli.commands) get_wavelength_ang() (in module ptyrad.optics.constants) grad_accumulation (ptyrad.params.recon_params.BatchSize attribute) GROUP_MODE (ptyrad.params.recon_params.ReconParams attribute) guess_radius_of_bright_field_disk() (in module ptyrad.utils.image_proc) gui() (in module ptyrad.cli.commands)

H

H (ptyrad.core.models.ptycho.PtychoModel attribute) handle_hdf5_types() (in module ptyrad.io.hierarchy) has_nan_or_inf() (in module ptyrad.utils.dev_tools)

hermite_like() (in module ptyrad.optics.probe) hypertune() (ptyrad.solver.ptyrad_solver.PtyRADSolver method) hypertune_params (ptyrad.params.ptyrad_params.PtyRADParams attribute)

I

idct_2d() (in module ptyrad.core.functional) if_hypertune (ptyrad.params.hypertune_params.HypertuneParams attribute) (ptyrad.solver.ptyrad_solver.PtyRADSolver attribute) ifftshift2() (in module ptyrad.core.functional) imshift_batch() (in module ptyrad.core.functional) INDICES_MODE (ptyrad.params.recon_params.ReconParams attribute) IndicesDataset (class in ptyrad.io.dataloader) init_all() (ptyrad.init.initializer.Initializer method) init_cache() (ptyrad.init.initializer.Initializer method) init_calibration() (ptyrad.init.initializer.Initializer method) init_check() (ptyrad.init.initializer.Initializer method) init_compilation_iters() (ptyrad.core.models.ptycho.PtychoModel method) init_constraint() (ptyrad.solver.ptyrad_solver.PtyRADSolver method) init_H() (ptyrad.init.initializer.Initializer method) init_initializer() (ptyrad.solver.ptyrad_solver.PtyRADSolver method) init_loss() (ptyrad.solver.ptyrad_solver.PtyRADSolver method)

init_measurements() (ptyrad.init.initializer.Initializer method) init_obj() (ptyrad.init.initializer.Initializer method) init_obj_tilts() (ptyrad.init.initializer.Initializer method) init_occu (ptyrad.params.init_params.ObjOmodeInitOccu attribute) init_omode_occu() (ptyrad.init.initializer.Initializer method) init_params (ptyrad.params.ptyrad_params.PtyRADParams attribute) init_pos() (ptyrad.init.initializer.Initializer method) init_probe() (ptyrad.init.initializer.Initializer method) init_project() (in module ptyrad.cli.commands) init_propagator_vars() (ptyrad.core.models.ptycho.PtychoModel method) init_provenance() (ptyrad.init.initializer.Initializer method) init_tilts (ptyrad.params.init_params.TiltParams attribute) Initializer (class in ptyrad.init.initializer) is_mig_enabled() (in module ptyrad.runtime.diagnostics) is_multislice (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property)

K

kernel_size (ptyrad.params.constraint_params.ObjRblur attribute) (ptyrad.params.constraint_params.ObjZblur attribute) key (ptyrad.params.init_params.FilePathWithKey attribute) kr_filter (ptyrad.params.constraint_params.ConstraintParams attribute)

kr_filter() (in module ptyrad.core.constraints) kr_thresh (ptyrad.params.constraint_params.ConstraintParams attribute) kwargs (ptyrad.params.hypertune_params.TuneParam attribute) kz_filter (ptyrad.params.constraint_params.ConstraintParams attribute) kz_filter() (in module ptyrad.core.constraints)

