pytme 0.1.9__cp311-cp311-macosx_14_0_arm64.whl → 0.2.0b0__cp311-cp311-macosx_14_0_arm64.whl

pytme-0.1.9.data/scripts/postprocess.py

@@ -1,625 +0,0 @@
-#!python
-""" CLI to simplify analysing the output of match_template.py.
-
-    Copyright (c) 2023 European Molecular Biology Laboratory
-
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
-"""
-from os import getcwd
-from os.path import join
-import argparse
-from sys import exit
-from typing import List, Tuple
-from os.path import splitext
-from dataclasses import dataclass
-
-import numpy as np
-from scipy.spatial.transform import Rotation
-from numpy.typing import NDArray
-
-from tme import Density, Structure
-from tme.analyzer import (
-    PeakCallerSort,
-    PeakCallerMaximumFilter,
-    PeakCallerFast,
-    PeakCallerRecursiveMasking,
-    PeakCallerScipy,
-)
-from tme.matching_utils import (
-    load_pickle,
-    euler_to_rotationmatrix,
-    euler_from_rotationmatrix,
-    centered_mask,
-)
-
-PEAK_CALLERS = {
-    "PeakCallerSort": PeakCallerSort,
-    "PeakCallerMaximumFilter": PeakCallerMaximumFilter,
-    "PeakCallerFast": PeakCallerFast,
-    "PeakCallerRecursiveMasking": PeakCallerRecursiveMasking,
-    "PeakCallerScipy": PeakCallerScipy,
-}
-
-
-def parse_args():
-    parser = argparse.ArgumentParser(
-        description="Peak Calling for Template Matching Outputs"
-    )
-    parser.add_argument(
-        "--input_file",
-        required=True,
-        help="Path to the output of match_template.py.",
-    )
-    parser.add_argument(
-        "--output_prefix",
-        required=True,
-        help="Prefix for the output file name. Extension depends on output_format.",
-    )
-    parser.add_argument(
-        "--number_of_peaks",
-        type=int,
-        default=1000,
-        help="Number of peaks to consider. Note, this is the number of called peaks "
-        ", subject to min_distance and min_boundary_distance filtering. Therefore, the "
-        "returned number of peaks will be at most equal to number_of_peaks. "
-        "Ignored when --orientations is provided.",
-    )
-    parser.add_argument(
-        "--min_distance",
-        type=int,
-        default=5,
-        help="Minimum distance between peaks. Ignored when --orientations is provided.",
-    )
-    parser.add_argument(
-        "--min_boundary_distance",
-        type=int,
-        default=0,
-        help="Minimum distance from target boundaries. Ignored when --orientations "
-        "is provided.",
-    )
-    parser.add_argument(
-        "--mask_edges",
-        action="store_true",
-        default=False,
-        help="Whether to mask edges of the input score array according to the template shape."
-        "Uses twice the value of --min_boundary_distance if boht are provided.",
-    )
-    parser.add_argument(
-        "--wedge_mask",
-        type=str,
-        default=None,
-        help="Path to Fourier space mask. Only considered if output_format is relion.",
-    )
-    parser.add_argument(
-        "--peak_caller",
-        choices=list(PEAK_CALLERS.keys()),
-        default="PeakCallerScipy",
-        help="Peak caller to use for analysis. Ignored if input_file contains peaks or when "
-        "--orientations is provided.",
-    )
-    parser.add_argument(
-        "--orientations",
-        default=None,
-        help="Path to orientations file to overwrite orientations computed from"
-        " match_template.py output.",
-    )
-    parser.add_argument(
-        "--output_format",
-        choices=["orientations", "alignment", "extraction", "relion"],
-        default="orientations",
-        help="Choose the output format. Available formats are: "
-        "orientations (translation, rotation, and score), "
-        "alignment (aligned template to target based on orientations), "
-        "extraction (extract regions around peaks from targets, i.e. subtomograms). "
-        "relion (perform extraction step and generate corresponding star files).",
-    )
-    args = parser.parse_args()
-
-    return args
-
-
-@dataclass
-class Orientations:
-    #: Return a numpy array with translations of each orientation (n x d).
-    translations: np.ndarray
-
-    #: Return a numpy array with euler angles of each orientation in zxy format (n x d).
-    rotations: np.ndarray
-
-    #: Return a numpy array with the score of each orientation (n, ).
-    scores: np.ndarray
-
-    #: Return a numpy array with additional orientation details (n, ).
