pytme 0.2.1__cp311-cp311-macosx_14_0_arm64.whl → 0.2.3__cp311-cp311-macosx_14_0_arm64.whl

tme/helpers.py

@@ -1,881 +0,0 @@
-""" General utility functions.
-
-    Copyright (c) 2023 European Molecular Biology Laboratory
-
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
-"""
-
-import os
-import yaml
-import pickle
-from itertools import product
-from typing import Tuple, Dict
-
-import numpy as np
-from numpy.typing import NDArray
-from scipy.special import iv as scipy_special_iv
-from scipy.ndimage import correlate1d, gaussian_filter
-from scipy.optimize import minimize
-from scipy.signal import convolve
-from scipy.interpolate import splrep, BSpline
-from scipy.stats import entropy
-
-
-def is_gzipped(filename: str) -> bool:
-    """Check if a file is a gzip file by reading its magic number."""
-    with open(filename, "rb") as f:
-        return f.read(2) == b"\x1f\x8b"
-
-
-def window_to_volume(window: NDArray) -> NDArray:
-    """
-    Convert a 1D window to a 3D volume.
-
-    Parameters
-    ----------
-    window : numpy.ndarray
-        1D window.
-
-    Returns
-    -------
-    numpy.ndarray
-        3D volume generated from the 1D window.
-    """
-    window /= np.trapz(window)
-    return (
-        window[:, np.newaxis, np.newaxis]
-        * window[np.newaxis, :, np.newaxis]
-        * window[np.newaxis, np.newaxis, :]
-    )
-
-
-def window_kaiserb(width: int, beta: float = 3.2, order: int = 0) -> NDArray:
-    """
-    Create a Kaiser-Bessel window.
-
-    Parameters
-    ----------
-    width : int
-        Width of the window.
-    beta : float, optional
-        Beta parameter of the Kaiser-Bessel window. Default is 3.2.
-    order : int, optional
-        Order of the Bessel function. Default is 0.
-
-    Returns
-    -------
-    NDArray
-        Kaiser-Bessel window.
-
-    References
-    ----------
-    .. [1]  Sorzano, Carlos et al (Mar. 2015). Fast and accurate conversion
-            of atomic models into electron density maps. AIMS Biophysics
-            2, 8–20.
-    """
-    window = np.arange(0, width)
-    alpha = (width - 1) / 2.0
-    arr = beta * np.sqrt(1 - ((window - alpha) / alpha) ** 2.0)
-
-    return bessel(order, arr) / bessel(order, beta)
-
-
-def window_blob(width: int, beta: float = 3.2, order: int = 2) -> NDArray:
-    """
-    Generate a blob window based on Bessel functions.
-
-    Parameters
-    ----------
-    width : int
-        Width of the window.
-    beta : float, optional
-        Beta parameter. Default is 3.2.
-    order : int, optional
-        Order of the Bessel function. Default is 2.
-
-    Returns
-    -------
-    NDArray
-        Blob window.
-
-    References
-    ----------
-    .. [1]  Sorzano, Carlos et al (Mar. 2015). Fast and accurate conversion
-            of atomic models into electron density maps. AIMS Biophysics
-            2, 8–20.
-    """
-    window = np.arange(0, width)
-    alpha = (width - 1) / 2.0
-    arr = beta * np.sqrt(1 - ((window - alpha) / alpha) ** 2.0)
-
-    arr = np.divide(np.power(arr, order) * bessel(order, arr), bessel(order, beta))
-    arr[arr != arr] = 0
-    return arr
-
-
-def window_sinckb(omega: float, d: float, dw: float):
-    """
-    Compute the sinc window combined with a Kaiser window.
-
-    Parameters
-    ----------
-    omega : float
-        Reduction factor.
-    d : float
-        Ripple.
-    dw : float
-        Delta w.
-
-    Returns
-    -------
-    ndarray
-        Impulse response of the low-pass filter.
-
-    References
-    ----------
-    .. [1]  Sorzano, Carlos et al (Mar. 2015). Fast and accurate conversion
-            of atomic models into electron density maps. AIMS Biophysics
-            2, 8–20.
-    """
-    kaiser = kaiser_mask(d, dw)
-    sinc_m = sinc_mask(np.zeros(kaiser.shape), omega)
-
-    mask = sinc_m * kaiser
-
-    return mask / np.sum(mask)
-
-
-def apply_window_filter(
-    arr: NDArray,
-    filter_window: NDArray,
-    mode: str = "reflect",
-    cval: float = 0.0,
-    origin: int = 0,
-):
-    """
-    Apply a window filter on an input array.
