pytme 0.2.5__tar.gz → 0.2.9.post1__tar.gz

{pytme-0.2.5 → pytme-0.2.9.post1}/MANIFEST.in

@@ -67,6 +67,7 @@ prune doc/_build
 prune doc/reference/api
 global-exclude tme/scoring.py
 global-exclude tme/package.py
+global-exclude tme/testing_utils.py
 global-exclude tme/transforms.py
 global-exclude tme/tests/test_packaging.py
 global-exclude scripts/match_template_devel.py

{pytme-0.2.5 → pytme-0.2.9.post1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pytme
-Version: 0.2.5
+Version: 0.2.9.post1
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
@@ -13,16 +13,17 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: mrcfile>=1.4.3
 Requires-Dist: numpy<2.0,>=1.22.2
+Requires-Dist: scipy>=1.9.1
 Requires-Dist: pyfftw>=0.13.1
 Requires-Dist: pytest>=6.2.5
 Requires-Dist: PyYAML>=6.0
 Requires-Dist: scikit-image>=0.19.0
 Requires-Dist: scikit_learn>=1.2.1
-Requires-Dist: scipy>=1.9.1
 Requires-Dist: pybind11
 Requires-Dist: psutil
-Requires-Dist: tifffile
 Requires-Dist: h5py
+Requires-Dist: importlib_resources
+Requires-Dist: joblib
 Provides-Extra: cupy
 Requires-Dist: cupy-cuda12x; extra == "cupy"
 Requires-Dist: voltools==0.6.0; extra == "cupy"
@@ -38,6 +39,9 @@ Requires-Dist: voltools==0.6.0; extra == "all"
 Requires-Dist: torch; extra == "all"
 Requires-Dist: jax; extra == "all"
 Requires-Dist: jaxlib; extra == "all"
+Requires-Dist: tifffile; extra == "all"
+Dynamic: author
+Dynamic: license-file
 
 # Python Template Matching Engine (PyTME)
 

{pytme-0.2.5 → pytme-0.2.9.post1}/pyproject.toml

@@ -7,23 +7,24 @@ name="pytme"
 authors = [
   { name = "Valentin Maurer", email = "valentin.maurer@embl-hamburg.de" },
 ]
-version="0.2.5"
+version="0.2.9.post1"
 description="Python Template Matching Engine"
 readme="README.md"
 requires-python = ">=3.11"
 dependencies=[
     "mrcfile>=1.4.3",
     "numpy>=1.22.2,<2.0",
+    "scipy>=1.9.1",
     "pyfftw>=0.13.1",
     "pytest>=6.2.5",
     "PyYAML>=6.0",
     "scikit-image>=0.19.0",
     "scikit_learn>=1.2.1",
-    "scipy>=1.9.1",
     "pybind11",
     "psutil",
-    "tifffile",
     "h5py",
+    "importlib_resources",
+    "joblib"
 ]
 license = {text = "Proprietary"}
 classifiers = [
@@ -40,7 +41,8 @@ all = [
     "voltools==0.6.0",
     "torch",
     "jax",
-    "jaxlib"
+    "jaxlib",
+    "tifffile"
 ]
 
 [project.scripts]

