pytme 0.2.0b0__cp311-cp311-macosx_14_0_arm64.whl → 0.2.2__cp311-cp311-macosx_14_0_arm64.whl

tme/preprocessing/tilt_series.py

@@ -0,0 +1,1011 @@
+""" Defines filters on tomographic tilt series.
+
+    Copyright (c) 2024 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+import re
+from typing import Tuple, Dict
+from dataclasses import dataclass
+
+import numpy as np
+
+from .. import Preprocessor
+from ..types import NDArray
+from ..backends import backend as be
+from ..matching_utils import euler_to_rotationmatrix
+from ._utils import (
+    frequency_grid_at_angle,
+    compute_tilt_shape,
+    crop_real_fourier,
+    fftfreqn,
+    shift_fourier,
+)
+
+
+def create_reconstruction_filter(
+    filter_shape: Tuple[int], filter_type: str, **kwargs: Dict
+):
+    """Create a reconstruction filter of given filter_type.
+
+    Parameters
+    ----------
+    filter_shape : tuple of int
+        Shape of the returned filter
+    filter_type: str
+        The type of created filter, available options are:
+
+        +---------------+----------------------------------------------------+
+        | ram-lak       | Returns |w|                                        |
+        +---------------+----------------------------------------------------+
+        | ramp-cont     | Principles of Computerized Tomographic Imaging Avin|
+        |               | ash C. Kak and Malcolm Slaney Chap 3 Eq. 61 [1]_   |
+        +---------------+----------------------------------------------------+
+        | ramp          | Like ramp-cont but considering tilt angles         |
+        +---------------+----------------------------------------------------+
+        | shepp-logan   | |w| * sinc(|w| / 2) [2]_                           |
+        +---------------+----------------------------------------------------+
+        | cosine        | |w| * cos(|w| * pi / 2) [2]_                       |
+        +---------------+----------------------------------------------------+
+        | hamming       | |w| * (.54 + .46 ( cos(|w| * pi))) [2]_            |
+        +---------------+----------------------------------------------------+
+    kwargs: Dict
+        Keyword arguments for particular filter_types.
+
+    Returns
+    -------
+    NDArray
+        Reconstruction filter
+
+    References
+    ----------
+    .. [1]  Principles of Computerized Tomographic Imaging Avinash C. Kak and Malcolm Slaney Chap 3 Eq. 61
+    .. [2]  https://odlgroup.github.io/odl/index.html
+    """
+    filter_type = str(filter_type).lower()
+    freq = fftfreqn(filter_shape, sampling_rate=0.5, compute_euclidean_norm=True)
+
+    if filter_type == "ram-lak":
+        ret = np.copy(freq)
+    elif filter_type == "ramp-cont":
+        ret, ndim = None, len(filter_shape)
+        for dim, size in enumerate(filter_shape):
+            n = np.concatenate(
+                (
+                    np.arange(1, size / 2 + 1, 2, dtype=int),
+                    np.arange(size / 2 - 1, 0, -2, dtype=int),
+                )
+            )
+            ret1d = np.zeros(size)
+            ret1d[0] = 0.25
+            ret1d[1::2] = -1 / (np.pi * n) ** 2
+            ret1d_shape = tuple(size if i == dim else 1 for i in range(ndim))
+            ret1d = ret1d.reshape(ret1d_shape)
+            if ret is None:
+                ret = ret1d
+            else:
+                ret = ret * ret1d
+        ret = 2 * np.real(np.fft.fftn(ret))
+    elif filter_type == "ramp":
+        tilt_angles = kwargs.get("tilt_angles", False)
+        if tilt_angles is False:
+            raise ValueError("'ramp' filter requires specifying tilt angles.")
+        size, odd = filter_shape[0], filter_shape[0] % 2
+        ret = np.arange(-size // 2 + odd, size // 2 + odd, 1, dtype=np.float32)
+        ret /= size // 2
+        ret *= 0.5
+        np.abs(ret, out=ret)
+
+        min_increment = np.radians(np.min(np.abs(np.diff(np.sort(tilt_angles)))))
+        ret *= min_increment * size
+        np.fmin(ret, 1, out=ret)
+
+        ret = np.tile(ret[:, np.newaxis], (1, filter_shape[1]))
+
+    elif filter_type == "shepp-logan":
+        ret = freq * np.sinc(freq / 2)
+    elif filter_type == "cosine":
+        ret = freq * np.cos(freq * np.pi / 2)
+    elif filter_type == "hamming":
+        ret = freq * (0.54 + 0.46 * np.cos(freq * np.pi))
+    else:
+        raise ValueError("Unsupported filter type")
+
+    return ret
+
+
+@dataclass
+class ReconstructFromTilt:
+    """Reconstruct a volume from a tilt series."""
