acryo.pick package

Module contents

class acryo.pick.DoGPicker(sigma_low: float = 3.5, sigma_high: float = 5.0)[source]

Bases: acryo.pick._base.BasePickerModel

Particle picking based on Difference of Gaussian.

get_params_and_depth(scale: float)[source]
pick_in_chunk(image: numpy.ndarray[Any, numpy.dtype[numpy.float32]], sigma_low: float, sigma_high: float) → tuple[numpy.ndarray[Any, numpy.dtype[numpy.float32]], numpy.ndarray[Any, numpy.dtype[numpy.uint16]], Any][source]
class acryo.pick.LoGPicker(sigma: float = 3.5)[source]

Bases: acryo.pick._base.BasePickerModel

Particle picking based on Laplacian of Gaussian.

get_params_and_depth(scale: float)[source]
pick_in_chunk(image: numpy.ndarray[Any, numpy.dtype[numpy.float32]], sigma: float) → tuple[numpy.ndarray[Any, numpy.dtype[numpy.float32]], numpy.ndarray[Any, numpy.dtype[numpy.uint16]], Any][source]
class acryo.pick.ZNCCTemplateMatcher(template: numpy.ndarray[Any, numpy.dtype[numpy.float32]] | acryo.pipe._classes.ImageProvider, rotation: Union[tuple[tuple[float, float], tuple[float, float], tuple[float, float]], scipy.spatial.transform._rotation.Rotation], tilt_range: tuple[float, float] = (- 60, 60), order: int = 1)[source]

Bases: acryo.pick._base.BaseTemplateMatcher

Particle picking based on ZNCC template matching.

Parameters

  • template (3D array or ImageProvider) – Template image.

  • rotation (range-like) – 3D rotation of template image in degrees.

  • tilt_range (tuple of float, default is (-60, 60)) – Tilt range in degrees.

  • order (int, default is 1) – Order of interpolation.

pick_in_chunk(image: numpy.ndarray[Any, numpy.dtype[numpy.float32]], templates: list[numpy.ndarray[Any, numpy.dtype[numpy.float32]]], min_distance: float, min_score: float)[source]
pick_molecules(image: dask.array.core.Array, scale: float = 1.0, *, min_distance: float = 1.0, min_score: float = 0.02) → acryo.molecules.core.Molecules[source]