Index

A

adjoint_frechet_derivative() (in module operators) adjoint_Frechet_derivative() (phaseretrieval.IRGN method) ADMM_CTF (class in phaseretrieval) align() (dataset.ESRF method) align_projection() (dataset.Dataset method) (dataset.ESRF method)

align_projections() (dataset.Dataset method) alpha (phaseretrieval.GradientDescent property) (phaseretrieval.NLCG property) Alpha (phaseretrieval.PhaseRetrievalAlgorithm2D property) amplitude_constraint() (in module operators) apply_transformation() (utilities.RegistrationAlgorithm method)

B

Backend (class in dataset)

backend_initialized (dataset.EDF property) (dataset.HDF5 property)

C

calculate_axis_position() (dataset.ESRF method) calculate_axis_positions() (dataset.ESRF method) calculate_motion() (dataset.ESRF method) calculate_reference_position() (dataset.ESRF method) close_all() (utilities.PyplotImageDisplayer method)

create_multimaterial_prior() (phaseretrieval.CTF method) CTF (class in phaseretrieval) (class in propagator) CTFHOM (class in phaseretrieval) CTFPurePhase (class in phaseretrieval)

D

dataset module Dataset (class in dataset) delta_beta (phaseretrieval.CTFHOM property) (phaseretrieval.TIEHOM property)

display() (utilities.PyplotImageDisplayer method) display_alignment() (dataset.ESRF method) display_Lcurve() (phaseretrieval.Mixed method) display_stack() (utilities.PyplotImageDisplayer method) div() (in module operators)

E

EDF (class in dataset) ElastixAffine (class in utilities) ElastixRigid (class in utilities) ElastixSimilar (class in utilities)

Elettra (class in dataset) error_estimate() (in module operators) error_reduction() (phaseretrieval.HIO_ER method) ESRF (class in dataset) ESRF_dev (class in dataset)

F

fit_alignment() (dataset.ESRF method) forward() (in module operators) ForwardProject() (tomography.PyHST method) frechet_derivative() (in module operators)

Frechet_derivative() (phaseretrieval.IRGN method) frequency_variable() (phaseretrieval.PhaseRetrievalAlgorithm2D method) Fresnel (class in propagator) Fresnel_number (phaseretrieval.PhaseRetrievalAlgorithm2D property)

G

GDTV (class in phaseretrieval) get_alignment() (dataset.Dataset method) (dataset.ESRF method) get_backend() (in module dataset) get_image() (dataset.EDF method) (dataset.ESRF method) (dataset.HDF5 method) get_motion() (dataset.ESRF method) get_prior() (phaseretrieval.Mixed method)

get_projection() (dataset.Elettra method) (dataset.ESRF method) (dataset.ESRF_dev method) (dataset.Nanomax method) (dataset.NanomaxPreprocessed2D method) (dataset.NanomaxPreprocessedTomo method) GetSinogram() (dataset.ESRF method) grad() (in module operators) GradientDescent (class in phaseretrieval)

H

HDF5 (class in dataset) HIO_ER (class in phaseretrieval)

HPR (class in phaseretrieval) hybrid_input_output() (phaseretrieval.HIO_ER method) hybrid_projection_reflection() (phaseretrieval.HPR method)

I

ID16B (class in dataset) ID19 (class in dataset) ImageDisplayer (class in utilities)

initialize_backend() (dataset.EDF method) (dataset.HDF5 method) inv_block_toeplitz_ctf_betaoverdelta() (phaseretrieval.ADMM_CTF method) IRGN (class in phaseretrieval)

L

Lambda (dataset.Dataset property) (phaseretrieval.PhaseRetrievalAlgorithm2D property)

Launch() (parallelizer.OAR method) Lcurve() (phaseretrieval.Mixed method)

M

Mixed (class in phaseretrieval) module dataset operators parallelizer phaseretrieval propagator tomography utilities

N

Nanomax (class in dataset) NanomaxPreprocessed (class in dataset) NanomaxPreprocessed2D (class in dataset) NanomaxPreprocessedTomo (class in dataset) nfx (dataset.Dataset property) (dataset.ESRF property) (phaseretrieval.PhaseRetrievalAlgorithm2D property)

nfy (dataset.Dataset property) (dataset.ESRF property) (phaseretrieval.PhaseRetrievalAlgorithm2D property) NLCG (class in phaseretrieval) NLPDHGM (class in phaseretrieval)

O

OAR (class in parallelizer) operator_ctf_adjoint() (phaseretrieval.ADMM_CTF method)

operator_to_inverse() (phaseretrieval.IRGN method) operators module

P

parallelizer module PDHGM_CTF (class in phaseretrieval) phaseretrieval module PhaseRetrievalAlgorithm2D (class in phaseretrieval) populate() (dataset.ESRF method) preprocess() (dataset.ESRF method)

preprocessing_initialised (dataset.HDF5 property) propagate_image() (propagator.Propagator method) propagate_projection() (propagator.Propagator method) PropagateProjection() (propagator.CTF method) propagator module Propagator (class in propagator) PyHST (class in tomography) PyplotImageDisplayer (class in utilities)

R

RAAR (class in phaseretrieval) read_parameters_backend() (dataset.EDF method) (dataset.HDF5 method) read_parameters_frontend() (dataset.Elettra method) (dataset.ESRF_dev method) (dataset.ID19 method) (dataset.Nanomax method) (dataset.NanomaxPreprocessed method) (dataset.NanomaxPreprocessed2D method) (dataset.NanomaxPreprocessedTomo method) reconstruct() (tomography.PyHST method) reconstruct_image() (phaseretrieval.PhaseRetrievalAlgorithm2D method) reconstruct_projection() (phaseretrieval.HIO_ER method) (phaseretrieval.HPR method) (phaseretrieval.NLPDHGM method) (phaseretrieval.PhaseRetrievalAlgorithm2D method) (phaseretrieval.RAAR method)

reconstruct_projections() (phaseretrieval.PhaseRetrievalAlgorithm2D method) register() (utilities.RegistrationAlgorithm method) RegistrationAlgorithm (class in utilities) relaxed_averaged_alternating_reflections() (phaseretrieval.RAAR method) resize() (in module utilities) retriever (phaseretrieval.GradientDescent property) (phaseretrieval.HIO_ER property) (phaseretrieval.HPR property) (phaseretrieval.NLCG property) (phaseretrieval.RAAR property)

S

Serial() (in module parallelizer) shrinkage() (in module operators)

simple_propagator() (phaseretrieval.PhaseRetrievalAlgorithm2D method) SLURM() (in module parallelizer) StackViewer (class in utilities)

T

TIEHOM (class in phaseretrieval) tomography module

Tomography (class in tomography)

U

update() (in module utilities)

utilities module

W

write_dark() (dataset.HDF5 method) write_flat() (dataset.HDF5 method) write_image() (dataset.EDF method) (dataset.ESRF method) (dataset.HDF5 method)

WriteOarFiles() (parallelizer.OAR method)