Source code for mantidimaging.core.operations.median_filter.median_filter

# 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 logging import getLogger
from typing import Callable, Dict, Any, TYPE_CHECKING, Tuple

import numpy as np
import scipy.ndimage as scipy_ndimage
from PyQt5.QtGui import QValidator
from PyQt5.QtWidgets import QSpinBox, QLabel, QSizePolicy

from mantidimaging import helper as h
from mantidimaging.core.gpu import utility as gpu
from mantidimaging.core.operations.base_filter import BaseFilter
from mantidimaging.core.parallel import shared as ps
from mantidimaging.core.utility.progress_reporting import Progress
from mantidimaging.gui.utility import add_property_to_form
from mantidimaging.gui.utility.qt_helpers import Type, on_change_and_disable

    from PyQt5.QtWidgets import QFormLayout  # pragma: no cover
    from import ImageStack

KERNEL_SIZE_TOOLTIP = "Size of the median filter kernel"

[docs]class KernelSpinBox(QSpinBox): def __init__(self, on_change: Callable): """ Spin box for entering kernel sizes that only accepts odd numbers. :param on_change: The function to be called when the value changes. """ super().__init__() self.setMinimum(3) self.setMaximum(999) self.setSingleStep(2) self.setKeyboardTracking(False) self.setToolTip(KERNEL_SIZE_TOOLTIP) self.setSizePolicy(QSizePolicy.Policy.Maximum, QSizePolicy.Policy.Fixed) self.valueChanged.connect(lambda: on_change_and_disable(self, on_change))
[docs] def validate(self, input: str, pos: int) -> Tuple[QValidator.State, str, int]: """ Validate the spin box input. Returns as Intermediate state if the input is empty or contains an even number, otherwise it returns Acceptable. """ if not input: return QValidator.State.Intermediate, input, pos kernel_size = int(input) if kernel_size % 2 != 0: return QValidator.State.Acceptable, input, pos return QValidator.State.Intermediate, input, pos
[docs]class MedianFilter(BaseFilter): """Applies Median filter to the data. Intended to be used on: Projections or reconstructed slices When: As a pre-processing or post-reconstruction step to reduce noise. Note: NaN values are preserved through the filter. They are treated as negative infinity while calculating neighbouring pixels. """ filter_name = "Median" link_histograms = True
[docs] @staticmethod def filter_func(data: ImageStack, size=None, mode="reflect", progress=None, force_cpu=True): """ :param data: Input data as an ImageStack object. :param size: Size of the kernel :param mode: The mode with which to handle the edges. One of [reflect, constant, nearest, mirror, wrap]. Modes are described in the `SciPy documentation <>`_. :param progress: The object for displaying the progress. :param force_cpu: Whether or not to use the CPU. :return: Returns the processed data """ h.check_data_stack(data) if not size or not size > 1: raise ValueError(f'Size parameter must be greater than 1, but value provided was {size}') if not force_cpu: _execute_gpu(, size, mode, progress) else: _execute(data, size, mode, progress) h.check_data_stack(data) return data
[docs] @staticmethod def register_gui(form: 'QFormLayout', on_change: Callable, view) -> Dict[str, Any]: # Create a spin box for kernel size without add_property_to_form in order to allow a custom validate method size_field = KernelSpinBox(on_change) size_field_label = QLabel("Kernel Size") size_field_label.setToolTip(KERNEL_SIZE_TOOLTIP) form.addRow(size_field_label, size_field) _, mode_field = add_property_to_form('Edge Mode', Type.CHOICE, valid_values=modes(), form=form, on_change=on_change, tooltip="Mode to handle the edges of the image") _, gpu_field = add_property_to_form('Use GPU', Type.BOOL, default_value=False, tooltip='Run the median filter on the GPU', form=form, on_change=on_change) return {'size_field': size_field, 'mode_field': mode_field, 'use_gpu_field': gpu_field}
[docs] @staticmethod def execute_wrapper(size_field=None, mode_field=None, use_gpu_field=None): return partial(MedianFilter.filter_func, size=size_field.value(), mode=mode_field.currentText(), force_cpu=not use_gpu_field.isChecked())
[docs]def modes(): return ['reflect', 'constant', 'nearest', 'mirror', 'wrap']
def _median_filter(data: np.ndarray, size: int, mode: str): # Replaces NaNs with negative infinity before median filter # so they do not effect neighbouring pixels nans = np.isnan(data) data = np.where(nans, -np.inf, data) data = scipy_ndimage.median_filter(data, size=size, mode=mode) # Put the original NaNs back data = np.where(nans, np.nan, data) return data def _execute(images: ImageStack, size, mode, progress=None): log = getLogger(__name__) progress = Progress.ensure_instance(progress, task_name='Median filter') # create the partial function to forward the parameters f = ps.create_partial(_median_filter, ps.return_to_self, size=size, mode=mode) with progress:"PARALLEL median filter, with pixel data type: {images.dtype}, filter size/width: {size}.") ps.execute(f, [images.shared_array],[0], progress, msg="Median filter") def _execute_gpu(data, size, mode, progress=None): log = getLogger(__name__) progress = Progress.ensure_instance(progress, num_steps=data.shape[0], task_name="Median filter GPU") cuda = gpu.CudaExecuter(data.dtype) with progress:"GPU median filter, with pixel data type: {data.dtype}, filter size/width: {size}.") cuda.median_filter(data, size, mode, progress)