pytme 0.2.3__tar.gz → 0.2.4__tar.gz

{pytme-0.2.3 → pytme-0.2.4}/MANIFEST.in

@@ -70,3 +70,9 @@ global-exclude tme/package.py
 global-exclude tme/transforms.py
 global-exclude tme/tests/test_packaging.py
 global-exclude scripts/match_template_devel.py
+
+# Explicit package data include
+include tme/data/*.npy
+include tme/data/metadata.yaml
+include tme/data/scattering_factors.pickle
+recursive-include tests/data *

{pytme-0.2.3 → pytme-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pytme
-Version: 0.2.3
+Version: 0.2.4
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>

{pytme-0.2.3 → pytme-0.2.4}/pyproject.toml

@@ -7,7 +7,7 @@ name="pytme"
 authors = [
   { name = "Valentin Maurer", email = "valentin.maurer@embl-hamburg.de" },
 ]
-version="0.2.3"
+version="0.2.4"
 description="Python Template Matching Engine"
 readme="README.md"
 requires-python = ">=3.11"
@@ -63,5 +63,5 @@ addopts = [
 
 [tool.coverage.run]
 omit = [
-    "tme/tests/*"
+    "tests/*"
 ]

{pytme-0.2.3 → pytme-0.2.4}/pytme.egg-info/SOURCES.txt

@@ -13,14 +13,55 @@ scripts/postprocess.py
 scripts/preprocess.py
 scripts/preprocessor_gui.py
 scripts/refine_matches.py
-src/extensions.cpp
+tests/__init__.py
+tests/test_analyzer.py
+tests/test_backends.py
+tests/test_density.py
+tests/test_extensions.py
+tests/test_matching_cli.py
+tests/test_matching_data.py
+tests/test_matching_exhaustive.py
+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_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
+tests/data/Blurring/hamming_width6.npy
+tests/data/Blurring/kaiserb_width18.npy
+tests/data/Blurring/localgaussian_sigma0510.npy
+tests/data/Blurring/mean_size5.npy
+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
+tests/data/Structures/1pdj.pdb
+tests/data/Structures/5khe.cif
+tests/data/Structures/5khe.ent
+tests/data/Structures/5khe.pdb
+tests/data/Structures/5uz4.cif
+tests/preprocessing/__init__.py
+tests/preprocessing/test_compose.py
+tests/preprocessing/test_frequency_filters.py
+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
-tme/matching_memory.py
 tme/matching_optimization.py
 tme/matching_scores.py
 tme/matching_utils.py
@@ -61,6 +102,8 @@ tme/data/c600v.npy
 tme/data/c600vc.npy
 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

{pytme-0.2.3 → pytme-0.2.4}/scripts/match_template.py

@@ -186,8 +186,10 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
         ReconstructFromTilt,
     )
 
+    needs_reconstruction = False
     template_filter, target_filter = [], []
     if args.tilt_angles is not None:
+        needs_reconstruction = args.tilt_weighting is not None
         try:
             wedge = Wedge.from_file(args.tilt_angles)
             wedge.weight_type = args.tilt_weighting
@@ -232,11 +234,12 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
                     angles=tilt_angles,
                     weight_wedge=args.tilt_weighting == "angle",
                     create_continuous_wedge=create_continuous_wedge,
+                    reconstruction_filter=args.reconstruction_filter,
                 )
                 wedge_target = WedgeReconstructed(
-                    angles=tilt_angles,
+                    angles=(np.abs(np.min(tilt_angles)), np.abs(np.max(tilt_angles))),
                     weight_wedge=False,
-                    create_continuous_wedge=create_continuous_wedge,
+                    create_continuous_wedge=True,
                 )
                 target_filter.append(wedge_target)
 
@@ -323,18 +326,13 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
             sampling_rate=template.sampling_rate,
         )
         template_filter.append(bandpass)
-
-        if not args.no_filter_target:
-            target_filter.append(bandpass)
+        target_filter.append(bandpass)
 
     if args.whiten_spectrum:
         whitening_filter = LinearWhiteningFilter()
         template_filter.append(whitening_filter)
         target_filter.append(whitening_filter)
 
-    needs_reconstruction = any(
-        [isinstance(t, ReconstructFromTilt) for t in template_filter]
-    )
     if needs_reconstruction and args.reconstruction_filter is None:
         warnings.warn(
             "Consider using a --reconstruction_filter such as 'ramp' to avoid artifacts."
@@ -342,6 +340,8 @@ def setup_filter(args, template: Density, target: Density) -> Tuple[Compose, Com
 
     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
 

{pytme-0.2.3 → pytme-0.2.4}/scripts/preprocess.py

@@ -79,6 +79,14 @@ def parse_args():
         action="store_true",
         help="Assumes the template is already centered and omits centering.",
     )
+    modulation_group.add_argument(
+        "--backend",
+        dest="backend",
+        type=str,
+        default=None,
+        choices=be.available_backends(),
+        help="Determines more suitable box size for the given compute backend.",
+    )
     args = parser.parse_args()
     return args
 
@@ -95,11 +103,18 @@ def main():
     if not args.no_centering:
         data, _ = data.centered(0)
 
-    recommended_box = be.compute_convolution_shapes([args.box_size], [1])[1][0]
-    if recommended_box != args.box_size:
-        warnings.warn(
-            f"Consider using --box_size {recommended_box} instead of {args.box_size}."
-        )
+    for name in be.available_backends():
+        be.change_backend(name, device="cpu")
+        box = be.compute_convolution_shapes([args.box_size], [1])[1][0]
+        if box != args.box_size and args.backend is None:
+            print(f"Consider --box_size {box} instead of {args.box_size} for {name}.")
+
+    if args.backend is not None:
+        be.change_backend(name, device="cpu")
+        box = be.compute_convolution_shapes([args.box_size], [1])[1][0]
+        if box != args.box_size:
+            print(f"Changed --box_size from {args.box_size} to {box}.")
+        args.box_size = box
 
     data.pad(
         np.multiply(args.box_size, np.divide(args.sampling_rate, data.sampling_rate)),
@@ -128,5 +143,6 @@ def main():
 
     data.to_file(args.output)
 
