pytme 0.3.1.post2__cp311-cp311-macosx_15_0_arm64.whl → 0.3.2__cp311-cp311-macosx_15_0_arm64.whl

scripts/match_template_devel.py

@@ -0,0 +1,1339 @@
+#!python3
+"""CLI 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 exists
+from tempfile import gettempdir
+
+import numpy as np
+
+from tme.backends import backend as be
+from tme import Density, __version__, Orientations
+from tme.matching_utils import scramble_phases, write_pickle, generate_tempfile_name
+from tme.matching_exhaustive import scan_subsets, MATCHING_EXHAUSTIVE_REGISTER
+from tme.rotations import (
+    get_cone_rotations,
+    get_rotation_matrices,
+    euler_to_rotationmatrix,
+)
+from tme.matching_data import MatchingData
+from tme.analyzer import (
+    MaxScoreOverRotations,
+    PeakCallerMaximumFilter,
+    MaxScoreOverRotationsConstrained,
+)
+from tme.filters import (
+    CTF,
+    Wedge,
+    Compose,
+    BandPass,
+    ShiftFourier,
+    CTFReconstructed,
+    WedgeReconstructed,
+    ReconstructFromTilt,
+    LinearWhiteningFilter,
+    BandPassReconstructed
+)
+from tme.cli import get_func_fullname, print_block, print_entry, check_positive
+
+
+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(
+            np.round(mask.sampling_rate, 2), np.round(mask_target.sampling_rate, 2)
+        ):
+            raise ValueError(
+                f"Expected sampling_rate of {mask_path} was {mask_target.sampling_rate}"
+                f", got f{mask.sampling_rate}"
+            )
+    return mask
+
+
+def parse_rotation_logic(args, ndim):
+    if args.particle_diameter is not None:
+        resolution = Density.from_file(args.target, use_memmap=True)
+        resolution = 360 * np.maximum(
+            np.max(2 * resolution.sampling_rate),
+            args.lowpass if args.lowpass is not None else 0,
+        )
+        args.angular_sampling = resolution / (3.14159265358979 * args.particle_diameter)
+
+    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_cone_rotations(
+        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,
+        axis=[0 if i != args.cone_axis else 1 for i in range(ndim)],
+        reference=[0, 0, -1],
+    )
+    return rotations
+
+
+def compute_schedule(
+    args,
+    matching_data: MatchingData,
+    callback_class,
+    pad_edges: bool = False,
+):
+    # User requested target padding
+    if args.pad_edges is True:
+        pad_edges = True
+
+    splits, schedule = matching_data.computation_schedule(
+        matching_method=args.score,
+        analyzer_method=callback_class.__name__,
+        use_gpu=args.use_gpu,
+        pad_fourier=False,
+        pad_target_edges=pad_edges,
+        available_memory=args.memory,
+        max_cores=args.cores,
+    )
+
+    if splits is None:
+        print(
+            "Found no suitable parallelization schedule. Consider increasing"
+            " available RAM or decreasing number of cores."
