CopickSectionAlignment

Bases: BaseModel

Rigid alignment of one tilt image.

A point p of the alignment's reference volume projects to the point q = drop_z(R @ p) + (shift_x, shift_y) of the image, with R = Rz(in_plane_rotation) @ Ry(tilt_angle) @ Rx(x_tilt) (active, right-handed). Positions are in Angstrom, relative to the CETS centres (floor(N/2)) of the image and of the reference volume (see copick.util.alignment_geometry).

Attributes:

• section (int) –

  Section of the image in the tilt series.

• tilt_angle (float) –

  Refined tilt angle in degrees.

• x_tilt (float) –

  Tilt about the x axis in degrees.

• in_plane_rotation (float) –

  In-plane rotation (tilt-axis angle) in degrees.

• shift_x (float) –

  Shift along x in Angstrom.

• shift_y (float) –

  Shift along y in Angstrom.

section: int

tilt_angle: float

x_tilt: float = 0.0

in_plane_rotation: float = 0.0

shift_x: float = 0.0

shift_y: float = 0.0

matrix() -> np.ndarray