Source code for mantidimaging.core.operations.remove_all_stripe.remove_all_stripe

# 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_all_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

if TYPE_CHECKING:
    from numpy import ndarray
    from mantidimaging.core.data.imagestack import ImageStack
    from PyQt5.QtWidgets import QSpinBox, QDoubleSpinBox


[docs] class RemoveAllStripesFilter(BaseFilter): """Stripe and ring artifact removal. Remove all types of stripe artifacts by combining algorithm 6, 5, and 3 in Vo et al., Optics Express 28396 (2018). Source: https://github.com/algotom/algotom 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 all stripes" link_histograms = True operate_on_sinograms = True
[docs] @staticmethod def filter_func(images: ImageStack, snr=3, la_size=61, sm_size=21, dim=1, progress=None): """ :param snr: The ratio used to segment between useful information and noise. Greater is less sensitive. :param la_size: The window size of the median filter to remove large stripes. :param sm_size: The window size of the median filter to remove small-to-medium stripes. :param dim: Whether to perform the median on 1D or 2D view of the data. :return: Remove all types of stripe artifacts. """ if images.num_projections < 2: return images params = {"snr": snr, "la_size": la_size, "sm_size": sm_size, "dim": dim} if images.is_sinograms: compute_func = RemoveAllStripesFilter.compute_function_sino else: compute_func = RemoveAllStripesFilter.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_all_stripe(array[index], **params)
[docs] @staticmethod def compute_function(index: int, array: ndarray, params: dict[str, Any]): array[:, index, :] = remove_all_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 # https://tomopy.readthedocs.io/en/latest/api/tomopy.prep.stripe.html#tomopy.prep.stripe.remove_all_stripe _, 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.") _, la_size = add_property_to_form('Large 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.") _, sm_size = add_property_to_form('Small stripe kernel', Type.INT, default_value=7, valid_values=(1, 100), form=form, on_change=on_change, tooltip="Window size of the median filter to remove small-to-medium stripes.") _, dim = add_property_to_form('Dimension of the window', Type.INT, default_value=2, valid_values=(1, 2), form=form, on_change=on_change, tooltip="Whether to perform the median on 1D or 2D view of the data") return {'snr': snr, 'la_size': la_size, 'sm_size': sm_size, 'dim': dim}
[docs] @staticmethod def execute_wrapper(snr: QDoubleSpinBox, la_size: QSpinBox, sm_size: QSpinBox, dim: QSpinBox): # type: ignore return partial(RemoveAllStripesFilter.filter_func, snr=snr.value(), la_size=la_size.value(), sm_size=sm_size.value(), dim=dim.value())
[docs] @staticmethod def group_name() -> FilterGroup: return FilterGroup.Advanced