+
+    #: Shape of the reconstruction.
+    shape: Tuple[int] = None
+    #: Angle of each individual tilt.
+    angles: Tuple[float] = None
+    #: The axis around which the volume is opened.
+    opening_axis: int = 0
+    #: Axis the plane is tilted over.
+    tilt_axis: int = 2
+    #: Whether to return a share compliant with rfftn.
+    return_real_fourier: bool = True
+    #: Interpolation order used for rotation
+    interpolation_order: int = 1
+    #: Filter window applied during reconstruction.
+    reconstruction_filter: str = None
+
+    def __call__(self, **kwargs):
+        func_args = vars(self).copy()
+        func_args.update(kwargs)
+
+        ret = self.reconstruct(**func_args)
+
+        return {
+            "data": ret,
+            "shape": ret.shape,
+            "shape_is_real_fourier": func_args["return_real_fourier"],
+            "angles": func_args["angles"],
+            "tilt_axis": func_args["tilt_axis"],
+            "opening_axis": func_args["opening_axis"],
+            "is_multiplicative_filter": False,
+        }
+
+    @staticmethod
+    def reconstruct(
+        data: NDArray,
+        shape: Tuple[int],
+        angles: Tuple[float],
+        opening_axis: int,
+        tilt_axis: int,
+        interpolation_order: int = 1,
+        return_real_fourier: bool = True,
+        reconstruction_filter: str = None,
+        **kwargs,
+    ):
+        """
+        Reconstruct a volume from a tilt series.
+
+        Parameters:
+        -----------
+        data : NDArray
+            The tilt series data.
+        shape : tuple of int
+            Shape of the reconstruction.
+        angles : tuple of float
+            Angle of each individual tilt.
+        opening_axis : int
+            The axis around which the volume is opened.
+        tilt_axis : int
+            Axis the plane is tilted over.
+        interpolation_order : int, optional
+            Interpolation order used for rotation, defautls to 1.
+        return_real_fourier : bool, optional
+           Whether to return a shape compliant with rfftn, defaults to True.
+        reconstruction_filter : bool, optional
+           Filter window applied during reconstruction.
+           See :py:meth:`create_reconstruction_filter` for available options.
+
+        Returns:
+        --------
+        NDArray
+            The reconstructed volume.
+        """
+        if data.shape == shape:
+            return data
+
+        data = be.to_backend_array(data)
+        volume_temp = be.zeros(shape, dtype=be._float_dtype)
+        volume_temp_rotated = be.zeros(shape, dtype=be._float_dtype)
+        volume = be.zeros(shape, dtype=be._float_dtype)
+
+        slices = tuple(slice(a, a + 1) for a in be.astype(be.divide(shape, 2), int))
+        subset = tuple(
+            slice(None) if i != opening_axis else slices[opening_axis]
+            for i in range(len(shape))
+        )
+        angles_loop = be.zeros(len(shape))
+        wedge_dim = [x for x in data.shape]
+        wedge_dim.insert(1 + opening_axis, 1)
+        wedges = be.reshape(data, wedge_dim)
+
+        rec_filter = 1
+        if reconstruction_filter is not None:
+            rec_filter = create_reconstruction_filter(
+                filter_type=reconstruction_filter,
+                filter_shape=tuple(x for x in wedges[0].shape if x != 1),
+                tilt_angles=angles,
+            )
+            if tilt_axis > 0:
+                rec_filter = rec_filter.T
+
+            # This is most likely an upstream bug
+            if tilt_axis == 1 and opening_axis == 0:
+                rec_filter = rec_filter.T
+
+            rec_filter = be.to_backend_array(rec_filter)
+            rec_filter = be.reshape(rec_filter, wedges[0].shape)
+
+        for index in range(len(angles)):
+            be.fill(angles_loop, 0)
+            be.fill(volume_temp, 0)
+            be.fill(volume_temp_rotated, 0)
+
+            volume_temp[subset] = wedges[index] * rec_filter
+
+            angles_loop[tilt_axis] = angles[index]
+            angles_loop = be.roll(angles_loop, (opening_axis - 1,), axis=0)
+            rotation_matrix = euler_to_rotationmatrix(be.to_numpy_array(angles_loop))
+            rotation_matrix = be.to_backend_array(rotation_matrix)
+
+            be.rigid_transform(
+                arr=volume_temp,
+                rotation_matrix=rotation_matrix,
+                out=volume_temp_rotated,
+                use_geometric_center=True,
+                order=interpolation_order,
+            )
+            be.add(volume, volume_temp_rotated, out=volume)
+
+        volume = shift_fourier(data=volume, shape_is_real_fourier=False)
+
+        if return_real_fourier:
+            volume = crop_real_fourier(volume)
+
+        return volume
+
+
+class Wedge:
+    """
+    Generate wedge mask for tomographic data.