+        )
+        exit(-1)
+
+    n_splits = np.prod(list(splits.values()))
+    if pad_edges is False and len(matching_data._target_dim) == 0 and n_splits > 1:
+        args.pad_edges = True
+        return compute_schedule(args, matching_data, callback_class, True)
+    return splits, schedule
+
+
+def extract_tilts(args, target):
+    from tme.projection import Projector
+    try:
+        wedge = Wedge.from_file(args.tilt_angles)
+        wedge.weight_type = args.tilt_weighting
+        if args.tilt_weighting in ("angle", None):
+            wedge = WedgeReconstructed(
+                angles=wedge.angles,
+                weight_wedge=args.tilt_weighting == "angle",
+            )
+    except (FileNotFoundError, AttributeError):
+        tilt_start, tilt_stop = args.tilt_angles.split(",")
+        tilt_start, tilt_stop = abs(float(tilt_start)), abs(float(tilt_stop))
+        wedge = WedgeReconstructed(
+            angles=(tilt_start, tilt_stop),
+            create_continuous_wedge=True,
+            weight_wedge=False,
+            reconstruction_filter=args.reconstruction_filter,
+        )
+    projector = Projector(target.data)
+    tilts = projector.extract_tilts(
+        tilt_angles=wedge.angles,
+    )
+    target = Density(tilts, sampling_rate=(1, *target.sampling_rate[1:]))
+    temp_path = generate_tempfile_name("h5")
+    target.to_file(temp_path)
+    return Density.from_file(temp_path, use_memmap = True)
+
+
+def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Compose]:
+    template_filter, target_filter = [], []
+
+    wedge = None
+    if args.tilt_angles is not None:
+        try:
+            wedge = Wedge.from_file(args.tilt_angles)
+            wedge.weight_type = args.tilt_weighting
+        except (FileNotFoundError, AttributeError):
+            raise ValueError(
+                "Projection matching angles need to be specified via angles file."
+            )
+
+        wedge_target = WedgeReconstructed(
+            angles=wedge.angles,
+            weight_wedge=False,
+            create_continuous_wedge=True,
+            opening_axis=args.wedge_axes[0],
+            tilt_axis=args.wedge_axes[1],
+        )
+        wedge.opening_axis = args.wedge_axes[0]
+        wedge.tilt_axis = args.wedge_axes[1]
+
+        target_filter.append(wedge_target)
+        template_filter.append(wedge)
+
+    args.ctf_file is not None
+    if args.ctf_file is not None or args.defocus is not None:
+        try:
+            ctf = CTF.from_file(args.ctf_file)
+            if (len(ctf.angles) == 0) and wedge is None:
+                raise ValueError(
+                    "You requested to specify the CTF per tilt, but did not specify "
+                    "tilt angles via --tilt_angles or --ctf_file (Warp/M XML format). "
+                )
+            if len(ctf.angles) == 0:
+                ctf.angles = wedge.angles
+
+            n_tilts_ctfs, n_tils_angles = len(ctf.defocus_x), len(wedge.angles)
+            if (n_tilts_ctfs != n_tils_angles) and isinstance(wedge, Wedge):
+                raise ValueError(
+                    f"CTF file contains {n_tilts_ctfs} tilt, but match_template "
+                    f"recieved {n_tils_angles} tilt angles. Expected one angle "
+                    "per tilt."
+                )
+
+        except (FileNotFoundError, AttributeError):
+            ctf = CTFReconstructed(defocus_x=args.defocus, phase_shift=args.phase_shift)
+
+        ctf.opening_axis, ctf.tilt_axis = args.wedge_axes
+        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
+        template_filter.append(ctf)
+
+    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 = BandPassReconstructed(
+            use_gaussian=args.no_pass_smooth,
+            lowpass=lowpass,
+            highpass=highpass,
+            sampling_rate=template.sampling_rate,
+        )
+        template_filter.append(bandpass)
+        target_filter.append(bandpass)
+
+    if args.whiten_spectrum:
+        whitening_filter = LinearWhiteningFilter()
+        template_filter.append(whitening_filter)
+        target_filter.append(whitening_filter)
+
+    rec_filt = (Wedge, CTF)
+    needs_reconstruction = sum(type(x) in rec_filt for x in template_filter)
+    if needs_reconstruction > 0 and args.reconstruction_filter is None:
+        warnings.warn(
+            "Consider using a --reconstruction_filter such as 'ram-lak' or 'ramp' "
+            "to avoid artifacts from reconstruction using weighted backprojection."
