# Scattering Calculations¶

Optical physicists and astronomers have worked out how to compute the scattering of light from many kinds of objects. HoloPy provides an easy interface for computing scattered fields, intensities, scattering matrices, cross-sections, and holograms generated by microscopic objects.

## A Simple Example¶

Let’s start by calculating an in-line hologram generated by a plane wave scattering from a microsphere.

import holopy as hp
from holopy.scattering import calc_holo, Sphere

sphere = Sphere(n = 1.59, r = .5, center = (4, 4, 5))
medium_index = 1.33
illum_wavelen = 0.660
illum_polarization = (1,0)
detector = hp.detector_grid(shape = 100, spacing = .1)

holo = calc_holo(detector, sphere, medium_index, illum_wavelen, illum_polarization)
hp.show(holo)


We’ll examine each section of code in turn. The first few lines :

import holopy as hp
from holopy.scattering import calc_holo, Sphere


load the relevant modules from HoloPy that we’ll need for doing our calculation. The next line describes the scatterer we would like to model:

sphere = Sphere(n = 1.59, r = .5, center = (4, 4, 5))


We will be scattering light off a Scatterer object, specifically a Sphere. A Scatterer object contains information about the geometry (position, size, shape) and optical properties (refractive index) of the object that is scattering light. We’ve defined a spherical scatterer with radius 0.5 microns and index of refraction 1.59. This refractive index is approximately that of polystyrene. Next, we need to describe how we are illuminating our sphere, and how that light will be detected:

medium_index = 1.33
illum_wavelen = 0.66
illum_polarization = (1,0)
detector = hp.detector_grid(shape = 100, spacing = .1)


We are going to be using red light (wavelength = 660 nm in vacuum) polarized in the x-direction to illuminate a sphere immersed in water (refractive index = 1.33). Refer to Units and Coordinate System if you’re confused about how the wavelength and polarization are specified.

The scattered light will be collected at a detector, which is frequently a digital camera mounted onto a microscope. We defined our detector as a 100 x 100 pixel array, with each square pixel of side length .1 microns. The shape argument tells HoloPy how many pixels are in the detector and affects computation time. The spacing argument tells HoloPy how far apart each pixel is. Both parameters affect the absolute size of the detector.

After getting everything ready, the actual scattering calculation is straightforward:

holo = calc_holo(detector, sphere, medium_index, illum_wavelen, illum_polarization)
hp.show(holo)


Congratulations! You just calculated the in-line hologram generated at the detector plane by interference between the scattered field and the reference wave. For an in-line hologram, the reference wave is simply the part of the field that is not scattered or absorbed by the particle.

You might have noticed that our scattering calculation requires much of the same metadata we specified when loading an image. If we have an experimental image from the system we would like to model, we can use that as an argument in calc_holo() instead of our detector object created from detector_grid(). HoloPy will calculate a hologram image with pixels at the same positions as the experimental image, and so we don’t need to worry about making a detector_grid() with the correct shape and spacing arguments.

from holopy.core.io import get_example_data_path
imagepath = get_example_data_path('image0002.h5')
holo = calc_holo(exp_img, sphere)


Note that we didn’t need to explicitly specify illumination information when calling calc_holo(), since our image contained saved metadata and HoloPy used its values. Passing an image to a scattering function is particularly useful when comparing simulated data to experimental results, since we can easily recreate our experimental conditions exactly.

So far all of the images we have calculated are holograms, or the interference pattern that results from the superposition of a scattered wave with a reference wave. Holopy can also be used to examine scattered fields on their own. Simply replace calc_holo() with calc_field() to look at scattered electric fields (complex) or calc_intensity() to look at field amplitudes, which is the typical measurement in a light scattering experiment.

## More Complex Scatterers¶

### Coated Spheres¶

HoloPy can also calculate holograms from coated (or multilayered) spheres. Constructing a coated sphere differs only in specifying a list of refractive indices and outer radii corresponding to the layers (starting from the core and working outwards).

coated_sphere = Sphere(center=(2.5, 5, 5), n=(1.59, 1.42), r=(0.3, 0.6))
holo = calc_holo(exp_img, coated_sphere)
hp.show(holo)


If you prefer thinking in terms of the thickness of subsequent layers, instead of their distance from the center, you can use LayeredSphere to achieve the same result:

from holopy.scattering import LayeredSphere
coated_sphere = LayeredSphere(center=(2.5, 5, 5), n=(1.59, 1.42), t=(0.3, 0.3))


### Collection of Spheres¶

If we want to calculate a hologram from a collection of spheres, we must first define the spheres individually, and then combine them into a Spheres object:

from holopy.scattering import Spheres
s1 = Sphere(center=(5, 5, 5), n = 1.59, r = .5)
s2 = Sphere(center=(4, 4, 5), n = 1.59, r = .5)
collection = Spheres([s1, s2])
holo = calc_holo(exp_img, collection)
hp.show(holo)


Adding more spheres to the cluster is as simple as defining more sphere objects and passing a longer list of spheres to the Spheres constructor.

