Index

_

__init__() (cdtools.datasets.CDataset method) (cdtools.datasets.Ptycho2DDataset method) (cdtools.models.Bragg2DPtycho method) (cdtools.models.CDIModel method) (cdtools.models.FancyPtycho method) (cdtools.models.Multislice2DPtycho method) (cdtools.models.MultislicePtycho method) (cdtools.models.RPI method) (cdtools.models.SimplePtycho method) (cdtools.reconstructors.AdamReconstructor method) (cdtools.reconstructors.LBFGSReconstructor method) (cdtools.reconstructors.Reconstructor method) (cdtools.reconstructors.SGDReconstructor method) (cdtools.tools.losses.AmplitudeMSENormalizer method) (cdtools.tools.losses.IntensityMSENormalizer method) (cdtools.tools.losses.SimplePoissonNLLNormalizer method)

_load() (cdtools.datasets.CDataset method) (cdtools.datasets.Ptycho2DDataset method)

A

accumulate() (cdtools.tools.losses.AmplitudeMSENormalizer method) (cdtools.tools.losses.IntensityMSENormalizer method), [1] (cdtools.tools.losses.SimplePoissonNLLNormalizer method), [1] Adam_optimize() (cdtools.models.CDIModel method) AdamReconstructor (class in cdtools.reconstructors) add_dark() (in module cdtools.tools.data) add_data() (in module cdtools.tools.data) add_detector() (in module cdtools.tools.data) add_entry_info() (in module cdtools.tools.data) add_mask() (in module cdtools.tools.data)

add_ptycho_translations() (in module cdtools.tools.data) add_qe_mask() (in module cdtools.tools.data) add_sample_info() (in module cdtools.tools.data) add_shot_to_shot_info() (in module cdtools.tools.data) add_source() (in module cdtools.tools.data) adjust_optimizer() (cdtools.reconstructors.AdamReconstructor method) (cdtools.reconstructors.LBFGSReconstructor method) (cdtools.reconstructors.Reconstructor method) (cdtools.reconstructors.SGDReconstructor method) amplitude_mse() (in module cdtools.tools.losses) AmplitudeMSENormalizer (class in cdtools.tools.losses)

B

Bragg2DPtycho (class in cdtools.models)

C

calc_consistency_prtf() (in module cdtools.tools.analysis) calc_deconvolved_cross_correlation() (in module cdtools.tools.analysis) calc_fidelity() (in module cdtools.tools.analysis) calc_frc() (in module cdtools.tools.analysis) calc_generalized_rms_error() (in module cdtools.tools.analysis) calc_mode_power_fractions() (in module cdtools.tools.analysis) calc_object_setup() (in module cdtools.tools.initializers) calc_rms_error() (in module cdtools.tools.analysis) calc_spectral_info() (in module cdtools.tools.analysis) calc_vn_entropy() (in module cdtools.tools.analysis) CDataset (class in cdtools.datasets) CDIModel (class in cdtools.models) cdtools.datasets module cdtools.models module cdtools.reconstructors module cdtools.tools.analysis module cdtools.tools.data module cdtools.tools.image_processing module

cdtools.tools.initializers module cdtools.tools.interactions module cdtools.tools.losses module cdtools.tools.measurements module cdtools.tools.plotting module cdtools.tools.propagators module center() (in module cdtools.tools.image_processing) center_probes() (cdtools.models.FancyPtycho method) (cdtools.models.MultislicePtycho method) centroid() (in module cdtools.tools.image_processing) centroid_sq() (in module cdtools.tools.image_processing) colorize() (in module cdtools.tools.plotting) compare() (cdtools.models.CDIModel method) convolve_1d() (in module cdtools.tools.image_processing) create_cxi() (in module cdtools.tools.data) crop_translations() (cdtools.datasets.Ptycho2DDataset method)

D

data_loader (cdtools.reconstructors.Reconstructor attribute)

downsample() (cdtools.datasets.Ptycho2DDataset method)