+
+    Parameters:
+    -----------
+    shape : tuple of int
+        The shape of the reconstruction volume.
+    tilt_axis : int
+        Axis the plane is tilted over.
+    opening_axis : int
+        The axis around which the volume is opened.
+    angles : tuple of float
+        The tilt angles.
+    weights : tuple of float
+        The weights corresponding to each tilt angle.
+    weight_type : str, optional
+        The type of weighting to apply, defaults to None.
+    frequency_cutoff : float, optional
+        The frequency cutoff value, defaults to 0.5.
+
+    Returns:
+    --------
+    Dict
+        A dictionary containing weighted wedges and related information.
+    """
+
+    def __init__(
+        self,
+        shape: Tuple[int],
+        tilt_axis: int,
+        opening_axis: int,
+        angles: Tuple[float],
+        weights: Tuple[float],
+        weight_type: str = None,
+        frequency_cutoff: float = 0.5,
+    ):
+        self.shape = shape
+        self.tilt_axis = tilt_axis
+        self.opening_axis = opening_axis
+        self.angles = angles
+        self.weights = weights
+        self.frequency_cutoff = frequency_cutoff
+
+    @classmethod
+    def from_file(cls, filename: str) -> "Wedge":
+        """
+        Generate a :py:class:`Wedge` instance by reading tilt angles and weights
+        from a tab-separated text file.
+
+        Parameters:
+        -----------
+        filename : str
+            The path to the file containing tilt angles and weights.
+
+        Returns:
+        --------
+        :py:class:`Wedge`
+           Class instance instance initialized with angles and weights from the file.
+        """
+        data = cls._from_text(filename)
+
+        angles, weights = data.get("angles", None), data.get("weights", None)
+        if angles is None:
+            raise ValueError(f"Could not find colum angles in {filename}")
+
+        if weights is None:
+            weights = [1] * len(angles)
+
+        if len(weights) != len(angles):
+            raise ValueError("Length of weights and angles differ.")
+
+        return cls(
+            shape=None,
+            tilt_axis=0,
+            opening_axis=2,
+            angles=np.array(angles, dtype=np.float32),
+            weights=np.array(weights, dtype=np.float32),
+        )
+
+    @staticmethod
+    def _from_text(filename: str, delimiter="\t") -> Dict:
+        """
+        Read column data from a text file.
+
+        Parameters:
+        -----------
+        filename : str
+            The path to the text file.
+        delimiter : str, optional
+            The delimiter used in the file, defaults to '\t'.
+
+        Returns:
+        --------
+        Dict
+            A dictionary with one key for each column.
+        """
+        with open(filename, mode="r", encoding="utf-8") as infile:
+            data = [x.strip() for x in infile.read().split("\n")]
+            data = [x.split("\t") for x in data if len(x)]
+
+        headers = data.pop(0)
+        ret = {header: list(column) for header, column in zip(headers, zip(*data))}
+
+        return ret
+
+    def __call__(self, **kwargs: Dict) -> NDArray:
+        func_args = vars(self).copy()
+        func_args.update(kwargs)
+
+        weight_types = {
+            None: self.weight_angle,
+            "angle": self.weight_angle,
+            "relion": self.weight_relion,
+            "grigorieff": self.weight_grigorieff,
+        }
+
+        weight_type = func_args.get("weight_type", None)
+        if weight_type not in weight_types:
+            raise ValueError(
+                f"Supported weight_types are {','.join(list(weight_types.keys()))}"
+            )
+
+        if weight_type == "angle":
+            func_args["weights"] = np.cos(np.radians(self.angles))
+
+        ret = weight_types[weight_type](**func_args)
+        ret = be.astype(be.to_backend_array(ret), be._float_dtype)
+
+        return {
+            "data": ret,
+            "angles": func_args["angles"],
+            "tilt_axis": func_args["tilt_axis"],
+            "opening_axis": func_args["opening_axis"],
+            "sampling_rate": func_args.get("sampling_rate", 1),
+            "is_multiplicative_filter": True,
+        }
+
+    @staticmethod
+    def weight_angle(
+        shape: Tuple[int],
+        weights: Tuple[float],
+        angles: Tuple[float],
+        opening_axis: int,
+        tilt_axis: int,
+        **kwargs,
+    ) -> NDArray:
+        """
+        Generate weighted wedges based on the cosine of the current angle.
