pytme 0.3b0__cp311-cp311-macosx_15_0_arm64.whl → 0.3b0.post1__cp311-cp311-macosx_15_0_arm64.whl

scripts/match_template_filters.py

@@ -0,0 +1,1200 @@
+#!python3
+""" CLI interface for basic pyTME template matching functions.
+
+    Copyright (c) 2023 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+import os
+import argparse
+import warnings
+from sys import exit
+from time import time
+from typing import Tuple
+from copy import deepcopy
+from os.path import abspath, exists
+
+import numpy as np
+
+from tme import Density, __version__
+from tme.matching_utils import (
+    get_rotation_matrices,
+    get_rotations_around_vector,
+    compute_parallelization_schedule,
+    scramble_phases,
+    generate_tempfile_name,
+    write_pickle,
+)
+from tme.matching_exhaustive import scan_subsets, MATCHING_EXHAUSTIVE_REGISTER
+from tme.matching_data import MatchingData
+from tme.analyzer import (
+    MaxScoreOverRotations,
+    PeakCallerMaximumFilter,
+)
+from tme.backends import backend as be
+from tme.preprocessing import Compose
+from tme.scoring import flc_scoring2
+
+def get_func_fullname(func) -> str:
+    """Returns the full name of the given function, including its module."""
+    return f"<function '{func.__module__}.{func.__name__}'>"
+
+
+def print_block(name: str, data: dict, label_width=20) -> None:
+    """Prints a formatted block of information."""
+    print(f"\n> {name}")
+    for key, value in data.items():
+        formatted_value = str(value)
+        print(f"  - {key + ':':<{label_width}} {formatted_value}")
+
+
+def print_entry() -> None:
+    width = 80
+    text = f" pytme v{__version__} "
+    padding_total = width - len(text) - 2
+    padding_left = padding_total // 2
+    padding_right = padding_total - padding_left
+
+    print("*" * width)
+    print(f"*{ ' ' * padding_left }{text}{ ' ' * padding_right }*")
+    print("*" * width)
+
+
+def check_positive(value):
+    ivalue = float(value)
+    if ivalue <= 0:
+        raise argparse.ArgumentTypeError("%s is an invalid positive float." % value)
+    return ivalue
+
+
+def load_and_validate_mask(mask_target: "Density", mask_path: str, **kwargs):
+    """
+    Loadsa mask in CCP4/MRC format and assess whether the sampling_rate
+    and shape matches its target.
+
+    Parameters
+    ----------
+    mask_target : Density
+        Object the mask should be applied to
+    mask_path : str
+        Path to the mask in CCP4/MRC format.
+    kwargs : dict, optional
+        Keyword arguments passed to :py:meth:`tme.density.Density.from_file`.
+    Raise
+    -----
+    ValueError
+        If shape or sampling rate do not match between mask_target and mask
+
+    Returns
+    -------
+    Density
+        A density instance if the mask was validated and loaded otherwise None
+    """
+    mask = mask_path
+    if mask is not None:
+        mask = Density.from_file(mask, **kwargs)
+        mask.origin = deepcopy(mask_target.origin)
+        if not np.allclose(mask.shape, mask_target.shape):
+            raise ValueError(
+                f"Expected shape of {mask_path} was {mask_target.shape},"
+                f" got f{mask.shape}"
+            )
+        if not np.allclose(mask.sampling_rate, mask_target.sampling_rate):
+            raise ValueError(
+                f"Expected sampling_rate of {mask_path} was {mask_target.sampling_rate}"
+                f", got f{mask.sampling_rate}"
+            )
+    return mask
+
+
+def crop_data(data: Density, cutoff: float, data_mask: Density = None) -> bool:
+    """
+    Crop the provided data and mask to a smaller box based on a cutoff value.
+
+    Parameters
+    ----------
+    data : Density
+        The data that should be cropped.
+    cutoff : float
+        The threshold value to determine which parts of the data should be kept.
+    data_mask : Density, optional
+        A mask for the data that should be cropped.
+
+    Returns
+    -------
+    bool
+        Returns True if the data was adjusted (cropped), otherwise returns False.
+
+    Notes
+    -----
+    Cropping is performed in place.
