pytme 0.2.9.post1__cp311-cp311-macosx_15_0_arm64.whl → 0.3b0.post1__cp311-cp311-macosx_15_0_arm64.whl

tme/memory.py

@@ -1,8 +1,9 @@
-""" Compute memory consumption of template matching components.
+"""
+Compute memory consumption of template matching components.
 
-    Copyright (c) 2023 European Molecular Biology Laboratory
+Copyright (c) 2023 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 
 from abc import ABC, abstractmethod

tme/orientations.py

@@ -1,10 +1,11 @@
-#!python3
-""" Handle template matching orientations and conversion between formats.
+"""
+Handle template matching orientations and conversion between formats.
 
-    Copyright (c) 2024 European Molecular Biology Laboratory
+Copyright (c) 2024 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
+
 from typing import List, Tuple
 from dataclasses import dataclass
 from string import ascii_lowercase, ascii_uppercase
@@ -14,7 +15,7 @@ import numpy as np
 from .parser import StarParser
 from .matching_utils import compute_extraction_box
 
-# Exceeds available numpy dimensions for default installations.
+# Exceeds available numpy dimensions for default installations
 NAMES = ["x", "y", "z", *ascii_lowercase[:-3], *ascii_uppercase]
 
 
@@ -81,7 +82,7 @@ class Orientations:
         self.translations = np.array(self.translations).astype(np.float32)
         self.rotations = np.array(self.rotations).astype(np.float32)
         self.scores = np.array(self.scores).astype(np.float32)
-        self.details = np.array(self.details).astype(np.float32)
+        self.details = np.array(self.details)
         n_orientations = set(
             [
                 self.translations.shape[0],
@@ -324,6 +325,7 @@ class Orientations:
             "_rlnAngleRot",
             "_rlnAngleTilt",
             "_rlnAnglePsi",
+            "_rlnClassNumber",
         ]
         if source_path is not None:
             header.append("_rlnMicrographName")
@@ -339,6 +341,7 @@ class Orientations:
             for index, (translation, rotation, score, detail) in enumerate(self):
                 line = [str(x) for x in translation]
                 line.extend([str(x) for x in rotation])
+                line.extend([str(detail)])
 
                 if source_path is not None:
                     line.append(source_path)
@@ -489,9 +492,12 @@ class Orientations:
     def _from_star(
         cls, filename: str, delimiter: str = "\t"
     ) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
-        ret = StarParser(filename, delimiter=delimiter)
+        parser = StarParser(filename, delimiter=delimiter)
+
+        ret = parser.get("data_particles", None)
+        if ret is None:
+            ret = parser.get("data_", None)
 
-        ret = ret.get("data_particles", None)
         if ret is None:
             raise ValueError(f"No data_particles section found in {filename}.")
 
@@ -500,13 +506,20 @@ class Orientations:
         )
         translation = translation.astype(np.float32).T
 
+        default_angle = np.zeros(translation.shape[0], dtype=np.float32)
+        for x in ("_rlnAngleRot", "_rlnAngleTilt", "_rlnAnglePsi"):
+            if x not in ret:
+                ret[x] = default_angle
+
         rotation = np.vstack(
             (ret["_rlnAngleRot"], ret["_rlnAngleTilt"], ret["_rlnAnglePsi"])
         )
         rotation = rotation.astype(np.float32).T
 
         default = np.zeros(translation.shape[0])
-        return translation, rotation, default, default
+
+        scores = ret.get("_pytmeScore", default)
+        return translation, rotation, scores, default
 
     @staticmethod
     def _from_tbl(

tme/parser.py

@@ -1,8 +1,9 @@
-""" Implements parsers for atomic structure file formats.
+"""
+Implements parsers for atomic structure file formats.
 
-    Copyright (c) 2023 European Molecular Biology Laboratory
+Copyright (c) 2023 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 
 import re
@@ -15,7 +16,14 @@ from typing import List, Dict, Union
 
 import numpy as np
 
-__all__ = ["PDBParser", "MMCIFParser", "GROParser", "StarParser", "XMLParser"]
+__all__ = [
+    "PDBParser",
+    "MMCIFParser",
+    "GROParser",
+    "StarParser",
+    "XMLParser",
+    "MDOCParser",
+]
 
 
 class Parser(ABC):
@@ -84,6 +92,34 @@ class Parser(ABC):
         """
         return key in self._data
 
