Alignment

The alignment module includes support for aligning projection data. The provided tools are:

Pre-alignment routines for tomographic data
Image stack shift finding

Pre-alignment

The class DetectorShiftsPRE offers support for both finding the vertical and horizontal shifts of tomographic projection data. They are exposed through the methods fit_v and fit_u.

class DetectorShiftsPRE(DetectorShiftsBase):
    """Compute the pre-alignment detector shifts for a given dataset."""

    def fit_v(
        self,
        use_derivative: bool = True,
        use_rfft: bool = True,
        normalize_fourier: bool = True,
    ) -> NDArrayFloat:
        ...

    def fit_u(
        self,
        fit_l1: bool = False,
        background: Union[float, NDArray, None] = None,
        method: str = "com",
    ) -> tuple[NDArrayFloat, float]:
        ...

The fit_v method computes the vertical shifts of the stack with 1D cross-correlations. The cross-correlation function is computed per angle on the intensity profile resulting from computing the integral of the projections along the U axis, and their derivative along the V axis.

The fit_u method computes the horizontal shifts of the stack, by computing the sinusoid that interpolates the chosen value of interest across all the rotation angles. The value of interest can include the center-of-mass (CoM) or the position of the highest intensity peak of the projections.