{pytme-0.2.5 → pytme-0.2.9.post1}/pytme.egg-info/SOURCES.txt

@@ -5,14 +5,10 @@ pyproject.toml
 setup.py
 scripts/__init__.py
 scripts/estimate_ram_usage.py
-scripts/eval.py
-scripts/extract_candidates.py
 scripts/match_template.py
-scripts/match_template_filters.py
 scripts/postprocess.py
 scripts/preprocess.py
 scripts/preprocessor_gui.py
-scripts/refine_matches.py
 tests/__init__.py
 tests/test_analyzer.py
 tests/test_backends.py
@@ -25,12 +21,10 @@ tests/test_matching_memory.py
 tests/test_matching_optimization.py
 tests/test_matching_utils.py
 tests/test_orientations.py
-tests/test_packaging.py
 tests/test_parser.py
+tests/test_rotations.py
 tests/test_structure.py
-tests/data/.DS_Store
 tests/data/README.md
-tests/data/Blurring/.DS_Store
 tests/data/Blurring/blob_width18.npy
 tests/data/Blurring/edgegaussian_sigma3.npy
 tests/data/Blurring/gaussian_sigma2.npy
@@ -42,7 +36,6 @@ tests/data/Blurring/ntree_sigma0510.npy
 tests/data/Blurring/rank_rank3.npy
 tests/data/Maps/.DS_Store
 tests/data/Maps/emd_8621.mrc.gz
-tests/data/Raw/.DS_Store
 tests/data/Raw/em_map.map
 tests/data/Structures/.DS_Store
 tests/data/Structures/1pdj.cif
@@ -58,7 +51,6 @@ tests/preprocessing/test_preprocessor.py
 tests/preprocessing/test_utils.py
 tme/__init__.py
 tme/__version__.py
-tme/analyzer.py
 tme/density.py
 tme/matching_data.py
 tme/matching_exhaustive.py
@@ -69,9 +61,15 @@ tme/memory.py
 tme/orientations.py
 tme/parser.py
 tme/preprocessor.py
+tme/rotations.py
 tme/structure.py
 tme/types.py
+tme/analyzer/__init__.py
+tme/analyzer/_utils.py
+tme/analyzer/aggregation.py
+tme/analyzer/peaks.py
 tme/backends/__init__.py
+tme/backends/_cupy_utils.py
 tme/backends/_jax_utils.py
 tme/backends/cupy_backend.py
 tme/backends/jax_backend.py
@@ -104,9 +102,11 @@ tme/data/metadata.yaml
 tme/data/quat_to_numpy.py
 tme/data/scattering_factors.pickle
 tme/external/bindings.cpp
-tme/preprocessing/__init__.py
-tme/preprocessing/_utils.py
-tme/preprocessing/composable_filter.py
-tme/preprocessing/compose.py
-tme/preprocessing/frequency_filters.py
-tme/preprocessing/tilt_series.py
+tme/filters/__init__.py
+tme/filters/_utils.py
+tme/filters/bandpass.py
+tme/filters/compose.py
+tme/filters/ctf.py
+tme/filters/reconstruction.py
+tme/filters/wedge.py
+tme/filters/whitening.py

{pytme-0.2.5 → pytme-0.2.9.post1}/scripts/match_template.py

@@ -12,26 +12,33 @@ from sys import exit
 from time import time
 from typing import Tuple
 from copy import deepcopy
-from os.path import abspath, exists
+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__
-from tme.matching_utils import (
+from tme.matching_utils import scramble_phases, write_pickle
+from tme.matching_exhaustive import scan_subsets, MATCHING_EXHAUSTIVE_REGISTER
+from tme.rotations import (
+    get_cone_rotations,
     get_rotation_matrices,
-    get_rotations_around_vector,
-    compute_parallelization_schedule,
-    scramble_phases,
-    write_pickle,
 )
-from tme.matching_exhaustive import scan_subsets, MATCHING_EXHAUSTIVE_REGISTER
 from tme.matching_data import MatchingData
 from tme.analyzer import (
     MaxScoreOverRotations,
     PeakCallerMaximumFilter,
 )
-from tme.backends import backend as be
-from tme.preprocessing import Compose
+from tme.filters import (
+    CTF,
+    Wedge,
+    Compose,
+    BandPassFilter,
+    WedgeReconstructed,
+    ReconstructFromTilt,
+    LinearWhiteningFilter,
+)
 
 
 def get_func_fullname(func) -> str:
@@ -43,6 +50,8 @@ def print_block(name: str, data: dict, label_width=20) -> None:
     """Prints a formatted block of information."""
     print(f"\n> {name}")
     for key, value in data.items():
+        if isinstance(value, np.ndarray):
+            value = value.shape
         formatted_value = str(value)
         print(f"  - {key + ':':<{label_width}} {formatted_value}")
 