+        )
+
+    template_filter = sorted(
+        template_filter, key=lambda x: type(x) in rec_filt, reverse=True
+    )
+    if needs_reconstruction > 0:
+        relevant_filters = [x for x in template_filter if type(x) in rec_filt]
+        if len(relevant_filters) == 0:
+            raise ValueError("Filters require ")
+
+        reconstruction_filter = ReconstructFromTilt(
+            reconstruction_filter=args.reconstruction_filter,
+            interpolation_order=args.reconstruction_interpolation_order,
+            angles=relevant_filters[0].angles,
+            opening_axis=args.wedge_axes[0],
+            tilt_axis=args.wedge_axes[1],
+        )
+        template_filter.insert(needs_reconstruction, reconstruction_filter)
+
+    template_filter = Compose(template_filter) if len(template_filter) else None
+    target_filter = Compose(target_filter) if len(target_filter) else None
+    if args.no_filter_target:
+        target_filter = None
+
+    return template_filter, target_filter
+
+
+def setup_projection_filter(args, template: Density, target: Density) -> Tuple[Compose, Compose]:
+    template_filter, target_filter = [], []
+
+    wedge = None
+    if args.tilt_angles is not None:
+        try:
+            wedge = Wedge.from_file(args.tilt_angles)
+            wedge.weight_type = args.tilt_weighting
+        except (FileNotFoundError, AttributeError):
+            raise ValueError(
+                "Projection matching angles need to be specified via angles file."
+            )
+        wedge.opening_axis = args.wedge_axes[0]
+        wedge.tilt_axis = args.wedge_axes[1]
+        template_filter.append(wedge)
+
+    args.ctf_file is not None
+    if args.ctf_file is not None or args.defocus is not None:
+        try:
+            ctf = CTF.from_file(args.ctf_file)
+            if (len(ctf.angles) == 0) and wedge is None:
+                raise ValueError(
+                    "You requested to specify the CTF per tilt, but did not specify "
+                    "tilt angles via --tilt_angles or --ctf_file (Warp/M XML format). "
+                )
+            if len(ctf.angles) == 0:
+                ctf.angles = wedge.angles
+
+            n_tilts_ctfs, n_tils_angles = len(ctf.defocus_x), len(wedge.angles)
+            if (n_tilts_ctfs != n_tils_angles) and isinstance(wedge, Wedge):
+                raise ValueError(
+                    f"CTF file contains {n_tilts_ctfs} tilt, but match_template "
+                    f"recieved {n_tils_angles} tilt angles. Expected one angle "
+                    "per tilt."
+                )
+
+        except (FileNotFoundError, AttributeError):
+            ctf = CTF(
+                defocus_x=args.defocus,
+                phase_shift=args.phase_shift,
+                angles=wedge.angles
+            )
+
+        ctf.opening_axis, ctf.tilt_axis = args.wedge_axes
+        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
+        template_filter.append(ctf)
+
+    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 = BandPass(
+            angles=wedge.angles,
+            use_gaussian=args.no_pass_smooth,
+            lowpass=lowpass,
+            highpass=highpass,
+            sampling_rate=template.sampling_rate,
+        )
+        template_filter.append(bandpass)
+        target_filter.append(bandpass)
+
+    if args.whiten_spectrum:
+        whitening_filter = LinearWhiteningFilter()
+        template_filter.append(whitening_filter)
+        target_filter.append(whitening_filter)
+
+    template_filter.append(ShiftFourier())
+    if len(target_filter):
+        target_filter.append(ShiftFourier())
+    template_filter = Compose(template_filter) if len(template_filter) else None
+    target_filter = Compose(target_filter) if len(target_filter) else None
+    if args.no_filter_target:
+        target_filter = None
+
+    return template_filter, target_filter
+
+
+def _format_sampling(arr, decimals: int = 2):
+    return tuple(round(float(x), decimals) for x in arr)
+
+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",
+        "--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",
+        "--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",
+        "--invert-target-contrast",
+        dest="invert_target_contrast",
+        action="store_true",
+        default=False,
+        help="Invert the target's contrast for cases where templates to-be-matched have "
+        "negative values, e.g. tomograms.",
+    )
+    io_group.add_argument(
+        "--scramble_phases",
+        "--scramble-phases",
+        dest="scramble_phases",
+        action="store_true",
+        default=False,
+        help="Phase scramble the template to generate a noise score background.",