+        """
+        tilt_shape = compute_tilt_shape(
+            shape=shape, opening_axis=opening_axis, reduce_dim=True
+        )
+        wedge, wedges = np.ones(tilt_shape), np.zeros((len(angles), *tilt_shape))
+        for index, angle in enumerate(angles):
+            wedge.fill(weights[index])
+            wedges[index] = wedge
+
+        return wedges
+
+    def weight_relion(self, **kwargs) -> NDArray:
+        """
+        Generate weighted wedges based on the RELION 1.4 formalism, weighting each
+        angle using the cosine of the angle and a Gaussian lowpass filter computed
+        with respect to the exposure per angstrom.
+
+        Returns:
+        --------
+        NDArray
+            Weighted wedges.
+        """
+        tilt_shape = compute_tilt_shape(
+            shape=self.shape, opening_axis=self.opening_axis, reduce_dim=True
+        )
+
+        wedges = np.zeros((len(self.angles), *tilt_shape))
+        for index, angle in enumerate(self.angles):
+            frequency_grid = frequency_grid_at_angle(
+                shape=self.shape,
+                opening_axis=self.opening_axis,
+                tilt_axis=self.tilt_axis,
+                angle=angle,
+                sampling_rate=1,
+            )
+            # frequency_mask = frequency_grid <= self.frequency_cutoff
+
+            sigma = np.sqrt(self.weights[index] * 4 / (8 * np.pi**2))
+            sigma = -2 * np.pi**2 * sigma**2
+            np.square(frequency_grid, out=frequency_grid)
+            np.multiply(sigma, frequency_grid, out=frequency_grid)
+            np.exp(frequency_grid, out=frequency_grid)
+            np.multiply(frequency_grid, np.cos(np.radians(angle)), out=frequency_grid)
+            # np.multiply(frequency_grid, frequency_mask, out=frequency_grid)
+
+            wedges[index] = frequency_grid
+
+        return wedges
+
+    def weight_grigorieff(
+        self,
+        amplitude: float = 0.245,
+        power: float = -1.665,
+        offset: float = 2.81,
+        **kwargs,
+    ) -> NDArray:
+        """
+        Generate weighted wedges based on the formalism introduced in [1]_.
+
+        Returns:
+        --------
+        NDArray
+            Weighted wedges.
+
+        References
+        ----------
+        .. [1]  Timothy GrantNikolaus Grigorieff (2015), eLife 4:e06980.
+        """
+        tilt_shape = compute_tilt_shape(
+            shape=self.shape,
+            opening_axis=self.opening_axis,
+            reduce_dim=True,
+        )
+
+        wedges = np.zeros((len(self.angles), *tilt_shape), dtype=be._float_dtype)
+        for index, angle in enumerate(self.angles):
+            frequency_grid = frequency_grid_at_angle(
+                shape=self.shape,
+                opening_axis=self.opening_axis,
+                tilt_axis=self.tilt_axis,
+                angle=angle,
+                sampling_rate=1,
+            )
+            # frequency_mask = frequency_grid <= self.frequency_cutoff
+
+            with np.errstate(divide="ignore"):
+                np.power(frequency_grid, power, out=frequency_grid)
+                np.multiply(amplitude, frequency_grid, out=frequency_grid)
+                np.add(frequency_grid, offset, out=frequency_grid)
+                np.multiply(-2, frequency_grid, out=frequency_grid)
+                np.divide(
+                    self.weights[index],
+                    frequency_grid,
+                    out=frequency_grid,
+                )
+
+            np.exp(frequency_grid, out=frequency_grid)
+            # np.multiply(frequency_grid, frequency_mask, out=frequency_grid)
+
+            wedges[index] = frequency_grid
+
+        return wedges
+
+
+class WedgeReconstructed:
+    """
+    Initialize :py:class:`WedgeReconstructed`.