@@ -122,19 +131,20 @@ def parse_rotation_logic(args, ndim):
     if args.axis_sampling is None:
         args.axis_sampling = args.cone_sampling
 
-    rotations = get_rotations_around_vector(
+    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,
-    target: Density,
     matching_data: MatchingData,
     callback_class,
     pad_edges: bool = False,
@@ -142,27 +152,15 @@ def compute_schedule(
     # User requested target padding
     if args.pad_edges is True:
         pad_edges = True
-    template_box = matching_data._output_template_shape
-    if not args.pad_fourier:
-        template_box = tuple(0 for _ in range(len(template_box)))
-
-    target_padding = tuple(0 for _ in range(len(template_box)))
-    if pad_edges:
-        target_padding = matching_data._output_template_shape
-
-    splits, schedule = compute_parallelization_schedule(
-        shape1=target.shape,
-        shape2=tuple(int(x) for x in template_box),
-        shape1_padding=tuple(int(x) for x in target_padding),
-        max_cores=args.cores,
-        max_ram=args.memory,
-        split_only_outer=args.use_gpu,
+
+    splits, schedule = matching_data.computation_schedule(
         matching_method=args.score,
         analyzer_method=callback_class.__name__,
-        backend=be._backend_name,
-        float_nbytes=be.datatype_bytes(be._float_dtype),
-        complex_nbytes=be.datatype_bytes(be._complex_dtype),
-        integer_nbytes=be.datatype_bytes(be._int_dtype),
+        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:
@@ -171,21 +169,15 @@ def compute_schedule(
             " available RAM or decreasing number of cores."
         )
         exit(-1)
+
     n_splits = np.prod(list(splits.values()))
-    if pad_edges is False and n_splits > 1:
+    if pad_edges is False and len(matching_data._target_dim) == 0 and n_splits > 1:
         args.pad_edges = True
-        return compute_schedule(args, target, matching_data, callback_class, True)
+        return compute_schedule(args, matching_data, callback_class, True)
     return splits, schedule
 
 
 def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Compose]:
-    from tme.preprocessing import LinearWhiteningFilter, BandPassFilter
-    from tme.preprocessing.tilt_series import (
-        Wedge,
-        WedgeReconstructed,
-        ReconstructFromTilt,
-    )
-
     needs_reconstruction = False
     template_filter, target_filter = [], []
     if args.tilt_angles is not None:
@@ -195,7 +187,10 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
             wedge.weight_type = args.tilt_weighting
             if args.tilt_weighting in ("angle", None) and args.ctf_file is None:
                 wedge = WedgeReconstructed(
-                    angles=wedge.angles, weight_wedge=args.tilt_weighting == "angle"
+                    angles=wedge.angles,
+                    weight_wedge=args.tilt_weighting == "angle",
+                    opening_axis=args.wedge_axes[0],
+                    tilt_axis=args.wedge_axes[1],
                 )
         except FileNotFoundError:
             tilt_step, create_continuous_wedge = None, True
@@ -235,16 +230,18 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
                     weight_wedge=args.tilt_weighting == "angle",
                     create_continuous_wedge=create_continuous_wedge,
                     reconstruction_filter=args.reconstruction_filter,
+                    opening_axis=args.wedge_axes[0],
+                    tilt_axis=args.wedge_axes[1],
                 )
                 wedge_target = WedgeReconstructed(
                     angles=(np.abs(np.min(tilt_angles)), np.abs(np.max(tilt_angles))),
                     weight_wedge=False,
                     create_continuous_wedge=True,
+                    opening_axis=args.wedge_axes[0],
+                    tilt_axis=args.wedge_axes[1],
                 )
                 target_filter.append(wedge_target)
 
