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Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
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 attribute)
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 attribute)
(Difference attribute)
(Scatterer attribute)
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_incident_field() (MieLensCalculator method)
calculate_pil_taul() (in module holopy.scattering.theory.mielensfunctions)
calculate_scattered_field() (ImageFormation method)
(MieLensCalculator method)
calculate_scattering_matrix() (ImageFormation method)
calculate_total_field() (MieLensCalculator method)
calculate_total_intensity() (MieLensCalculator method)
can_handle() (holopy.scattering.theory.dda.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 attribute)
(Spheroid attribute)
center_find() (in module holopy.core.process.centerfinder)
CenteredScatterer (class in holopy.scattering.scatterer.scatterer)
centers (Spheres attribute)
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)
configuration() (in module holopy.scattering.theory.mie_f.setup)
(in module holopy.scattering.theory.tmatrix_f.setup)
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)
cv() (Accumulator method)
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)
(LeastSquaresScipyStrategy method)
(Model method)
(NmpfitStrategy method)
(in module holopy.inference.interface)
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() (holopy.core.holopy_object.HoloPyObject class method)
(holopy.inference.model.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 attribute)
(TransformedPrior attribute)
guess_hologram (FitResult attribute)
guess_parameters (FitResult attribute)
guess_scatterer (FitResult attribute)
H
hologram (FitResult attribute)
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.mie_f.setup (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)
holopy.scattering.theory.tmatrix_f.setup (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 attribute)
illum_wavelen (Model attribute)
imag (ComplexPrior attribute)
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 attribute)
Indicators (class in holopy.scattering.scatterer.scatterer)
indicators (Ellipsoid attribute)
(JanusSphere_Tapered attribute)
(JanusSphere_Uniform attribute)
(Sphere attribute)
(Spheroid attribute)
initial_guess (Model attribute)
initial_guess_scatterer (Model attribute)
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 attribute)
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 attribute)
(TransformedPrior attribute)
map_transformed_prior() (Mapper method)
map_xarray() (Mapper method)
Mapper (class in holopy.core.mapping)
max_dpl_size (DDA attribute)
max_lnprob (FitResult attribute)
mean() (Accumulator method)
medium_index (Model attribute)
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)
Multisphere (class in holopy.scattering.theory.multisphere)
MultisphereFailure
must_be_specified (AberratedMieLensCalculator attribute)
(MieLensCalculator attribute)
N
n (LayeredSphere attribute)
(Sphere attribute)
(Spheres attribute)
(Spheroid attribute)
n_cpu (DDA attribute)
n_imag (Spheres attribute)
n_real (Spheres attribute)
ndarray_representer() (in module holopy.core.io.serialize)
niter (Multisphere attribute)
NmpfitStrategy (class in holopy.inference.nmpfit)
noise_sd (Model attribute)
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 attribute)
(Sphere attribute)
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 attribute)
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 attribute)
(Model attribute)
(Scatterer attribute)
(ScatteringTheory attribute)
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 attribute)
(Sphere attribute)
(Spheres attribute)
(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 attribute)
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)
(Model method)
(TemperedStrategy method)
(TransformedPrior method)
(Uniform method)
(in module holopy.inference.interface)
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)
(Show2D method)
(in module holopy.core.io.serialize)
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 attribute)
(Model attribute)
scatterer_from_parameters() (Model method)
Scatterers (class in holopy.scattering.scatterer.composite)
scatterers (RigidCluster attribute)
(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)
subimage() (in module holopy.core.process.img_proc)
SuppressOutput (class in holopy.core.utils)
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() (holopy.core.holopy_object.HoloPyObject class method)
(holopy.core.holopy_object.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 attribute)
VisualizationNotImplemented
voxelate() (Scatterer method)
voxelate_domains() (Scatterer method)
W
warn (Spheres attribute)
X
x (Scatterer attribute)
(Spheres attribute)
Y
y (Scatterer attribute)
(Spheres attribute)
Z
z (Scatterer attribute)
(Spheres attribute)
zero_filter() (in module holopy.core.process.img_proc)
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