+    """
+    if cutoff is None:
+        return False
+
+    box = data.trim_box(cutoff=cutoff)
+    box_mask = box
+    if data_mask is not None:
+        box_mask = data_mask.trim_box(cutoff=cutoff)
+    box = tuple(
+        slice(min(arr.start, mask.start), max(arr.stop, mask.stop))
+        for arr, mask in zip(box, box_mask)
+    )
+    if box == tuple(slice(0, x) for x in data.shape):
+        return False
+
+    data.adjust_box(box)
+
+    if data_mask:
+        data_mask.adjust_box(box)
+
+    return True
+
+
+def parse_rotation_logic(args, ndim):
+    if args.angular_sampling is not None:
+        rotations = get_rotation_matrices(
+            angular_sampling=args.angular_sampling,
+            dim=ndim,
+            use_optimized_set=not args.no_use_optimized_set,
+        )
+        if args.angular_sampling >= 180:
+            rotations = np.eye(ndim).reshape(1, ndim, ndim)
+        return rotations
+
+    if args.axis_sampling is None:
+        args.axis_sampling = args.cone_sampling
+
+    rotations = get_rotations_around_vector(
+        cone_angle=args.cone_angle,
+        cone_sampling=args.cone_sampling,
+        axis_angle=args.axis_angle,
+        axis_sampling=args.axis_sampling,
+        n_symmetry=args.axis_symmetry,
+    )
+    return rotations
+
+
+# TODO: Think about whether wedge mask should also be added to target
+# For now leave it at the cost of incorrect upper bound on the scores
+def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Compose]:
+    from tme.preprocessing import LinearWhiteningFilter, BandPassFilter
+    from tme.preprocessing.tilt_series import (
+        Wedge,
+        WedgeReconstructed,
+        ReconstructFromTilt,
+    )
+
+    template_filter, target_filter = [], []
+    if args.tilt_angles is not None:
+        try:
+            wedge = Wedge.from_file(args.tilt_angles)
+            wedge.weight_type = args.tilt_weighting
+            if args.tilt_weighting in ("angle", None) and args.ctf_file is None:
+                wedge = WedgeReconstructed(
+                    angles=wedge.angles, weight_wedge=args.tilt_weighting == "angle"
+                )
+        except FileNotFoundError:
+            tilt_step, create_continuous_wedge = None, True
+            tilt_start, tilt_stop = args.tilt_angles.split(",")
+            if ":" in tilt_stop:
+                create_continuous_wedge = False
+                tilt_stop, tilt_step = tilt_stop.split(":")
+            tilt_start, tilt_stop = float(tilt_start), float(tilt_stop)
+            tilt_angles = (tilt_start, tilt_stop)
+            if tilt_step is not None:
+                tilt_step = float(tilt_step)
+                tilt_angles = np.arange(
+                    -tilt_start, tilt_stop + tilt_step, tilt_step
+                ).tolist()
+
+            if args.tilt_weighting is not None and tilt_step is None:
+                raise ValueError(
+                    "Tilt weighting is not supported for continuous wedges."
+                )
+            if args.tilt_weighting not in ("angle", None):
+                raise ValueError(
+                    "Tilt weighting schemes other than 'angle' or 'None' require "
+                    "a specification of electron doses via --tilt_angles."
+                )
+
+            wedge = Wedge(
+                angles=tilt_angles,
+                opening_axis=args.wedge_axes[0],
+                tilt_axis=args.wedge_axes[1],
+                shape=None,
+                weight_type=None,
+                weights=np.ones_like(tilt_angles),
+            )
+            if args.tilt_weighting in ("angle", None) and args.ctf_file is None:
+                wedge = WedgeReconstructed(
+                    angles=tilt_angles,
+                    weight_wedge=args.tilt_weighting == "angle",
+                    create_continuous_wedge=create_continuous_wedge,
+                )
+
+        wedge.opening_axis = args.wedge_axes[0]
+        wedge.tilt_axis = args.wedge_axes[1]
+        wedge.sampling_rate = template.sampling_rate
+        template_filter.append(wedge)
+        if not isinstance(wedge, WedgeReconstructed):
+            template_filter.append(
+                ReconstructFromTilt(
+                    reconstruction_filter=args.reconstruction_filter,
+                    interpolation_order=args.reconstruction_interpolation_order,
+                )
+            )
+
+    if args.ctf_file is not None or args.defocus is not None:
+        from tme.preprocessing.tilt_series import CTF
+
+        needs_reconstruction = True
+        if args.ctf_file is not None:
+            ctf = CTF.from_file(args.ctf_file)
+            n_tilts_ctfs, n_tils_angles = len(ctf.defocus_x), len(wedge.angles)
+            if n_tilts_ctfs != n_tils_angles:
+                raise ValueError(
+                    f"CTF file contains {n_tilts_ctfs} micrographs, but match_template "
+                    f"recieved {n_tils_angles} tilt angles. Expected one angle "
+                    "per micrograph."
+                )
+            ctf.angles = wedge.angles
+            ctf.opening_axis, ctf.tilt_axis = args.wedge_axes
+        else:
+            needs_reconstruction = False
+            ctf = CTF(
+                defocus_x=[args.defocus],
+                phase_shift=[args.phase_shift],
+                defocus_y=None,
+                angles=[0],
+                shape=None,
+                return_real_fourier=True,
+            )
+        ctf.sampling_rate = template.sampling_rate
+        ctf.flip_phase = args.no_flip_phase
+        ctf.amplitude_contrast = args.amplitude_contrast
+        ctf.spherical_aberration = args.spherical_aberration
+        ctf.acceleration_voltage = args.acceleration_voltage * 1e3
+        ctf.correct_defocus_gradient = args.correct_defocus_gradient
+
+        if not needs_reconstruction:
+            template_filter.append(ctf)
+        elif isinstance(template_filter[-1], ReconstructFromTilt):
+            template_filter.insert(-1, ctf)
+        else:
+            template_filter.insert(0, ctf)
+            template_filter.insert(
+                1,
+                ReconstructFromTilt(
+                    reconstruction_filter=args.reconstruction_filter,
+                    interpolation_order=args.reconstruction_interpolation_order,
+                ),
+            )
+
+    if args.lowpass or args.highpass is not None:
+        lowpass, highpass = args.lowpass, args.highpass
+        if args.pass_format == "voxel":
+            if lowpass is not None:
+                lowpass = np.max(np.multiply(lowpass, template.sampling_rate))
+            if highpass is not None:
+                highpass = np.max(np.multiply(highpass, template.sampling_rate))
+        elif args.pass_format == "frequency":
+            if lowpass is not None:
+                lowpass = np.max(np.divide(template.sampling_rate, lowpass))
+            if highpass is not None:
+                highpass = np.max(np.divide(template.sampling_rate, highpass))
+
+        try:
+            if args.lowpass >= args.highpass:
+                warnings.warn("--lowpass should be smaller than --highpass.")