### Non-spherical Objects¶

To define a non-spherical scatterer, use Spheroid or Cylinder objects. These axisymmetric scatterers are defined by two dimensions, and can describe scatterers that are elongated or squashed along one direction. By default, these objects are aligned with the z-axis, but they can be rotated into any orientation by passing a set of Euler angles to the rotation argument when defining the scatterer. See Rotations of Scatterers for information on how these angles are defined. As an example, here is a hologram produced by a cylinder aligned with the vertical axis (x-axis according to the HoloPy Coordinate System). Note that the hologram image is elongated in the horizontal direction since the sides of the cylinder scatter light more than the ends.

import numpy as np
from holopy.scattering import Cylinder
c = Cylinder(center=(5, 5, 7), n = 1.59, d=0.5, h=2, rotation=(0,np.pi/2, 0))
holo = calc_holo(exp_img, c)
hp.show(holo)


## Customizing Scattering Calculations¶

While the examples above will be sufficient for most purposes, there are a few additional options that are useful in certain scenarios.

### Scattering Theories in HoloPy¶

HoloPy contains a number of scattering theories to model the scattering from different kinds of scatterers. By default, scattering from single spheres is calculated using Mie theory, which is the exact solution to Maxwell’s equations for the scattered field from a spherical particle, originally derived by Gustav Mie and (independently) by Ludvig Lorenz in the early 1900s.

A scatterer composed of multiple spheres can exhibit multiple scattering and coupling of the near-fields of neighbouring particles. Mie theory doesn’t include these effects, so Spheres objects are by default calculated using the SCSMFO package from Daniel Mackowski. This calculation uses T-matrix methods to give the exact solution to Maxwell’s equation for the scattering from an arbitrary arrangement of non-overlapping spheres.

Sometimes you might want to calculate scattering from multiple spheres using Mie theory if you are worried about computation time or if you are using multi-layered spheres (HoloPy’s implementation of the multisphere theory can’t currently handle coated spheres). You can specify Mie theory manually when calling the calc_holo() function:

from holopy.scattering import Mie
holo = calc_holo(exp_img, collection, theory = Mie)


Similarly, HoloPy calculates scattering from cylindrical or spheroidal particles by using T-matrix code from Michael Mishchenko, but these scatterer types are not compatible with Mie theory.

Holopy can also access a discrete dipole approximation (DDA) theory to model arbitrary non-spherical objects. See the Scattering from Arbitrary Structures with DDA tutorial for more details. It is fairly easy to add your own scattering theory to HoloPy. See Adding a new scattering theory for details. If you think your new scattering theory may be useful for other users, please consider submitting a pull request.

### Detector Types in HoloPy¶

The detector_grid() function we saw earlier creates holograms that display nicely and are easily compared to experimental images. However, they can be computationally expensive, as they require calculations of the electric field at many points. If you only need to calculate values at a few points, or if your points of interest are not arranged in a 2D grid, you can use detector_points(), which accepts either a dictionary of coordinates or indvidual coordinate dimensions:

x = [0, 1, 0, 1, 2]
y = [0, 0, 1, 1, 1]
z = -1
coord_dict = {'x': x, 'y': y, 'z': z}
detector = hp.detector_points(x = x, y = y, z = z)
detector = hp.detector_points(coord_dict)


The coordinates for detector_points() can be specified in terms of either Cartesian or spherical coordinates. If spherical coordinates are used, the center value of your scatterer is ignored and the coordinates are interpreted as being relative to the scatterer.

## Static light scattering calculations¶

### Scattering Matrices¶

In a static light scattering measurement you record the scattered intensity at a number of locations. A common experimental setup contains multiple detectors at a constant radial distance from a sample (or a single detector on a goniometer arm that can swing to multiple angles.) In this kind of experiment you are usually assuming that the detector is far enough away from the particles that the far-field approximation is valid, and you are usually not interested in the exact distance of the detector from the particles. So, it’s most convenient to work with amplitude scattering matrices that are angle-dependent. (See [Bohren1983] for further mathematical description.)

import numpy as np
from holopy.scattering import calc_scat_matrix

detector = hp.detector_points(theta = np.linspace(0, np.pi, 100), phi = 0)
distant_sphere = Sphere(r=0.5, n=1.59)
matr = calc_scat_matrix(detector, distant_sphere, medium_index, illum_wavelen)


Here we omit specifying the location (center) of the scatterer. This is only valid when you’re calculating a far-field quantity. Similarly, note that our detector, defined from a detector_points() function, includes information about direction but not distance. It is typical to look at scattering matrices on a semilog plot. You can make one as follows:

import matplotlib.pyplot as plt
plt.figure()
plt.semilogy(np.linspace(0, np.pi, 100), abs(matr[:,0,0])**2)
plt.semilogy(np.linspace(0, np.pi, 100), abs(matr[:,1,1])**2)
plt.show()


You are usually interested in the intensities of the scattered fields, which are proportional to the modulus squared of the amplitude scattering matrix. The diagonal elements give the intensities for the incident light and the scattered light both polarized parallel and perpendicular to the scattering plane, respectively.

### Scattering Cross-Sections¶

The scattering cross section provides a measure of how much light from an incident beam is scattered by a particular scatterer. Similar to calculating scattering matrices, we can omit the position of the scatterer for calculation of cross sections. Since cross sections integrates over all angles, we can also omit the detector argument entirely:

from holopy.scattering import calc_cross_sections
x_sec = calc_cross_sections(distant_sphere, medium_index, illum_wavelen, illum_polarization)


x_sec returns an array containing four elements. The first element is the scattering cross section, specified in terms of the same units as wavelength and particle size. The second and third elements are the absorption and extinction cross sections, respectively. The final element is the average value of the cosine of the scattering angle.