holopy.scattering.scatterer package¶

Modules for defining different types of scatterers, including scattering primitives such as Spheres, and more complex objects such as Clusters.

Submodules¶

Defines cylinder scatterers.

class Bisphere(n=None, h=None, d=None, center=None, rotation=(0, 0, 0))¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

Scattering object representing bisphere scatterers

Parameters:	n (complex) – Index of refraction h (distance between centers) – d (diameter) – center (3-tuple, list or numpy array) – specifies coordinates of center of the scatterer rotation (3-tuple, list or numpy.array) – specifies the Euler angles (alpha, beta, gamma) in radians defined in a-dda manual section 8.1

Defines capsule scatterers.

class Capsule(n=None, h=None, d=None, center=None, rotation=(0, 0, 0))¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

A cylinder with semi-spherical caps.

A particle with no rotation has its long axis pointing along +z, specify other orientations by euler angle rotations from that reference.

Parameters:	n (complex) – Index of refraction h (height of cylinder) – d (diameter) – center (3-tuple, list or numpy array) – specifies coordinates of center of the scatterer rotation (3-tuple, list or numpy.array) – specifies the Euler angles (alpha, beta, gamma) in radians

indicators¶

Defines Scatterers, a scatterer that consists of other scatterers, including scattering primitives (e.g. Sphere) or other Scatterers scatterers (e.g. two trimers).

class Scatterers(scatterers=None)¶

Bases: holopy.scattering.scatterer.scatterer.Scatterer

Contains optical and geometrical properties of a a composite scatterer. A Scatterers can consist of multiple scattering primitives (e.g. Sphere) or other Scatterers scatterers.

scatterers¶

List of scatterers that make up this object

Type:	list

parameters [property]: Dictionary of composite’s parameters

add(scatterer)¶: Adds a new scatterer to the composite.

from_parameters()¶

translated()¶

rotated()¶

Notes

Stores information about components in a tree. This is the most generic container for a collection of scatterers.

add(scatterer)

from_parameters(new_parameters)

Makes a new object similar to self with values as given in parameters. This returns a physical object, so any priors are replaced with their guesses if not included in passed-in parameters.

Parameters:	parameters (dict) – dictionary of parameters to use in the new object. Keys should match those of self.parameters. overwrite (bool (optional)) – if True, constant values are replaced by those in parameters

get_component_list()¶

in_domain(points)¶

Tell which domain of a scatterer points are in

Parameters:	points (np.ndarray (Nx3)) – Point or list of points to evaluate
Returns:	domain – The domain of each point. Domain 0 means not in the particle
Return type:	np.ndarray (N)

index_at(point)¶

rotated(ang1, ang2=None, ang3=None)

translated(coord1, coord2=None, coord3=None)

Make a copy of this scatterer translated to a new location

Parameters:	y, z (x,) – Value of the translation along each axis
Returns:	translated – A copy of this scatterer translated to a new location
Return type:	Scatterer

Do Constructive Solid Geometry (CSG) with scatterers. Currently only useful with the DDA th

class CsgScatterer(s1, s2)¶

Bases: holopy.scattering.scatterer.scatterer.Scatterer

bounds¶

rotated(alpha, beta, gamma)¶

class Difference(s1, s2)¶

Bases: holopy.scattering.scatterer.csg.CsgScatterer

bounds¶

in_domain(points)¶

Tell which domain of a scatterer points are in

Parameters:	points (np.ndarray (Nx3)) – Point or list of points to evaluate
Returns:	domain – The domain of each point. Domain 0 means not in the particle
Return type:	np.ndarray (N)

class Intersection(s1, s2)¶

Bases: holopy.scattering.scatterer.csg.CsgScatterer

in_domain(points)¶

Tell which domain of a scatterer points are in

Parameters:	points (np.ndarray (Nx3)) – Point or list of points to evaluate
Returns:	domain – The domain of each point. Domain 0 means not in the particle
Return type:	np.ndarray (N)

class Union(s1, s2)¶

Bases: holopy.scattering.scatterer.csg.CsgScatterer

in_domain(points)¶

Tell which domain of a scatterer points are in

Parameters:	points (np.ndarray (Nx3)) – Point or list of points to evaluate
Returns:	domain – The domain of each point. Domain 0 means not in the particle
Return type:	np.ndarray (N)

Defines cylinder scatterers.

class Cylinder(n=None, h=None, d=None, center=None, rotation=(0, 0, 0))¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

Scattering object representing cylinder scatterers

Parameters:	n (complex) – Index of refraction h (height of cylinder) – d (diameter) – center (3-tuple, list or numpy array) – specifies coordinates of center of the scatterer rotation (3-tuple, list or numpy.array) – specifies the Euler angles (alpha, beta, gamma) in radians defined in a-dda manual section 8.1

Defines ellipsoidal scatterers.

class Ellipsoid(n=None, r=None, center=None, rotation=(0, 0, 0))¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

Scattering object representing ellipsoidal scatterers

Parameters:	n (complex) – Index of refraction r (float or (float, float, float)) – x, y, z semi-axes of the ellipsoid center (3-tuple, list or numpy array) – specifies coordinates of center of the scatterer rotation (3-tuple, list or numpy.array) – specifies the Euler angles (alpha, beta, gamma) in radians defined in a-dda manual section 8.1

indicators¶

Ellipsoid indicators does not currently apply rotations

Type:	NOTE

Defines two types of Janus (two faced) Spheres as scattering primitives.

