Index

A

Align() (dataset.ESRF method) (parallelizer.OAR method) AlignProjection() (dataset.Dataset method) (dataset.ESRF method)

AlignProjections() (dataset.Dataset method) alpha() (phaseretrieval.HIO_ER property) Alpha() (phaseretrieval.PhaseRetrievalAlgorithm2D property) AmplitudeConstraint() (phaseretrieval.HIO_ER method) ApplyTransformation() (utilities.RegistrationAlgorithm method)

C

CalculateAxisPosition() (dataset.ESRF method) CalculateAxisPositions() (dataset.ESRF method) CalculateMotion() (dataset.ESRF method) CalculateReferenceDistance() (dataset.ESRF method) ClearShifts() (dataset.ESRF method) CloseAll() (utilities.PyplotImageDisplayer method) ComputeFactors() (phaseretrieval.CTF method) (phaseretrieval.PhaseRetrievalAlgorithm2D method)

CreateMultimaterialPrior() (phaseretrieval.Mixed method) CreateParameterFile() (tomography.PyHST method) CreateReconstructionFiles() (tomography.PyHST method) CTF (class in phaseretrieval) (class in propagator) CTFPurePhase (class in phaseretrieval)

D

dataset module Dataset (class in dataset) Difference() (dataset.ESRF method) DifferenceProjection() (dataset.ESRF method)

DifferenceProjections() (dataset.ESRF method) Display() (utilities.PyplotImageDisplayer method) DisplayLcurve() (phaseretrieval.Mixed method) DisplayShifts() (dataset.ESRF method) DisplayStack() (utilities.PyplotImageDisplayer method)

E

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

ErrorEstimate() (phaseretrieval.HIO_ER method) ErrorReduction() (phaseretrieval.HIO_ER method) ESRF (class in dataset)

F

FitShifts() (dataset.ESRF method) ForwardProject() (tomography.PyHST method)

FrequencyVariable() (phaseretrieval.PhaseRetrievalAlgorithm2D method) Fresnel (class in propagator) Fresnel_number() (phaseretrieval.PhaseRetrievalAlgorithm2D property)

G

GetAlignment() (dataset.Dataset method) (dataset.ESRF method) GetAttenuation() (dataset.ESRF method) GetImage() (dataset.Dataset method) (dataset.ESRF method) GetMotion() (dataset.ESRF method)

GetPhase() (dataset.ESRF method) GetPrior() (phaseretrieval.Mixed method) GetProjection() (dataset.ESRF method) (dataset.Nanomax method) (dataset.NanomaxPreprocessed2D method) (dataset.NanomaxPreprocessedTomo method) GetSinogram() (dataset.ESRF method)

H

HIO_ER (class in phaseretrieval)

HybridInputOutput() (phaseretrieval.HIO_ER method)

I

ImageDisplayer (class in utilities)

Initialise() (dataset.Dataset method) Iterative (class in phaseretrieval)

L

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

Launch() (parallelizer.OAR method) Lcurve() (phaseretrieval.Mixed method) LogisticImageFilter (class in utilities)

M

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

N

Nanomax (class in dataset) NanomaxPreprocessed (class in dataset)

NanomaxPreprocessed2D (class in dataset) NanomaxPreprocessedTomo (class in dataset) NLCG (class in phaseretrieval)

O

OAR (class in parallelizer)

on_key() (utilities.StackViewer method)

P

Parallelize() (in module parallelizer) parallelizer module phaseretrieval module PhaseRetrievalAlgorithm2D (class in phaseretrieval) Populate() (dataset.ESRF method) Preprocess() (dataset.ESRF method)

Propagate() (propagator.Propagator method) PropagateProjection() (propagator.CTF method) (propagator.Fresnel method) PropagateProjections() (propagator.Propagator method) propagator module Propagator (class in propagator) PyHST (class in tomography) PyplotImageDisplayer (class in utilities)

R

ReadParameterFile() (dataset.ESRF method) Reconstruct() (phaseretrieval.Iterative method) (phaseretrieval.PhaseRetrievalAlgorithm2D method) (tomography.PyHST method) (tomography.TomoPy method) ReconstructDifference() (phaseretrieval.PhaseRetrievalAlgorithm2D method) ReconstructProjection() (phaseretrieval.CTF method) (phaseretrieval.CTFPurePhase method) (phaseretrieval.HIO_ER method) (phaseretrieval.Mixed method) (phaseretrieval.NLCG method)

ReconstructProjections() (phaseretrieval.PhaseRetrievalAlgorithm2D method) Register() (utilities.RegistrationAlgorithm method) RegistrationAlgorithm (class in utilities) Resize() (in module utilities)

S

Serial() (in module parallelizer) SetShift() (dataset.ESRF method)

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

T

tomography module

Tomography (class in tomography) TomoPy (class in tomography)

U

update() (in module utilities) (utilities.StackViewer method) UpdateAttenuation() (dataset.ESRF method)

UpdatePhase() (dataset.ESRF method) utilities module

W

WriteImage() (dataset.Dataset method) (dataset.ESRF method)

WriteOarFiles() (parallelizer.OAR method) WriteParameterFile() (dataset.ESRF method)