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)

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

A

AD_optimize() (cdtools.models.CDIModel method) Adam_optimize() (cdtools.models.CDIModel method) 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_sample_info() (in module cdtools.tools.data) add_shot_to_shot_info() (in module cdtools.tools.data) add_source() (in module cdtools.tools.data) amplitude_mse() (in module 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.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

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_ptycho_translations() (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) inverse_far_field() (in module cdtools.tools.propagators) inverse_near_field() (in module cdtools.tools.propagators)

L

LBFGS_optimize() (cdtools.models.CDIModel method)

M

module cdtools.datasets cdtools.models 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)

O

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_imag() (in module cdtools.tools.plotting) 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) 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) remove_translations_mask() (cdtools.datasets.Ptycho2DDataset method)

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

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) SGD_optimize() (cdtools.models.CDIModel method)

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