+    )
+
+    sampling_group = parser.add_argument_group("Sampling")
+    sampling_group.add_argument(
+        "--orientations",
+        dest="orientations",
+        default=None,
+        required=False,
+        help="Path to a file readable via Orientations.from_file containing "
+        "translations and rotations of candidate peaks to refine.",
+    )
+    sampling_group.add_argument(
+        "--orientations_scaling",
+        "--orientations-scaling",
+        required=False,
+        type=float,
+        default=1.0,
+        help="Scaling factor to map candidate translations onto the target. "
+        "Assuming coordinates are in Å and target sampling rate are 3Å/voxel, "
+        "the corresponding orientations_scaling would be 3.",
+    )
+    sampling_group.add_argument(
+        "--orientations_cone",
+        "--orientations-cone",
+        required=False,
+        type=float,
+        default=20.0,
+        help="Accept orientations within specified cone angle of each orientation.",
+    )
+    sampling_group.add_argument(
+        "--orientations_uncertainty",
+        "--orientations-uncertainty",
+        required=False,
+        type=str,
+        default="10",
+        help="Accept translations within the specified radius of each orientation. "
+        "Can be a single value or comma-separated string for per-axis uncertainty.",
+    )
+
+    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",
+        "--angular_sampling",
+        "--angular-sampling",
+        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",
+        "--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_exclusive.add_argument(
+        "--particle_diameter",
+        "--particle-diameter",
+        dest="particle_diameter",
+        type=check_positive,
+        default=None,
+        help="Particle diameter in units of sampling rate.",
+    )
+    angular_group.add_argument(
+        "--cone_axis",
+        "--cone-axis",
+        dest="cone_axis",
+        type=check_positive,
+        default=2,
+        help="Principal axis to build cone around.",
+    )
+    angular_group.add_argument(
+        "--invert_cone",
+        "--invert-cone",
+        dest="invert_cone",
+        action="store_true",
+        help="Invert cone handedness direction from up to down.",
+    )
+    angular_group.add_argument(
+        "--cone_sampling",
+        "--cone-sampling",
+        dest="cone_sampling",
+        type=check_positive,
+        default=None,
+        help="Sampling rate of the cone in degrees.",
+    )
+    angular_group.add_argument(
+        "--axis_angle",
+        "--axis-angle",
+        dest="axis_angle",
+        type=check_positive,
+        default=360.0,
+        required=False,
+        help="Sampling angle along the principal axis of the cone.",
+    )
+    angular_group.add_argument(
+        "--axis_sampling",
+        "--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",
+        "--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",
+        "--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",
+        "--use-gpu",
+        dest="use_gpu",
+        action="store_true",
+        default=False,
+        help="Whether to perform computations on the GPU.",
+    )
+    computation_group.add_argument(
+        "--gpu_indices",
+        "--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(
+        "--memory",
+        dest="memory",
+        required=False,
+        type=int,
+        default=None,
+        help="Amount of memory that can be used in bytes.",
+    )
+    computation_group.add_argument(
+        "--memory_scaling",
+        "--memory-scaling",
+        dest="memory_scaling",
+        required=False,
+        type=float,
+        default=0.85,
+        help="Fraction of available memory to be used. Ignored if --memory is set.",
+    )
+    computation_group.add_argument(
+        "--temp_directory",
+        "--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=be._backend_name,
+        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",
+        "--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",
+        "--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. "
+        "Defaults to unit of sampling_rate, e.g., 40 Angstrom.",
+    )
+    filter_group.add_argument(
+        "--whiten_spectrum",
+        "--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",
+        "--wedge-axes",
+        dest="wedge_axes",
+        type=str,
+        required=False,
+        default="2,0",
+        help="Indices of projection (wedge opening) and tilt axis, e.g., '2,0' "
+        "for the typical projection over z and tilting over the x-axis.",
+    )