+    def __repr__(self) -> str:
+        """
+        String representation of the Parser showing available keys and their lengths.
+
+        Returns
+        -------
+        str
+            A formatted string showing each key and the length of its value.
+        """
+        if not self._data:
+            return f"{self.__class__.__name__}(empty)"
+
+        lines = [f"{self.__class__.__name__}:"]
+        try:
+            for key, value in sorted(self._data.items()):
+                if isinstance(value, (list, tuple)):
+                    lines.append(f"  {key}: length {len(value)}")
+                elif isinstance(value, dict):
+                    lines.append(f"  {key}: dict with {len(value)} keys")
+                elif isinstance(value, str):
+                    lines.append(f"  {key}: str")
+                else:
+                    lines.append(f"  {key}: {type(value).__name__}")
+        except Exception:
+            pass
+
+        return "\n".join(lines)
+
     def get(self, key, default=None):
         """
         Retrieve a value from the internal data using a given key. If the
@@ -247,19 +283,6 @@ class MMCIFParser(Parser):
     """
 
     def parse_input(self, lines: deque) -> Dict:
-        """
-        Parse a list of lines from an MMCIF file and convert the data into a dictionary.
-
-        Parameters
-        ----------
-        lines : deque of str
-            The lines of an MMCIF file to parse.
-
-        Returns
-        -------
-        dict
-            A dictionary containing the parsed data from the MMCIF file.
-        """
         lines = self._consolidate_strings(lines)
         blocks = self._split_in_blocks(lines)
         mmcif_dict = {}
@@ -448,21 +471,6 @@ class GROParser(Parser):
     """
 
     def parse_input(self, lines, **kwargs) -> Dict:
-        """
-        Parse a list of lines from a GRO file and convert the data into a dictionary.
-
-        Parameters
-        ----------
-        lines : deque of str
-            The lines of a GRO file to parse.
-        kwargs : Dict, optional
-            Optional keyword arguments.
-
-        Returns
-        -------
-        dict
-            A dictionary containing the parsed data from the GRO file.
-        """
         data = {
             "title": [],
             "num_atoms": [],
@@ -560,7 +568,7 @@ class StarParser(MMCIFParser):
     .. [1]  https://www.iucr.org/__data/assets/file/0013/11416/star.5.html
     """
 
-    def parse_input(self, lines: List[str], delimiter: str = "\t") -> Dict:
+    def parse_input(self, lines: List[str], delimiter: str = None) -> Dict:
         pattern = re.compile(r"\s*#.*")
 
         ret, category, block = {}, None, []
@@ -683,3 +691,76 @@ class XMLParser(Parser):
             pass
 
         return value_str
+
+
+class MDOCParser(Parser):
+    """
+    Convert MDOC file (SerialEM metadata) into a dictionary representation.
+
+    MDOC files contain global parameters and per-tilt metadata for cryo-ET
+    tilt series, with sections marked by [ZValue = N] for individual tilts.
+    """
+
+    def parse_input(self, lines: deque, **kwargs) -> Dict:
+        data = {}
+        global_params = {}
+        in_zvalue_section = False
+        zvalue_pattern = re.compile(r"\[ZValue\s*=\s*(\d+)\]")
+        section_pattern = re.compile(r"\[T\s*=\s*(.*?)\]")
+
+        if not lines:
+            return data
+
+        while lines:
+            line = lines.popleft().strip()
+
+            if not line:
+                continue
+
+            # Check for ZValue section header
+            zvalue_match = zvalue_pattern.match(line)
+            if zvalue_match:
+                in_zvalue_section = True
+
+                zvalue = int(zvalue_match.group(1))
+                if "ZValue" not in data:
+                    data["ZValue"] = []
+                data["ZValue"].append(zvalue)
+                continue
+
+            # Check for T section header (comments/metadata)
+            section_match = section_pattern.match(line)
+            if section_match:
+                section_content = section_match.group(1)
+                if "sections" not in global_params:
+                    global_params["sections"] = []
+                global_params["sections"].append(section_content)
+                continue
+
+            # Parse key-value pairs
+            if "=" in line:
+                try:
+                    key, value = line.split("=", 1)
+                    key = key.strip()
+                    value = value.strip()
+
+                    try:
+                        if "." not in value and "e" not in value.lower():
+                            parsed_value = int(value)
+                        else:
+                            parsed_value = float(value)
+                    except ValueError:
+                        parsed_value = value
+
+                    if not in_zvalue_section:
+                        global_params[key] = parsed_value
+                    else:
+                        if key not in data:
+                            data[key] = []
+                        data[key].append(parsed_value)
+
+                except ValueError:
+                    continue
+
+        data.update(global_params)
+        return data

tme/preprocessor.py

@@ -1,8 +1,9 @@
-""" Implements Preprocessor class for filtering operations.
+"""
+Implements Preprocessor class for filtering operations.
 