-
-    Parameters
-    ----------
-    arr : NDArray,
-        Input array.
-    filter_window : NDArray,
-        Window filter to apply.
-    mode : str, optional
-        Mode for the filtering, default is "reflect".
-    cval : float, optional
-        Value to fill when mode is "constant", default is 0.0.
-    origin : int, optional
-        Origin of the filter window, default is 0.
-
-    Returns
-    -------
-    NDArray,
-        Array after filtering.
-
-    """
-    filter_window = filter_window[::-1]
-    for axs in range(arr.ndim):
-        correlate1d(
-            input=arr,
-            weights=filter_window,
-            axis=axs,
-            output=arr,
-            mode=mode,
-            cval=cval,
-            origin=origin,
-        )
-    return arr
-
-
-def sinc_mask(mask: NDArray, omega: float) -> NDArray:
-    """
-    Create a sinc mask.
-
-    Parameters
-    ----------
-    mask : NDArray
-        Input mask.
-    omega : float
-        Reduction factor.
-
-    Returns
-    -------
-    NDArray
-        Sinc mask.
-    """
-    # Move filter origin to the center of the mask
-    mask_origin = int((mask.size - 1) / 2)
-    dist = np.arange(-mask_origin, mask_origin + 1)
-
-    return np.multiply(omega / np.pi, np.sinc((omega / np.pi) * dist))
-
-
-def kaiser_mask(d: float, dw: float) -> NDArray:
-    """
-    Create a Kaiser mask.
-
-    Parameters
-    ----------
-    d : float
-        Ripple.
-    dw : float
-        Delta-w.
-
-    Returns
-    -------
-    NDArray
-        Kaiser mask.
-    """
-    # convert dw from a frequency normalized to 1 to a frequency normalized to pi
-    dw *= np.pi
-    A = -20 * np.log10(d)
-    M = max(1, np.ceil((A - 8) / (2.285 * dw)))
-
-    beta = 0
-    if A > 50:
-        beta = 0.1102 * (A - 8.7)
-    elif A >= 21:
-        beta = 0.5842 * np.power(A - 21, 0.4) + 0.07886 * (A - 21)
-
-    mask_values = np.abs(np.arange(-M, M + 1))
-    mask = np.sqrt(1 - np.power(mask_values / M, 2))
-
-    return np.divide(bessel(0, beta * mask), bessel(0, beta))
-
-
-def bessel(order: int, arr: NDArray) -> NDArray:
-    """
-    Compute the modified Bessel function of the first kind.
-
-    Parameters
-    ----------
-    order : int
-        Order of the Bessel function.
-    arr : NDArray
-        Input array.
-
-    Returns
-    -------
-    NDArray
-        Bessel function values.
-
-    """
-    return scipy_special_iv(order, arr)
-
-
-def electron_factor(
-    dist: NDArray, method: str, atom: str, fourier: bool = False
-) -> NDArray:
-    """
-    Compute the electron factor.
-
-    Parameters
-    ----------
-    dist : NDArray
-        Distance.
-    method : str
-        Method name.
-    atom : str
-        Atom type.
-    fourier : bool, optional
-        Whether to compute the electron factor in Fourier space.
-
-    Returns
-    -------
-    NDArray
-        Computed electron factor.
-    """
-    data = get_scattering_factors(method)
-    n_range = len(data.get(atom, [])) // 2
-    default = np.zeros(n_range * 3)
-
-    res = 0.0
-    a_values = data.get(atom, default)[:n_range]
-    b_values = data.get(atom, default)[n_range : 2 * n_range]
-
-    if method == "dt1969":
-        b_values = data.get(atom, default)[1 : (n_range + 1)]
-
-    for i in range(n_range):
-        a = a_values[i]
-        b = b_values[i]
-
-        if fourier:
-            temp = a * np.exp(-b * np.power(dist, 2))
-        else:
-            b = b / (4 * np.power(np.pi, 2))
-            temp = a * np.sqrt(np.pi / b) * np.exp(-np.power(dist, 2) / (4 * b))
-
-        if not np.isnan(temp).any():
-            res += temp
-
-    return res / (2 * np.pi)
-
-
-def optimize_hlfp(profile, M, T, atom, method, filter_method):
-    """
-    Optimize high-low pass filter (HLFP).
-
-    Parameters
-    ----------
-    profile : NDArray
-        Input profile.
-    M : int
-        Scaling factor.