-    details: np.ndarray
-
-    def __iter__(self) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
-        """
-        Iterate over the current class instance. Each iteration returns a orientation
-        defined by its translation, rotation, score and additional detail.
-
-        Yields
-        ------
-        Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]
-            A tuple of arrays defining the given orientation.
-        """
-        yield from zip(self.translations, self.rotations, self.scores, self.details)
-
-    def __getitem__(self, indices: List[int]) -> "Orientations":
-        """
-        Retrieve a subset of orientations based on the provided indices.
-
-        Parameters
-        ----------
-        indices : List[int]
-            A list of indices specifying the orientations to be retrieved.
-
-        Returns
-        -------
-        :py:class:`Orientations`
-            A new :py:class:`Orientations`instance containing only the selected orientations.
-        """
-        indices = np.asarray(indices)
-        attributes = (
-            "translations",
-            "rotations",
-            "scores",
-            "details",
-        )
-        kwargs = {attr: getattr(self, attr)[indices] for attr in attributes}
-        return self.__class__(**kwargs)
-
-    def to_file(self, filename: str, file_format: type, **kwargs) -> None:
-        """
-        Save the current class instance to a file in the specified format.
-
-        Parameters
-        ----------
-        filename : str
-            The name of the file where the orientations will be saved.
-        file_format : type
-            The format in which to save the orientations. Supported formats are 'text' and 'relion'.
-        **kwargs : dict
-            Additional keyword arguments specific to the file format.
-
-        Raises
-        ------
-        ValueError
-            If an unsupported file format is specified.
-        """
-        mapping = {
-            "text": self._to_text,
-            "relion": self._to_relion_star,
-        }
-
-        func = mapping.get(file_format, None)
-        if func is None:
-            raise ValueError(
-                f"{file_format} not implemented. Supported are {','.join(mapping.keys())}."
-            )
-
-        return func(filename=filename, **kwargs)
-
-    def _to_text(self, filename: str) -> None:
-        """
-        Save orientations in a text file format.
-
-        Parameters
-        ----------
-        filename : str
-            The name of the file to save the orientations.
-
-        Notes
-        -----
-        The file is saved with a header specifying each column: z, y, x, euler_z,
-        euler_y, euler_x, score, detail. Each row in the file corresponds to an orientation.
-        """
-        header = "\t".join(
-            ["z", "y", "x", "euler_z", "euler_y", "euler_x", "score", "detail"]
-        )
-        with open(filename, mode="w", encoding="utf-8") as ofile:
-            _ = ofile.write(f"{header}\n")
-            for translation, angles, score, detail in self:
-                translation_string = "\t".join([str(x) for x in translation])
-                angle_string = "\t".join([str(x) for x in angles])
-                _ = ofile.write(
-                    f"{translation_string}\t{angle_string}\t{score}\t{detail}\n"
-                )
-        return None
-
-    def _to_relion_star(
-        self,
-        filename: str,
-        name_prefix: str = None,
-        ctf_image: str = None,
-        sampling_rate: float = 1.0,
-        subtomogram_size: int = 0,
-    ) -> None:
-        """
-        Save orientations in RELION's STAR file format.
-
-        Parameters
-        ----------
-        filename : str
-            The name of the file to save the orientations.
-        name_prefix : str, optional
-            A prefix to add to the image names in the STAR file.
-        ctf_image : str, optional
-            Path to CTF or wedge mask RELION.
-        sampling_rate : float, optional
-            Subtomogram sampling rate in angstrom per voxel
-        subtomogram_size : int, optional
-            Size of the square shaped subtomogram.
-
-        Notes
-        -----
-        The file is saved with a standard header used in RELION STAR files.
-        Each row in the file corresponds to an orientation.