+        except Exception:
+            pass
+
+        bandpass = BandPassFilter(
+            use_gaussian=args.no_pass_smooth,
+            lowpass=lowpass,
+            highpass=highpass,
+            sampling_rate=template.sampling_rate,
+        )
+        template_filter.append(bandpass)
+
+        if not args.no_filter_target:
+            target_filter.append(bandpass)
+
+    if args.whiten_spectrum:
+        whitening_filter = LinearWhiteningFilter()
+        template_filter.append(whitening_filter)
+        target_filter.append(whitening_filter)
+
+    needs_reconstruction = any(
+        [isinstance(t, ReconstructFromTilt) for t in template_filter]
+    )
+    if needs_reconstruction and args.reconstruction_filter is None:
+        warnings.warn(
+            "Consider using a --reconstruction_filter such as 'ramp' to avoid artifacts."
+        )
+
+    template_filter = Compose(template_filter) if len(template_filter) else None
+    target_filter = Compose(target_filter) if len(target_filter) else None
+
+    return template_filter, target_filter
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description="Perform template matching.",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+
+    io_group = parser.add_argument_group("Input / Output")
+    io_group.add_argument(
+        "-m",
+        "--target",
+        dest="target",
+        type=str,
+        required=True,
+        help="Path to a target in CCP4/MRC, EM, H5 or another format supported by "
+        "tme.density.Density.from_file "
+        "https://kosinskilab.github.io/pyTME/reference/api/tme.density.Density.from_file.html",
+    )
+    io_group.add_argument(
+        "--target_mask",
+        dest="target_mask",
+        type=str,
+        required=False,
+        help="Path to a mask for the target in a supported format (see target).",
+    )
+    io_group.add_argument(
+        "-i",
+        "--template",
+        dest="template",
+        type=str,
+        required=True,
+        help="Path to a template in PDB/MMCIF or other supported formats (see target).",
+    )
+    io_group.add_argument(
+        "--template_mask",
+        dest="template_mask",
+        type=str,
+        required=False,
+        help="Path to a mask for the template in a supported format (see target).",
+    )
+    io_group.add_argument(
+        "-o",
+        "--output",
+        dest="output",
+        type=str,
+        required=False,
+        default="output.pickle",
+        help="Path to the output pickle file.",
+    )
+    io_group.add_argument(
+        "--invert_target_contrast",
+        dest="invert_target_contrast",
+        action="store_true",
+        default=False,
+        help="Invert the target's contrast and rescale linearly between zero and one. "
+        "This option is intended for targets where templates to-be-matched have "
+        "negative values, e.g. tomograms.",
+    )
+    io_group.add_argument(
+        "--scramble_phases",
+        dest="scramble_phases",
+        action="store_true",
+        default=False,
+        help="Phase scramble the template to generate a noise score background.",
+    )
+
+    scoring_group = parser.add_argument_group("Scoring")
+    scoring_group.add_argument(
+        "-s",
+        dest="score",
+        type=str,
+        default="FLCSphericalMask",
+        choices=list(MATCHING_EXHAUSTIVE_REGISTER.keys()),
+        help="Template matching scoring function.",
+    )
+
+    angular_group = parser.add_argument_group("Angular Sampling")
+    angular_exclusive = angular_group.add_mutually_exclusive_group(required=True)
+
+    angular_exclusive.add_argument(
+        "-a",
+        dest="angular_sampling",
+        type=check_positive,
+        default=None,
+        help="Angular sampling rate using optimized rotational sets."
+        "A lower number yields more rotations. Values >= 180 sample only the identity.",
+    )
+    angular_exclusive.add_argument(
+        "--cone_angle",
+        dest="cone_angle",
+        type=check_positive,
+        default=None,
+        help="Half-angle of the cone to be sampled in degrees. Allows to sample a "
+        "narrow interval around a known orientation, e.g. for surface oversampling.",
+    )
+    angular_group.add_argument(
+        "--cone_sampling",
+        dest="cone_sampling",
+        type=check_positive,
+        default=None,
+        help="Sampling rate of the cone in degrees.",
+    )
+    angular_group.add_argument(
+        "--axis_angle",
+        dest="axis_angle",
+        type=check_positive,
+        default=360.0,
+        required=False,
+        help="Sampling angle along the z-axis of the cone.",
+    )
+    angular_group.add_argument(
+        "--axis_sampling",
+        dest="axis_sampling",
+        type=check_positive,
+        default=None,
+        required=False,
+        help="Sampling rate along the z-axis of the cone. Defaults to --cone_sampling.",
+    )
+    angular_group.add_argument(
+        "--axis_symmetry",
+        dest="axis_symmetry",
+        type=check_positive,
+        default=1,
+        required=False,
+        help="N-fold symmetry around z-axis of the cone.",
+    )
+    angular_group.add_argument(
+        "--no_use_optimized_set",
+        dest="no_use_optimized_set",
+        action="store_true",
+        default=False,
+        required=False,
+        help="Whether to use random uniform instead of optimized rotation sets.",
+    )
+
+    computation_group = parser.add_argument_group("Computation")
+    computation_group.add_argument(
+        "-n",
+        dest="cores",
+        required=False,
+        type=int,
+        default=4,
+        help="Number of cores used for template matching.",
+    )
+    computation_group.add_argument(
+        "--use_gpu",
+        dest="use_gpu",
+        action="store_true",
+        default=False,
+        help="Whether to perform computations on the GPU.",
+    )
+    computation_group.add_argument(
+        "--gpu_indices",
+        dest="gpu_indices",
+        type=str,
+        default=None,
+        help="Comma-separated list of GPU indices to use. For example,"
+        " 0,1 for the first and second GPU. Only used if --use_gpu is set."