E

exit_wave_geometry() (in module cdtools.tools.initializers)

F

FancyPtycho (class in cdtools.models) far_field() (in module cdtools.tools.propagators) find_pixel_shift() (in module cdtools.tools.image_processing) find_shift() (in module cdtools.tools.image_processing)

find_subpixel_shift() (in module cdtools.tools.image_processing) forward() (cdtools.models.CDIModel method) from_cxi() (cdtools.datasets.CDataset class method) (cdtools.datasets.Ptycho2DDataset class method)

G

gaussian() (in module cdtools.tools.initializers) gaussian_probe() (in module cdtools.tools.initializers) generate_angular_spectrum_propagator() (in module cdtools.tools.propagators) generate_generalized_angular_spectrum_propagator() (in module cdtools.tools.propagators) generate_high_NA_k_intensity_map() (in module cdtools.tools.propagators) generate_subdominant_modes() (in module cdtools.tools.initializers) get_as() (cdtools.datasets.CDataset method) get_dark() (in module cdtools.tools.data) get_data() (in module cdtools.tools.data) get_detector_geometry() (cdtools.models.CDIModel method) (in module cdtools.tools.data)

get_entry_info() (in module cdtools.tools.data) get_mask() (in module cdtools.tools.data) get_obj_shape_and_n_modes() (cdtools.models.RPI method) get_probe_intensities() (cdtools.models.FancyPtycho method) get_ptycho_translations() (in module cdtools.tools.data) get_qe_mask() (in module cdtools.tools.data) get_sample_info() (in module cdtools.tools.data) get_shot_to_shot_info() (in module cdtools.tools.data) get_units_factor() (in module cdtools.tools.plotting) get_wavelength() (in module cdtools.tools.data)

H

h5_to_nested_dict() (in module cdtools.tools.data)

hann_window() (in module cdtools.tools.image_processing) high_NA_far_field() (in module cdtools.tools.propagators)

I

incoherent_sum() (in module cdtools.tools.measurements) inspect() (cdtools.datasets.CDataset method) (cdtools.datasets.Ptycho2DDataset method) (cdtools.models.CDIModel method)

intensity() (in module cdtools.tools.measurements) intensity_mse() (in module cdtools.tools.losses) IntensityMSENormalizer (class in cdtools.tools.losses) inverse_far_field() (in module cdtools.tools.propagators) inverse_near_field() (in module cdtools.tools.propagators)

L

LBFGS_optimize() (cdtools.models.CDIModel method)

LBFGSReconstructor (class in cdtools.reconstructors)

M

model (cdtools.reconstructors.Reconstructor attribute) module cdtools.datasets cdtools.models cdtools.reconstructors cdtools.tools.analysis cdtools.tools.data cdtools.tools.image_processing cdtools.tools.initializers cdtools.tools.interactions cdtools.tools.losses cdtools.tools.measurements cdtools.tools.plotting cdtools.tools.propagators

Multislice2DPtycho (class in cdtools.models) MultislicePtycho (class in cdtools.models)

N

near_field() (in module cdtools.tools.propagators) nested_dict_to_h5() (in module cdtools.tools.data) nested_dict_to_numpy() (in module cdtools.tools.data)

nested_dict_to_torch() (in module cdtools.tools.data) normalize_loss() (cdtools.tools.losses.AmplitudeMSENormalizer method) (cdtools.tools.losses.IntensityMSENormalizer method), [1] (cdtools.tools.losses.SimplePoissonNLLNormalizer method), [1]

O

optimize() (cdtools.reconstructors.AdamReconstructor method) (cdtools.reconstructors.LBFGSReconstructor method) (cdtools.reconstructors.Reconstructor method) (cdtools.reconstructors.SGDReconstructor method)

optimizer (cdtools.reconstructors.Reconstructor attribute) orthogonalize_probes() (in module cdtools.tools.analysis)