L

lambd (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) list_nested_keys() (in module ptyrad.io.hierarchy) ln_order (ptyrad.params.loss_params.LossSparse attribute) load_array_from_file() (in module ptyrad.io.handlers) load_hdf5() (in module ptyrad.io.hierarchy) load_hdf5_ND_with_selection() (in module ptyrad.io.hierarchy) load_json_params() (in module ptyrad.params.parser) load_mat() (in module ptyrad.io.hierarchy) load_ND_with_key() (in module ptyrad.io.hierarchy) load_npy() (in module ptyrad.io.generic) load_params() (in module ptyrad.params) (in module ptyrad.params.parser) load_provenance_from_h5() (in module ptyrad.io.provenance) load_pt() (in module ptyrad.io.hierarchy) load_ptyrad() (in module ptyrad.io.load)

load_py_params() (in module ptyrad.params.parser) load_raw() (in module ptyrad.io.generic) load_state (ptyrad.params.model_params.OptimizerParams attribute) (ptyrad.params.model_params.SchedulerParams attribute) load_tif() (in module ptyrad.io.generic) load_toml_params() (in module ptyrad.params.parser) load_yml_params() (in module ptyrad.params.parser) load_zarr() (in module ptyrad.io.hierarchy) LoggingManager (class in ptyrad.runtime.logging) loss_logger() (in module ptyrad.solver.reconstruction) loss_pacbed (ptyrad.params.loss_params.LossParams attribute) loss_params (ptyrad.params.ptyrad_params.PtyRADParams attribute) loss_poissn (ptyrad.params.loss_params.LossParams attribute) loss_simlar (ptyrad.params.loss_params.LossParams attribute) loss_single (ptyrad.params.loss_params.LossParams attribute) loss_sparse (ptyrad.params.loss_params.LossParams attribute) lr_params (ptyrad.core.models.ptycho.PtychoModel attribute)

M

mag (ptyrad.optics.aberrations.AberrationValue attribute) main() (in module ptyrad.cli.entry) make_aberration_surface_krivanek_cartesian() (in module ptyrad.optics.probe) make_aberration_surface_krivanek_complex() (in module ptyrad.optics.probe) make_aberration_surface_krivanek_polar() (in module ptyrad.optics.probe) make_batches() (in module ptyrad.solver.reconstruction) make_freq_grid_2d() (in module ptyrad.core.functional) make_fzp_probe() (in module ptyrad.optics.probe) make_gaussian_mask() (in module ptyrad.utils.image_proc) make_mixed_probe() (in module ptyrad.optics.probe) make_output_folder() (in module ptyrad.io.save) make_real_grid_2d() (in module ptyrad.core.functional) make_save_dict() (in module ptyrad.io.save) make_sigmoid_mask() (in module ptyrad.core.functional) make_stem_probe() (in module ptyrad.optics.probe) make_super_gaussian_mask() (in module ptyrad.core.functional) max_shift (ptyrad.params.constraint_params.ObjZRecenter attribute) meas_add_detector_blur (ptyrad.params.init_params.InitParams attribute) meas_add_poisson_noise (ptyrad.params.init_params.InitParams attribute) meas_add_source_size (ptyrad.params.init_params.InitParams attribute) meas_calibration (ptyrad.params.init_params.InitParams attribute) meas_crop (ptyrad.params.init_params.InitParams attribute) meas_export (ptyrad.params.init_params.InitParams attribute) meas_flipT (ptyrad.params.init_params.InitParams attribute) meas_normalization (ptyrad.params.init_params.InitParams attribute) meas_Npix (ptyrad.params.init_params.InitParams attribute) meas_pad (ptyrad.params.init_params.InitParams attribute) meas_params (ptyrad.params.init_params.InitParams attribute) meas_permute (ptyrad.params.init_params.InitParams attribute) meas_remove_neg_values (ptyrad.params.init_params.InitParams attribute) meas_resample (ptyrad.params.init_params.InitParams attribute) meas_reshape (ptyrad.params.init_params.InitParams attribute) meas_source (ptyrad.params.init_params.InitParams attribute) MeasDataLoader (class in ptyrad.io.dataloader) measurements (ptyrad.core.models.ptycho.PtychoModel attribute) mfft2() (in module ptyrad.utils.image_proc) mirrored_amp (ptyrad.params.constraint_params.ConstraintParams attribute) mode (ptyrad.params.init_params.MeasCalibration attribute) (ptyrad.params.init_params.MeasNormalization attribute) (ptyrad.params.init_params.MeasPad attribute) (ptyrad.params.init_params.MeasRemoveNegValues attribute) (ptyrad.params.init_params.MeasResample attribute) (ptyrad.params.init_params.ObjZResample attribute) (ptyrad.params.init_params.ProbeNormalization attribute) (ptyrad.params.recon_params.CompilerConfigs attribute) (ptyrad.params.recon_params.IndicesMode attribute) model (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) model_attrs (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) model_params (ptyrad.params.ptyrad_params.PtyRADParams attribute) module ptyrad.analysis ptyrad.analysis.analyzer ptyrad.analysis.extract ptyrad.cli ptyrad.cli.commands ptyrad.cli.entry ptyrad.cli.templates ptyrad.core ptyrad.core.constraints ptyrad.core.forward ptyrad.core.functional ptyrad.core.losses ptyrad.core.models ptyrad.core.models.ptycho ptyrad.init ptyrad.init.initializer ptyrad.io ptyrad.io.adapter ptyrad.io.dataloader ptyrad.io.generic ptyrad.io.handlers ptyrad.io.hierarchy ptyrad.io.load ptyrad.io.provenance ptyrad.io.save ptyrad.optics ptyrad.optics.aberrations ptyrad.optics.constants ptyrad.optics.probe ptyrad.optics.propagator ptyrad.params ptyrad.params.constraint_params ptyrad.params.hypertune_params ptyrad.params.init_params ptyrad.params.loss_params ptyrad.params.model_params ptyrad.params.parser ptyrad.params.ptyrad_params ptyrad.params.recon_params ptyrad.plotting ptyrad.plotting.basic ptyrad.plotting.model ptyrad.runtime ptyrad.runtime.convergence ptyrad.runtime.device ptyrad.runtime.diagnostics ptyrad.runtime.logging ptyrad.runtime.seed ptyrad.solver ptyrad.solver.grouping ptyrad.solver.hypertune ptyrad.solver.ptyrad_solver ptyrad.solver.reconstruction ptyrad.utils ptyrad.utils.affine ptyrad.utils.dev_tools ptyrad.utils.image_proc ptyrad.utils.time