+        " If not provided but --use_gpu is set, CUDA_VISIBLE_DEVICES will"
+        " be respected.",
+    )
+    computation_group.add_argument(
+        "-r",
+        "--ram",
+        dest="memory",
+        required=False,
+        type=int,
+        default=None,
+        help="Amount of memory that can be used in bytes.",
+    )
+    computation_group.add_argument(
+        "--memory_scaling",
+        dest="memory_scaling",
+        required=False,
+        type=float,
+        default=0.85,
+        help="Fraction of available memory to be used. Ignored if --ram is set."
+    )
+    computation_group.add_argument(
+        "--temp_directory",
+        dest="temp_directory",
+        default=None,
+        help="Directory for temporary objects. Faster I/O improves runtime.",
+    )
+    computation_group.add_argument(
+        "--backend",
+        dest="backend",
+        default=None,
+        choices=be.available_backends(),
+        help="[Expert] Overwrite default computation backend.",
+    )
+
+    filter_group = parser.add_argument_group("Filters")
+    filter_group.add_argument(
+        "--lowpass",
+        dest="lowpass",
+        type=float,
+        required=False,
+        help="Resolution to lowpass filter template and target to in the same unit "
+        "as the sampling rate of template and target (typically Ångstrom).",
+    )
+    filter_group.add_argument(
+        "--highpass",
+        dest="highpass",
+        type=float,
+        required=False,
+        help="Resolution to highpass filter template and target to in the same unit "
+        "as the sampling rate of template and target (typically Ångstrom).",
+    )
+    filter_group.add_argument(
+        "--no_pass_smooth",
+        dest="no_pass_smooth",
+        action="store_false",
+        default=True,
+        help="Whether a hard edge filter should be used for --lowpass and --highpass.",
+    )
+    filter_group.add_argument(
+        "--pass_format",
+        dest="pass_format",
+        type=str,
+        required=False,
+        default="sampling_rate",
+        choices=["sampling_rate", "voxel", "frequency"],
+        help="How values passed to --lowpass and --highpass should be interpreted. ",
+    )
+    filter_group.add_argument(
+        "--whiten_spectrum",
+        dest="whiten_spectrum",
+        action="store_true",
+        default=None,
+        help="Apply spectral whitening to template and target based on target spectrum.",
+    )
+    filter_group.add_argument(
+        "--wedge_axes",
+        dest="wedge_axes",
+        type=str,
+        required=False,
+        default=None,
+        help="Indices of wedge opening and tilt axis, e.g. 0,2 for a wedge that is open "
+        "in z-direction and tilted over the x axis.",
+    )
+    filter_group.add_argument(
+        "--tilt_angles",
+        dest="tilt_angles",
+        type=str,
+        required=False,
+        default=None,
+        help="Path to a tab-separated file containing the column angles and optionally "
+        " weights, or comma separated start and stop stage tilt angle, e.g. 50,45, which "
+        " yields a continuous wedge mask. Alternatively, a tilt step size can be "
+        "specified like 50,45:5.0 to sample 5.0 degree tilt angle steps.",
+    )
+    filter_group.add_argument(
+        "--tilt_weighting",
+        dest="tilt_weighting",
+        type=str,
+        required=False,
+        choices=["angle", "relion", "grigorieff"],
+        default=None,
+        help="Weighting scheme used to reweight individual tilts. Available options: "
+        "angle (cosine based weighting), "
+        "relion (relion formalism for wedge weighting) requires,"
+        "grigorieff (exposure filter as defined in Grant and Grigorieff 2015)."
