Index

A

AberratedMieLens (class in holopy.scattering.theory.mielens) AberratedMieLensCalculator (class in holopy.scattering.theory.mielensfunctions) Accumulator (class in holopy.core.io.io) add() (Scatterers method), [1] (Spheres method) add_attr() (FitResult method) add_noise() (in module holopy.core.process.img_proc)

add_parameter() (Mapper method) add_stage_strategy() (TemperedStrategy method) add_tie() (Model method) AlBlFunctions (class in holopy.scattering.theory.mielensfunctions) alpha (AlphaModel property) AlphaModel (class in holopy.inference.model) asymmetry_parameter() (in module holopy.scattering.theory.mie_f.miescatlib) AutoTheoryFailed

B

BadImage best_fit() (FitResult method) bg_correct() (in module holopy.core.process.img_proc) Bisphere (class in holopy.scattering.scatterer.bisphere) bound_union() (in module holopy.scattering.scatterer.scatterer)

BoundedGaussian (class in holopy.core.prior) bounds (CsgScatterer property) (Difference property) (Scatterer property) burn_in() (SamplingResult method)

C

calc_cross_sections() (in module holopy.scattering.interface) calc_field() (in module holopy.scattering.interface) calc_holo() (in module holopy.scattering.interface) calc_intensity() (in module holopy.scattering.interface) calc_residuals() (NmpfitStrategy method) calc_scat_matrix() (in module holopy.scattering.interface) calculate_al_bl() (AlBlFunctions static method) (in module holopy.scattering.theory.mielensfunctions) calculate_cross_sections() (ImageFormation method) calculate_pil_taul() (in module holopy.scattering.theory.mielensfunctions) calculate_scattered_field() (ImageFormation method) (MieLensCalculator method), [1] calculate_scattering_matrix() (ImageFormation method) calculate_total_field() (MieLensCalculator method), [1] calculate_total_intensity() (MieLensCalculator method), [1] can_handle() (DDA class method) (Lens method) (Mie method) (MieLens method) (Multisphere method) (ScatteringTheory method) (Tmatrix method) Capsule (class in holopy.scattering.scatterer.capsule) cartesian_distance() (in module holopy.core.math) center (LayeredSphere attribute) (Sphere attribute) (Spheres property) (Spheroid attribute)

center_find() (in module holopy.core.process.centerfinder) CenteredScatterer (class in holopy.scattering.scatterer.scatterer) centers (Spheres property) check() (LimitOverlaps method) check_display() (in module holopy.core.io.vis) check_for_ties() (Mapper method) chisq() (in module holopy.core.math) choose_pool() (in module holopy.core.utils) class_loader() (in module holopy.core.io.serialize) class_representer() (in module holopy.core.io.serialize) clean_concat() (in module holopy.core.metadata) cleanup_from_fit() (NmpfitStrategy method) click() (Show2D method) close() (NonePool method) CmaStrategy (class in holopy.inference.cmaes) complex_constructor() (in module holopy.core.io.serialize) complex_representer() (in module holopy.core.io.serialize) ComplexPrior (class in holopy.core.prior) contains() (Scatterer method) convert_to_map() (Mapper method) CoordSysError copy_metadata() (in module holopy.core.metadata) cross_sections() (in module holopy.scattering.theory.mie_f.miescatlib) CsgScatterer (class in holopy.scattering.scatterer.csg) Cylinder (class in holopy.scattering.scatterer.cylinder)

D

data_grid() (in module holopy.core.metadata) DDA (class in holopy.scattering.theory.dda) default_extension() (in module holopy.core.io.io) DependencyMissing DeprecationError desired_coordinate_system (Lens attribute) (MieLens attribute) (ScatteringTheory attribute)

detector_grid() (in module holopy.core.metadata) detector_points() (in module holopy.core.metadata) determine_default_theory_for() (in module holopy.scattering.interface) detrend() (in module holopy.core.process.img_proc) dict_to_array() (in module holopy.core.metadata) dict_without() (in module holopy.core.utils) Difference (class in holopy.scattering.scatterer.csg) display_image() (in module holopy.core.io.vis) draw() (Show2D method)

E

edit_map_indices() (in module holopy.core.mapping) Ellipsoid (class in holopy.scattering.scatterer.ellipsoid) emcee_lnprobs_DataArray() (in module holopy.inference.emcee) emcee_samples_DataArray() (in module holopy.inference.emcee) EmceeStrategy (class in holopy.inference.emcee) ensure_array() (in module holopy.core.utils)

ensure_listlike() (in module holopy.core.utils) ensure_parameters_are_listlike() (Model method) ensure_scalar() (in module holopy.core.utils) eps (Multisphere attribute) evaluate() (LnpostWrapper method) ExactModel (class in holopy.inference.model)

