Index

_

__init__() (PyLorentz.dataset.base_dataset.BaseDataset method) (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries method) (PyLorentz.phase.AD_phase.ADPhase method) (PyLorentz.phase.base_tie.BaseTIE method) (PyLorentz.phase.DIP_NN.conv2dblock method) (PyLorentz.phase.DIP_NN.DIP_NN method) (PyLorentz.phase.DIP_NN.upsample_block method) (PyLorentz.phase.sitie.SITIE method) (PyLorentz.phase.tie.TIE method) (PyLorentz.sim.base_sim.BaseSim method) (PyLorentz.sim.sim.SimLTEM method) (PyLorentz.utils.microscopes.Microscope method)

A

ADPhase (class in PyLorentz.phase.AD_phase)

apply_transforms() (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries method)

B

B0 (PyLorentz.sim.base_sim.BaseSim property) backpropagate_wave() (PyLorentz.utils.microscopes.Microscope method) bandpass_filter() (in module PyLorentz.utils.filter) BaseDataset (class in PyLorentz.dataset.base_dataset) BaseSim (class in PyLorentz.sim.base_sim) BaseTIE (class in PyLorentz.phase.base_tie) beam_energy (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) (PyLorentz.phase.base_tie.BaseTIE property) (PyLorentz.sim.base_sim.BaseSim property)

best_amp (PyLorentz.phase.AD_phase.ADPhase property) best_amp_full (PyLorentz.phase.AD_phase.ADPhase property) best_phase (PyLorentz.phase.AD_phase.ADPhase property) best_phase_full (PyLorentz.phase.AD_phase.ADPhase property) bloch() (in module PyLorentz.utils.magnetizations) blochII() (in module PyLorentz.utils.magnetizations)

C

Ca (PyLorentz.utils.microscopes.Microscope attribute) Cc (PyLorentz.utils.microscopes.Microscope attribute) circ4() (in module PyLorentz.utils.utils) color_im() (in module PyLorentz.visualize.colorwheel) compute_diffraction_pattern() (PyLorentz.utils.microscopes.Microscope method)

compute_image() (PyLorentz.utils.microscopes.Microscope method) compute_phase() (PyLorentz.sim.sim.SimLTEM method) conv2dblock (class in PyLorentz.phase.DIP_NN) copy() (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) (PyLorentz.sim.sim.SimLTEM method) Cs (PyLorentz.utils.microscopes.Microscope attribute)

D

data_dir (PyLorentz.dataset.base_dataset.BaseDataset property) def_spr (PyLorentz.utils.microscopes.Microscope attribute) defocus (PyLorentz.utils.microscopes.Microscope attribute) DefocusedDataset (class in PyLorentz.dataset.defocused_dataset) defvals (PyLorentz.dataset.defocused_dataset.DefocusedDataset property) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property)

defvals_index (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) device (PyLorentz.phase.AD_phase.ADPhase property) DIP_NN (class in PyLorentz.phase.DIP_NN) dist4() (in module PyLorentz.utils.utils) (in module PyLorentz.visualize.colorwheel)

E

E (PyLorentz.utils.microscopes.Microscope attribute)

energy (PyLorentz.dataset.defocused_dataset.DefocusedDataset property) extract_patches() (in module PyLorentz.utils.filter)

F

filter() (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries method) filter_hotpix() (in module PyLorentz.utils.filter) flat_shape_func (PyLorentz.sim.base_sim.BaseSim property) flip (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) (PyLorentz.phase.tie.TIE property) flipstack (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) format_defocus() (in module PyLorentz.io.write)

forward() (PyLorentz.phase.DIP_NN.conv2dblock method) (PyLorentz.phase.DIP_NN.DIP_NN method) (PyLorentz.phase.DIP_NN.upsample_block method) fov (PyLorentz.dataset.base_dataset.BaseDataset property) from_array() (PyLorentz.phase.sitie.SITIE class method) from_files() (PyLorentz.dataset.through_focal_series.ThroughFocalSeries class method) from_TFS() (PyLorentz.dataset.defocused_dataset.DefocusedDataset class method) full_defvals (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) full_stack (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property)

G

gamma (PyLorentz.utils.microscopes.Microscope attribute) gaussian_sigma (PyLorentz.phase.AD_phase.ADPhase property) get_cmap() (in module PyLorentz.visualize.colorwheel) get_flat_shape_func() (PyLorentz.sim.base_sim.BaseSim method) get_optimum_defocus() (PyLorentz.utils.microscopes.Microscope method)

get_scherzer_defocus() (PyLorentz.utils.microscopes.Microscope method) get_shape_func() (PyLorentz.sim.base_sim.BaseSim method) get_TFs() (PyLorentz.phase.AD_phase.ADPhase method) get_transfer_function() (PyLorentz.utils.microscopes.Microscope method) guess_amp (PyLorentz.phase.AD_phase.ADPhase property) guess_phase (PyLorentz.phase.AD_phase.ADPhase property)