+        "relion and grigorieff require electron doses in --tilt_angles weights column.",
+    )
+    filter_group.add_argument(
+        "--reconstruction_filter",
+        dest="reconstruction_filter",
+        type=str,
+        required=False,
+        choices=["ram-lak", "ramp", "ramp-cont", "shepp-logan", "cosine", "hamming"],
+        default=None,
+        help="Filter applied when reconstructing (N+1)-D from N-D filters.",
+    )
+    filter_group.add_argument(
+        "--reconstruction_interpolation_order",
+        dest="reconstruction_interpolation_order",
+        type=int,
+        default=1,
+        required=False,
+        help="Analogous to --interpolation_order but for reconstruction.",
+    )
+    filter_group.add_argument(
+        "--no_filter_target",
+        dest="no_filter_target",
+        action="store_true",
+        default=False,
+        help="Whether to not apply potential filters to the target.",
+    )
+
+    ctf_group = parser.add_argument_group("Contrast Transfer Function")
+    ctf_group.add_argument(
+        "--ctf_file",
+        dest="ctf_file",
+        type=str,
+        required=False,
+        default=None,
+        help="Path to a file with CTF parameters from CTFFIND4. Each line will be "
+        "interpreted as tilt obtained at the angle specified in --tilt_angles. ",
+    )
+    ctf_group.add_argument(
+        "--defocus",
+        dest="defocus",
+        type=float,
+        required=False,
+        default=None,
+        help="Defocus in units of sampling rate (typically Ångstrom). "
+        "Superseded by --ctf_file.",
+    )
+    ctf_group.add_argument(
+        "--phase_shift",
+        dest="phase_shift",
+        type=float,
+        required=False,
+        default=0,
+        help="Phase shift in degrees. Superseded by --ctf_file.",
+    )
+    ctf_group.add_argument(
+        "--acceleration_voltage",
+        dest="acceleration_voltage",
+        type=float,
+        required=False,
+        default=300,
+        help="Acceleration voltage in kV.",
+    )
+    ctf_group.add_argument(
+        "--spherical_aberration",
+        dest="spherical_aberration",
+        type=float,
+        required=False,
+        default=2.7e7,
+        help="Spherical aberration in units of sampling rate (typically Ångstrom).",
+    )
+    ctf_group.add_argument(
+        "--amplitude_contrast",
+        dest="amplitude_contrast",
+        type=float,
+        required=False,
+        default=0.07,
+        help="Amplitude contrast.",
+    )
+    ctf_group.add_argument(
+        "--no_flip_phase",
+        dest="no_flip_phase",
+        action="store_false",
+        required=False,
+        help="Perform phase-flipping CTF correction.",
+    )
+    ctf_group.add_argument(
+        "--correct_defocus_gradient",
+        dest="correct_defocus_gradient",
+        action="store_true",
+        required=False,
+        help="[Experimental] Whether to compute a more accurate 3D CTF incorporating "
+        "defocus gradients.",
+    )
+
+    performance_group = parser.add_argument_group("Performance")
+    performance_group.add_argument(
+        "--cutoff_target",
+        dest="cutoff_target",
+        type=float,
+        required=False,
+        default=None,
+        help="Target contour level (used for cropping).",
+    )
+    performance_group.add_argument(
+        "--cutoff_template",
+        dest="cutoff_template",
+        type=float,
+        required=False,
+        default=None,
+        help="Template contour level (used for cropping).",
+    )
+    performance_group.add_argument(
+        "--no_centering",
+        dest="no_centering",
+        action="store_true",
+        help="Assumes the template is already centered and omits centering.",
+    )
+    performance_group.add_argument(
+        "--no_edge_padding",
+        dest="no_edge_padding",
+        action="store_true",
+        default=False,
+        help="Whether to not pad the edges of the target. Can be set if the target"
+        " has a well defined bounding box, e.g. a masked reconstruction.",
+    )
+    performance_group.add_argument(
+        "--no_fourier_padding",
+        dest="no_fourier_padding",
+        action="store_true",
+        default=False,
+        help="Whether input arrays should not be zero-padded to full convolution shape "
+        "for numerical stability. When working with very large targets, e.g. tomograms, "
+        "it is safe to use this flag and benefit from the performance gain.",
+    )
+    performance_group.add_argument(
+        "--no_filter_padding",
+        dest="no_filter_padding",
+        action="store_true",
+        default=False,
+        help="Omits padding of optional template filters. Particularly effective when "
+        "the target is much larger than the template. However, for fast osciliating "
+        "filters setting this flag can introduce aliasing effects.",
+    )
+    performance_group.add_argument(
+        "--interpolation_order",
+        dest="interpolation_order",
+        required=False,
+        type=int,
+        default=3,
+        help="Spline interpolation used for rotations.",
+    )
+    performance_group.add_argument(
+        "--use_mixed_precision",
+        dest="use_mixed_precision",
+        action="store_true",
+        default=False,
+        help="Use float16 for real values operations where possible.",
+    )
+    performance_group.add_argument(
+        "--use_memmap",
+        dest="use_memmap",
+        action="store_true",
+        default=False,
+        help="Use memmaps to offload large data objects to disk. "
+        "Particularly useful for large inputs in combination with --use_gpu.",
+    )
+
+    analyzer_group = parser.add_argument_group("Analyzer")
+    analyzer_group.add_argument(
+        "--score_threshold",
+        dest="score_threshold",
+        required=False,
+        type=float,
+        default=0,
+        help="Minimum template matching scores to consider for analysis.",
+    )
+    analyzer_group.add_argument(
+        "-p",
+        dest="peak_calling",
+        action="store_true",
+        default=False,
+        help="Perform peak calling instead of score aggregation.",
+    )
+    analyzer_group.add_argument(
+        "--number_of_peaks",
+        dest="number_of_peaks",
+        action="store_true",
+        default=1000,
+        help="Number of peaks to call, 1000 by default..",
+    )
+    args = parser.parse_args()
+    args.version = __version__
+
+    if args.interpolation_order < 0:
+        args.interpolation_order = None
+
+    if args.temp_directory is None:
+        default = abspath(".")