-    T : float
-        Time step.
-    atom : str
-        Atom type.
-    method : str
-        Method name.
-    filter_method : str
-        Filter method name.
-
-    Returns
-    -------
-    float
-        Fitness value.
-
-    References
-    ----------
-    .. [1]  Sorzano, Carlos et al (Mar. 2015). Fast and accurate conversion
-            of atomic models into electron density maps. AIMS Biophysics
-            2, 8–20.
-    """
-    # omega, d, dw
-    initial_params = [1.0, 0.01, 1.0 / 8.0]
-    if filter_method == "brute":
-        best_fitness = float("inf")
-        OMEGA, D, DW = np.meshgrid(
-            np.arange(0.7, 1.3, 0.015),
-            np.arange(0.01, 0.2, 0.015),
-            np.arange(0.05, 0.2, 0.015),
-        )
-        for omega, d, dw in zip(OMEGA.ravel(), D.ravel(), DW.ravel()):
-            current_fitness = _hlpf_fitness([omega, d, dw], T, M, profile, atom, method)
-            if current_fitness < best_fitness:
-                best_fitness = current_fitness
-                initial_params = [omega, d, dw]
-        final_params = np.array(initial_params)
-    else:
-        res = minimize(
-            _hlpf_fitness,
-            initial_params,
-            args=tuple([T, M, profile, atom, method]),
-            method="SLSQP",
-            bounds=([0.2, 2], [1e-3, 2], [1e-3, 1]),
-        )
-        final_params = res.x
-        if np.any(final_params != final_params):
-            print(f"Solver returned NAs for atom {atom} at {M}" % (atom, M))
-            final_params = final_params
-
-    final_params[0] *= np.pi / M
-    mask = window_sinckb(*final_params)
-
-    if profile.shape[0] > mask.shape[0]:
-        profile_origin = int((profile.size - 1) / 2)
-        mask = window(mask, profile_origin, profile_origin)
-
-    return mask
-
-
-def _hlpf_fitness(
-    params: Tuple[float], T: float, M: float, profile: NDArray, atom: str, method: str
-) -> float:
-    """
-    Fitness function for high-low pass filter optimization.
-
-    Parameters
-    ----------
-    params : tuple of float
-        Parameters [omega, d, dw] for optimization.
-    T : float
-        Time step.
-    M : int
-        Scaling factor.
-    profile : NDArray
-        Input profile.
-    atom : str
-        Atom type.
-    method : str
-        Method name.
-
-    Returns
-    -------
-    float
-        Fitness value.
-
-    References
-    ----------
-    .. [1]  Sorzano, Carlos et al (Mar. 2015). Fast and accurate conversion
-            of atomic models into electron density maps. AIMS Biophysics
-            2, 8–20.
-    .. [2]  https://github.com/I2PC/xmipp/blob/707f921dfd29cacf5a161535034d28153b58215a/src/xmipp/libraries/data/pdb.cpp#L1344
-    """
-    omega, d, dw = params
-
-    if not (0.7 <= omega <= 1.3) and (0 <= d <= 0.2) and (1e-3 <= dw <= 0.2):
-        return 1e38 * np.random.randint(1, 100)
-
-    mask = window_sinckb(omega=omega * np.pi / M, d=d, dw=dw)
-
-    if profile.shape[0] > mask.shape[0]:
-        profile_origin = int((profile.size - 1) / 2)
-        mask = window(mask, profile_origin, profile_origin)
-    else:
-        filter_origin = int((mask.size - 1) / 2)
-        profile = window(profile, filter_origin, filter_origin)
-
-    f_mask = convolve(profile, mask)
-
-    orig = int((f_mask.size - 1) / 2)
-    dist = np.arange(-orig, orig + 1) * T
-    t, c, k = splrep(x=dist, y=f_mask, k=3)
-    i_max = np.ceil(np.divide(f_mask.shape, M))
-    coarse_mask = np.arange(-i_max, i_max + 1) * M
-    spline = BSpline(t, c, k)
-    coarse_values = spline(coarse_mask)
-
-    # padding to retain longer fourier response
-    aux = window(
-        coarse_values, x0=10 * coarse_values.shape[0], xf=10 * coarse_values.shape[0]
-    )
-    f_filter = np.fft.fftn(aux)
-    f_filter_mag = np.abs(f_filter)
-    freq = np.fft.fftfreq(f_filter.size)
-    freq /= M * T
-    amplitude_f = mask.sum() / coarse_values.sum()
-
-    size_f = f_filter_mag.shape[0] * amplitude_f
-    fourier_form_f = electron_factor(dist=freq, atom=atom, method=method, fourier=True)
-
-    valid_freq_mask = freq >= 0
-    f1_values = np.log10(f_filter_mag[valid_freq_mask] * size_f)
-    f2_values = np.log10(np.divide(T, fourier_form_f[valid_freq_mask]))
-    squared_differences = np.square(f1_values - f2_values)
-    error = np.sum(squared_differences)
-    error /= np.sum(valid_freq_mask)
-
-    return error
-
-
-def window(arr, x0, xf, constant_values=0):
-    """
-    Window an array by slicing between x0 and xf and padding if required.