multislice_forward() (in module ptyrad.core.forward)

N

N_scan_fast (ptyrad.core.models.ptycho.PtychoModel attribute) N_scan_slow (ptyrad.core.models.ptycho.PtychoModel attribute) n_trials (ptyrad.params.hypertune_params.HypertuneParams attribute) name (ptyrad.params.hypertune_params.PrunerParams attribute) (ptyrad.params.hypertune_params.SamplerParams attribute) (ptyrad.params.model_params.OptimizerParams attribute) (ptyrad.params.model_params.SchedulerParams attribute) ndarrays_to_tensors() (in module ptyrad.io.adapter) near_field_evolution() (in module ptyrad.optics.propagator) near_field_evolution_torch() (in module ptyrad.core.functional) niter (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property)

NITER (ptyrad.params.recon_params.ReconParams attribute) Nlayer (ptyrad.params.hypertune_params.TuneParams attribute) nm (ptyrad.optics.aberrations.AberrationValue attribute) (ptyrad.optics.aberrations.ParsedKey attribute) normalize_by_bit_depth() (in module ptyrad.utils.image_proc) normalize_constraint_params() (in module ptyrad.params.parser) normalize_from_zero_to_one() (in module ptyrad.utils.image_proc) normalize_probe_params() (in module ptyrad.params.parser) nslice (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property)