-        """
-        optics_header = [
-            "# version 30001",
-            "data_optics",
-            "",
-            "loop_",
-            "_rlnOpticsGroup",
-            "_rlnOpticsGroupName",
-            "_rlnSphericalAberration",
-            "_rlnVoltage",
-            "_rlnImageSize",
-            "_rlnImageDimensionality",
-            "_rlnImagePixelSize",
-        ]
-        optics_data = [
-            "1",
-            "opticsGroup1",
-            "2.700000",
-            "300.000000",
-            str(int(subtomogram_size)),
-            "3",
-            str(float(sampling_rate)),
-        ]
-        optics_header = "\n".join(optics_header)
-        optics_data = "\t".join(optics_data)
-
-        header = [
-            "data_particles",
-            "",
-            "loop_",
-            "_rlnCoordinateX",
-            "_rlnCoordinateY",
-            "_rlnCoordinateZ",
-            "_rlnImageName",
-            "_rlnAngleRot",
-            "_rlnAngleTilt",
-            "_rlnAnglePsi",
-            "_rlnOpticsGroup",
-        ]
-        if ctf_image is not None:
-            header.append("_rlnCtfImage")
-
-        ctf_image = "" if ctf_image is None else f"\t{ctf_image}"
-
-        header = "\n".join(header)
-        name_prefix = "" if name_prefix is None else name_prefix
-
-        with open(filename, mode="w", encoding="utf-8") as ofile:
-            _ = ofile.write(f"{optics_header}\n")
-            _ = ofile.write(f"{optics_data}\n")
-
-            _ = ofile.write("\n# version 30001\n")
-            _ = ofile.write(f"{header}\n")
-
-            # pyTME uses a zyx data layout
-            for index, (translation, rotation, score, detail) in enumerate(self):
-                rotation = Rotation.from_euler("zyx", rotation, degrees=True)
-                rotation = rotation.as_euler(seq="xyx", degrees=True)
-
-                translation_string = "\t".join([str(x) for x in translation][::-1])
-                angle_string = "\t".join([str(x) for x in rotation])
-                name = f"{name_prefix}_{index}.mrc"
-                _ = ofile.write(
-                    f"{translation_string}\t{name}\t{angle_string}\t1{ctf_image}\n"
-                )
-
-        return None
-
-    @classmethod
-    def from_file(cls, filename: str, file_format: type, **kwargs) -> "Orientations":
-        """
-        Create an instance of :py:class:`Orientations` from a file.
-
-        Parameters
-        ----------
-        filename : str
-            The name of the file from which to read the orientations.
-        file_format : type
-            The format of the file. Currently, only 'text' format is supported.
-        **kwargs : dict
-            Additional keyword arguments specific to the file format.
-
-        Returns
-        -------
-        :py:class:`Orientations`
-            An instance of :py:class:`Orientations` populated with data from the file.
-
-        Raises
-        ------
-        ValueError
-            If an unsupported file format is specified.
-        """
-        mapping = {
-            "text": cls._from_text,
-        }
-
-        func = mapping.get(file_format, None)
-        if func is None:
-            raise ValueError(
-                f"{file_format} not implemented. Supported are {','.join(mapping.keys())}."
-            )
-
-        translations, rotations, scores, details, *_ = func(filename=filename, **kwargs)
-        return cls(
-            translations=translations,
-            rotations=rotations,
-            scores=scores,
-            details=details,
-        )
-
-    @staticmethod
-    def _from_text(
-        filename: str,
-    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
-        """
-        Read orientations from a text file.
-
-        Parameters
-        ----------
-        filename : str
-            The name of the file from which to read the orientations.
-
-        Returns
-        -------
-        Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]
-            A tuple containing numpy arrays for translations, rotations, scores,
-            and details.
-
-        Notes
-        -----
-        The text file is expected to have a header and data in columns corresponding to
-        z, y, x, euler_z, euler_y, euler_x, score, detail.
