scatterers¶
Implementations of Feature the model scattering objects.
Provides some basic implementations of scattering objects that are frequently used.
Classes¶
- Scatterer
Abstract base class for scatterers
- PointParticle
Generates point particles
- Ellipse
Generetes 2-d elliptical particles
- Sphere
Generates 3-d spheres
- Ellipsoid
Generates 3-d ellipsoids
Module classes¶
Ellipse¶
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class
deeptrack.scatterers.Ellipse(radius, rotation, **kwargs)¶ Generates an elliptical disk scatterer
- Parameters
radius (float or array_like [float (, float)]) – Radius of the ellipse in meters. If only one value, assume circular.
rotation (float) – Orientation angle of the ellipse in the camera plane in radians.
position (array_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.
z (float) – The position in the direction normal to the camera plane. Used if position is of length 2.
value (float) – 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).
upsample (int) – Upsamples the calculations of the pixel occupancy fraction.
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get(*ignore, radius, rotation, voxel_size, **kwargs)¶ Method for altering an image Abstract method that define how the feature transforms the input. The current value of all properties will be passed as keyword arguments.
Ellipsoid¶
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class
deeptrack.scatterers.Ellipsoid(radius, rotation=0, **kwargs)¶ Generates an ellipsoidal scatterer
- Parameters
radius (float or array_like[float (, float, float)]) – Radius of the ellipsoid in meters. If only one value, assume spherical.
rotation (float) – Rotation of the ellipsoid in about the x, y and z axis.
position (array_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.
z (float) – The position in the direction normal to the camera plane. Used if position is of length 2.
value (float) – 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).
upsample (int) – Upsamples the calculations of the pixel occupancy fraction.
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get(image, radius, rotation, voxel_size, **kwargs)¶ Method for altering an image Abstract method that define how the feature transforms the input. The current value of all properties will be passed as keyword arguments.
PointParticle¶
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class
deeptrack.scatterers.PointParticle(**kwargs)¶ Generates a point particle
A point particle is approximated by the size of a pixel. For subpixel positioning, the position is interpolated linearly.
- Parameters
position (array_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.
z (float) – The position in the direction normal to the camera plane. Used if position is of length 2.
value (float) – 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).
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get(image, **kwargs)¶ Method for altering an image Abstract method that define how the feature transforms the input. The current value of all properties will be passed as keyword arguments.
Scatterer¶
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class
deeptrack.scatterers.Scatterer(position, z=0.0, value=1.0, position_unit='meter', upsample=1, **kwargs)¶ 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
position (array_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.
z (float) – The position in the direction normal to the camera plane. Used if position is of length 2.
value (float) – 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_axes (tuple of ints) – Sets the axes along which the calculation is upsampled (default is None, which implies all axes are upsampled).
crop_zeros (bool) – Whether to remove slices in which all elements are zero.
Sphere¶
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class
deeptrack.scatterers.Sphere(radius, **kwargs)¶ Generates a spherical scatterer
- Parameters
radius (float) – Radius of the sphere in meters.
position (array_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.
z (float) – The position in the direction normal to the camera plane. Used if position is of length 2.
value (float) – 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).
upsample (int) – Upsamples the calculations of the pixel occupancy fraction.
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get(image, radius, voxel_size, **kwargs)¶ Method for altering an image Abstract method that define how the feature transforms the input. The current value of all properties will be passed as keyword arguments.