O

oalr (ptyrad.params.hypertune_params.TuneParams attribute) obj_dim (ptyrad.params.recon_params.ResultModes attribute) obj_Nlayer (ptyrad.params.init_params.InitParams attribute) obj_omode_init_occu (ptyrad.params.init_params.InitParams attribute) obj_omode_max (ptyrad.params.init_params.InitParams attribute) obj_params (ptyrad.params.init_params.InitParams attribute) obj_rblur (ptyrad.params.constraint_params.ConstraintParams attribute) obj_slice_thickness (ptyrad.params.init_params.InitParams attribute) obj_source (ptyrad.params.init_params.InitParams attribute) obj_tilts (ptyrad.params.model_params.UpdateParams attribute) obj_type (ptyrad.params.constraint_params.ComplexRatio attribute) (ptyrad.params.constraint_params.KrFilter attribute) (ptyrad.params.constraint_params.KrThresh attribute) (ptyrad.params.constraint_params.KzFilter attribute) (ptyrad.params.constraint_params.ObjRblur attribute) (ptyrad.params.constraint_params.ObjZblur attribute) (ptyrad.params.loss_params.LossSimlar attribute) obj_z_crop (ptyrad.params.init_params.InitParams attribute) obj_z_pad (ptyrad.params.init_params.InitParams attribute) obj_z_recenter (ptyrad.params.constraint_params.ConstraintParams attribute) obj_z_resample (ptyrad.params.init_params.InitParams attribute) obj_zblur (ptyrad.params.constraint_params.ConstraintParams attribute) obja (ptyrad.params.model_params.UpdateParams attribute) obja_thresh (ptyrad.params.constraint_params.ConstraintParams attribute)

objp (ptyrad.params.model_params.UpdateParams attribute) objp_postiv (ptyrad.params.constraint_params.ConstraintParams attribute) occu_type (ptyrad.params.init_params.ObjOmodeInitOccu attribute) offset (ptyrad.params.init_params.FilePathWithKey attribute) omode (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) omode_occu (ptyrad.core.models.ptycho.PtychoModel attribute) oplr (ptyrad.params.hypertune_params.TuneParams attribute) opt_obj_tilts (ptyrad.core.models.ptycho.PtychoModel attribute) opt_obja (ptyrad.core.models.ptycho.PtychoModel attribute) opt_objp (ptyrad.core.models.ptycho.PtychoModel attribute) opt_probe (ptyrad.core.models.ptycho.PtychoModel attribute) opt_probe_pos_shifts (ptyrad.core.models.ptycho.PtychoModel attribute) opt_tensors (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) optimizable_tensors (ptyrad.core.models.ptycho.PtychoModel attribute) optimizer (ptyrad.params.hypertune_params.TuneParams attribute) optimizer_params (ptyrad.params.model_params.ModelParams attribute) options (ptyrad.params.recon_params.CompilerConfigs attribute) optuna_objective() (in module ptyrad.solver.hypertune) ortho_pmode (ptyrad.params.constraint_params.ConstraintParams attribute) orthogonalize_modes_vec() (in module ptyrad.core.constraints) orthogonalize_modes_vec_np() (in module ptyrad.optics.probe) output_dir (ptyrad.params.recon_params.ReconParams attribute) output_shape (ptyrad.params.init_params.MeasExport attribute)