F

fft() (in module holopy.core.process.fourier) finalize() (in module holopy.scattering.interface) find_bounds() (in module holopy.scattering.scatterer.scatterer) find_transformation_function() (in module holopy.core.math) fit() (CmaStrategy method) (in module holopy.inference.interface) (LeastSquaresScipyStrategy method) (Model method) (NmpfitStrategy method) FitResult (class in holopy.inference.result) flat() (in module holopy.core.metadata)

format_coord() (Show2D method) forward() (FitResult method) (Model method) from_flat() (in module holopy.core.metadata) from_parameters() (RigidCluster method) (Scatterer method) (Scatterers method), [1] (ScatteringTheory method) from_yaml() (HoloPyObject class method) (Model class method) ft_coord() (in module holopy.core.process.fourier) ft_coords() (in module holopy.core.process.fourier)

G

gauss_legendre_pts_wts() (in module holopy.scattering.theory.lens) (in module holopy.scattering.theory.mielensfunctions) Gaussian (class in holopy.core.prior) generate_guess() (in module holopy.core.prior) (Model method) get_component_list() (Scatterers method) get_errors_from_minimizer() (NmpfitStrategy method) get_example_data() (in module holopy.core.io.io) get_example_data_path() (in module holopy.core.io.io) get_extents() (in module holopy.core.metadata)

get_parameter_index() (Mapper method) get_spacing() (in module holopy.core.metadata) (in module holopy.core.process.fourier) get_values() (in module holopy.core.metadata) get_wavevec_from() (in module holopy.scattering.imageformation) guess (Gaussian property) (TransformedPrior property) guess_hologram (FitResult property) guess_parameters (FitResult property) guess_scatterer (FitResult property)

H

hologram (FitResult property) holopy module holopy.core module holopy.core.errors module holopy.core.holopy_object module holopy.core.io module holopy.core.io.io module holopy.core.io.serialize module holopy.core.io.vis module holopy.core.mapping module holopy.core.math module holopy.core.metadata module holopy.core.prior module holopy.core.process module holopy.core.process.centerfinder module holopy.core.process.fourier module holopy.core.process.img_proc module holopy.core.utils module holopy.inference module holopy.inference.cmaes module holopy.inference.emcee module holopy.inference.interface module holopy.inference.model module holopy.inference.nmpfit module holopy.inference.result module holopy.inference.scipyfit module holopy.propagation module holopy.propagation.convolution_propagation module holopy.propagation.point_source_propagate module holopy.scattering module

holopy.scattering.errors module holopy.scattering.imageformation module holopy.scattering.interface module holopy.scattering.scatterer module holopy.scattering.scatterer.bisphere module holopy.scattering.scatterer.capsule module holopy.scattering.scatterer.composite module holopy.scattering.scatterer.csg module holopy.scattering.scatterer.cylinder module holopy.scattering.scatterer.ellipsoid module holopy.scattering.scatterer.janus module holopy.scattering.scatterer.scatterer module holopy.scattering.scatterer.sphere module holopy.scattering.scatterer.spherecluster module holopy.scattering.scatterer.spheroid module holopy.scattering.theory module holopy.scattering.theory.dda module holopy.scattering.theory.lens module holopy.scattering.theory.mie module holopy.scattering.theory.mie_f module holopy.scattering.theory.mie_f.mie_specfuncs module holopy.scattering.theory.mie_f.miescatlib module holopy.scattering.theory.mie_f.multilayer_sphere_lib module holopy.scattering.theory.mielens module holopy.scattering.theory.mielensfunctions module holopy.scattering.theory.multisphere module holopy.scattering.theory.scatteringtheory module holopy.scattering.theory.tmatrix module holopy.scattering.theory.tmatrix_f module HoloPyObject (class in holopy.core.holopy_object) hough() (in module holopy.core.process.centerfinder)

I

ifft() (in module holopy.core.process.fourier) ift_coord() (in module holopy.core.process.fourier) ift_coords() (in module holopy.core.process.fourier) ignore_aliases() (in module holopy.core.io.serialize) illum_polarization (Model property) illum_wavelen (Model property) imag (ComplexPrior property) image_gradient() (in module holopy.core.process.centerfinder) ImageFormation (class in holopy.scattering.imageformation) in_domain() (Difference method) (Intersection method) (Scatterer method) (Scatterers method) (Union method) index_at() (Scatterer method) (Scatterers method) indicators (Capsule property)