+    filter_group.add_argument(
+        "--tilt_angles",
+        "--tilt-angles",
+        dest="tilt_angles",
+        type=str,
+        required=False,
+        default=None,
+        help="Path to a file specifying tilt angles. This can be a Warp/M XML file, "
+        "a tomostar STAR file, a tab-separated file with column name 'angles', or a "
+        "single column file without header. Exposure will be taken from the input file "
+        ", if you are using a tab-separated file, the column names 'angles' and "
+        "'weights' need to be present. It is also possible to specify a continuous "
+        "wedge mask using e.g., -50,45.",
+    )
+    filter_group.add_argument(
+        "--tilt_weighting",
+        "--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",
+        "--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",
+        "--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",
+        "--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",
+        "--ctf-file",
+        dest="ctf_file",
+        type=str,
+        required=False,
+        default=None,
+        help="Path to a file with CTF parameters. This can be a Warp/M XML file "
+        "a GCTF/Relion STAR file, or the output of CTFFIND4. If the file does not "
+        "specify tilt angles, the angles specified with --tilt_angles are used.",
+    )
+    ctf_group.add_argument(
+        "--defocus",
+        dest="defocus",
+        type=float,
+        required=False,
+        default=None,
+        help="Defocus in units of sampling rate (typically Ångstrom), e.g., 30000 "
+        "for a defocus of 3 micrometer. Superseded by --ctf_file.",
+    )
+    ctf_group.add_argument(
+        "--phase_shift",
+        "--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",
+        "--acceleration-voltage",
+        dest="acceleration_voltage",
+        type=float,
+        required=False,
+        default=300,
+        help="Acceleration voltage in kV.",
+    )
+    ctf_group.add_argument(
+        "--spherical_aberration",
+        "--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",
+        "--amplitude-contrast",
+        dest="amplitude_contrast",
+        type=float,
+        required=False,
+        default=0.07,
+        help="Amplitude contrast.",
+    )
+    ctf_group.add_argument(
+        "--no_flip_phase",
+        "--no-flip-phase",
+        dest="no_flip_phase",
+        action="store_false",
+        required=False,
+        help="Do not perform phase-flipping CTF correction.",
+    )
+    ctf_group.add_argument(
+        "--correct_defocus_gradient",
+        "--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(
+        "--no_centering",
+        "--no-centering",
+        dest="no_centering",
+        action="store_true",
+        help="Assumes the template is already centered and omits centering.",
+    )
+    performance_group.add_argument(
+        "--pad_edges",
+        "--pad-edges",
+        dest="pad_edges",
+        action="store_true",
+        default=False,
+        help="Whether to pad the edges of the target. Useful if the target does not "
+        "a well-defined bounding box. Defaults to True if splitting is required.",
+    )
+    performance_group.add_argument(
+        "--pad_filter",
+        "--pad-filter",
+        dest="pad_filter",
+        action="store_true",
+        default=False,
+        help="Pads the filter to the shape of the target. Particularly useful for fast "
+        "oscilating filters to avoid aliasing effects.",
+    )
+    performance_group.add_argument(
+        "--interpolation_order",
+        "--interpolation-order",
+        dest="interpolation_order",
+        required=False,
+        type=int,
+        default=None,
+        help="Spline interpolation used for rotations.",
+    )
+    performance_group.add_argument(
+        "--use_mixed_precision",
+        "--use-mixed-precision",
+        dest="use_mixed_precision",
+        action="store_true",
+        default=False,
+        help="Use float16 for real values operations where possible. Not supported "
+        "for jax backend.",
+    )
+    performance_group.add_argument(
+        "--use_memmap",
+        "--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",
+        "--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",
+        "--peak-calling",
+        dest="peak_calling",
+        action="store_true",
+        default=False,
+        help="Perform peak calling instead of score aggregation.",
+    )
+    analyzer_group.add_argument(
+        "--num_peaks",
+        "--num-peaks",
+        dest="num_peaks",
+        default=1000,
+        help="Number of peaks to call, 1000 by default.",
+    )
+