+        if os.environ.get("TMPDIR", None) is not None:
+            default = os.environ.get("TMPDIR")
+        args.temp_directory = default
+
+    os.environ["TMPDIR"] = args.temp_directory
+
+    args.pad_target_edges = not args.no_edge_padding
+    args.pad_fourier = not args.no_fourier_padding
+
+    if args.score not in MATCHING_EXHAUSTIVE_REGISTER:
+        raise ValueError(
+            f"score has to be one of {', '.join(MATCHING_EXHAUSTIVE_REGISTER.keys())}"
+        )
+
+    gpu_devices = os.environ.get("CUDA_VISIBLE_DEVICES", None)
+    if args.gpu_indices is not None:
+        os.environ["CUDA_VISIBLE_DEVICES"] = args.gpu_indices
+
+    if args.use_gpu:
+        gpu_devices = os.environ.get("CUDA_VISIBLE_DEVICES", None)
+        if gpu_devices is None:
+            print(
+                "No GPU indices provided and CUDA_VISIBLE_DEVICES is not set.",
+                "Assuming device 0.",
+            )
+            os.environ["CUDA_VISIBLE_DEVICES"] = "0"
+        args.gpu_indices = [
+            int(x) for x in os.environ["CUDA_VISIBLE_DEVICES"].split(",")
+        ]
+
+    if args.tilt_angles is not None:
+        if args.wedge_axes is None:
+            raise ValueError("Need to specify --wedge_axes when --tilt_angles is set.")
+        if not exists(args.tilt_angles):
+            try:
+                float(args.tilt_angles.split(",")[0])
+            except ValueError:
+                raise ValueError(f"{args.tilt_angles} is not a file nor a range.")
+
+    if args.ctf_file is not None and args.tilt_angles is None:
+        raise ValueError("Need to specify --tilt_angles when --ctf_file is set.")
+
+    if args.wedge_axes is not None:
+        args.wedge_axes = tuple(int(i) for i in args.wedge_axes.split(","))
+
+    return args
+
+
+def main():
+    args = parse_args()
+    print_entry()
+
+    target = Density.from_file(args.target, use_memmap=True)
+
+    try:
+        template = Density.from_file(args.template)
+    except Exception:
+        drop = target.metadata.get("batch_dimension", ())
+        keep = [i not in drop for i in range(target.data.ndim)]
+        template = Density.from_structure(
+            filename_or_structure=args.template,
+            sampling_rate=target.sampling_rate[keep],
+        )
+
+    if target.sampling_rate.size == template.sampling_rate.size:
+        if not np.allclose(target.sampling_rate, template.sampling_rate):
+            print(
+                f"Resampling template to {target.sampling_rate}. "
+                "Consider providing a template with the same sampling rate as the target."
+            )
+            template = template.resample(target.sampling_rate, order=3)
+
+    template_mask = load_and_validate_mask(
+        mask_target=template, mask_path=args.template_mask
+    )
+    target_mask = load_and_validate_mask(
+        mask_target=target, mask_path=args.target_mask, use_memmap=True
+    )
+
+    initial_shape = target.shape
+    is_cropped = crop_data(
+        data=target, data_mask=target_mask, cutoff=args.cutoff_target
+    )
+    print_block(
+        name="Target",
+        data={
+            "Initial Shape": initial_shape,
+            "Sampling Rate": tuple(np.round(target.sampling_rate, 2)),
+            "Final Shape": target.shape,
+        },
+    )
+    if is_cropped:
+        args.target = generate_tempfile_name(suffix=".mrc")
+        target.to_file(args.target)
+
+        if target_mask:
+            args.target_mask = generate_tempfile_name(suffix=".mrc")
+            target_mask.to_file(args.target_mask)
+
+    if target_mask:
+        print_block(
+            name="Target Mask",
+            data={
+                "Initial Shape": initial_shape,
+                "Sampling Rate": tuple(np.round(target_mask.sampling_rate, 2)),
+                "Final Shape": target_mask.shape,
+            },
+        )
+
+    initial_shape = template.shape
+    _ = crop_data(data=template, data_mask=template_mask, cutoff=args.cutoff_template)
+
+    translation = np.zeros(len(template.shape), dtype=np.float32)
+    if not args.no_centering:
+        template, translation = template.centered(0)
+    print_block(
+        name="Template",
+        data={
+            "Initial Shape": initial_shape,
+            "Sampling Rate": tuple(np.round(template.sampling_rate, 2)),
+            "Final Shape": template.shape,
+        },
+    )
+
+    if template_mask is None:
+        template_mask = template.empty
+        if not args.no_centering:
+            enclosing_box = template.minimum_enclosing_box(
+                0, use_geometric_center=False
+            )
+            template_mask.adjust_box(enclosing_box)
+
+        template_mask.data[:] = 1
+        translation = np.zeros_like(translation)
+
+    template_mask.pad(template.shape, center=False)
+    origin_translation = np.divide(
+        np.subtract(template.origin, template_mask.origin), template.sampling_rate
+    )
+    translation = np.add(translation, origin_translation)
+
+    template_mask = template_mask.rigid_transform(
+        rotation_matrix=np.eye(template_mask.data.ndim),
+        translation=-translation,
+        order=1,
+    )
+    template_mask.origin = template.origin.copy()
+    print_block(
+        name="Template Mask",
+        data={
+            "Inital Shape": initial_shape,
+            "Sampling Rate": tuple(np.round(template_mask.sampling_rate, 2)),
+            "Final Shape": template_mask.shape,
+        },
+    )
+    print("\n" + "-" * 80)
+
+    if args.scramble_phases:
+        template.data = scramble_phases(
+            template.data, noise_proportion=1.0, normalize_power=True
+        )
+
+    # Determine suitable backend for the selected operation
+    available_backends = be.available_backends()
+    if args.backend is not None:
+        req_backend = args.backend
+        if req_backend not in available_backends:
+            raise ValueError(
+                "Requested backend is not available."
