Source code for mantidimaging.core.reconstruct.base_recon

# Copyright (C) 2024 ISIS Rutherford Appleton Laboratory UKRI
# SPDX - License - Identifier: GPL-3.0-or-later
from __future__ import annotations

from typing import TYPE_CHECKING

import numpy as np
from numpy.polynomial import Polynomial

    from import ImageStack
    from mantidimaging.core.utility.data_containers import ScalarCoR, ProjectionAngles, ReconstructionParameters
    from mantidimaging.core.utility.progress_reporting import Progress

[docs] class BaseRecon:
[docs] @staticmethod def find_cor(images: ImageStack, slice_idx: int, start_cor: float, recon_params: ReconstructionParameters) -> float: raise NotImplementedError("Base class call")
[docs] @staticmethod def prepare_sinogram(data: np.ndarray, recon_params: ReconstructionParameters): logged_data = BaseRecon.negative_log(data) if recon_params.beam_hardening_coefs is not None: coefs = np.array([0.0, 1.0] + recon_params.beam_hardening_coefs) bhc_poly = Polynomial(coefs.astype(data.dtype)) return bhc_poly(logged_data) else: return logged_data
[docs] @staticmethod def negative_log(data: np.ndarray) -> np.ndarray: return -np.log(data)
[docs] @staticmethod def single_sino(sino: np.ndarray, cor: ScalarCoR, proj_angles: ProjectionAngles, recon_params: ReconstructionParameters, progress: Progress | None = None) -> np.ndarray: """ Reconstruct a single sinogram :param sino: The 2D sinogram as a numpy array :param cor: Center of rotation for parallel geometry. It will be converted to vector geometry before reconstructing :param proj_angles: Projection angles :param recon_params: Reconstruction parameters to configure which algorithm/filter/etc is used :return: 2D image data for reconstructed slice """ raise NotImplementedError("Base class call")
[docs] @staticmethod def full(images: ImageStack, cors: list[ScalarCoR], recon_params: ReconstructionParameters, progress: Progress | None = None) -> ImageStack: """ Performs a volume reconstruction using sample data provided as sinograms. :param images: Array of sinogram images :param cors: Array of centre of rotation values :param proj_angles: Array of projection angles :param recon_params: Reconstruction Parameters :param progress: Optional progress reporter :return: 3D image data for reconstructed volume """ raise NotImplementedError("Base class call")
[docs] @staticmethod def allowed_filters() -> list[str]: return []