+    projection_group = parser.add_argument_group("Projection")
+    projection_group.add_argument(
+        "--projection_matching",
+        "--projection-matching",
+        dest="projection_matching",
+        action="store_true",
+        help="Perform projection matching instead of nD-nD matching.",
+    )
+    projection_group.add_argument(
+        "--extract_tilts",
+        "--extract-tilts",
+        dest="extract_tilts",
+        action="store_true",
+        help="Assume target is a reconstruction we have to extract tilts from. If the "
+        "target is a tilt series already, this flag can be omitted.",
+    )
+
+
+    args = parser.parse_args()
+    args.version = __version__
+
+    if args.interpolation_order is None:
+        args.interpolation_order = 3
+        if args.backend in ("jax", "pytorch"):
+            args.interpolation_order = 1
+
+    if args.interpolation_order < 0:
+        args.interpolation_order = None
+
+    if args.temp_directory is None:
+        args.temp_directory = gettempdir()
+
+    os.environ["TMPDIR"] = args.temp_directory
+    if args.score not in MATCHING_EXHAUSTIVE_REGISTER:
+        raise ValueError(
+            f"score has to be one of {', '.join(MATCHING_EXHAUSTIVE_REGISTER.keys())}"
+        )
+
+    if args.gpu_indices is not None:
+        os.environ["CUDA_VISIBLE_DEVICES"] = args.gpu_indices
+
+    if args.use_gpu:
+        warnings.warn(
+            "The use_gpu flag is no longer required and automatically "
+            "determined based on the selected backend."
+        )
+
+    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.extract_tilts:
+        args.projection_matching = True
+
+    if args.extract_tilts and args.tilt_angles is None:
+        raise ValueError("Need to specify --tilt_angles when --extract_tilts is set.")
+
+    if args.projection_matching and args.backend != "jax":
+        raise ValueError("Projection matching is only supported for --backend jax.")
+
+    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(","))
+
+    if args.orientations is not None:
+        orientations = Orientations.from_file(args.orientations)
+        orientations.translations = np.divide(
+            orientations.translations, args.orientations_scaling
+        )
+        args.orientations = orientations
+
+    return args
+
+
+def main():
+    args = parse_args()
+    print_entry()
+
+    target = Density.from_file(args.target, use_memmap=True)
+    if args.extract_tilts:
+        target = extract_tilts(args=args, target=target)
+
+    try:
+        template = Density.from_file(args.template)
+    except Exception:
+        template = Density.from_structure(
+            filename_or_structure=args.template,
+            sampling_rate=target.sampling_rate,
+        )
+
+    if target.sampling_rate.size == template.sampling_rate.size:
+        if not np.allclose(
+            np.round(target.sampling_rate, 2), np.round(template.sampling_rate, 2)
+        ) and not args.projection_matching:
+            print(
+                "Target and template sampling rate do not match. "
+                "Make sure this is intended."
+            )
+
+    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
+    print_block(
+        name="Target",
+        data={
+            "Initial Shape": initial_shape,
+            "Sampling Rate": _format_sampling(target.sampling_rate),
+            "Final Shape": target.shape,
+        },
+    )
+
+    if target_mask:
+        print_block(
+            name="Target Mask",
+            data={
+                "Initial Shape": initial_shape,
+                "Sampling Rate": _format_sampling(target_mask.sampling_rate),
+                "Final Shape": target_mask.shape,
+            },
+        )
+
+    initial_shape = template.shape
+    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": _format_sampling(template.sampling_rate),
+            "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": _format_sampling(template_mask.sampling_rate),
+            "Final Shape": template_mask.shape,
+        },
+    )
+    print("\n" + "-" * 80)
+
+    if args.scramble_phases:
+        template.data = scramble_phases(
+            template.data, noise_proportion=1.0, normalize_power=False
+        )
+
+    callback_class = MaxScoreOverRotations
+    if args.peak_calling:
+        callback_class = PeakCallerMaximumFilter
+
+    if args.orientations is not None:
+        callback_class = MaxScoreOverRotationsConstrained
+
+    # Determine suitable backend for the selected operation
+    available_backends = be.available_backends()
+    if args.backend not in available_backends:
+        raise ValueError("Requested backend is not available.")