P

pad_layers (ptyrad.params.init_params.ObjZPad attribute) pad_types (ptyrad.params.init_params.ObjZPad attribute) padding_type (ptyrad.params.init_params.MeasPad attribute) param (ptyrad.optics.aberrations.ParsedKey attribute) params (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) (ptyrad.solver.ptyrad_solver.PtyRADSolver attribute) parse_hypertune_params_to_str() (in module ptyrad.solver.hypertune) parse_sec_to_time_str() (in module ptyrad.utils.time) parse_torch_compile_configs() (in module ptyrad.solver.reconstruction) ParsedKey (class in ptyrad.optics.aberrations) path (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) (ptyrad.params.init_params.FilePathWithKey attribute) percentile_range (ptyrad.params.recon_params.ConvergenceMonitorParams attribute) plot_affine_transformation() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_convergence_dashboard() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_dashboard() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plot_forward_pass() (in module ptyrad.plotting.model) (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plot_learning_rates_schedule() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_loss() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plot_loss_curves() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_obj_tilts() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_obj_tilts_avg() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_pos_grouping() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_positions() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plot_probe() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plot_probe_modes() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_scan_positions() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_sigmoid_mask() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) plot_slice_thickness() (in module ptyrad.plotting) (in module ptyrad.plotting.basic) (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plot_summary() (in module ptyrad.plotting.model) (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plot_tilts() (ptyrad.analysis.Analyzer method) (ptyrad.analysis.analyzer.Analyzer method) plr (ptyrad.params.hypertune_params.TuneParams attribute) pmode (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) pmode_max (ptyrad.params.hypertune_params.TuneParams attribute) pos_N_scan_fast (ptyrad.params.init_params.InitParams attribute) pos_N_scan_slow (ptyrad.params.init_params.InitParams attribute) pos_N_scans (ptyrad.params.init_params.InitParams attribute) pos_params (ptyrad.params.init_params.InitParams attribute) pos_recenter (ptyrad.params.constraint_params.ConstraintParams attribute) pos_scan_affine (ptyrad.params.init_params.InitParams attribute) pos_scan_flipT (ptyrad.params.init_params.InitParams attribute) pos_scan_rand_std (ptyrad.params.init_params.InitParams attribute) pos_scan_step_size (ptyrad.params.init_params.InitParams attribute) pos_source (ptyrad.params.init_params.InitParams attribute) postfix (ptyrad.params.recon_params.ReconParams attribute) power (ptyrad.params.constraint_params.MirroredAmp attribute) power_law() (in module ptyrad.utils.image_proc) power_thresh (ptyrad.params.constraint_params.ProbeMaskK attribute) prefix (ptyrad.params.recon_params.ReconParams attribute) prefix_time (ptyrad.params.recon_params.ReconParams attribute) preload_data (ptyrad.params.model_params.ModelParams attribute) prepare_recon() (in module ptyrad.solver.reconstruction) pretty_print() (ptyrad.optics.aberrations.Aberrations method) print_gpu_info() (in module ptyrad.runtime.diagnostics) print_info() (in module ptyrad.cli.commands) print_init_params() (ptyrad.init.initializer.Initializer method) print_model_summary() (ptyrad.core.models.ptycho.PtychoModel method) print_nested_dict() (in module ptyrad.io.hierarchy) print_package_tree() (in module ptyrad.utils.dev_tools) print_packages_info() (in module ptyrad.runtime.diagnostics) print_system_info() (in module ptyrad.runtime.diagnostics) probe (ptyrad.params.model_params.UpdateParams attribute) probe_aberrations (ptyrad.params.init_params.InitParams attribute) probe_conv_angle (ptyrad.params.init_params.InitParams attribute) probe_D_FZP (ptyrad.params.init_params.InitParams attribute) probe_D_H (ptyrad.params.init_params.InitParams attribute) probe_dRn (ptyrad.params.init_params.InitParams attribute) probe_illum_type (ptyrad.params.init_params.InitParams attribute) probe_int_sum (ptyrad.core.models.ptycho.PtychoModel attribute) probe_kv (ptyrad.params.init_params.InitParams attribute) probe_Ls (ptyrad.params.init_params.InitParams attribute) probe_mask_k (ptyrad.params.constraint_params.ConstraintParams attribute) probe_mask_r (ptyrad.params.constraint_params.ConstraintParams attribute) probe_normalization (ptyrad.params.init_params.InitParams attribute) probe_params (ptyrad.params.init_params.InitParams attribute) probe_permute (ptyrad.params.init_params.InitParams attribute) probe_pmode_init_pows (ptyrad.params.init_params.InitParams attribute) probe_pmode_max (ptyrad.params.init_params.InitParams attribute) probe_pos_shifts (ptyrad.params.model_params.UpdateParams attribute) probe_Rn (ptyrad.params.init_params.InitParams attribute) probe_shape (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) probe_source (ptyrad.params.init_params.InitParams attribute) probe_z_shift (ptyrad.params.init_params.InitParams attribute) provenance (ptyrad.analysis.Analyzer property) (ptyrad.analysis.analyzer.Analyzer property) pruner_params (ptyrad.params.hypertune_params.HypertuneParams attribute) PtychoModel (class in ptyrad.core.models.ptycho) ptyrad.analysis module

