Source code for mantidimaging.core.operations.remove_dead_stripe.remove_dead_stripe

# Copyright (C) 2023 ISIS Rutherford Appleton Laboratory UKRI
# SPDX - License - Identifier: GPL-3.0-or-later
from __future__ import annotations

from functools import partial
from typing import Dict, Any, TYPE_CHECKING

from algotom.prep.removal import remove_dead_stripe

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 QDoubleSpinBox, QSpinBox

[docs]class RemoveDeadStripesFilter(BaseFilter): """Stripe and ring artifact removal. Algorithm 6 in Vo et al., Optics Express 28396 (2018). Remove unresponsive or fluctuating stripes by: locating stripes, correction by interpolation. 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 dead stripes" link_histograms = True operate_on_sinograms = True
[docs] @classmethod def filter_func(cls, images: ImageStack, snr=3, size=61, progress=None): """ :param snr: The ratio value. :param size: The window size of the median filter to remove dead stripes. :return: The ImageStack object with the dead stripes removed. """ if images.num_projections < 2: return images params = {"snr": snr, "size": size, "residual": False} if images.is_sinograms: compute_func = cls.compute_function_sino else: compute_func = cls.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_dead_stripe(array[index], **params)
[docs] @staticmethod def compute_function(index: int, array: ndarray, params: Dict[str, Any]): array[:, index, :] = remove_dead_stripe(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) # defaults taken from TomoPy integration # _, snr = add_property_to_form('Stripe ratio', Type.FLOAT, default_value=3, form=form, on_change=on_change, tooltip="Ratio used to segment between useful information and noise" ". Greater is less sensitive.") _, size = add_property_to_form('Stripe kernel', Type.INT, default_value=21, valid_values=(1, 100), form=form, on_change=on_change, tooltip="Window size of the median filter to remove large stripes.") return {'snr': snr, 'size': size}
[docs] @staticmethod def execute_wrapper(snr: QDoubleSpinBox, size: QSpinBox): # type: ignore return partial(RemoveDeadStripesFilter.filter_func, snr=snr.value(), size=size.value())
[docs] @staticmethod def group_name() -> FilterGroup: return FilterGroup.Advanced