+
+    Parameters:
+    -----------
+    angles : Tuple[float], optional
+        The tilt angles, defaults to None.
+    opening_axis : int, optional
+        The axis around which the wedge is opened, defaults to 0.
+    tilt_axis : int, optional
+        The axis along which the tilt is applied, defaults to 2.
+    **kwargs : Dict
+        Additional keyword arguments.
+    """
+
+    def __init__(
+        self,
+        angles: Tuple[float] = None,
+        start_tilt: float = None,
+        stop_tilt: float = None,
+        opening_axis: int = 0,
+        tilt_axis: int = 2,
+        weight_wedge: bool = False,
+        create_continuous_wedge: bool = False,
+        **kwargs: Dict,
+    ):
+        self.angles = angles
+        self.opening_axis = opening_axis
+        self.tilt_axis = tilt_axis
+        self.weight_wedge = weight_wedge
+        self.create_continuous_wedge = create_continuous_wedge
+
+    def __call__(self, shape: Tuple[int], **kwargs: Dict) -> Dict:
+        """
+        Generate the reconstructed wedge.
+
+        Parameters:
+        -----------
+        shape : tuple of int
+            The shape of the reconstruction volume.
+        **kwargs : Dict
+            Additional keyword arguments.
+
+        Returns:
+        --------
+        Dict
+            A dictionary containing the reconstructed wedge and related information.
+        """
+        func_args = vars(self).copy()
+        func_args.update(kwargs)
+
+        if kwargs.get("is_fourier_shape", False):
+            print("Cannot create continuous wedge mask basde on real fourier shape.")
+
+        func = self.step_wedge
+        if func_args.get("create_continuous_wedge", False):
+            func = self.continuous_wedge
+
+        ret = func(shape=shape, **func_args)
+        ret = be.astype(be.to_backend_array(ret), be._float_dtype)
+
+        return {
+            "data": ret,
+            "shape_is_real_fourier": func_args["return_real_fourier"],
+            "shape": ret.shape,
+            "tilt_axis": func_args["tilt_axis"],
+            "opening_axis": func_args["opening_axis"],
+            "is_multiplicative_filter": True,
+            "angles": func_args["angles"],
+        }
+
+    @staticmethod
+    def continuous_wedge(
+        shape: Tuple[int],
+        angles: Tuple[float],
+        opening_axis: int,
+        tilt_axis: int,
+        return_real_fourier: bool,
+        **kwargs: Dict,
+    ) -> NDArray:
+        """
+        Generate a continuous reconstructed wedge.
+
+        Parameters:
+        -----------
+        shape : tuple of int
+            The shape of the reconstruction volume.
+        angles : tuple of float
+            Start and stop tilt angle.
+        opening_axis : int
+            The axis around which the wedge is opened.
+        tilt_axis : int
+            The axis along which the tilt is applied.
+        return_real_fourier : bool
+            Whether to return the real part of the Fourier transform.
+
+        Returns:
+        --------
+        NDArray
+            The reconstructed wedge.
+        """
+        preprocessor = Preprocessor()
+        start_tilt, stop_tilt = angles
+        ret = preprocessor.continuous_wedge_mask(
+            start_tilt=start_tilt,
+            stop_tilt=stop_tilt,
+            shape=shape,
+            opening_axis=opening_axis,
+            tilt_axis=tilt_axis,
+            omit_negative_frequencies=return_real_fourier,
+            infinite_plane=False,
+        )
+
+        return ret
+
+    @staticmethod
+    def step_wedge(
+        shape: Tuple[int],
+        angles: Tuple[float],
+        opening_axis: int,
+        tilt_axis: int,
+        return_real_fourier: bool,
+        weight_wedge: bool = False,
+        **kwargs: Dict,
+    ) -> NDArray:
+        """
+        Generate a step-wise reconstructed wedge.
+
+        Parameters:
+        -----------
+        shape : tuple of int
+            The shape of the reconstruction volume.
+        angles : tuple of float
+            The tilt angles.
+        opening_axis : int
+            The axis around which the wedge is opened.
+        tilt_axis : int
+            The axis along which the tilt is applied.
+        weight_wedge : bool, optional
+            Whether to weight the wedge by the cosine of the angle.
+        return_real_fourier : bool
+            Whether to return the real part of the Fourier transform.