ptyrad.analysis.analyzer module ptyrad.analysis.extract module ptyrad.cli module ptyrad.cli.commands module ptyrad.cli.entry module ptyrad.cli.templates module ptyrad.core module ptyrad.core.constraints module ptyrad.core.forward module ptyrad.core.functional module ptyrad.core.losses module ptyrad.core.models module ptyrad.core.models.ptycho module ptyrad.init module ptyrad.init.initializer module ptyrad.io module ptyrad.io.adapter module ptyrad.io.dataloader module ptyrad.io.generic module ptyrad.io.handlers module ptyrad.io.hierarchy module ptyrad.io.load module ptyrad.io.provenance module ptyrad.io.save module ptyrad.optics module ptyrad.optics.aberrations module ptyrad.optics.constants module ptyrad.optics.probe module ptyrad.optics.propagator module ptyrad.params module ptyrad.params.constraint_params module ptyrad.params.hypertune_params module ptyrad.params.init_params module ptyrad.params.loss_params module ptyrad.params.model_params module ptyrad.params.parser module ptyrad.params.ptyrad_params module ptyrad.params.recon_params module ptyrad.plotting module ptyrad.plotting.basic module ptyrad.plotting.model module ptyrad.runtime module ptyrad.runtime.convergence module ptyrad.runtime.device module ptyrad.runtime.diagnostics module ptyrad.runtime.logging module ptyrad.runtime.seed module ptyrad.solver module ptyrad.solver.grouping module ptyrad.solver.hypertune module ptyrad.solver.ptyrad_solver module ptyrad.solver.reconstruction module ptyrad.utils module ptyrad.utils.affine module ptyrad.utils.dev_tools module ptyrad.utils.image_proc module ptyrad.utils.time module PtyRADSolver (class in ptyrad.solver.ptyrad_solver)

R

radius (ptyrad.params.constraint_params.KrFilter attribute) (ptyrad.params.constraint_params.ProbeMaskK attribute) random_seed (ptyrad.params.init_params.InitParams attribute) RankZeroFilter (class in ptyrad.runtime.logging) recon_dir_affixes (ptyrad.params.recon_params.ReconParams attribute) recon_loop() (in module ptyrad.solver.reconstruction) recon_params (ptyrad.params.ptyrad_params.PtyRADParams attribute) recon_step() (in module ptyrad.solver.reconstruction) reconstruct() (ptyrad.solver.ptyrad_solver.PtyRADSolver method) relax (ptyrad.params.constraint_params.MirroredAmp attribute) (ptyrad.params.constraint_params.ObjaThresh attribute) (ptyrad.params.constraint_params.ObjpPostiv attribute) (ptyrad.params.constraint_params.PosRecenter attribute)

remap_batches_to_global() (in module ptyrad.solver.grouping) report() (in module ptyrad.runtime.logging) resolve_seed_priority() (in module ptyrad.runtime.seed) result_modes (ptyrad.params.recon_params.ReconParams attribute) rotation (ptyrad.params.hypertune_params.TuneParams attribute) run() (in module ptyrad.cli.commands) (ptyrad.solver.ptyrad_solver.PtyRADSolver method)