Indicators (class in holopy.scattering.scatterer.scatterer) indicators (Ellipsoid property) (JanusSphere_Tapered property) (JanusSphere_Uniform property) (Sphere property) (Spheroid property) initial_guess (Model property) initial_guess_scatterer (Model property) initialize_fit() (NmpfitStrategy method) instancemethod_constructor() (in module holopy.core.io.serialize) instancemethod_representer() (in module holopy.core.io.serialize) internal_coeffs() (in module holopy.scattering.theory.mie_f.miescatlib) interpolate2D() (in module holopy.propagation.point_source_propagate) interpret_theory() (in module holopy.scattering.interface) Intersection (class in holopy.scattering.scatterer.csg) interval (Uniform property) InvalidScatterer iterate_mapping() (Mapper method)

J

j2() (in module holopy.scattering.theory.mielensfunctions)

JanusSphere_Tapered (class in holopy.scattering.scatterer.janus) JanusSphere_Uniform (class in holopy.scattering.scatterer.janus)

K

keep_in_same_coordinates() (in module holopy.core.math)

keep_raw_calculations (DDA attribute)

L

largest_overlap() (Spheres method) LayeredSphere (class in holopy.scattering.scatterer.sphere) LeastSquaresScipyStrategy (class in holopy.inference.scipyfit) Lens (class in holopy.scattering.theory.lens) LimitOverlaps (class in holopy.inference.model) lnlike() (Model method) lnposterior() (Model method) LnpostWrapper (class in holopy.core.utils) lnprior() (Model method) lnprob() (BoundedGaussian method) (ComplexPrior method) (Gaussian method) (TransformedPrior method) (Uniform method)

load() (in module holopy.core.io.io) (in module holopy.core.io.serialize) load_average() (in module holopy.core.io.io) load_image() (in module holopy.core.io.io) LoadError log_der_1() (in module holopy.scattering.theory.mie_f.mie_specfuncs) log_der_13() (in module holopy.scattering.theory.mie_f.mie_specfuncs)

M

make_center_priors() (in module holopy.core.prior) make_coords() (in module holopy.core.metadata) make_default_model() (in module holopy.inference.interface) make_subset_data() (in module holopy.core.metadata) make_uniform() (in module holopy.inference.interface) make_xarray() (in module holopy.core.mapping) map() (NonePool method) map_dictionary() (Mapper method) map_keys (ComplexPrior property) (TransformedPrior property) map_transformed_prior() (Mapper method) map_xarray() (Mapper method) Mapper (class in holopy.core.mapping) max_dpl_size (DDA attribute) max_lnprob (FitResult property) mean() (Accumulator method) medium_index (Model property) meth (Multisphere attribute) Mie (class in holopy.scattering.theory.mie) MieLens (class in holopy.scattering.theory.mielens) MieLensCalculator (class in holopy.scattering.theory.mielensfunctions) MieScatteringMatrix (class in holopy.scattering.theory.mielensfunctions) minimize() (LeastSquaresScipyStrategy method) (NmpfitStrategy method) MissingParameter mkdir_p() (in module holopy.core.utils) Model (class in holopy.inference.model) module holopy holopy.core holopy.core.errors holopy.core.holopy_object holopy.core.io holopy.core.io.io holopy.core.io.serialize holopy.core.io.vis holopy.core.mapping holopy.core.math holopy.core.metadata holopy.core.prior holopy.core.process holopy.core.process.centerfinder holopy.core.process.fourier holopy.core.process.img_proc holopy.core.utils holopy.inference holopy.inference.cmaes holopy.inference.emcee holopy.inference.interface holopy.inference.model holopy.inference.nmpfit holopy.inference.result holopy.inference.scipyfit holopy.propagation holopy.propagation.convolution_propagation holopy.propagation.point_source_propagate holopy.scattering holopy.scattering.errors holopy.scattering.imageformation holopy.scattering.interface holopy.scattering.scatterer holopy.scattering.scatterer.bisphere holopy.scattering.scatterer.capsule holopy.scattering.scatterer.composite holopy.scattering.scatterer.csg holopy.scattering.scatterer.cylinder holopy.scattering.scatterer.ellipsoid holopy.scattering.scatterer.janus holopy.scattering.scatterer.scatterer holopy.scattering.scatterer.sphere holopy.scattering.scatterer.spherecluster holopy.scattering.scatterer.spheroid holopy.scattering.theory holopy.scattering.theory.dda holopy.scattering.theory.lens holopy.scattering.theory.mie holopy.scattering.theory.mie_f holopy.scattering.theory.mie_f.mie_specfuncs holopy.scattering.theory.mie_f.miescatlib holopy.scattering.theory.mie_f.multilayer_sphere_lib holopy.scattering.theory.mielens holopy.scattering.theory.mielensfunctions holopy.scattering.theory.multisphere holopy.scattering.theory.scatteringtheory holopy.scattering.theory.tmatrix holopy.scattering.theory.tmatrix_f