-        """
-        with open(filename, mode="r", encoding="utf-8") as infile:
-            data = [x.strip().split("\t") for x in infile.read().split("\n")]
-            _ = data.pop(0)
-
-        translation, rotation, score, detail = [], [], [], []
-        for candidate in data:
-            if len(candidate) <= 1:
-                continue
-            if len(candidate) != 8:
-                candidate.append(-1)
-
-            candidate = [float(x) for x in candidate]
-            translation.append((candidate[0], candidate[1], candidate[2]))
-            rotation.append((candidate[3], candidate[4], candidate[5]))
-            score.append(candidate[6])
-            detail.append(candidate[7])
-
-        translation = np.vstack(translation).astype(int)
-        rotation = np.vstack(rotation).astype(float)
-        score = np.array(score).astype(float)
-        detail = np.array(detail).astype(float)
-
-        return translation, rotation, score, detail
-
-
-def load_template(filepath: str, sampling_rate: NDArray) -> "Density":
-    try:
-        template = Density.from_file(filepath)
-        template, _ = template.centered(0)
-        center_of_mass = template.center_of_mass(template.data)
-    except ValueError:
-        template = Structure.from_file(filepath)
-        center_of_mass = template.center_of_mass()[::-1]
-        template = Density.from_structure(template, sampling_rate=sampling_rate)
-
-    return template, center_of_mass
-
-
-def main():
-    args = parse_args()
-    data = load_pickle(args.input_file)
-
-    meta = data[-1]
-    target_origin, _, sampling_rate, cli_args = meta
-
-    if args.orientations is not None:
-        orientations = Orientations.from_file(
-            filename=args.orientations, file_format="text"
-        )
-
-    else:
-        translations, rotations, scores, details = [], [], [], []
-        # Output is MaxScoreOverRotations
-        if data[0].ndim == data[2].ndim:
-            scores, offset, rotation_array, rotation_mapping, meta = data
-            if args.mask_edges:
-                template, center_of_mass = load_template(
-                    cli_args.template, sampling_rate=sampling_rate
-                )
-                if not cli_args.no_centering:
-                    template, *_ = template.centered(0)
-                mask_size = template.shape
-                if args.min_boundary_distance > 0:
-                    mask_size = 2 * args.min_boundary_distance
-                scores = centered_mask(scores, np.subtract(scores.shape, mask_size) + 1)
-
-            peak_caller = PEAK_CALLERS[args.peak_caller](
-                number_of_peaks=args.number_of_peaks,
-                min_distance=args.min_distance,
-                min_boundary_distance=args.min_boundary_distance,
-            )
-            peak_caller(scores, rotation_matrix=np.eye(3))
-            candidates = peak_caller.merge(
-                candidates=[tuple(peak_caller)],
-                number_of_peaks=args.number_of_peaks,
-                min_distance=args.min_distance,
-                min_boundary_distance=args.min_boundary_distance,
-            )
-            if len(candidates) == 0:
-                exit(
-                    "Found no peaks. Try reducing min_distance or min_boundary_distance."
-                )
-
-            for translation, _, score, detail in zip(*candidates):
-                rotations.append(rotation_mapping[rotation_array[tuple(translation)]])
-
-        else:
-            candidates = data
-            translation, rotation, score, detail, *_ = data
-            for i in range(translation.shape[0]):
-                rotations.append(euler_from_rotationmatrix(rotation[i]))
-
-        rotations = np.vstack(rotations).astype(float)
-        translations, scores, details = candidates[0], candidates[2], candidates[3]
-        orientations = Orientations(
-            translations=translations,
-            rotations=rotations,
-            scores=scores,
-            details=details,
-        )
-
-    if args.output_format == "orientations":
-        orientations.to_file(filename=f"{args.output_prefix}.tsv", file_format="text")
-        exit(0)
-
-    _, template_extension = splitext(cli_args.template)
-    template, center_of_mass = load_template(
-        filepath=cli_args.template, sampling_rate=sampling_rate
-    )
-    template_is_density, index = isinstance(template, Density), 0
-
-    if args.output_format == "relion":
-        new_shape = np.add(template.shape, np.mod(template.shape, 2))
-        new_shape = np.repeat(new_shape.max(), new_shape.size).astype(int)
-        print(f"Padding template from {template.shape} to {new_shape} for RELION.")
-        template.pad(new_shape)
-
-    if args.output_format in ("extraction", "relion"):
-        target = Density.from_file(cli_args.target)
-
-        if not np.all(np.divide(target.shape, template.shape) > 2):
-            print(
-                "Target might be too small relative to template to extract"
-                " meaningful particles."
-                f" Target : {target.shape}, template : {template.shape}."
-            )
-
-        peaks = orientations.translations.astype(int)
-        max_shape = np.max(template.shape).astype(int)
-        half_shape = max_shape // 2
-
-        left_pad = half_shape
-        right_pad = np.add(half_shape, max_shape % 2)
-        starts = np.subtract(peaks, left_pad)
-        stops = np.add(peaks, right_pad)
-
-        candidate_starts = np.maximum(starts, 0).astype(int)
-        candidate_stops = np.minimum(stops, target.shape).astype(int)
-        keep_peaks = (
-            np.sum(
-                np.multiply(starts == candidate_starts, stops == candidate_stops),
-                axis=1,
-            )
-            == peaks.shape[1]
-        )
-
-        orientations = orientations[keep_peaks]
-        working_directory = getcwd()
-        if args.output_format == "relion":
-            orientations.to_file(
-                filename=f"{args.output_prefix}.star",
-                file_format="relion",
-                name_prefix=join(working_directory, args.output_prefix),
-                ctf_image=args.wedge_mask,
-                sampling_rate=target.sampling_rate.max(),
-                subtomogram_size=template.shape[0],
-            )
-
-        peaks = peaks[keep_peaks,]
-        starts = starts[keep_peaks,]
-        stops = stops[keep_peaks,]
-        candidate_starts = candidate_starts[keep_peaks,]
-        candidate_stops = candidate_stops[keep_peaks,]
-
-        if not len(peaks):
-            print(
-                "No peak remaining after filtering. Started with"
-                f" {orientations.translations.shape[0]} filtered to {peaks.shape[0]}."
