Scatterer

class deeptrack.optical.scatterers.Scatterer(position: tuple[float, float] | tuple[float, float, float] = (32.0, 32.0), z: float = 0.0, value: float = 1.0, position_unit: str = 'pixel', upsample: int = 1, voxel_size: tuple | None = None, pixel_size: tuple | None = None, **kwargs)

Bases: Feature

Base abstract class for scatterers.

A Scatterer defines an object or optical source term to be evaluated on a discrete spatial grid. Depending on the subclass, the result may represent either a voxelized volume (VolumeScatterer) or a complex field (FieldScatterer).

Parameters

position: tuple[float, float] | tuple[float, float, float], optional

The position of the particle, length 2 or 3. Third index is optional, and represents the position in the direction normal to the camera plane. Default is (32.0, 32.0).

z: float, optional

The position in the direction normal to the camera plane. Used if position is of length 2. Default is 0.0.

value: float, optional

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). Default is 1.0.

position_unit: str, optional

The unit of the provided position property. Can be “meter” or “pixel”. Default is “pixel”.

upsample: int, optional

Geometry supersampling factor for volume-based scatterers. The scatterer is evaluated on a finer grid and downsampled by average pooling. Ignored by field-based scatterers.

upsample_axes: tuple of int, optional

Deprecated. Previously selected the axes along which supersampling was applied. This parameter is now ignored.

voxel_size: array-like, optional

The size of the voxels in meters. If not provided, it is obtained from the active optics configuration.

pixel_size: array-like, optional

The size of the pixels in meters. If not provided, it is obtained from the active optics configuration.

**kwargs: Any

Additional feature properties forwarded to the parent Feature class.

Methods

_antialias_volume(volume, factor) -> array

Geometry-only supersampling anti-aliasing.

_process_properties(properties) -> dict

Preprocess the input to the method .get(). This method is called before the scatterer is evaluated.

_process_and_get(…) -> list[array]

Post-processes the created object.

_wrap_output(array, props) -> ScatteredVolume or ScatteredField

Wraps the output of the scatterer in the appropriate class.

Notes

For developers extending the class hierarchy: __list_merge_strategy__: str

The strategy for merging lists of properties when multiple scatterers are combined. Default is “append”, which concatenates the lists.

__distributed__: bool

Determines whether .get(image, **kwargs) is applied to each element of the input list independently (__distributed__ = True) or to the list as a whole (__distributed__ = False).

__conversion_table__: ConversionTable

A table defining the physical units of the scatterer’s properties and how to convert them to the internal units used for calculations.