+
+        Returns:
+        --------
+        NDArray
+            The reconstructed wedge.
+        """
+        preprocessor = Preprocessor()
+
+        angles = np.asarray(be.to_numpy_array(angles))
+        weights = np.ones(angles.size)
+        if weight_wedge:
+            weights = np.cos(np.radians(angles))
+        ret = preprocessor.step_wedge_mask(
+            tilt_angles=angles,
+            weights=weights,
+            start_tilt=None,
+            stop_tilt=None,
+            tilt_step=None,
+            shape=shape,
+            opening_axis=opening_axis,
+            tilt_axis=tilt_axis,
+            omit_negative_frequencies=return_real_fourier,
+        )
+
+        return ret
+
+
+@dataclass
+class CTF:
+    """
+    Representation of a contrast transfer function (CTF) [1]_.
+
+    References
+    ----------
+    .. [1]  CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
+            Alexis Rohou and Nikolaus Grigorieff. Journal of Structural Biology 2015.
+    """
+
+    #: The shape of the to-be reconstructed volume.
+    shape: Tuple[int]
+    #: The defocus value in x direction.
+    defocus_x: float
+    #: The tilt angles.
+    angles: Tuple[float] = None
+    #: The axis around which the wedge is opened, defaults to None.
+    opening_axis: int = None
+    #: The axis along which the tilt is applied, defaults to None.
+    tilt_axis: int = None
+    #: Whether to correct defocus gradient, defaults to False.
+    correct_defocus_gradient: bool = False
+    #: The sampling rate, defaults to 1.
+    sampling_rate: Tuple[float] = 1
+    #: The acceleration voltage in Volts, defaults to 300e3.
+    acceleration_voltage: float = 300e3
+    #: The spherical aberration coefficient, defaults to 2.7e7.
+    spherical_aberration: float = 2.7e7
+    #: The amplitude contrast, defaults to 0.07.
+    amplitude_contrast: float = 0.07
+    #: The phase shift, defaults to 0.
+    phase_shift: float = 0
+    #: The defocus angle, defaults to 0.
+    defocus_angle: float = 0
+    #: The defocus value in y direction, defaults to None.
+    defocus_y: float = None
+    #: Whether the returned CTF should be phase-flipped.
+    flip_phase: bool = True
+    #: Whether to return a format compliant with rfft. Only relevant for single angles.
+    return_real_fourier: bool = False
+
+    @classmethod
+    def from_file(cls, filename: str) -> "CTF":
+        """
+        Initialize :py:class:`CTF` from file.
+
+        Parameters:
+        -----------
+        filename : str
+            The path to a file with ctf parameters. Supports the following formats:
+            - CTFFIND4
+        """
+        data = cls._from_ctffind(filename=filename)
+
+        return cls(
+            shape=None,
+            angles=None,
+            defocus_x=data["defocus_1"],
+            sampling_rate=data["pixel_size"],
+            acceleration_voltage=data["acceleration_voltage"],
+            spherical_aberration=data["spherical_aberration"],
+            amplitude_contrast=data["amplitude_contrast"],
+            phase_shift=data["additional_phase_shift"],
+            defocus_angle=np.degrees(data["azimuth_astigmatism"]),
+            defocus_y=data["defocus_2"],
+        )
+
+    @staticmethod
+    def _from_ctffind(filename: str):
+        parameter_regex = {
+            "pixel_size": r"Pixel size: ([0-9.]+) Angstroms",
+            "acceleration_voltage": r"acceleration voltage: ([0-9.]+) keV",
+            "spherical_aberration": r"spherical aberration: ([0-9.]+) mm",
+            "amplitude_contrast": r"amplitude contrast: ([0-9.]+)",
+        }
+
+        with open(filename, mode="r", encoding="utf-8") as infile:
+            lines = [x.strip() for x in infile.read().split("\n")]
+            lines = [x for x in lines if len(x)]
+
+        def _screen_params(line, params, output):
+            for parameter, regex_pattern in parameter_regex.items():
+                match = re.search(regex_pattern, line)
+                if match:
+                    output[parameter] = float(match.group(1))
+
+        columns = {
+            "micrograph_number": 0,
+            "defocus_1": 1,
+            "defocus_2": 2,
+            "azimuth_astigmatism": 3,
+            "additional_phase_shift": 4,
+            "cross_correlation": 5,
+            "spacing": 6,
+        }
+        output = {k: [] for k in columns.keys()}
+        for line in lines:
+            if line.startswith("#"):
+                _screen_params(line, params=parameter_regex, output=output)
+                continue
+
+            values = line.split()
+            for key, value in columns.items():
+                output[key].append(float(values[value]))
+
+        for key in columns:
+            output[key] = np.array(output[key])
+
+        return output
+
+    def __post_init__(self):
+        self.defocus_angle = np.radians(self.defocus_angle)
+
+        kwargs = {
+            "defocus_x": self.defocus_x,
+            "defocus_y": self.defocus_y,
+            "spherical_aberration": self.spherical_aberration,
+        }
+        kwargs = {k: v for k, v in kwargs.items() if v is not None}
+        self._update_parameters(
+            electron_wavelength=self._compute_electron_wavelength(), **kwargs
+        )
+
+    def _compute_electron_wavelength(self, acceleration_voltage: int = None):
+        """Computes the wavelength of an electron in angstrom."""
