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# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
"""Filtering computation module.
--------------------------------
This module provides spatial and frequency-based filtering operations for images.
Filtering functions are essential for enhancing image quality and removing noise.
Main features include:
* Gaussian, median, moving average and Wiener filters
* Butterworth and frequency domain Gaussian filters.
Filtering functions are essential for enhancing image quality
and removing noise prior to further analysis.
"""
# pylint: disable=invalid-name # Allows short names like x, y...
# Note:
# ----
# - All `guidata.dataset.DataSet` parameter classes must also be imported in the
# `sigima.params` module.
# - All functions decorated with `computation_function` must be imported in the upper
# level `sigima.proc.image` module.
from __future__ import annotations
import guidata.dataset as gds # type: ignore[import]
import scipy.ndimage as spi # type: ignore[import]
import scipy.signal as sps # type: ignore[import]
from skimage import filters # type: ignore[import]
import sigima.tools.image
from sigima.config import _
from sigima.objects.image import ImageObj
from sigima.proc.base import (
GaussianParam,
MovingAverageParam,
MovingMedianParam,
)
from sigima.proc.decorator import computation_function
from sigima.proc.image.base import Wrap1to1Func, dst_1_to_1, restore_data_outside_roi
# NOTE: Only parameter classes DEFINED in this module should be included in __all__.
# Parameter classes imported from other modules (like sigima.proc.base) should NOT
# be re-exported to avoid Sphinx cross-reference conflicts. The sigima.params module
# serves as the central API point that imports and re-exports all parameter classes.
__all__ = [
"ButterworthParam",
"GaussianFreqFilterParam",
"butterworth",
"gaussian_filter",
"gaussian_freq_filter",
"moving_average",
"moving_median",
"wiener",
]
# MARK: Noise reduction filters
@computation_function()
def gaussian_filter(src: ImageObj, p: GaussianParam) -> ImageObj:
"""Compute gaussian filter with :py:func:`scipy.ndimage.gaussian_filter`.
Args:
src: Input image object.
p: Parameters.
Returns:
Output image object.
"""
return Wrap1to1Func(spi.gaussian_filter, sigma=p.sigma)(src)
@computation_function()
def moving_average(src: ImageObj, p: MovingAverageParam) -> ImageObj:
"""Compute moving average with :py:func:`scipy.ndimage.uniform_filter`.
Args:
src: Input image object.
p: Parameters.
Returns:
Output image object.
"""
return Wrap1to1Func(
spi.uniform_filter, size=p.n, mode=p.mode, func_name="moving_average"
)(src)
@computation_function()
def moving_median(src: ImageObj, p: MovingMedianParam) -> ImageObj:
"""Compute moving median with :py:func:`scipy.ndimage.median_filter`.
Args:
src: Input image object.
p: Parameters.
Returns:
Output image object.
"""
return Wrap1to1Func(
spi.median_filter, size=p.n, mode=p.mode, func_name="moving_median"
)(src)
@computation_function()
def wiener(src: ImageObj) -> ImageObj:
"""Compute Wiener filter with :py:func:`scipy.signal.wiener`
Args:
src: Input image object.
Returns:
Output image object.
"""
return Wrap1to1Func(sps.wiener)(src)
class ButterworthParam(gds.DataSet):
"""Butterworth filter parameters."""
cut_off = gds.FloatItem(
_("Cut-off frequency ratio"),
default=0.005,
min=0.0,
max=0.5,
help=_("Cut-off frequency ratio"),
)
high_pass = gds.BoolItem(
_("High-pass filter"),
default=False,
help=_("If True, apply high-pass filter instead of low-pass"),
)
order = gds.IntItem(
_("Order"),
default=2,
min=1,
help=_("Order of the Butterworth filter"),
)
# MARK: Frequency filters
@computation_function()
def butterworth(src: ImageObj, p: ButterworthParam) -> ImageObj:
"""Compute Butterworth filter with :py:func:`skimage.filters.butterworth`.
Args:
src: Input image object.
p: Parameters.
Returns:
Output image object.
"""
dst = dst_1_to_1(
src,
"butterworth",
f"cut_off={p.cut_off:.3f}, order={p.order}, high_pass={p.high_pass}",
)
dst.data = filters.butterworth(src.data, p.cut_off, p.high_pass, p.order)
restore_data_outside_roi(dst, src)
return dst
class GaussianFreqFilterParam(GaussianParam):
"""Parameters for Gaussian filter applied in the frequency domain."""
sigma = gds.FloatItem(
"σ",
default=1.0,
unit="pixel⁻¹",
min=0.0,
help=_("Standard deviation of the Gaussian filter"),
)
f0 = gds.FloatItem(
_("Center frequency"),
default=1.0,
unit="pixel⁻¹",
min=0.0,
help=_("Center frequency of the Gaussian filter"),
)
sigma = gds.FloatItem(
"σ",
default=0.5,
unit="pixels⁻¹",
min=0.0,
help=_("Standard deviation of the Gaussian filter"),
)
ifft_result_type = gds.ChoiceItem(
_("Inverse FFT result"),
(("real", _("Real part")), ("abs", _("Absolute value"))),
default="real",
help=_("How to return the inverse FFT result"),
)
@computation_function()
def gaussian_freq_filter(src: ImageObj, p: GaussianFreqFilterParam) -> ImageObj:
"""Apply a Gaussian filter in the frequency domain.
Args:
src: Source image object.
p: Parameters.
Returns:
Output image object.
"""
dst = dst_1_to_1(
src,
"frequency_domain_gaussian_filter",
f"sigma={p.sigma:.3f}, f0={p.f0:.3f}",
)
dst.data = sigima.tools.image.gaussian_freq_filter(src.data, p.f0, p.sigma)
restore_data_outside_roi(dst, src)
return dst
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