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

tme/preprocessing/composable_filter.py

@@ -0,0 +1,31 @@
+""" Defines a specification for filters that can be used with
+    :py:class:`tme.preprocessing.compose.Compose`.
+
+    Copyright (c) 2024 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+from typing import Dict
+from abc import ABC, abstractmethod
+
+
+class ComposableFilter(ABC):
+    """
+    Strategy class for composable filters.
+    """
+
+    @abstractmethod
+    def __call__(self, *args, **kwargs) -> Dict:
+        """
+        Parameters:
+        -----------
+        *args : tuple
+            Variable length argument list.
+        **kwargs : dict
+            Arbitrary keyword arguments.
+
+        Returns:
+        --------
+        Dict
+            A dictionary representing the result of the filtering operation.
+        """

tme/preprocessing/compose.py

@@ -0,0 +1,55 @@
+""" Combine filters using an interface analogous to pytorch's Compose.
+
+    Copyright (c) 2024 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+
+from typing import Tuple, Dict
+
+from tme.backends import backend as be
+
+
+class Compose:
+    """
+    Compose a series of transformations.
+
+    This class allows composing multiple transformations together. Each transformation
+    is expected to be a callable that accepts keyword arguments and returns metadata.
+
+    Parameters:
+    -----------
+    transforms : Tuple[object]
+        A tuple containing transformation objects.
+
+    Returns:
+    --------
+    Dict
+        Metadata resulting from the composed transformations.
+
+    """
+
+    def __init__(self, transforms: Tuple[object]):
+        self.transforms = transforms
+
+    def __call__(self, **kwargs: Dict) -> Dict:
+        meta = {}
+        if not len(self.transforms):
+            return meta
+
+        meta = self.transforms[0](**kwargs)
+        for transform in self.transforms[1:]:
+            kwargs.update(meta)
+            ret = transform(**kwargs)
+
+            if "data" not in ret:
+                continue
+
+            if ret.get("is_multiplicative_filter", False):
+                prev_data = meta.pop("data")
+                ret["data"] = be.multiply(ret["data"], prev_data, out=ret["data"])
+                ret["merge"], prev_data = None, None
+
+            meta = ret
+
+        return meta

tme/preprocessing/frequency_filters.py

@@ -0,0 +1,388 @@
+""" Defines Fourier frequency filters.
+
+    Copyright (c) 2024 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+from math import log, sqrt
+from typing import Tuple, Dict
+
+import numpy as np
+from scipy.ndimage import mean as ndimean
+from scipy.ndimage import map_coordinates
+
+from ..types import BackendArray
+from ..backends import backend as be
+from ._utils import fftfreqn, crop_real_fourier, shift_fourier, compute_fourier_shape
+
+
+class BandPassFilter:
+    """
+    This class provides methods to generate bandpass filters in Fourier space,
+    either by directly specifying the frequency cutoffs (discrete_bandpass) or
+    by using Gaussian functions (gaussian_bandpass).
+
+    Parameters:
+    -----------
+    lowpass : float, optional
+        The lowpass cutoff, defaults to None.
+    highpass : float, optional
+        The highpass cutoff, defaults to None.
+    sampling_rate : Tuple[float], optional
+        The sampling r_position_to_molmapate in Fourier space, defaults to 1.
+    use_gaussian : bool, optional
+        Whether to use Gaussian bandpass filter, defaults to True.
+    return_real_fourier : bool, optional
+        Whether to return only the real Fourier space, defaults to False.
+    shape_is_real_fourier : bool, optional
+        Whether the shape represents the real Fourier space, defaults to False.