+    if args.backend == "jax" and callback_class != MaxScoreOverRotations:
+        raise ValueError(
+            "Jax backend only supports the MaxScoreOverRotations analyzer."
+        )
+
+    if args.interpolation_order == 3 and args.backend in ("jax", "pytorch"):
+        warnings.warn(
+            "Jax and pytorch do not support interpolation order 3, setting it to 1."
+        )
+        args.interpolation_order = 1
+
+    if args.backend in ("pytorch", "cupy", "jax"):
+        gpu_devices = os.environ.get("CUDA_VISIBLE_DEVICES", None)
+        if gpu_devices is None:
+            warnings.warn(
+                "No GPU indices provided and CUDA_VISIBLE_DEVICES is not set. "
+                "Assuming device 0.",
+            )
+            os.environ["CUDA_VISIBLE_DEVICES"] = "0"
+
+        args.cores = len(os.environ["CUDA_VISIBLE_DEVICES"].split(","))
+        args.gpu_indices = [
+            int(x) for x in os.environ["CUDA_VISIBLE_DEVICES"].split(",")
+        ]
+
+    # Finally set the desired backend
+    device = "cuda"
+    be.change_backend(args.backend)
+    if args.backend in ("jax", "pytorch", "cupy"):
+        args.use_gpu = True
+
+    if args.backend == "pytorch":
+        try:
+            be.change_backend("pytorch", device=device)
+            # Trigger exception if not compiled with device
+            be.get_available_memory()
+        except Exception as e:
+            print(e)
+            device = "cpu"
+            args.use_gpu = True
+            be.change_backend("pytorch", device=device)
+
+    if args.use_mixed_precision:
+        be.change_backend(
+            backend_name=args.backend,
+            float_dtype=be._array_backend.float16,
+            complex_dtype=be._array_backend.complex64,
+            int_dtype=be._array_backend.int16,
+            device=device,
+        )
+
+    available_memory = be.get_available_memory() * be.device_count()
+    if args.memory is None:
+        args.memory = int(args.memory_scaling * available_memory)
+
+    if args.orientations_uncertainty is not None:
+        args.orientations_uncertainty = tuple(
+            int(x) for x in args.orientations_uncertainty.split(",")
+        )
+
+    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),
+    )
+
+    setup_filt = setup_filter
+    if args.projection_matching:
+        setup_filt = setup_projection_filter
+        matching_data.set_matching_dimension(target_dim=0)
+
+    matching_setup, matching_score = MATCHING_EXHAUSTIVE_REGISTER[args.score]
+    matching_data.template_filter, matching_data.target_filter = setup_filt(
+        args, template, target
+    )
+
+    splits, schedule = compute_schedule(args, matching_data, callback_class)
+
+    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 Target Edges": args.pad_edges,
+        "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,
+        "Extend Filter Grid": args.pad_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,
+        "num_peaks": args.num_peaks,
+        "min_distance": max(template.shape) // 3,
+        "use_memmap": args.use_memmap,
+    }
+    if args.orientations is not None:
+        analyzer_args["reference"] = (0, 0, 1)
+        analyzer_args["cone_angle"] = args.orientations_cone
+        analyzer_args["acceptance_radius"] = args.orientations_uncertainty
+        analyzer_args["positions"] = args.orientations.translations
+        analyzer_args["rotations"] = euler_to_rotationmatrix(
+            args.orientations.rotations
+        )
+
+    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_edges,
+        pad_template_filter=args.pad_filter,
+        interpolation_order=args.interpolation_order,
+        match_projection=args.projection_matching
+    )
+
+    candidates = list(candidates) if candidates is not None else []
+    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()