Scatterer

class deeptrack.scatterers.Scatterer(position: Tuple[float, ...] | List[float] | ndarray | Callable[[...], Tuple[float, ...] | List[float] | ndarray] = (32, 32), z: float | Callable[[...], float] = 0.0, value: float | Callable[[...], float] = 1.0, position_unit: str | Callable[[...], str] = 'pixel', upsample: int | Callable[[...], int] = 1, voxel_size=None, pixel_size=None, **kwargs)

Bases: Feature

Base abstract class for scatterers.

A scatterer is defined by a 3-dimensional volume of voxels. To each voxel corresponds an occupancy factor, i.e., how much of that voxel does the scatterer occupy. However, this number is not necessarily limited to the [0, 1] range. It can be any number, and its interpretation is left to the optical device that images the scatterer.

This abstract class implements the _process_properties method to convert the position to voxel units, as well as the _process_and_get method to upsample the calculation and crop empty slices.

Parameters

positionarray_like of length 2 or 3

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.

valuefloat

A default value of the characteristic of the particle. Used by optics unless a more direct property is set (eg. refractive_index for Brightfield and intensity for Fluorescence).

position_unit“meter” or “pixel”

The unit of the provided position property.

Other Parameters

upsample_axestuple of ints

Sets the axes along which the calculation is upsampled (default is None, which implies all axes are upsampled).

crop_zerosbool

Whether to remove slices in which all elements are zero.