+    """
+
+    def __init__(
+        self,
+        lowpass: float = None,
+        highpass: float = None,
+        sampling_rate: Tuple[float] = 1,
+        use_gaussian: bool = True,
+        return_real_fourier: bool = False,
+        shape_is_real_fourier: bool = False,
+    ):
+        self.lowpass = lowpass
+        self.highpass = highpass
+        self.use_gaussian = use_gaussian
+        self.return_real_fourier = return_real_fourier
+        self.shape_is_real_fourier = shape_is_real_fourier
+        self.sampling_rate = sampling_rate
+
+    @staticmethod
+    def discrete_bandpass(
+        shape: Tuple[int],
+        lowpass: float,
+        highpass: float,
+        sampling_rate: Tuple[float],
+        return_real_fourier: bool = False,
+        shape_is_real_fourier: bool = False,
+        **kwargs,
+    ) -> BackendArray:
+        """
+        Generate a bandpass filter using discrete frequency cutoffs.
+
+        Parameters:
+        -----------
+        shape : tuple of int
+            The shape of the bandpass filter.
+        lowpass : float
+            The lowpass cutoff in units of sampling rate.
+        highpass : float
+            The highpass cutoff in units of sampling rate.
+        return_real_fourier : bool, optional
+            Whether to return only the real Fourier space, defaults to False.
+        sampling_rate : float
+            The sampling rate in Fourier space.
+        shape_is_real_fourier : bool, optional
+            Whether the shape represents the real Fourier space, defaults to False.
+        **kwargs : dict
+            Additional keyword arguments.
+
+        Returns:
+        --------
+        BackendArray
+            The bandpass filter in Fourier space.
+        """
+        if shape_is_real_fourier:
+            return_real_fourier = False
+
+        grid = fftfreqn(
+            shape=shape,
+            sampling_rate=0.5,
+            shape_is_real_fourier=shape_is_real_fourier,
+            compute_euclidean_norm=True,
+        )
+
+        lowpass = 0 if lowpass is None else lowpass
+        highpass = 1e10 if highpass is None else highpass
+
+        highcut = grid.max()
+        if lowpass > 0:
+            highcut = np.max(2 * sampling_rate / lowpass)
+        lowcut = np.max(2 * sampling_rate / highpass)
+
+        bandpass_filter = ((grid <= highcut) & (grid >= lowcut)) * 1.0
+
+        bandpass_filter = shift_fourier(
+            data=bandpass_filter, shape_is_real_fourier=shape_is_real_fourier
+        )
+
+        if return_real_fourier:
+            bandpass_filter = crop_real_fourier(bandpass_filter)
+
+        return bandpass_filter
+
+    @staticmethod
+    def gaussian_bandpass(
+        shape: Tuple[int],
+        lowpass: float,
+        highpass: float,
+        sampling_rate: float,
+        return_real_fourier: bool = False,
+        shape_is_real_fourier: bool = False,
+        **kwargs,
+    ) -> BackendArray:
+        """
+        Generate a bandpass filter using Gaussian functions.
+
+        Parameters:
+        -----------
+        shape : tuple of int
+            The shape of the bandpass filter.
+        lowpass : float
+            The lowpass cutoff in units of sampling rate.
+        highpass : float
+            The highpass cutoff in units of sampling rate.
+        sampling_rate : float
+            The sampling rate in Fourier space.
+        return_real_fourier : bool, optional
+            Whether to return only the real Fourier space, defaults to False.
+        shape_is_real_fourier : bool, optional
+            Whether the shape represents the real Fourier space, defaults to False.
+        **kwargs : dict
+            Additional keyword arguments.
+
+        Returns:
+        --------
+        BackendArray
+            The bandpass filter in Fourier space.