-        wedge.opening_axis = args.wedge_axes[0]
-        wedge.tilt_axis = args.wedge_axes[1]
         wedge.sampling_rate = template.sampling_rate
         template_filter.append(wedge)
         if not isinstance(wedge, WedgeReconstructed):
@@ -255,8 +252,6 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
             template_filter.append(reconstruction_filter)
 
     if args.ctf_file is not None or args.defocus is not None:
-        from tme.preprocessing.tilt_series import CTF
-
         needs_reconstruction = True
         if args.ctf_file is not None:
             ctf = CTF.from_file(args.ctf_file)
@@ -268,6 +263,7 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
                     "per micrograph."
                 )
             ctf.angles = wedge.angles
+            ctf.no_reconstruction = False
             ctf.opening_axis, ctf.tilt_axis = args.wedge_axes
         else:
             needs_reconstruction = False
@@ -439,6 +435,19 @@ def parse_args():
         help="Half-angle of the cone to be sampled in degrees. Allows to sample a "
         "narrow interval around a known orientation, e.g. for surface oversampling.",
     )
+    angular_group.add_argument(
+        "--cone_axis",
+        dest="cone_axis",
+        type=check_positive,
+        default=2,
+        help="Principal axis to build cone around.",
+    )
+    angular_group.add_argument(
+        "--invert_cone",
+        dest="invert_cone",
+        action="store_true",
+        help="Invert cone handedness.",
+    )
     angular_group.add_argument(
         "--cone_sampling",
         dest="cone_sampling",
@@ -581,8 +590,8 @@ def parse_args():
         type=str,
         required=False,
         default=None,
-        help="Indices of wedge opening and tilt axis, e.g. 0,2 for a wedge that is open "
-        "in z-direction and tilted over the x axis.",
+        help="Indices of wedge opening and tilt axis, e.g. '2,0' for a wedge open "
+        "in z and tilted over the x-axis.",
     )
     filter_group.add_argument(
         "--tilt_angles",
@@ -715,14 +724,6 @@ def parse_args():
         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_fourier",
-        dest="pad_fourier",
-        action="store_true",
-        default=False,
-        help="Whether input arrays should not be zero-padded to full convolution shape "
-        "for numerical stability. Typically only useful when working with small data.",
-    )
     performance_group.add_argument(
         "--pad_filter",
         dest="pad_filter",
@@ -785,13 +786,9 @@ def parse_args():
         args.interpolation_order = None
 
     if args.temp_directory is None:
-        default = abspath(".")
-        if os.environ.get("TMPDIR", None) is not None:
-            default = os.environ.get("TMPDIR")
-        args.temp_directory = default
+        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())}"
@@ -1007,7 +1004,11 @@ def main():
         args, template, target
     )
 
-    splits, schedule = compute_schedule(args, target, matching_data, callback_class)
+    matching_data.set_matching_dimension(
+        target_dim=target.metadata.get("batch_dimension", None),
+        template_dim=template.metadata.get("batch_dimension", None),
+    )
+    splits, schedule = compute_schedule(args, matching_data, callback_class)
 
     n_splits = np.prod(list(splits.values()))
     target_split = ", ".join(
@@ -1020,7 +1021,6 @@ def main():
         "Center Template": not args.no_centering,
         "Scramble Template": args.scramble_phases,
         "Invert Contrast": args.invert_target_contrast,
-        "Extend Fourier Grid": args.pad_fourier,
         "Extend Target Edges": args.pad_edges,
         "Interpolation Order": args.interpolation_order,
         "Setup Function": f"{get_func_fullname(matching_setup)}",
@@ -1106,13 +1106,12 @@ def main():
         callback_class_args=analyzer_args,
         target_splits=splits,
         pad_target_edges=args.pad_edges,
-        pad_fourier=args.pad_fourier,
         pad_template_filter=args.pad_filter,
         interpolation_order=args.interpolation_order,
     )
 
     candidates = list(candidates) if candidates is not None else []
-    if callback_class == MaxScoreOverRotations:
+    if issubclass(callback_class, MaxScoreOverRotations):
         if target_mask is not None and args.score != "MCC":
             candidates[0] *= target_mask.data
         with warnings.catch_warnings():