+            )
+        available_backends = [req_backend,]
+
+    be_selection = ("numpyfftw", "pytorch", "jax", "mlx")
+    if args.use_gpu:
+        args.cores = len(args.gpu_indices)
+        be_selection = ("pytorch", "cupy", "jax")
+    if args.use_mixed_precision:
+        be_selection = tuple(x for x in be_selection if x in ("cupy", "numpyfftw"))
+
+    available_backends = [x for x in available_backends if x in be_selection]
+    if args.peak_calling:
+        if "jax" in available_backends:
+            available_backends.remove("jax")
+        if args.use_gpu and "pytorch" in available_backends:
+            available_backends = ("pytorch",)
+            if args.interpolation_order == 3:
+                raise NotImplementedError(
+                    "Pytorch does not support --interpolation_order 3, 1 is supported."
+                )
+    ndim = len(template.shape)
+    if len(target.shape) == ndim and ndim <= 3 and args.use_gpu:
+        available_backends = ["jax", ]
+
+    backend_preference = ("numpyfftw", "pytorch", "jax", "mlx")
+    if args.use_gpu:
+        backend_preference = ("cupy", "jax", "pytorch")
+    for pref in backend_preference:
+        if pref not in available_backends:
+            continue
+        be.change_backend(pref)
+        if pref == "pytorch":
+            be.change_backend(pref, device = "cuda" if args.use_gpu else "cpu")
+
+        if args.use_mixed_precision:
+            be.change_backend(
+                backend_name=pref,
+                default_dtype=be._array_backend.float16,
+                complex_dtype=be._array_backend.complex64,
+                default_dtype_int=be._array_backend.int16,
+            )
+        break
+
+    available_memory = be.get_available_memory() * be.device_count()
+    if args.memory is None:
+        args.memory = int(args.memory_scaling * available_memory)
+
+    callback_class = MaxScoreOverRotations
+    if args.peak_calling:
+        callback_class = PeakCallerMaximumFilter
+
+    matching_data = MatchingData(
+        target=target,
+        template=template.data,
+        target_mask=target_mask,
+        template_mask=template_mask,
+        invert_target=args.invert_target_contrast,
+        rotations=parse_rotation_logic(args=args, ndim=template.data.ndim),
+    )
+
+    matching_data.template_filter, matching_data.target_filter  = setup_filter(
+        args, template, target
+    )
+
+    target_dims = target.metadata.get("batch_dimension", None)
+    matching_data._set_matching_dimension(target_dims=target_dims, template_dims=None)
+    args.score = "FLC" if target_dims is not None else args.score
+    args.target_batch, args.template_batch = target_dims, None
+
+    template_box = matching_data._output_template_shape
+    if not args.pad_fourier:
+        template_box = tuple(0 for _ in range(len(template_box)))
+
+    target_padding = tuple(0 for _ in range(len(template_box)))
+    if args.pad_target_edges:
+        target_padding = matching_data._output_template_shape
+
+    splits, schedule = compute_parallelization_schedule(
+        shape1=target.shape,
+        shape2=tuple(int(x) for x in template_box),
+        shape1_padding=tuple(int(x) for x in target_padding),
+        max_cores=args.cores,
+        max_ram=args.memory,
+        split_only_outer=args.use_gpu,
+        matching_method=args.score,
+        analyzer_method=callback_class.__name__,
+        backend=be._backend_name,
+        float_nbytes=be.datatype_bytes(be._float_dtype),
+        complex_nbytes=be.datatype_bytes(be._complex_dtype),
+        integer_nbytes=be.datatype_bytes(be._int_dtype),
+        split_axes=target_dims,
+    )
+
+    if splits is None:
+        print(
+            "Found no suitable parallelization schedule. Consider increasing"
+            " available RAM or decreasing number of cores."