+
+        if acceleration_voltage is None:
+            acceleration_voltage = self.acceleration_voltage
+
+        # Physical constants expressed in SI units
+        planck_constant = 6.62606896e-34
+        electron_charge = 1.60217646e-19
+        electron_mass = 9.10938215e-31
+        light_velocity = 299792458
+
+        energy = electron_charge * acceleration_voltage
+        denominator = energy**2
+        denominator += 2 * energy * electron_mass * light_velocity**2
+        electron_wavelength = np.divide(
+            planck_constant * light_velocity, np.sqrt(denominator)
+        )
+        electron_wavelength *= 1e10
+        return electron_wavelength
+
+    def _update_parameters(self, **kwargs):
+        """Update multiple parameters of the CTF instance."""
+        voxel_based = [
+            "electron_wavelength",
+            "spherical_aberration",
+            "defocus_x",
+            "defocus_y",
+        ]
+        if "sampling_rate" in kwargs:
+            self.sampling_rate = kwargs["sampling_rate"]
+
+        if "acceleration_voltage" in kwargs:
+            kwargs["electron_wavelength"] = self._compute_electron_wavelength()
+
+        for key, value in kwargs.items():
+            if key in voxel_based and value is not None:
+                value = np.divide(value, np.max(self.sampling_rate))
+            setattr(self, key, value)
+
+    def __call__(self, **kwargs) -> NDArray:
+        func_args = vars(self).copy()
+        func_args.update(kwargs)
+
+        if len(func_args["angles"]) != len(func_args["defocus_x"]):
+            func_args["angles"] = self.angles
+            func_args["return_real_fourier"] = False
+            func_args["tilt_axis"] = None
+            func_args["opening_axis"] = None
+
+        ret = self.weight(**func_args)
+        ret = be.astype(be.to_backend_array(ret), be._float_dtype)
+        return {
+            "data": ret,
+            "angles": func_args["angles"],
+            "tilt_axis": func_args["tilt_axis"],
+            "opening_axis": func_args["opening_axis"],
+            "is_multiplicative_filter": True,
+        }
+
+    def weight(
+        self,
+        shape: Tuple[int],
+        defocus_x: Tuple[float],
+        angles: Tuple[float],
+        electron_wavelength: float = None,
+        opening_axis: int = None,
+        tilt_axis: int = None,
+        amplitude_contrast: float = 0.07,
+        phase_shift: Tuple[float] = 0,
+        defocus_angle: Tuple[float] = 0,
+        defocus_y: Tuple[float] = None,
+        correct_defocus_gradient: bool = False,
+        sampling_rate: Tuple[float] = 1,
+        acceleration_voltage: float = 300e3,
+        spherical_aberration: float = 2.7e3,
+        flip_phase: bool = True,
+        return_real_fourier: bool = False,
+        **kwargs: Dict,
+    ) -> NDArray:
+        """
+        Compute the CTF weight tilt stack.
+
+        Parameters:
+        -----------
+        shape : tuple of int
+            The shape of the CTF.
+        defocus_x : tuple of float
+            The defocus value in x direction.
+        angles : tuple of float
+            The tilt angles.
+        electron_wavelength : float, optional
+            The electron wavelength, defaults to None.
+        opening_axis : int, optional
+            The axis around which the wedge is opened, defaults to None.
+        tilt_axis : int, optional
+            The axis along which the tilt is applied, defaults to None.
+        amplitude_contrast : float, optional
+            The amplitude contrast, defaults to 0.07.