Multisphere (class in holopy.scattering.theory.multisphere) MultisphereFailure must_be_specified (AberratedMieLensCalculator attribute) (MieLensCalculator attribute)

N

n (LayeredSphere attribute) (Sphere attribute) (Spheres property) (Spheroid attribute) n_cpu (DDA attribute) n_imag (Spheres property) n_real (Spheres property) ndarray_representer() (in module holopy.core.io.serialize) niter (Multisphere attribute) NmpfitStrategy (class in holopy.inference.nmpfit) noise_sd (Model property) NoMetadata NonePool (class in holopy.core.utils)

normalize() (in module holopy.core.process.img_proc) normalize_polarization() (in module holopy.scattering.theory.multisphere) nstop() (in module holopy.scattering.theory.mie_f.miescatlib) num_domains (Scatterer property) (Sphere property) numexpr_integrand_prefactor1 (Lens attribute) numexpr_integrand_prefactor2 (Lens attribute) numexpr_integrand_prefactor3 (Lens attribute) numexpr_integrandl (Lens attribute) numexpr_integrandr (Lens attribute) numpy_float_representer() (in module holopy.core.io.serialize) numpy_int_representer() (in module holopy.core.io.serialize) numpy_ufunc_constructor() (in module holopy.core.io.serialize) numpy_ufunc_representer() (in module holopy.core.io.serialize)

O

overlaps (Spheres property)

OverlapWarning

P

pack_attrs() (in module holopy.core.io.io) parameter_names (AberratedMieLens attribute) (Lens attribute) (MieLens attribute) (ScatteringTheory attribute) parameterize_scatterer() (in module holopy.inference.interface) parameters (FitResult property) (Model property) (Scatterer property) (ScatteringTheory property) parameters() (Scatterers method) ParameterSpecificationError PerformanceWarning

PiecewiseChebyshevApproximant (class in holopy.scattering.theory.mielensfunctions) prep_schema() (in module holopy.scattering.interface) Prior (class in holopy.core.prior) prob() (BoundedGaussian method) (ComplexPrior method) (Gaussian method) (TransformedPrior method) (Uniform method) propagate() (in module holopy.propagation.convolution_propagation) ps_propagate() (in module holopy.propagation.point_source_propagate) ps_propagate_plane() (in module holopy.propagation.point_source_propagate) pts_wts_for_phi_integrals() (in module holopy.scattering.theory.lens) push() (Accumulator method)

Q

qeps1 (Multisphere attribute)

qeps2 (Multisphere attribute) Qratio() (in module holopy.scattering.theory.mie_f.mie_specfuncs)

R

r (LayeredSphere property) (Sphere attribute) (Spheres property) (Spheroid attribute) R_psi() (in module holopy.scattering.theory.mie_f.mie_specfuncs) raise_fitting_api_error() (in module holopy.core.errors) raw_cross_sections() (Mie method) (Multisphere method) (ScatteringTheory method) raw_fields() (Lens method) (Mie method) (MieLens method) (Multisphere method) (ScatteringTheory method) (Tmatrix method) raw_scat_matrs() (DDA method) (Mie method) (Multisphere method) (ScatteringTheory method) (Tmatrix method)

read_map() (in module holopy.core.mapping) real (ComplexPrior property) renamed() (Prior method) repeat_sing_dims() (in module holopy.core.utils) replace_center() (in module holopy.inference.interface) required_spacing() (DDA method) riccati_psi_xi() (in module holopy.scattering.theory.mie_f.mie_specfuncs) riccati_psin() (AlBlFunctions static method) riccati_xin() (AlBlFunctions static method) RigidCluster (class in holopy.scattering.scatterer.spherecluster) rotate_points() (in module holopy.core.math) rotated() (CsgScatterer method) (Scatterers method), [1] (Sphere method) rotation (Spheroid attribute) rotation_matrix() (in module holopy.core.math) rsq() (in module holopy.core.math) run_cma() (in module holopy.inference.cmaes)