+        """
+        if shape_is_real_fourier:
+            return_real_fourier = False
+
+        grid = fftfreqn(
+            shape=shape,
+            sampling_rate=0.5,
+            shape_is_real_fourier=shape_is_real_fourier,
+            compute_euclidean_norm=True,
+        )
+        grid = be.to_backend_array(grid)
+        grid = -be.square(grid)
+
+        lowpass_filter, highpass_filter = 1, 1
+        norm = float(sqrt(2 * log(2)))
+        upper_sampling = float(
+            be.max(be.multiply(2, be.to_backend_array(sampling_rate)))
+        )
+
+        if lowpass is not None:
+            lowpass = float(lowpass)
+            lowpass = be.maximum(lowpass, be.eps(be._float_dtype))
+        if highpass is not None:
+            highpass = float(highpass)
+            highpass = be.maximum(highpass, be.eps(be._float_dtype))
+
+        if lowpass is not None:
+            lowpass = upper_sampling / (lowpass * norm)
+            lowpass = be.multiply(2, be.square(lowpass))
+            lowpass_filter = be.exp(be.divide(grid, lowpass))
+        if highpass is not None:
+            highpass = upper_sampling / (highpass * norm)
+            highpass = be.multiply(2, be.square(highpass))
+            highpass_filter = 1 - be.exp(be.divide(grid, highpass))
+
+        bandpass_filter = be.multiply(lowpass_filter, highpass_filter)
+        bandpass_filter = shift_fourier(
+            data=bandpass_filter, shape_is_real_fourier=shape_is_real_fourier
+        )
+
+        if return_real_fourier:
+            bandpass_filter = crop_real_fourier(bandpass_filter)
+
+        return bandpass_filter
+
+    def __call__(self, **kwargs):
+        func_args = vars(self)
+        func_args.update(kwargs)
+
+        func = self.discrete_bandpass
+        if func_args.get("use_gaussian"):
+            func = self.gaussian_bandpass
+
+        mask = func(**func_args)
+
+        return {
+            "data": be.to_backend_array(mask),
+            "sampling_rate": func_args.get("sampling_rate", 1),
+            "is_multiplicative_filter": True,
+        }
+
+
+class LinearWhiteningFilter:
+    """
+    This class provides methods to compute the spectrum of the input data and
+    apply linear whitening to the Fourier coefficients.
+
+    Parameters:
+    -----------
+    **kwargs : Dict, optional
+        Additional keyword arguments.
+
+
+    References
+    ----------
+    .. [1] de Teresa-Trueba, I.; Goetz, S. K.; Mattausch, A.; Stojanovska, F.; Zimmerli, C. E.;
+        Toro-Nahuelpan, M.; Cheng, D. W. C.; Tollervey, F.; Pape, C.; Beck, M.; Diz-Munoz,
+        A.; Kreshuk, A.; Mahamid, J.; Zaugg, J. B. Nat. Methods 2023, 20, 284–294.
+    .. [2]  M. L. Chaillet, G. van der Schot, I. Gubins, S. Roet,
+        R. C. Veltkamp, and F. Förster, Int. J. Mol. Sci. 24,
+        13375 (2023)
+    """
+
+    def __init__(self, **kwargs):
+        pass
+
+    @staticmethod
+    def _compute_spectrum(
+        data_rfft: BackendArray, n_bins: int = None, batch_dimension: int = None
+    ) -> Tuple[BackendArray, BackendArray]:
+        """
+        Compute the spectrum of the input data.
+
+        Parameters:
+        -----------
+        data_rfft : BackendArray
+            The Fourier transform of the input data.
+        n_bins : int, optional
+            The number of bins for computing the spectrum, defaults to None.
+        batch_dimension : int, optional
+            Batch dimension to average over.
+
+        Returns:
+        --------
+        bins : BackendArray
+            Array containing the bin indices for the spectrum.
+        radial_averages : BackendArray
+            Array containing the radial averages of the spectrum.