-
-    Parameters
-    ----------
-    arr : ndarray
-        Input array to be windowed.
-    x0 : int
-        Start of the window.
-    xf : int
-        End of the window.
-    constant_values : int or float, optional
-        The constant values to use for padding, by default 0.
-
-    Returns
-    -------
-    ndarray
-        Windowed array.
-    """
-    origin = int((arr.size - 1) / 2)
-
-    xs = origin - x0
-    xe = origin - xf
-
-    if xs >= 0 and xe <= arr.shape[0]:
-        if xs <= arr.shape[0] and xe > 0:
-            arr = arr[xs:xe]
-            xs = 0
-            xe = 0
-        elif xs <= arr.shape[0]:
-            arr = arr[xs:]
-            xs = 0
-    elif xe >= 0 and xe <= arr.shape[0]:
-        arr = arr[:xe]
-        xe = 0
-
-    xs *= -1
-    xe *= -1
-
-    return np.pad(
-        arr, (int(xs), int(xe)), mode="constant", constant_values=constant_values
-    )
-
-
-def atom_profile(
-    M, atom, T=0.08333333, method="peng1995", lfilter=True, filter_method="minimize"
-):
-    """
-    Generate an atom profile using a variety of methods.
-
-    Parameters
-    ----------
-    M : float
-        Down sampling factor.
-    atom : Any
-        Type or representation of the atom.
-    T : float, optional
-        Sampling rate in angstroms/pixel, by default 0.08333333.
-    method : str, optional
-        Method to be used for generating the profile, by default "peng1995".
-    lfilter : bool, optional
-        Whether to apply filter on the profile, by default True.
-    filter_method : str, optional
-        The method for the filter, by default "minimize".
-
-    Returns
-    -------
-    BSpline
-        A spline representation of the atom profile.
-
-    References
-    ----------
-    .. [1]  Sorzano, Carlos et al (Mar. 2015). Fast and accurate conversion
-            of atomic models into electron density maps. AIMS Biophysics
-            2, 8–20.
-    .. [2]  https://github.com/I2PC/xmipp/blob/707f921dfd29cacf5a161535034d28153b58215a/src/xmipp/libraries/data/pdb.cpp#L1344
-    """
-    M = M / T
-    imax = np.ceil(4 / T * np.sqrt(76.7309 / (2 * np.power(np.pi, 2))))
-    dist = np.arange(-imax, imax + 1) * T
-
-    profile = electron_factor(dist, method, atom)
-
-    if lfilter:
-        window = optimize_hlfp(
-            profile=profile,
-            M=M,
-            T=T,
-            atom=atom,
-            method=method,
-            filter_method=filter_method,
-        )
-        profile = convolve(profile, window)
-
-        indices = np.where(profile > 1e-3)
-        min_indices = np.maximum(np.amin(indices, axis=1), 0)
-        max_indices = np.minimum(np.amax(indices, axis=1) + 1, profile.shape)
-        slices = tuple(slice(*coord) for coord in zip(min_indices, max_indices))
-        profile = profile[slices]
-
-    profile_origin = int((profile.size - 1) / 2)
-    dist = np.arange(-profile_origin, profile_origin + 1) * T
-    t, c, k = splrep(x=dist, y=profile, k=3)
-
-    return BSpline(t, c, k)
-
-
-def get_scattering_factors(method: str) -> Dict:
-    """
-    Retrieve scattering factors from a stored file based on the given method.
-
-    Parameters
-    ----------
-    method : str
-        Method name used to get the scattering factors.
-
-    Returns
-    -------
-    Dict
-        Dictionary containing scattering factors for the given method.
-
-    Raises
-    ------
-    ValueError
-        If the method is not found in the stored data.