S

safe_filename() (in module ptyrad.io.save) SafeJSONEncoder (class in ptyrad.io.provenance) sampler_params (ptyrad.params.hypertune_params.HypertuneParams attribute) save_array() (in module ptyrad.io.handlers) save_dict_to_hdf5() (in module ptyrad.io.save) SAVE_ITERS (ptyrad.params.recon_params.ReconParams attribute) save_provenance_to_hdf5() (in module ptyrad.io.provenance) save_result (ptyrad.params.recon_params.ReconParams attribute) save_results() (in module ptyrad.io.save) scale (ptyrad.optics.aberrations.ParsedKey attribute) (ptyrad.params.constraint_params.MirroredAmp attribute) (ptyrad.params.constraint_params.ObjZRecenter attribute) (ptyrad.params.hypertune_params.TuneParams attribute) scale_factor (ptyrad.params.loss_params.LossSimlar attribute) scale_factors (ptyrad.params.init_params.MeasResample attribute) scan_affine (ptyrad.core.models.ptycho.PtychoModel attribute) scheduler_params (ptyrad.params.model_params.ModelParams attribute) scrub_legacy_keys() (ptyrad.params.hypertune_params.TuneParams method) select_scan_indices() (in module ptyrad.solver.reconstruction) selected_figs (ptyrad.params.recon_params.ReconParams attribute) selection (ptyrad.params.init_params.FilePathWithKey attribute) serialize_model() (ptyrad.params.init_params.InitParams method) (ptyrad.params.model_params.OptimizerParams method) (ptyrad.params.model_params.SchedulerParams method) set_accelerator() (in module ptyrad.runtime.device) set_gpu_device() (in module ptyrad.runtime.device) set_random_seed() (in module ptyrad.runtime.seed) set_variables_dict() (ptyrad.init.initializer.Initializer method) shape (ptyrad.params.init_params.FilePathWithKey attribute) shear (ptyrad.params.hypertune_params.TuneParams attribute) shift_obj_along_z() (in module ptyrad.core.constraints) should_step() (ptyrad.runtime.convergence.ConvergenceMonitor method) simu_match_mode (ptyrad.params.init_params.InitParams attribute) simu_Npix (ptyrad.params.init_params.InitParams attribute) size (ptyrad.params.recon_params.BatchSize attribute) slice_thickness (ptyrad.core.models.ptycho.PtychoModel attribute) (ptyrad.params.model_params.UpdateParams attribute) slr (ptyrad.params.hypertune_params.TuneParams attribute) sort_by_mode_int() (in module ptyrad.core.constraints) sort_by_mode_int_np() (in module ptyrad.optics.probe) sparse_sampler_fps() (in module ptyrad.solver.grouping) sparse_sampler_hilbert() (in module ptyrad.solver.grouping) start_iter (ptyrad.params.constraint_params.ComplexRatio attribute) (ptyrad.params.constraint_params.FixProbeInt attribute) (ptyrad.params.constraint_params.KrFilter attribute) (ptyrad.params.constraint_params.KrThresh attribute) (ptyrad.params.constraint_params.KzFilter attribute) (ptyrad.params.constraint_params.MirroredAmp attribute) (ptyrad.params.constraint_params.ObjaThresh attribute) (ptyrad.params.constraint_params.ObjpPostiv attribute) (ptyrad.params.constraint_params.ObjRblur attribute) (ptyrad.params.constraint_params.ObjZblur attribute) (ptyrad.params.constraint_params.ObjZRecenter attribute) (ptyrad.params.constraint_params.OrthoPmode attribute) (ptyrad.params.constraint_params.PosRecenter attribute) (ptyrad.params.constraint_params.ProbeMaskK attribute) (ptyrad.params.constraint_params.TiltSmooth attribute)

state (ptyrad.params.hypertune_params.TuneParam attribute) (ptyrad.params.loss_params.LossPacbed attribute) (ptyrad.params.loss_params.LossPoissn attribute) (ptyrad.params.loss_params.LossSimlar attribute) (ptyrad.params.loss_params.LossSingle attribute) (ptyrad.params.loss_params.LossSparse attribute) std (ptyrad.params.constraint_params.ObjRblur attribute) (ptyrad.params.constraint_params.ObjZblur attribute) (ptyrad.params.constraint_params.TiltSmooth attribute) step (ptyrad.params.constraint_params.ComplexRatio attribute) (ptyrad.params.constraint_params.FixProbeInt attribute) (ptyrad.params.constraint_params.KrFilter attribute) (ptyrad.params.constraint_params.KrThresh attribute) (ptyrad.params.constraint_params.KzFilter attribute) (ptyrad.params.constraint_params.MirroredAmp attribute) (ptyrad.params.constraint_params.ObjaThresh attribute) (ptyrad.params.constraint_params.ObjpPostiv attribute) (ptyrad.params.constraint_params.ObjRblur attribute) (ptyrad.params.constraint_params.ObjZblur attribute) (ptyrad.params.constraint_params.ObjZRecenter attribute) (ptyrad.params.constraint_params.OrthoPmode attribute) (ptyrad.params.constraint_params.PosRecenter attribute) (ptyrad.params.constraint_params.ProbeMaskK attribute) (ptyrad.params.constraint_params.TiltSmooth attribute) step() (ptyrad.runtime.convergence.ConvergenceMonitor method) step_unit (ptyrad.params.model_params.SchedulerParams attribute) storage_path (ptyrad.params.hypertune_params.HypertuneParams attribute) study_name (ptyrad.params.hypertune_params.HypertuneParams attribute) subscan_fast (ptyrad.params.recon_params.IndicesMode attribute) subscan_slow (ptyrad.params.recon_params.IndicesMode attribute) suggest (ptyrad.params.hypertune_params.TuneParam attribute)