H

hopfion() (in module PyLorentz.utils.magnetizations)

hopfion_cylinder() (in module PyLorentz.utils.magnetizations)

I

image (PyLorentz.dataset.defocused_dataset.DefocusedDataset property) images (PyLorentz.dataset.defocused_dataset.DefocusedDataset property) images_cropped (PyLorentz.dataset.defocused_dataset.DefocusedDataset property)

images_filtered (PyLorentz.dataset.defocused_dataset.DefocusedDataset property) imstack (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) infocus (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) input_DIP (PyLorentz.phase.AD_phase.ADPhase property)

L

lam (PyLorentz.utils.microscopes.Microscope attribute) len_tfs (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) lillihook() (in module PyLorentz.utils.magnetizations)

lineplot_im() (in module PyLorentz.visualize.show) LinsupPhase (class in PyLorentz.sim.comp_phase) load() (PyLorentz.dataset.defocused_dataset.DefocusedDataset class method) load_ovf() (PyLorentz.sim.sim.SimLTEM class method)

M

mags (PyLorentz.sim.base_sim.BaseSim property) make_colorwheel() (in module PyLorentz.visualize.colorwheel) make_colorwheelz() (in module PyLorentz.visualize.colorwheel) MansuripurPhase (class in PyLorentz.sim.comp_phase) mem_thickness (PyLorentz.sim.base_sim.BaseSim property) mem_V0 (PyLorentz.sim.base_sim.BaseSim property) mem_xip0 (PyLorentz.sim.base_sim.BaseSim property) Microscope (class in PyLorentz.utils.microscopes) module PyLorentz.dataset.base_dataset PyLorentz.dataset.defocused_dataset PyLorentz.dataset.through_focal_series PyLorentz.io.ovf PyLorentz.io.read PyLorentz.io.write PyLorentz.phase.AD_phase PyLorentz.phase.base_tie PyLorentz.phase.DIP_NN PyLorentz.phase.sitie PyLorentz.phase.tie PyLorentz.sim.base_sim PyLorentz.sim.comp_phase PyLorentz.sim.sim PyLorentz.utils.filter PyLorentz.utils.magnetizations PyLorentz.utils.microscopes PyLorentz.utils.utils PyLorentz.visualize.colorwheel PyLorentz.visualize.show PyLorentz.visualize.vector_show

Mx (PyLorentz.sim.base_sim.BaseSim property) My (PyLorentz.sim.base_sim.BaseSim property) Mz (PyLorentz.sim.base_sim.BaseSim property)

N

neel() (in module PyLorentz.utils.magnetizations)

norm_image() (in module PyLorentz.utils.utils)

O

orig_infocus (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) orig_shape2D (PyLorentz.dataset.base_dataset.BaseDataset property)

overwrite_rename() (in module PyLorentz.io.write) overwrite_rename_dir() (in module PyLorentz.io.write)

P

pad (PyLorentz.phase.AD_phase.ADPhase property) phase_B (PyLorentz.sim.base_sim.BaseSim property) phase_B_full (PyLorentz.phase.AD_phase.ADPhase property) phase_E (PyLorentz.phase.tie.TIE property) (PyLorentz.sim.base_sim.BaseSim property) phase_method (PyLorentz.sim.base_sim.BaseSim property) phase_shape (PyLorentz.sim.base_sim.BaseSim property) phase_T (PyLorentz.sim.base_sim.BaseSim property) phi_a (PyLorentz.utils.microscopes.Microscope attribute) prep_dict_for_json() (in module PyLorentz.io.write) preprocess() (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries method) PyLorentz.dataset.base_dataset module PyLorentz.dataset.defocused_dataset module PyLorentz.dataset.through_focal_series module PyLorentz.io.ovf module PyLorentz.io.read module PyLorentz.io.write module PyLorentz.phase.AD_phase module PyLorentz.phase.base_tie module

PyLorentz.phase.DIP_NN module PyLorentz.phase.sitie module PyLorentz.phase.tie module PyLorentz.sim.base_sim module PyLorentz.sim.comp_phase module PyLorentz.sim.sim module PyLorentz.utils.filter module PyLorentz.utils.magnetizations module PyLorentz.utils.microscopes module PyLorentz.utils.utils module PyLorentz.visualize.colorwheel module PyLorentz.visualize.show module PyLorentz.visualize.vector_show module

Q

qc (PyLorentz.phase.base_tie.BaseTIE property)

R

read_image() (in module PyLorentz.io.read) read_json() (in module PyLorentz.io.read) read_ovf() (in module PyLorentz.io.ovf) recon_amp (PyLorentz.phase.AD_phase.ADPhase property) recon_amp_full (PyLorentz.phase.AD_phase.ADPhase property) recon_defval (PyLorentz.phase.sitie.SITIE property) (PyLorentz.phase.tie.TIE property) recon_phase (PyLorentz.phase.AD_phase.ADPhase property)

recon_phase_full (PyLorentz.phase.AD_phase.ADPhase property) reconstruct() (PyLorentz.phase.AD_phase.ADPhase method) (PyLorentz.phase.sitie.SITIE method) (PyLorentz.phase.tie.TIE method) reset_transforms() (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries method) rng_seed() (in module PyLorentz.phase.DIP_NN) roll_cmap() (in module PyLorentz.visualize.colorwheel)