+        """
+        shape = tuple(x for i, x in enumerate(data_rfft.shape) if i != batch_dimension)
+
+        max_bins = max(max(shape[:-1]) // 2 + 1, shape[-1])
+        n_bins = max_bins if n_bins is None else n_bins
+        n_bins = int(min(n_bins, max_bins))
+
+        bins = fftfreqn(
+            shape=shape,
+            sampling_rate=0.5,
+            shape_is_real_fourier=True,
+            compute_euclidean_norm=True,
+        )
+        bins = be.to_numpy_array(bins)
+
+        # Implicit lowpass to nyquist
+        bins = np.floor(bins * (n_bins - 1) + 0.5).astype(int)
+        fft_shift_axes = tuple(
+            i for i in range(data_rfft.ndim - 1) if i != batch_dimension
+        )
+        fourier_spectrum = np.fft.fftshift(data_rfft, axes=fft_shift_axes)
+        fourier_spectrum = np.abs(fourier_spectrum)
+        np.square(fourier_spectrum, out=fourier_spectrum)
+
+        radial_averages = ndimean(
+            fourier_spectrum, labels=bins, index=np.arange(n_bins)
+        )
+        np.sqrt(radial_averages, out=radial_averages)
+        np.reciprocal(radial_averages, out=radial_averages)
+        np.divide(radial_averages, radial_averages.max(), out=radial_averages)
+
+        return bins, radial_averages
+
+    @staticmethod
+    def _interpolate_spectrum(
+        spectrum: BackendArray,
+        shape: Tuple[int],
+        shape_is_real_fourier: bool = True,
+        order: int = 1,
+    ) -> BackendArray:
+        """
+        References
+        ----------
+        .. [1]  M. L. Chaillet, G. van der Schot, I. Gubins, S. Roet,
+            R. C. Veltkamp, and F. Förster, Int. J. Mol. Sci. 24,
+            13375 (2023)
+        """
+        grid = fftfreqn(
+            shape=shape,
+            sampling_rate=0.5,
+            shape_is_real_fourier=shape_is_real_fourier,
+            compute_euclidean_norm=True,
+        )
+        grid = be.to_numpy_array(grid)
+        np.multiply(grid, (spectrum.shape[0] - 1), out=grid) + 0.5
+        spectrum = map_coordinates(spectrum, grid.reshape(1, -1), order=order)
+        return spectrum.reshape(grid.shape)
+
+    def __call__(
+        self,
+        data: BackendArray = None,
+        data_rfft: BackendArray = None,
+        n_bins: int = None,
+        batch_dimension: int = None,
+        order: int = 1,
+        **kwargs: Dict,
+    ) -> Dict:
+        """
+        Apply linear whitening to the data and return the result.
+
+        Parameters:
+        -----------
+        data : BackendArray, optional
+            The input data, defaults to None.
+        data_rfft : BackendArray, optional
+            The Fourier transform of the input data, defaults to None.
+        n_bins : int, optional
+            The number of bins for computing the spectrum, defaults to None.
+        batch_dimension : int, optional
+            Batch dimension to average over.
+        order : int, optional
+            Interpolation order to use.
+        **kwargs : Dict
+            Additional keyword arguments.
+
+        Returns:
+        --------
+        Dict
+           Filter data and associated parameters.
+        """
+        if data_rfft is None:
+            data_rfft = np.fft.rfftn(be.to_numpy_array(data))
+
+        data_rfft = be.to_numpy_array(data_rfft)
+
+        bins, radial_averages = self._compute_spectrum(
+            data_rfft, n_bins, batch_dimension
+        )
+
+        if order is None:
+            cutoff = bins < radial_averages.size
+            filter_mask = np.zeros(bins.shape, radial_averages.dtype)
+            filter_mask[cutoff] = radial_averages[bins[cutoff]]
+        else:
+            shape = bins.shape
+            if kwargs.get("shape", False):
+                shape = compute_fourier_shape(
+                    shape=kwargs.get("shape"),
+                    shape_is_real_fourier=kwargs.get("shape_is_real_fourier", False),
+                )
+
+            filter_mask = self._interpolate_spectrum(
+                spectrum=radial_averages,
+                shape=shape,
+                shape_is_real_fourier=True,
+            )
+
+        filter_mask = np.fft.ifftshift(
+            filter_mask,
+            axes=tuple(i for i in range(data_rfft.ndim - 1) if i != batch_dimension),
+        )
+
+        return {
+            "data": be.to_backend_array(filter_mask),
+            "is_multiplicative_filter": True,
+        }