-
-    """
-    path = os.path.join(os.path.dirname(__file__), "data", "scattering_factors.pickle")
-    with open(path, "rb") as infile:
-        data = pickle.load(infile)
-
-    if method not in data:
-        raise ValueError(f"{method} is not valid. Use {', '.join(data.keys())}.")
-    return data[method]
-
-
-def load_quaternions_by_angle(angle: float) -> (NDArray, NDArray, float):
-    """
-    Get orientations and weights proportional to the given angle.
-
-    Parameters
-    ----------
-    angle : float
-        Given angle.
-
-    Returns
-    -------
-    tuple
-        quaternions : NDArray
-            Quaternion representations of orientations.
-        weights : NDArray
-            Weights associated with each orientation.
-        angle : float
-            The closest angle to the provided angle from the metadata.
-    """
-    # Metadata contains (N orientations, rotational sampling, coverage as values)
-    with open(
-        os.path.join(os.path.dirname(__file__), "data", "metadata.yaml"), "r"
-    ) as infile:
-        metadata = yaml.full_load(infile)
-
-    set_diffs = {
-        setname: abs(angle - set_angle)
-        for setname, (_, set_angle, _) in metadata.items()
-    }
-    fname = min(set_diffs, key=set_diffs.get)
-
-    infile = os.path.join(os.path.dirname(__file__), "data", fname)
-    quat_weights = np.load(infile)
-
-    quat = quat_weights[:, :4]
-    weights = quat_weights[:, -1]
-    angle = metadata[fname][0]
-
-    return quat, weights, angle
-
-
-def quaternion_to_rotation_matrix(quaternions: NDArray) -> NDArray:
-    """
-    Convert quaternions to rotation matrices.
-
-    Parameters
-    ----------
-    quaternions : NDArray
-        Array containing quaternions.
-
-    Returns
-    -------
-    NDArray
-        Rotation matrices corresponding to the given quaternions.
-    """
-    q0 = quaternions[:, 0]
-    q1 = quaternions[:, 1]
-    q2 = quaternions[:, 2]
-    q3 = quaternions[:, 3]
-
-    s = np.linalg.norm(quaternions, axis=1) * 2
-    rotmat = np.zeros((quaternions.shape[0], 3, 3), dtype=np.float64)
-
-    rotmat[:, 0, 0] = 1.0 - s * ((q2 * q2) + (q3 * q3))
-    rotmat[:, 0, 1] = s * ((q1 * q2) - (q0 * q3))
-    rotmat[:, 0, 2] = s * ((q1 * q3) + (q0 * q2))
-
-    rotmat[:, 1, 0] = s * ((q2 * q1) + (q0 * q3))
-    rotmat[:, 1, 1] = 1.0 - s * ((q3 * q3) + (q1 * q1))
-    rotmat[:, 1, 2] = s * ((q2 * q3) - (q0 * q1))
-
-    rotmat[:, 2, 0] = s * ((q3 * q1) - (q0 * q2))
-    rotmat[:, 2, 1] = s * ((q3 * q2) + (q0 * q1))
-    rotmat[:, 2, 2] = 1.0 - s * ((q1 * q1) + (q2 * q2))
-
-    np.around(rotmat, decimals=8, out=rotmat)
-
-    return rotmat
-
-
-def reverse(arr: NDArray) -> NDArray:
-    """
-    Reverse the order of elements in an array along all its axes.
-
-    Parameters
-    ----------
-    arr : NDArray
-        Input array.
-
-    Returns
-    -------
-    NDArray
-        Reversed array.
-    """
-    return arr[(slice(None, None, -1),) * arr.ndim]
-
-
-class Ntree:
-    """
-    N-dimensional dyadic tree.
-
-    Each array dimension is split into two similarly sized halves. The amount of
-    subvolumes per split equals 2**n with n being the dimension of the input array.
-
-    Attributes
-    ----------
-    nleaves : int
-        Number of leaves in the Ntree.
-
-    """
-
-    def __init__(self, arr: NDArray):
-        """
-        Initialize the Ntree with the given array.
-
-        Parameters
-        ----------
-        arr : np.ndarray
-            Input array to build the N-dimensional dyadic tree.
-
-        """
-        arr = np.asarray(arr)
-        self._subvolumes = []
-        self._sd = []
-        self._arr = arr.copy()
-        self._arr += np.abs(np.min(self._arr))
-
-        np.seterr(divide="ignore", invalid="ignore")
-        self._create_node(self._arr, np.zeros(arr.ndim, dtype=int), 0)
-        np.seterr(divide="warn", invalid="warn")
-
-    @property
-    def nleaves(self):
-        return len(self._subvolumes)
-
-    def _create_node(self, arr: NDArray, offset: NDArray, ig: float):
-        """
-        Recursively split the array into nodes based on specific criteria.