S

sample_params (PyLorentz.sim.base_sim.BaseSim property) sample_V0 (PyLorentz.sim.base_sim.BaseSim property) sample_xip0 (PyLorentz.sim.base_sim.BaseSim property) save_results() (PyLorentz.phase.AD_phase.ADPhase method) (PyLorentz.phase.sitie.SITIE method) (PyLorentz.phase.tie.TIE method) save_tif() (in module PyLorentz.io.write) scale (PyLorentz.dataset.base_dataset.BaseDataset property) (PyLorentz.sim.base_sim.BaseSim property) (PyLorentz.utils.microscopes.Microscope property) scope (PyLorentz.phase.AD_phase.ADPhase property) select_ROI() (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries method) set_best_iter() (PyLorentz.phase.AD_phase.ADPhase method) set_sample_params() (PyLorentz.sim.base_sim.BaseSim method) shape (PyLorentz.dataset.base_dataset.BaseDataset property) (PyLorentz.dataset.defocused_dataset.DefocusedDataset property) (PyLorentz.dataset.through_focal_series.ThroughFocalSeries property) (PyLorentz.phase.AD_phase.ADPhase property) (PyLorentz.sim.base_sim.BaseSim property) shape_full (PyLorentz.phase.AD_phase.ADPhase property) shape_func (PyLorentz.sim.base_sim.BaseSim property) shift_cmap_center() (in module PyLorentz.visualize.colorwheel) show_2D() (in module PyLorentz.visualize.vector_show)

show_3D() (in module PyLorentz.visualize.vector_show) show_all() (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) show_best() (PyLorentz.phase.AD_phase.ADPhase method) show_fft() (in module PyLorentz.visualize.show) show_final() (PyLorentz.phase.AD_phase.ADPhase method) show_im() (in module PyLorentz.visualize.show) (PyLorentz.dataset.defocused_dataset.DefocusedDataset method) show_im_peaks() (in module PyLorentz.visualize.show) show_mags() (PyLorentz.sim.base_sim.BaseSim method) show_phase() (PyLorentz.sim.base_sim.BaseSim method) show_phase_B() (PyLorentz.sim.base_sim.BaseSim method) show_phase_E() (PyLorentz.phase.tie.TIE method) (PyLorentz.sim.base_sim.BaseSim method) show_prediction() (PyLorentz.phase.AD_phase.ADPhase method) show_sims() (in module PyLorentz.visualize.show) show_stack() (in module PyLorentz.visualize.show) show_tfs() (PyLorentz.dataset.through_focal_series.ThroughFocalSeries method) show_thickness_map() (PyLorentz.sim.base_sim.BaseSim method) sigma (PyLorentz.utils.microscopes.Microscope attribute) sim_images() (PyLorentz.sim.sim.SimLTEM method) sim_TFS() (PyLorentz.sim.sim.SimLTEM method) SimLTEM (class in PyLorentz.sim.sim) SITIE (class in PyLorentz.phase.sitie) splitnum() (in module PyLorentz.io.write) sym (PyLorentz.phase.base_tie.BaseTIE property)

T

theta_c (PyLorentz.utils.microscopes.Microscope attribute) ThroughFocalSeries (class in PyLorentz.dataset.through_focal_series) tick_label_formatter() (in module PyLorentz.visualize.show) TIE (class in PyLorentz.phase.tie)

tilt_x (PyLorentz.sim.base_sim.BaseSim property) tilt_y (PyLorentz.sim.base_sim.BaseSim property) transforms (PyLorentz.dataset.base_dataset.BaseDataset property) tukey2d() (in module PyLorentz.utils.utils) tukey2D() (in module PyLorentz.visualize.show)

U

upsample_block (class in PyLorentz.phase.DIP_NN)

V

visualize() (PyLorentz.phase.AD_phase.ADPhase method) (PyLorentz.phase.sitie.SITIE method) (PyLorentz.phase.tie.TIE method) (PyLorentz.sim.base_sim.BaseSim method)

vprint() (PyLorentz.dataset.base_dataset.BaseDataset method) (PyLorentz.sim.base_sim.BaseSim method)

W

warning_on_one_line() (in module PyLorentz.phase.base_tie) weight_reset() (in module PyLorentz.phase.DIP_NN) write_json() (in module PyLorentz.io.write)

write_ovf() (in module PyLorentz.io.ovf) write_tif() (in module PyLorentz.io.write) write_tiff() (in module PyLorentz.io.write)

Z

zscale (PyLorentz.sim.base_sim.BaseSim property)