MieScatterer

class deeptrack.scatterers.MieScatterer(coefficients: Callable[[...], Callable[[int], Tuple[Tuple[T, ...] | List[T] | ndarray, Tuple[T, ...] | List[T] | ndarray]]], input_polarization=0, output_polarization=0, offset_z: str | Callable[[...], str] = 'auto', collection_angle: str | Callable[[...], str] = 'auto', L: str | Callable[[...], str] = 'auto', refractive_index_medium=None, wavelength=None, NA=None, padding=(0, 0, 0, 0), output_region=None, polarization_angle=None, working_distance=1000000, position_objective=(0, 0), return_fft=False, coherence_length=None, illumination_angle=0, amp_factor=1, phase_shift_correction=False, **kwargs)

Bases: Scatterer

Base implementation of a Mie particle.

New Mie-theory scatterers can be implemented by extending this class, and passing a function that calculates the coefficients of the harmonics up to order L. To beprecise, the feature expects a wrapper function that takes the current values of the properties, as well as a inner function that takes an integer as the only parameter, and calculates the coefficients up to that integer. The return format is expected to be a tuple with two values, corresponding to an and bn. See deeptrack.backend.mie.coefficients for an example.

Parameters

coefficientsCallable[int] -> Tuple[ndarray, ndarray]

Function that returns the harmonics coefficients.

offset_z“auto” or float

Distance from the particle in the z direction the field is evaluated. If “auto”, this is calculated from the pixel size and collection_angle

collection_angle“auto” or float

The maximum collection angle in radians. If “auto”, this is calculated from the objective NA (which is true if the objective is the limiting aperature).

input_polarization: float or Quantity

Defines the polarization angle of the input. For simulating circularly polarized light we recommend a coherent sum of two simulated fields. For unpolarized light we recommend a incoherent sum of two simulated fields. If defined as “circular”, the coefficients are set to 1/2.

output_polarization: float or Quantity or None

If None, the output light is not polarized. Otherwise defines the angle of the polarization filter after the sample. For off-axis, keep the same as input_polarization. If defined as “circular”, the coefficients are multiplied by 1. I.e. no change.

Lint or str

The number of terms used to evaluate the mie theory. If “auto”, it determines the number of terms automatically.

positionarray_like[float, float (, float)]

The position of the particle. Third index is optional, and represents the position in the direction normal to the camera plane.

zfloat

The position in the direction normal to the camera plane. Used if position is of length 2.

return_fftbool

If True, the feature returns the fft of the field, rather than the field itself.

coherence_lengthfloat

The temporal coherence length of a partially coherent light given in meters. If None, the illumination is assumed to be coherent.

amp_factorfloat

A factor that scales the amplification of the field. This is useful for scaling the field to the correct intensity. Default is 1.

phase_shift_correctionbool

If True, the feature applies a phase shift correction to the output field. This is necessary for ISCAT simulations. The correction depends on the k-vector and z according to the formula: arr*=np.exp(1j * k * z + 1j * np.pi / 2)

Methods Summary

get(inp, position, voxel_size, padding, ...)	Transform an image [abstract method].
get_XY(shape, voxel_size)
get_detector_mask(X, Y, radius)
get_plane_in_polar_coords(shape, voxel_size, ...)
get_xy_size(output_region, padding)

Methods Documentation

get(inp, position, voxel_size, padding, wavelength, refractive_index_medium, L, collection_angle, input_polarization, output_polarization, coefficients, offset_z, z, working_distance, position_objective, return_fft, coherence_length, output_region, illumination_angle, amp_factor, phase_shift_correction, **kwargs)

Transform an image [abstract method].

Abstract method that defines how the feature transforms the input. The current value of all properties will be passed as keyword arguments.

Parameters

image‘Image’ or List[‘Image’]

The Image or list of images to transform.

**kwargsDict[str, Any]

The current value of all properties in properties as well as any global arguments.

Returns

‘Image’ or List[‘Image’]

The transformed image or list of images.

Raises

NotImplementedError

Must be overridden by subclasses.

get_XY(shape, voxel_size)

get_detector_mask(X, Y, radius)

get_plane_in_polar_coords(shape, voxel_size, plane_position, illumination_angle)

get_xy_size(output_region, padding)