+        phase_shift : tuple of float, optional
+            The phase shift, defaults to 0.
+        defocus_angle : tuple of float, optional
+            The defocus angle, defaults to 0.
+        defocus_y : tuple of float, optional
+            The defocus value in y direction, defaults to None.
+        correct_defocus_gradient : bool, optional
+            Whether to correct defocus gradient, defaults to False.
+        sampling_rate : tuple of float, optional
+            The sampling rate, defaults to 1.
+        acceleration_voltage : float, optional
+            The acceleration voltage in electron microscopy, defaults to 300e3.
+        spherical_aberration : float, optional
+            The spherical aberration coefficient, defaults to 2.7e3.
+        flip_phase : bool, optional
+            Whether the returned CTF should be phase-flipped.
+        **kwargs : Dict
+            Additional keyword arguments.
+
+        Returns:
+        --------
+        NDArray
+            A stack containing the CTF weight.
+        """
+        defoci_x = np.atleast_1d(defocus_x)
+        defoci_y = np.atleast_1d(defocus_y)
+        phase_shift = np.atleast_1d(phase_shift)
+        angles = np.atleast_1d(angles)
+        defocus_angle = np.atleast_1d(defocus_angle)
+
+        sampling_rate = np.max(sampling_rate)
+        tilt_shape = compute_tilt_shape(
+            shape=shape, opening_axis=opening_axis, reduce_dim=True
+        )
+        stack = np.zeros((len(angles), *tilt_shape))
+
+        correct_defocus_gradient &= len(shape) == 3
+        correct_defocus_gradient &= tilt_axis is not None
+        correct_defocus_gradient &= opening_axis is not None
+
+        for index, angle in enumerate(angles):
+            defocus_x, defocus_y = defoci_x[index], defoci_y[index]
+
+            if correct_defocus_gradient or defocus_y is not None:
+                grid = fftfreqn(
+                    shape=shape,
+                    sampling_rate=be.divide(sampling_rate, shape),
+                    return_sparse_grid=True,
+                )
+
+            # This should be done after defocus_x computation
+            if correct_defocus_gradient:
+                angle_rad = np.radians(angle)
+
+                defocus_gradient = np.multiply(grid[1], np.sin(angle_rad))
+                remaining_axis = tuple(
+                    i for i in range(len(shape)) if i not in (opening_axis, tilt_axis)
+                )[0]
+
+                if tilt_axis > remaining_axis:
+                    defocus_x = np.add(defocus_x, defocus_gradient)
+                elif tilt_axis < remaining_axis and defocus_y is not None:
+                    defocus_y = np.add(defocus_y, defocus_gradient.T)
+
+            if defocus_y is not None:
+                defocus_sum = np.add(defocus_x, defocus_y)
+                defocus_difference = np.subtract(defocus_x, defocus_y)
+                angular_grid = np.arctan2(grid[0], grid[1])
+                defocus_difference *= np.cos(2 * (angular_grid - defocus_angle[index]))
+                defocus_x = np.add(defocus_sum, defocus_difference)
+                defocus_x *= 0.5
+
+            frequency_grid = frequency_grid_at_angle(
+                shape=shape,
+                opening_axis=opening_axis,
+                tilt_axis=tilt_axis,
+                angle=angle,
+                sampling_rate=1,
+            )
+            np.square(frequency_grid, out=frequency_grid)
+
+            electron_aberration = spherical_aberration * electron_wavelength**2
+            chi = defocus_x - 0.5 * electron_aberration * frequency_grid
+            np.multiply(chi, np.pi * electron_wavelength, out=chi)
+            np.multiply(chi, frequency_grid, out=chi)
+
+            chi += phase_shift[index]
+            chi += np.arctan(
+                np.divide(
+                    amplitude_contrast,
+                    np.sqrt(1 - np.square(amplitude_contrast)),
+                )
+            )
+            np.sin(-chi, out=chi)
+            stack[index] = chi
+
+        # Avoid contrast inversion
+        np.negative(stack, out=stack)
+        if flip_phase:
+            np.abs(stack, out=stack)
+
+        stack = np.squeeze(stack)
+        stack = be.to_backend_array(stack)
+
+        if len(angles) == 1:
+            stack = shift_fourier(data=stack, shape_is_real_fourier=False)
+            if return_real_fourier:
+                stack = crop_real_fourier(stack)
+
+        return stack