T

target_Npix (ptyrad.params.init_params.MeasPad attribute) tensors (ptyrad.params.recon_params.ConvergenceMonitorParams attribute) tensors_to_ndarrays() (in module ptyrad.io.adapter) test_constraint_fn() (in module ptyrad.utils.dev_tools) test_loss_fn() (in module ptyrad.utils.dev_tools) thresh (ptyrad.params.constraint_params.KrThresh attribute) (ptyrad.params.constraint_params.ObjaThresh attribute) (ptyrad.params.constraint_params.ObjZRecenter attribute) threshold (ptyrad.params.init_params.MeasPad attribute) tilt_obj (ptyrad.core.models.ptycho.PtychoModel attribute) tilt_params (ptyrad.params.init_params.InitParams attribute)

tilt_smooth (ptyrad.params.constraint_params.ConstraintParams attribute) tilt_source (ptyrad.params.init_params.InitParams attribute) tilt_type (ptyrad.params.init_params.TiltParams attribute) tilt_x (ptyrad.params.hypertune_params.TuneParams attribute) tilt_y (ptyrad.params.hypertune_params.TuneParams attribute) time_sync() (in module ptyrad.solver.reconstruction) timeout (ptyrad.params.hypertune_params.HypertuneParams attribute) tlr (ptyrad.params.hypertune_params.TuneParams attribute) toggle_grad_requires() (in module ptyrad.solver.reconstruction) torch_phasor() (in module ptyrad.core.functional) tune_params (ptyrad.params.hypertune_params.HypertuneParams attribute)

U

unit (ptyrad.params.init_params.MeasAddPoissonNoise attribute)

update_params (ptyrad.params.model_params.ModelParams attribute)

V

validate_params() (in module ptyrad.cli.commands) value (ptyrad.params.init_params.MeasAddPoissonNoise attribute) (ptyrad.params.init_params.MeasCalibration attribute) (ptyrad.params.init_params.MeasNormalization attribute) (ptyrad.params.init_params.MeasPad attribute) (ptyrad.params.init_params.MeasRemoveNegValues attribute) (ptyrad.params.init_params.ObjZResample attribute) (ptyrad.params.init_params.ProbeNormalization attribute)

verbosity (ptyrad.params.hypertune_params.HypertuneParams attribute)

W

weight (ptyrad.params.loss_params.LossPacbed attribute) (ptyrad.params.loss_params.LossPoissn attribute) (ptyrad.params.loss_params.LossSimlar attribute) (ptyrad.params.loss_params.LossSingle attribute) (ptyrad.params.loss_params.LossSparse attribute)

width (ptyrad.params.constraint_params.KrFilter attribute) (ptyrad.params.constraint_params.ProbeMaskK attribute) write_hdf5() (in module ptyrad.io.hierarchy) write_npy() (in module ptyrad.io.generic) write_tif() (in module ptyrad.io.generic)

Y

yaml2json() (in module ptyrad.params.parser)

Z

z_shift (ptyrad.params.hypertune_params.TuneParams attribute)

zarr_kwargs (ptyrad.params.init_params.FilePathWithKey attribute)