+        )
+        exit(-1)
+
+    matching_setup, matching_score = MATCHING_EXHAUSTIVE_REGISTER[args.score]
+    if target_dims is not None:
+        matching_score = flc_scoring2
+    n_splits = np.prod(list(splits.values()))
+    target_split = ", ".join(
+        [":".join([str(x) for x in axis]) for axis in splits.items()]
+    )
+    gpus_used = 0 if args.gpu_indices is None else len(args.gpu_indices)
+    options = {
+        "Angular Sampling": f"{args.angular_sampling}"
+        f" [{matching_data.rotations.shape[0]} rotations]",
+        "Center Template": not args.no_centering,
+        "Scramble Template": args.scramble_phases,
+        "Invert Contrast": args.invert_target_contrast,
+        "Extend Fourier Grid": not args.no_fourier_padding,
+        "Extend Target Edges": not args.no_edge_padding,
+        "Interpolation Order": args.interpolation_order,
+        "Setup Function": f"{get_func_fullname(matching_setup)}",
+        "Scoring Function": f"{get_func_fullname(matching_score)}",
+    }
+
+    print_block(
+        name="Template Matching",
+        data=options,
+        label_width=max(len(key) for key in options.keys()) + 3,
+    )
+
+    compute_options = {
+        "Backend" :be._BACKEND_REGISTRY[be._backend_name],
+        "Compute Devices" : f"CPU [{args.cores}], GPU [{gpus_used}]",
+        "Use Mixed Precision": args.use_mixed_precision,
+        "Assigned Memory [MB]": f"{args.memory // 1e6} [out of {available_memory//1e6}]",
+        "Temporary Directory": args.temp_directory,
+        "Target Splits": f"{target_split} [N={n_splits}]",
+    }
+    print_block(
+        name="Computation",
+        data=compute_options,
+        label_width=max(len(key) for key in options.keys()) + 3,
+    )
+
+    filter_args = {
+        "Lowpass": args.lowpass,
+        "Highpass": args.highpass,
+        "Smooth Pass": args.no_pass_smooth,
+        "Pass Format": args.pass_format,
+        "Spectral Whitening": args.whiten_spectrum,
+        "Wedge Axes": args.wedge_axes,
+        "Tilt Angles": args.tilt_angles,
+        "Tilt Weighting": args.tilt_weighting,
+        "Reconstruction Filter": args.reconstruction_filter,
+    }
+    if args.ctf_file is not None or args.defocus is not None:
+        filter_args["CTF File"] = args.ctf_file
+        filter_args["Defocus"] = args.defocus
+        filter_args["Phase Shift"] = args.phase_shift
+        filter_args["Flip Phase"] = args.no_flip_phase
+        filter_args["Acceleration Voltage"] = args.acceleration_voltage
+        filter_args["Spherical Aberration"] = args.spherical_aberration
+        filter_args["Amplitude Contrast"] = args.amplitude_contrast
+        filter_args["Correct Defocus"] = args.correct_defocus_gradient
+
+    filter_args = {k: v for k, v in filter_args.items() if v is not None}
+    if len(filter_args):
+        print_block(
+            name="Filters",
+            data=filter_args,
+            label_width=max(len(key) for key in options.keys()) + 3,
+        )
+
+    analyzer_args = {
+        "score_threshold": args.score_threshold,
+        "number_of_peaks": args.number_of_peaks,
+        "min_distance" : max(template.shape) // 2,
+        "min_boundary_distance" : max(template.shape) // 2,
+        "use_memmap": args.use_memmap,
+    }
+    print_block(
+        name="Analyzer",
+        data={"Analyzer": callback_class, **analyzer_args},
+        label_width=max(len(key) for key in options.keys()) + 3,
+    )
+    print("\n" + "-" * 80)
+
+    outer_jobs = f"{schedule[0]} job{'s' if schedule[0] > 1 else ''}"
+    inner_jobs = f"{schedule[1]} core{'s' if schedule[1] > 1 else ''}"
+    n_splits = f"{n_splits} split{'s' if n_splits > 1 else ''}"
+    print(f"\nDistributing {n_splits} on {outer_jobs} each using {inner_jobs}.")
+
+    start = time()
+    print("Running Template Matching. This might take a while ...")
+    candidates = scan_subsets(
+        matching_data=matching_data,
+        job_schedule=schedule,
+        matching_score=matching_score,
+        matching_setup=matching_setup,
+        callback_class=callback_class,
+        callback_class_args=analyzer_args,
+        target_splits=splits,
+        pad_target_edges=args.pad_target_edges,
+        pad_fourier=args.pad_fourier,
+        pad_template_filter=not args.no_filter_padding,
+        interpolation_order=args.interpolation_order,
+    )
+
+    candidates = list(candidates) if candidates is not None else []
+    if callback_class == MaxScoreOverRotations:
+        if target_mask is not None and args.score != "MCC":
+            candidates[0] *= target_mask.data
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore", category=UserWarning)
+            nbytes = be.datatype_bytes(be._float_dtype)
+            dtype = np.float32 if nbytes == 4 else np.float16
+            rot_dim = matching_data.rotations.shape[1]
+            candidates[3] = {
+                x: np.frombuffer(i, dtype=dtype).reshape(rot_dim, rot_dim)
+                for i, x in candidates[3].items()
+            }
+    print(np.where(candidates[0] == candidates[0].max()), candidates[0].max())
+    candidates.append((target.origin, template.origin, template.sampling_rate, args))
+    write_pickle(data=candidates, filename=args.output)
+
+    runtime = time() - start
+    print("\n" + "-" * 80)
+    print(f"\nRuntime real: {runtime:.3f}s user: {(runtime * args.cores):.3f}s.")
+
+
+if __name__ == "__main__":
+    main()