pytme 0.2.9.post1__cp311-cp311-macosx_15_0_arm64.whl → 0.3b0__cp311-cp311-macosx_15_0_arm64.whl

tme/matching_optimization.py

@@ -1,8 +1,9 @@
-""" Implements methods for non-exhaustive template matching.
+"""
+Implements methods for non-exhaustive template matching.
 
-    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
@@ -1308,4 +1309,4 @@ def optimize_match(
         result.x = np.zeros_like(result.x)
     translation, rotation = result.x[:ndim], result.x[ndim:]
     rotation_matrix = euler_to_rotationmatrix(rotation)
-    return translation, rotation_matrix, result.fun
+    return translation, rotation_matrix, float(result.fun)

tme/matching_scores.py

@@ -1,8 +1,9 @@
-""" Implements a range of cross-correlation coefficients.
+"""
+Implements a range of cross-correlation coefficients.
 
-    Copyright (c) 2023-2024 European Molecular Biology Laboratory
+Copyright (c) 2023-2024 European Molecular Biology Laboratory
 
-    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
 """
 
 import warnings

tme/matching_utils.py

@@ -1,8 +1,9 @@
-""" Utility functions for template matching.
+"""
+Utility functions for template matching.
 
-    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
@@ -1150,3 +1151,40 @@ def compute_extraction_box(
     keep = be.multiply(keep, clamp_change == 0)
 
     return obs_beg_clamp, obs_end_clamp, cand_beg, cand_end, keep
+
+
+class TqdmParallel(Parallel):
+    """
+    A minimal Parallel implementation using tqdm for progress reporting.
+
+    Parameters:
+    -----------
+    tqdm_args : dict, optional
+        Dictionary of arguments passed to tqdm.tqdm
+    *args, **kwargs:
+        Arguments to pass to joblib.Parallel
+    """
+
+    def __init__(self, tqdm_args: Dict = {}, *args, **kwargs):
+        from tqdm import tqdm
+
+        super().__init__(*args, **kwargs)
+        self.pbar = tqdm(**tqdm_args)
+
+    def __call__(self, iterable, *args, **kwargs):
+        self.n_tasks = len(iterable) if hasattr(iterable, "__len__") else None
+        return super().__call__(iterable, *args, **kwargs)
+
+    def print_progress(self):
+        if self.n_tasks is None:
+            return super().print_progress()
+
+        if self.n_tasks != self.pbar.total:
+            self.pbar.total = self.n_tasks
+            self.pbar.refresh()
+
+        self.pbar.n = self.n_completed_tasks
+        self.pbar.refresh()
+
+        if self.n_completed_tasks >= self.n_tasks:
+            self.pbar.close()

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)

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
@@ -560,7 +561,7 @@ 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, []

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

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