S

sample() (BoundedGaussian method) (EmceeStrategy method) (Gaussian method) (in module holopy.inference.interface) (Model method) (TemperedStrategy method) (TransformedPrior method) (Uniform method) sample_emcee() (in module holopy.inference.emcee) sample_one_sigma_gaussian() (in module holopy.inference.emcee) SamplingResult (class in holopy.inference.result) save() (in module holopy.core.io.io) (in module holopy.core.io.serialize) (Show2D method) save_all() (Show2D method) save_image() (in module holopy.core.io.io) save_images() (in module holopy.core.io.io) save_plot() (in module holopy.core.io.vis) scale() (Prior method) scatcoeffs() (in module holopy.scattering.theory.mie_f.miescatlib) scatcoeffs_multi() (in module holopy.scattering.theory.mie_f.multilayer_sphere_lib) scattered_field_to_hologram() (in module holopy.scattering.interface) Scatterer (class in holopy.scattering.scatterer.scatterer)

scatterer (FitResult property) (Model property) scatterer_from_parameters() (Model method) Scatterers (class in holopy.scattering.scatterer.composite) scatterers (RigidCluster property) (Scatterers attribute) ScatteringTheory (class in holopy.scattering.theory.scatteringtheory) select_scatterer_by_illumination() (in module holopy.scattering.imageformation) Serializable (class in holopy.core.holopy_object) SerializableMetaclass (class in holopy.core.holopy_object) show() (in module holopy.core.io.vis) Show2D (class in holopy.core.io.vis) show_scatterer_slices() (in module holopy.core.io.vis) show_sphere_cluster() (in module holopy.core.io.vis) simulate_noise() (in module holopy.core.process.img_proc) Sphere (class in holopy.scattering.scatterer.sphere) Spheres (class in holopy.scattering.scatterer.spherecluster) spheres (Spheres attribute) spherical_h1n() (in module holopy.scattering.theory.mielensfunctions) spherical_h2n() (in module holopy.scattering.theory.mielensfunctions) Spheroid (class in holopy.scattering.scatterer.spheroid) std() (Accumulator method) subimage() (in module holopy.core.process.img_proc)

T

t (LayeredSphere attribute) TemperedSamplingResult (class in holopy.inference.result) TemperedStrategy (class in holopy.inference.emcee) theory_from_parameters() (Model method) TheoryNotCompatibleError Tmatrix (class in holopy.scattering.theory.tmatrix) TmatrixFailure to_cartesian() (in module holopy.core.math) to_vector() (in module holopy.core.metadata) to_yaml() (HoloPyObject class method) (Serializable class method) trans_func() (in module holopy.propagation.convolution_propagation)

transform_cartesian_to_cylindrical() (in module holopy.core.math) transform_cartesian_to_spherical() (in module holopy.core.math) transform_cylindrical_to_cartesian() (in module holopy.core.math) transform_cylindrical_to_spherical() (in module holopy.core.math) transform_metadata() (in module holopy.core.process.fourier) transform_spherical_to_cartesian() (in module holopy.core.math) transform_spherical_to_cylindrical() (in module holopy.core.math) transformed_prior() (in module holopy.core.mapping) TransformedPrior (class in holopy.core.prior) translated() (Scatterer method) (Scatterers method), [1] tuple_representer() (in module holopy.core.io.serialize)

U

UncertainValue (class in holopy.inference.result) Uniform (class in holopy.core.prior) Union (class in holopy.scattering.scatterer.csg) unpack_attrs() (in module holopy.core.io.io) unscale() (Prior method)

unscale_pars_from_minimizer() (LeastSquaresScipyStrategy method) (NmpfitStrategy method) update_metadata() (in module holopy.core.metadata) updated() (in module holopy.core.prior) (in module holopy.core.utils) use_indicators (DDA attribute)

V

validate_scatterer() (in module holopy.scattering.interface) validate_strategy() (in module holopy.inference.interface) variance (Gaussian property)

VisualizationNotImplemented voxelate() (Scatterer method) voxelate_domains() (Scatterer method)

W

warn (Spheres attribute)

X

x (Scatterer property) (Spheres property)

Y

y (Scatterer property) (Spheres property)

Z

z (Scatterer property) (Spheres property)

zero_filter() (in module holopy.core.process.img_proc)