-
-        Parameters
-        ----------
-        arr : NDArray
-            The array to split into nodes.
-        offset : NDArray
-            The offset for the current split in the array.
-        ig : float
-            Information gain value.
-
-        """
-        coordinates = self._split_arr(arr)
-        sd_arr = np.std(arr)
-
-        for chunk in coordinates:
-            sd_chunk = np.std(arr[chunk])
-            split_needed = False
-
-            if np.count_nonzero(arr[chunk]) == 0 or sd_chunk == 0:
-                split_needed = False
-            elif not np.all(np.greater(arr[chunk].shape, 3)):
-                split_needed = False
-            else:
-                new_split = self._split_arr(arr[chunk])
-                igo = self._information_gain(arr[chunk], new_split)
-                if sd_chunk < sd_arr or igo > ig:
-                    split_needed = True
-
-            if split_needed:
-                new_offset = np.add(offset, [n.start for n in chunk])
-                self._create_node(arr[chunk], new_offset, igo)
-            else:
-                final_coordinates = tuple(
-                    slice(n.start + offset[i], n.stop + offset[i])
-                    for i, n in enumerate(chunk)
-                )
-                self._subvolumes.append(final_coordinates)
-                self._sd.append(np.sum(arr[tuple(chunk)] != 0))
-
-    @staticmethod
-    def _information_gain(arr: NDArray, chunks: Tuple[NDArray]):
-        """
-        Calculate the information gain of splitting the array.
-
-        Parameters
-        ----------
-        arr : NDArray
-            The array from which to calculate information gain.
-        chunks : Tuple
-            List of sub-arrays (chunks) created by splitting.
-
-        Returns
-        -------
-        float
-            The information gain of the split.
-
-        """
-        if not isinstance(chunks, list) and not isinstance(chunks, tuple):
-            chunks = [chunks]
-
-        arr_entropy = entropy(arr.ravel())
-        weighted_split_entropy = [
-            (arr[tuple(i)].size / arr.size) * entropy(arr[tuple(i)].ravel())
-            for i in chunks
-        ]
-        return arr_entropy - np.sum(weighted_split_entropy)
-
-    @staticmethod
-    def _split_arr(arr: NDArray) -> Tuple[NDArray]:
-        """
-        Split the given array into multiple similarly sized chunks.
-
-        Parameters
-        ----------
-        arr : NDArray
-            The array to split.
-
-        Returns
-        -------
-        tuple
-            Tuple containing the slices to split the array.
-
-        """
-        old_shape = np.asarray(arr.shape).astype(int)
-        new_shape = np.divide(arr.shape, 2).astype(int)
-        split = tuple(
-            product(
-                *[
-                    (slice(0, n_shape), slice(n_shape, o_shape))
-                    for n_shape, o_shape in np.nditer([new_shape, old_shape])
-                ]
-            )
-        )
-        return split
-
-    def _sd_to_range(self, scale_range: Tuple[float, float] = (0.1, 20)) -> NDArray:
-        """
-        Scale the standard deviation values to a specific range.
-
-        Parameters
-        ----------
-        scale_range : tuple of float, optional
-            The range to scale the standard deviation to.
-
-        Returns
-        -------
-        NDArray
-            Array of scaled standard deviation values.
-
-        """
-        scaled_sd = np.interp(
-            self._sd, (np.min(self._sd), np.max(self._sd)), scale_range
-        )
-        return np.round(scaled_sd, decimals=0)
-
-    def filter_chunks(
-        self, arr: NDArray = None, sigma_range: Tuple[float, float] = (0.2, 10)
-    ) -> NDArray:
-        """
-        Apply Gaussian filter to each chunk and return the filtered array.
-
-        Parameters
-        ----------
-        arr : NDArray, optional
-            The array to filter. If None, the original array is used.
-        sigma_range : tuple of float, optional
-            Range of sigma values for the Gaussian filter.
-
-        Returns
-        -------
-        NDArray
-            The filtered array.
-
-        """
-        if arr is None:
-            arr = self._arr
-        result = np.zeros_like(arr)
-        chunk_sigmas = self._sd_to_range(sigma_range)
-
-        for chunk, sigma in zip(self._subvolumes, chunk_sigmas):
-            result[chunk] = gaussian_filter(arr[chunk], sigma)
-
-        return result