P

pad() (cdtools.datasets.Ptycho2DDataset method) pixel_to_translations() (in module cdtools.tools.interactions) plot_amplitude() (in module cdtools.tools.plotting) plot_colorized() (in module cdtools.tools.plotting) plot_illumination_intensity() (cdtools.models.FancyPtycho method) plot_imag() (in module cdtools.tools.plotting) plot_loss_history() (cdtools.models.CDIModel method) plot_mean_pattern() (cdtools.datasets.Ptycho2DDataset method) plot_nanomap() (in module cdtools.tools.plotting) plot_nanomap_with_images() (in module cdtools.tools.plotting)

plot_phase() (in module cdtools.tools.plotting) plot_real() (in module cdtools.tools.plotting) plot_translations() (in module cdtools.tools.plotting) plot_translations_and_originals() (cdtools.models.FancyPtycho method) poisson_nll() (in module cdtools.tools.losses) product_svd() (in module cdtools.tools.analysis) project_translations_to_sample() (in module cdtools.tools.interactions) Ptycho2DDataset (class in cdtools.datasets) ptycho_2D_linear() (in module cdtools.tools.interactions) ptycho_2D_round() (in module cdtools.tools.interactions) ptycho_2D_sinc() (in module cdtools.tools.interactions)

Q

quadratic_background() (in module cdtools.tools.measurements)

R

random_init() (cdtools.models.RPI method) Reconstructor (class in cdtools.reconstructors) remove_translations_mask() (cdtools.datasets.Ptycho2DDataset method)

report() (cdtools.models.CDIModel method) RPI (class in cdtools.models) RPI_interaction() (in module cdtools.tools.interactions) run_epoch() (cdtools.reconstructors.Reconstructor method)

S

save_figures() (cdtools.models.CDIModel method) save_on_exception() (cdtools.models.CDIModel method) save_on_exit() (cdtools.models.CDIModel method) save_results() (cdtools.models.Bragg2DPtycho method) (cdtools.models.CDIModel method) (cdtools.models.FancyPtycho method) (cdtools.models.Multislice2DPtycho method) (cdtools.models.MultislicePtycho method) (cdtools.models.RPI method) (cdtools.models.SimplePtycho method) save_to_h5() (cdtools.models.CDIModel method) scheduler (cdtools.reconstructors.Reconstructor attribute) setup_dataloader() (cdtools.reconstructors.Reconstructor method) SGD_optimize() (cdtools.models.CDIModel method)

SGDReconstructor (class in cdtools.reconstructors) SHARP_style_near_field_probe() (in module cdtools.tools.initializers) SHARP_style_probe() (in module cdtools.tools.initializers) SimplePoissonNLLNormalizer (class in cdtools.tools.losses) SimplePtycho (class in cdtools.models) sinc_subpixel_shift() (in module cdtools.tools.image_processing) skip_computation() (cdtools.models.CDIModel method) spectral_init() (cdtools.models.RPI method) split() (cdtools.datasets.Ptycho2DDataset method) standardize() (in module cdtools.tools.analysis) standardize_reconstruction_pair() (in module cdtools.tools.analysis) standardize_reconstruction_set() (in module cdtools.tools.analysis) STEM_style_probe() (in module cdtools.tools.initializers) store_detector_geometry() (cdtools.models.CDIModel method) synthesize_reconstructions() (in module cdtools.tools.analysis)

T

tidy_probes() (cdtools.models.FancyPtycho method) (cdtools.models.Multislice2DPtycho method) (cdtools.models.MultislicePtycho method) to() (cdtools.datasets.CDataset method) (cdtools.datasets.Ptycho2DDataset method) (cdtools.models.Multislice2DPtycho method)

to_cxi() (cdtools.datasets.CDataset method) (cdtools.datasets.Ptycho2DDataset method) translations_to_pixel() (in module cdtools.tools.interactions)

U

uniform_init() (cdtools.models.RPI method)