+
 if __name__ == "__main__":
-    main()
+    main()

{pytme-0.2.3 → pytme-0.2.4}/scripts/preprocessor_gui.py

@@ -147,9 +147,7 @@ def wedge(
     tilt_step: float = 0,
     opening_axis: int = 0,
     tilt_axis: int = 1,
-    gaussian_sigma: float = 0,
     omit_negative_frequencies: bool = True,
-    extrude_plane: bool = True,
     infinite_plane: bool = True,
 ) -> NDArray:
     template_ft = np.fft.rfftn(template)
@@ -161,9 +159,7 @@ def wedge(
             tilt_axis=tilt_axis,
             opening_axis=opening_axis,
             shape=template.shape,
-            sigma=gaussian_sigma,
             omit_negative_frequencies=omit_negative_frequencies,
-            extrude_plane=extrude_plane,
             infinite_plane=infinite_plane,
         )
         np.multiply(template_ft, wedge_mask, out=template_ft)
@@ -177,7 +173,6 @@ def wedge(
         tilt_step=tilt_step,
         opening_axis=opening_axis,
         shape=template.shape,
-        sigma=gaussian_sigma,
         omit_negative_frequencies=omit_negative_frequencies,
     )
     np.multiply(template_ft, wedge_mask, out=template_ft)
@@ -483,10 +478,9 @@ def wedge_mask(
     tilt_step: float = 0,
     opening_axis: int = 0,
     tilt_axis: int = 2,
-    gaussian_sigma: float = 0,
     omit_negative_frequencies: bool = False,
-    extrude_plane: bool = True,
-    infinite_plane: bool = True,
+    infinite_plane: bool = False,
+    weight_angle: bool = False,
     **kwargs,
 ) -> NDArray:
     if tilt_step <= 0:
@@ -496,22 +490,23 @@ def wedge_mask(
             tilt_axis=tilt_axis,
             opening_axis=opening_axis,
             shape=template.shape,
-            sigma=gaussian_sigma,
             omit_negative_frequencies=omit_negative_frequencies,
-            extrude_plane=extrude_plane,
             infinite_plane=infinite_plane,
         )
         wedge_mask = np.fft.fftshift(wedge_mask)
         return wedge_mask
 
+    weights = None
+    tilt_angles = np.arange(-tilt_start, tilt_stop + tilt_step, tilt_step)
+    if weight_angle:
+        weights = np.cos(np.radians(tilt_angles))
+
     wedge_mask = preprocessor.step_wedge_mask(
-        start_tilt=tilt_start,
-        stop_tilt=tilt_stop,
+        tilt_angles=tilt_angles,
         tilt_axis=tilt_axis,
-        tilt_step=tilt_step,
         opening_axis=opening_axis,
         shape=template.shape,
-        sigma=gaussian_sigma,
+        weights=weights,
         omit_negative_frequencies=omit_negative_frequencies,
     )
 

pytme-0.2.4/setup.py

@@ -0,0 +1,65 @@
+import os
+import platform
+
+from setuptools import setup, find_packages
+from pybind11.setup_helpers import Pybind11Extension, build_ext
+
+about = {}
+with open(os.path.join("tme", "__version__.py"), mode="r") as f:
+    exec(f.read(), about)
+__version__ = about["__version__"]
+
+if platform.processor() in ("arm", "i386"):
+    c_args = ["-O3", "-ftree-vectorize", "-std=c17"]
+    cpp_args = [
+        "-O3",
+        "-ftree-vectorize",
+        "-std=c++11",
+        "-funroll-loops",
+        "-ffast-math",
+    ]
+else:
+    c_args = ["-O3", "-march=native", "-std=c17"]
+    cpp_args = [
+        "-O3",
+        "-march=native",
+        "-std=c++11",
+        "-funroll-loops",
+        "-ffast-math",
+    ]
+
+ext_modules = [
+    Pybind11Extension(
+        "tme.extensions",
+        ["tme/external/bindings.cpp"],
+        define_macros=[("VERSION_INFO", __version__)],
+        extra_compile_args=cpp_args,
+    ),
+]
+
+package_data = {
+    "tme": [
+        os.path.join("data", "*.npy"),
+        os.path.join("data", "metadata.yaml"),
+        os.path.join("data", "scattering_factors.pickle"),
+    ],
+    "tests": ["data/Blurring/*", "data/Structures/*", "data/Raw/*", "data/Maps/*"],
+}
+setup(
+    name="pytme",
+    author="Valentin Maurer",
+    author_email="valentin.maurer@embl-hamburg.de",
+    version=__version__,
+    description="Data-intensive n-dimensional template matching using CPUs and GPUs.",
+    package_data=package_data,
+    packages=find_packages(),
+    scripts=[
+        "scripts/match_template.py",
+        "scripts/estimate_ram_usage.py",
+        "scripts/preprocessor_gui.py",
+        "scripts/preprocess.py",
+        "scripts/postprocess.py",
+    ],
+    ext_modules=ext_modules,
+    cmdclass={"build_ext": build_ext},
+)

pytme-0.2.4/tests/data/README.md

@@ -0,0 +1,2 @@
+Test data was derived from EMD-8249
+https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-8249