class JanusSphere_Tapered(n=None, r=None, rotation=(0, 0), center=None)¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

indicators¶

class JanusSphere_Uniform(n=None, r=None, rotation=(0, 0, 0), center=None)¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

indicators¶

The abstract base class for all scattering objects

class CenteredScatterer(center=None)¶: Bases: holopy.scattering.scatterer.scatterer.Scatterer

class Indicators(functions, bound=None)¶

Bases: holopy.core.holopy_object.HoloPyObject

Class holding functions describing a scatterer

One or more functions (one per domain) that take Nx3 arrays of points and return a boolean array of membership in each domain. More than one indicator is allowed to return true for a given point, in that case the point is considered a member of the first domain with a true value.

class Scatterer(indicators, n, center)¶

Bases: holopy.core.holopy_object.HoloPyObject

Base class for scatterers

bounds¶

contains(points)¶

from_parameters(parameters)¶

Create a Scatterer from a dictionary of parameters

Parameters:	parameters (dict) – Parameters for a scatterer. This should be of the form returned by Scatterer.parameters.
Returns:	scatterer – A scatterer with the given parameter values
Return type:	Scatterer class

in_domain(points)¶

Tell which domain of a scatterer points are in

Parameters:	points (np.ndarray (Nx3)) – Point or list of points to evaluate
Returns:	domain – The domain of each point. Domain 0 means not in the particle
Return type:	np.ndarray (N)

index_at(points, background=0)¶

num_domains¶

parameters¶

Get a dictionary of this scatterer’s parameters

Parameters:	None –
Returns:	parameters – A dictionary of this scatterer’s parameters. This dict can be passed to Scatterer.from_parameters to make a copy of this scatterer
Return type:	dict

translated(coord1, coord2=None, coord3=None)¶

Make a copy of this scatterer translated to a new location

Parameters:	y, z (x,) – Value of the translation along each axis
Returns:	translated – A copy of this scatterer translated to a new location
Return type:	Scatterer

voxelate(spacing, medium_index=0)¶

Represent a scatterer by discretizing into voxels

Parameters:	spacing (float) – The spacing between voxels in the returned voxelation medium_index (float) – The background index of refraction to fill in at regions where the scatterer is not present
Returns:	voxelation – An array with refractive index at every pixel
Return type:	np.ndarray

voxelate_domains(spacing)¶

x¶

y¶

z¶

bound_union(d1, d2)¶

find_bounds(indicator)¶

Finds the bounds needed to contain an indicator function

Notes

Will probably determine incorrect bounds for functions which are not convex

Defines Sphere, a scattering primitive

class LayeredSphere(n=None, t=None, center=None)¶

Bases: holopy.scattering.scatterer.sphere.Sphere

Alternative description of a sphere where you specify layer thicknesses instead of radii

n¶

Index of each each layer

Type:	list of complex

t¶

Thickness of each layer

Type:	list of float

center¶

specifies coordinates of center of sphere

Type:	length 3 listlike

r¶

class Sphere(n=None, r=0.5, center=None)¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

Contains optical and geometrical properties of a sphere, a scattering primitive.

This can be a multiple layered sphere by making r and n lists.

n¶

index of refraction of each layer of the sphere

Type:	complex or list of complex

r¶

radius of the sphere or outer radius of each sphere.

Type:	float or list of float

center¶

specifies coordinates of center of sphere

Type:	length 3 listlike

indicators¶

num_domains¶

rotated(alpha, beta, gamma)¶

Defines Spheres, a Scatterers scatterer consisting of Spheres

class RigidCluster(spheres, translation=(0, 0, 0), rotation=(0, 0, 0))¶

Bases: holopy.scattering.scatterer.spherecluster.Spheres

from_parameters(parameters)¶

Makes a new object similar to self with values as given in parameters. This returns a physical object, so any priors are replaced with their guesses if not included in passed-in parameters.

Parameters:	parameters (dict) – dictionary of parameters to use in the new object. Keys should match those of self.parameters. overwrite (bool (optional)) – if True, constant values are replaced by those in parameters

scatterers¶

class Spheres(scatterers, warn=True)¶

Bases: holopy.scattering.scatterer.composite.Scatterers

Contains optical and geometrical properties of a cluster of spheres.

spheres¶

Spheres which will make up the cluster

Type:	list of Spheres

warn¶

if True, overlapping spheres raise warnings.

Type:	bool

Notes

add(scatterer)¶

center¶

centers¶

largest_overlap()¶

n¶

n_imag¶

n_real¶

overlaps¶

r¶

x¶

y¶

z¶

Defines spheroidal scatterers.

class Spheroid(n=None, r=None, rotation=(0, 0, 0), center=None)¶

Bases: holopy.scattering.scatterer.scatterer.CenteredScatterer

Scattering object representing spheroidal scatterers

n¶

Index of refraction

Type:	complex

r¶

length of xy and z semi-axes of the spheroid

Type:	(float, float)

rotation¶

specifies the Euler angles (alpha, beta, gamma) in radians

Type:	3-tuple, list or numpy array

center¶

specifies coordinates of center of the scatterer

Type:	3-tuple, list or numpy array

indicators¶