-                " Consider reducing min_distance, increase num_peaks or use"
-                " a different peak caller."
-            )
-            exit(-1)
-
-        observation_starts = np.subtract(candidate_starts, starts).astype(int)
-        observation_stops = np.subtract(np.add(max_shape, candidate_stops), stops)
-        observation_stops = observation_stops.astype(int)
-
-        candidate_slices = [
-            tuple(slice(s, e) for s, e in zip(start_row, stop_row))
-            for start_row, stop_row in zip(candidate_starts, candidate_stops)
-        ]
-
-        observation_slices = [
-            tuple(slice(s, e) for s, e in zip(start_row, stop_row))
-            for start_row, stop_row in zip(observation_starts, observation_stops)
-        ]
-        observations = np.zeros(
-            (len(candidate_slices), max_shape, max_shape, max_shape)
-        )
-
-        slices = zip(candidate_slices, observation_slices)
-        for idx, (cand_slice, obs_slice) in enumerate(slices):
-            observations[idx][:] = np.mean(target.data[cand_slice])
-            observations[idx][obs_slice] = target.data[cand_slice]
-
-        for index in range(observations.shape[0]):
-            out_density = Density(
-                data=observations[index],
-                sampling_rate=sampling_rate,
-                origin=candidate_starts[index] * sampling_rate,
-            )
-            # out_density.data = out_density.data * template_mask.data
-            out_density.to_file(
-                join(working_directory, f"{args.output_prefix}_{index}.mrc")
-            )
-
-        exit(0)
-
-    for translation, angles, *_ in orientations:
-        rotation_matrix = euler_to_rotationmatrix(angles)
-
-        if template_is_density:
-            translation = np.subtract(translation, center_of_mass)
-            transformed_template = template.rigid_transform(
-                rotation_matrix=rotation_matrix
-            )
-            new_origin = np.add(target_origin / sampling_rate, translation)
-            transformed_template.origin = np.multiply(new_origin, sampling_rate)
-        else:
-            new_center_of_mass = np.add(
-                np.multiply(translation, sampling_rate), target_origin
-            )
-            translation = np.subtract(new_center_of_mass, center_of_mass)
-            transformed_template = template.rigid_transform(
-                translation=translation[::-1],
-                rotation_matrix=rotation_matrix[::-1, ::-1],
-            )
-        # template_extension should contain the extension '.'
-        transformed_template.to_file(
-            f"{args.output_prefix}_{index}{template_extension}"
-        )
-        index += 1
-
-
-if __name__ == "__main__":
-    main()

pytme-0.1.9.dist-info/RECORD

@@ -1,61 +0,0 @@
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-pytme-0.1.9.data/scripts/match_template.py,sha256=moMpH8mLk42ZkW0vXzd_TMCWsTUKXohxuWrqHLh8lks,25743
-pytme-0.1.9.data/scripts/postprocess.py,sha256=MKyIgsXWRlO6cU8qGqe_tSSKIF2pNTRSuaDoyXZ22G8,21938
-pytme-0.1.9.data/scripts/preprocess.py,sha256=zog-l2Je-GeouJ6SnamOMuHgTn7fFPiGnO5X03y5qSY,2527
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-scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-scripts/estimate_ram_usage.py,sha256=rN7haobnHg3YcgGJIp81FNiCzy8-saJGeEurQlmQmNQ,2768
-scripts/match_template.py,sha256=dEvw9KDqgR7vZcIVn5Bld6FcRt_rp7nblybVuJhLYbs,25744
-scripts/postprocess.py,sha256=NDTo9qbnAzhxo_tbnR8oWlDrsflUGu-Sj4ULqOPix1U,21939
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-scripts/preprocessor_gui.py,sha256=E0F6quZnu32yZsBle38KDel5naHpC3Aci0uMCyo8DzY,29001
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