Source code for mantidimaging.core.operations.remove_stripe_sorting_fitting.remove_stripe_sorting_fitting

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

from functools import partial
from typing import Any, TYPE_CHECKING

from algotom.prep.removal import remove_stripe_based_fitting

from mantidimaging.core.operations.base_filter import BaseFilter, FilterGroup
from mantidimaging.core.parallel import shared as ps
from mantidimaging.gui.utility.qt_helpers import Type

    from numpy import ndarray
    from import ImageStack
    from PyQt5.QtWidgets import QSpinBox

[docs] class RemoveStripeSortingFittingFilter(BaseFilter): """Stripe and ring artifact removal. Combination of algorithm 3 and 1 in Vo et al., Optics Express 28396 (2018). Remove stripes using the sorting and fitting technique. Source: Intended to be used on: Sinograms When: If stripes artifacts are present that have not been removed with outliers + flat-fielding the projections Caution: Horizontal stripes caused by changes in image intensity (pixel values) should be fixed by ROI Normalisation instead! """ filter_name = "Remove stripes with sorting and fitting" link_histograms = True operate_on_sinograms = True
[docs] @staticmethod def filter_func(images: ImageStack, order=1, sigma=3, progress=None): """ :param order: The polynomial fit order. Check algotom docs for more information. :param sigma: The sigma of the Gaussian window in the x-direction. :return: The ImageStack object with the stripes removed using the sorting and fitting technique. """ if images.num_projections < 2: return images params = {'order': order, 'sigma': sigma, 'sort': True} if images.is_sinograms: compute_func = RemoveStripeSortingFittingFilter.compute_function_sino else: compute_func = RemoveStripeSortingFittingFilter.compute_function ps.run_compute_func(compute_func, images.num_sinograms, images.shared_array, params, progress) return images
[docs] @staticmethod def compute_function_sino(index: int, array: ndarray, params: dict[str, Any]): array[index] = remove_stripe_based_fitting(array[index], **params)
[docs] @staticmethod def compute_function(index: int, array: ndarray, params: dict[str, Any]): array[:, index, :] = remove_stripe_based_fitting(array[:, index, :], **params)
[docs] @staticmethod def register_gui(form, on_change, view): from mantidimaging.gui.utility import add_property_to_form label, _ = add_property_to_form(BaseFilter.SINOGRAM_FILTER_INFO, Type.LABEL, form=form, on_change=on_change) _, order = add_property_to_form('Polynomial fit order', Type.INT, default_value=1, form=form, on_change=on_change, tooltip="Polynomial fit order. Check algotom docs for more information") _, sigma = add_property_to_form('Sigma', Type.INT, default_value=3, form=form, on_change=on_change, tooltip="Sigma of the Gaussian window in the x-direction") return {'order': order, 'sigma': sigma}
[docs] @staticmethod def execute_wrapper(order: QSpinBox, sigma: QSpinBox): # type: ignore return partial(RemoveStripeSortingFittingFilter.filter_func, order=order.value(), sigma=sigma.value())
[docs] @staticmethod def group_name() -> FilterGroup: return FilterGroup.Advanced