-    Copyright (c) 2023 European Molecular Biology Laboratory
+Copyright (c) 2023 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 
 import os
@@ -669,9 +670,9 @@ class Preprocessor:
         NDArray
             Bandpass filtered.
         """
-        from .filters import BandPassFilter
+        from .filters import BandPassReconstructed
 
-        return BandPassFilter(
+        return BandPassReconstructed(
             sampling_rate=sampling_rate,
             lowpass=lowpass,
             highpass=highpass,

tme/rotations.py

@@ -1,8 +1,9 @@
-""" Implements various means of generating rotation matrices.
+"""
+Implements various means of generating rotation matrices.
 
-    Copyright (c) 2023-2025 European Molecular Biology Laboratory
+Copyright (c) 2023-2025 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 
 import yaml
@@ -183,12 +184,14 @@ def euler_to_rotationmatrix(angles: Tuple[float], seq: str = "zyz") -> NDArray:
     NDArray
         The generated rotation matrix.
     """
+    angles = np.asarray(angles)
+
     n_angles = len(angles)
-    angle_convention = seq[:n_angles]
-    if n_angles == 1:
-        angles = (angles, 0, 0)
+    if angles.ndim == 2:
+        n_angles = angles.shape[1]
+
     rotation_matrix = Rotation.from_euler(
-        seq=angle_convention, angles=angles, degrees=True
+        seq=seq[:n_angles], angles=angles, degrees=True
     )
     return rotation_matrix.as_matrix().astype(np.float32)
 

tme/structure.py

@@ -1,8 +1,9 @@
-""" Implements class Structure to represent atomic structures.
+"""
+Implements class Structure to represent atomic structures.
 
-    Copyright (c) 2023 European Molecular Biology Laboratory
+Copyright (c) 2023 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 
 import warnings

pytme-0.2.9.post1.data/scripts/estimate_ram_usage.py

@@ -1,97 +0,0 @@
-#!python
-""" Estimate RAM requirements for template matching jobs.
-
-    Copyright (c) 2023 European Molecular Biology Laboratory
-
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
-"""
-import numpy as np
-import argparse
-from tme import Density
-from tme.matching_utils import estimate_ram_usage
-from tme.matching_exhaustive import MATCHING_EXHAUSTIVE_REGISTER
-
-
-def parse_args():
-    parser = argparse.ArgumentParser(
-        description="Estimate RAM usage for template matching."
-    )
-    parser.add_argument(
-        "-m",
-        "--target",
-        dest="target",
-        type=str,
-        required=True,
-        help="Path to a target in CCP4/MRC format.",
-    )
-    parser.add_argument(
-        "-i",
-        "--template",
-        dest="template",
-        type=str,
-        required=True,
-        help="Path to a template in PDB/MMCIF or CCP4/MRC format.",
-    )
-    parser.add_argument(
-        "--matching_method",
-        required=False,
-        default=None,
-        help="Analyzer method to use.",
-    )
-    parser.add_argument(
-        "-s",
-        dest="score",
-        type=str,
-        default="FLCSphericalMask",
-        help="Template matching scoring function.",
-        choices=MATCHING_EXHAUSTIVE_REGISTER.keys(),
-    )
-    parser.add_argument(
-        "--ncores", type=int, help="Number of cores for parallelization.", required=True
-    )
-    parser.add_argument(
-        "--no_edge_padding",
-        dest="no_edge_padding",
-        action="store_true",
-        default=False,
-        help="Whether to pad the edges of the target. This is useful, if the target"
-        " has a well defined bounding box, e.g. a density map.",
-    )
-    parser.add_argument(
-        "--no_fourier_padding",
-        dest="no_fourier_padding",
-        action="store_true",
-        default=False,
-        help="Whether input arrays should be zero-padded to the full convolution shape"
-        " for numerical stability. When working with very large targets such as"
-        " tomograms it is safe to use this flag and benefit from the performance gain.",
-    )
-    args = parser.parse_args()
-    return args
-
-
-def main():
-    args = parse_args()
-    target = Density.from_file(args.target)
-    template = Density.from_file(args.template)
-
-    target_box = target.shape
-    if not args.no_edge_padding:
-        target_box = np.add(target_box, template.shape)
-
-    template_box = template.shape
-    if args.no_fourier_padding:
-        template_box = np.ones(len(template_box), dtype=int)
-
-    result = estimate_ram_usage(
-        shape1=target_box,
-        shape2=template_box,
-        matching_method=args.score,
-        ncores=args.ncores,
-        analyzer_method="MaxScoreOverRotations",
-    )
-    print(result)
-
-
-if __name__ == "__main__":
-    main()

pytme-0.2.9.post1.dist-info/RECORD

@@ -1,119 +0,0 @@
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