pytme 0.2.4__tar.gz → 0.2.5__tar.gz

{pytme-0.2.4 → pytme-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pytme
-Version: 0.2.4
+Version: 0.2.5
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>

{pytme-0.2.4 → pytme-0.2.5}/pyproject.toml

@@ -7,7 +7,7 @@ name="pytme"
 authors = [
   { name = "Valentin Maurer", email = "valentin.maurer@embl-hamburg.de" },
 ]
-version="0.2.4"
+version="0.2.5"
 description="Python Template Matching Engine"
 readme="README.md"
 requires-python = ">=3.11"

{pytme-0.2.4 → pytme-0.2.5}/tests/test_matching_optimization.py

@@ -101,56 +101,6 @@ class TestMatchDensityToCoordinates:
         score = instance()
         assert isinstance(score, float)
 
-    def test_map_coordinates_to_array(self):
-        ret = _MatchCoordinatesToDensity.map_coordinates_to_array(
-            coordinates=self.coordinates.astype(np.float32),
-            array_shape=self.target.shape,
-            array_origin=np.zeros(self.target.ndim),
-            sampling_rate=np.ones(self.target.ndim),
-        )
-        assert len(ret) == 2
-
-        in_vol, in_vol_mask = ret
-
-        assert in_vol_mask is None
-        assert np.allclose(in_vol.shape, self.coordinates.shape[1])
-
-    def test_map_coordinates_to_array_mask(self):
-        ret = _MatchCoordinatesToDensity.map_coordinates_to_array(
-            coordinates=self.coordinates.astype(np.float32),
-            array_shape=self.target.shape,
-            array_origin=self.origin,
-            sampling_rate=self.sampling_rate,
-            coordinates_mask=self.coordinates.astype(np.float32),
-        )
-        assert len(ret) == 2
-
-        in_vol, in_vol_mask = ret
-        assert np.allclose(in_vol, in_vol_mask)
-
-    def test_array_from_coordinates(self):
-        ret = _MatchCoordinatesToDensity.array_from_coordinates(
-            coordinates=self.coordinates,
-            weights=self.coordinates_weights,
-            sampling_rate=self.sampling_rate,
-        )
-        assert len(ret) == 3
-        arr, positions, origin = ret
-        assert arr.ndim == self.coordinates.shape[0]
-        assert positions.shape == self.coordinates.shape
-        assert origin.shape == (self.coordinates.shape[0],)
-
-        assert np.allclose(origin, self.coordinates.min(axis=1))
-
-        ret = _MatchCoordinatesToDensity.array_from_coordinates(
-            coordinates=self.coordinates,
-            weights=self.coordinates_weights,
-            sampling_rate=self.sampling_rate,
-            origin=self.origin,
-        )
-        arr, positions, origin = ret
-        assert np.allclose(origin, self.origin)
-
 
 class TestMatchCoordinateToCoordinates:
     def setup_method(self):

pytme-0.2.5/tme/__version__.py

@@ -0,0 +1 @@
+__version__ = "0.2.5"

{pytme-0.2.4 → pytme-0.2.5}/tme/backends/jax_backend.py

@@ -208,13 +208,6 @@ class JaxBackend(NumpyFFTWBackend):
         # Applying the filter leads to more FFTs
         fastt_shape = matching_data._template.shape
         if create_template_filter:
-            # _, fastt_shape, _, tshift = matching_data._fourier_padding(
-            #     target_shape=self.to_numpy_array(matching_data._template.shape),
-            #     template_shape=self.to_numpy_array(
-            #         [1 for _ in matching_data._template.shape]
-            #     ),
-            #     pad_fourier=False,
-            # )
             fastt_shape = matching_data._template.shape
 
         ret, template_filter, target_filter = [], 1, 1
@@ -260,8 +253,8 @@ class JaxBackend(NumpyFFTWBackend):
             base, targets = None, self._array_backend.stack(targets)
             scores, rotations = scan_inner(
                 targets,
-                self.topleft_pad(matching_data.template, fastt_shape),
-                self.topleft_pad(matching_data.template_mask, fastt_shape),
+                matching_data.template,
+                matching_data.template_mask,
                 matching_data.rotations,
                 template_filter,
                 target_filter,

{pytme-0.2.4 → pytme-0.2.5}/tme/density.py

@@ -697,8 +697,7 @@ class Density:
         References
         ----------
         .. [1]  Sorzano, Carlos et al (Mar. 2015). Fast and accurate conversion
-            of atomic models into electron density maps. AIMS Biophysics
-            2, 8–20.
+            of atomic models into electron density maps. AIMS Biophysics 2, 8–20.
 
         Examples
         --------
@@ -743,17 +742,16 @@ class Density:
         >>>    filter_by_residues = {"SER", "THR", "CYS", "ASN", "GLN", "TYR"}
         >>> )
 
-        :py:meth:`Density.from_structure` supports a variety of methods to convert
-        atoms into densities
+        In addtion, :py:meth:`Density.from_structure` supports a variety of methods
+        to convert atoms into densities, such as Gaussians
 
         >>> density = Density.from_structure(
         >>>    filename_or_structure = path_to_structure,
         >>>    weight_type = "gaussian",
-        >>>    weight_type_args={"resolution": "20"}
+        >>>    weight_type_args={"resolution": 20}
         >>> )
 
-        In addition its possible to use experimentally determined scattering factors
-        from various sources:
+        experimentally determined scattering factors
 
         >>> density = Density.from_structure(
         >>>    filename_or_structure = path_to_structure,
@@ -1688,11 +1686,10 @@ class Density:
             Resampling method to use, defaults to `spline`. Availabe options are:
 
             +---------+----------------------------------------------------------+
-            | spline  | Smooth spline interpolation via :obj:`scipy.ndimage.zoom`|
+            | spline  | Spline interpolation using :obj:`scipy.ndimage.zoom`     |
             +---------+----------------------------------------------------------+
-            | fourier | Frequency preserving Fourier cropping                    |
+            | fourier | Fourier cropping                                         |
             +---------+----------------------------------------------------------+
-
         order : int, optional
             Order of spline used for interpolation, by default 1. Ignored when
             ``method`` is `fourier`.

{pytme-0.2.4 → pytme-0.2.5}/tme/matching_data.py

@@ -478,7 +478,8 @@ class MatchingData:
         shape_diff = np.multiply(
             np.subtract(target_shape, template_shape), 1 - batch_mask
         )
-        if np.sum(shape_diff < 0):
+        shape_mask = shape_diff < 0
+        if np.sum(shape_mask):
             shape_shift = np.divide(shape_diff, 2)
             offset = np.mod(shape_diff, 2)
             if pad_fourier:
@@ -491,8 +492,7 @@ class MatchingData:
                     "Template is larger than target and padding is turned off. Consider "
                     "swapping them or activate padding. Correcting the shift for now."
                 )
-
-            shape_shift = np.add(shape_shift, offset)
+            shape_shift = np.multiply(np.add(shape_shift, offset), shape_mask)
             fourier_shift = np.subtract(fourier_shift, shape_shift).astype(int)
 
         fourier_shift = tuple(fourier_shift.astype(int))

{pytme-0.2.4 → pytme-0.2.5}/tme/matching_exhaustive.py

@@ -90,12 +90,12 @@ def _setup_template_filter_apply_target_filter(
         #     pad_fourier=False,
         # )
         fastt_shape = matching_data._template.shape
-        matching_data.template = be.reverse(
-            be.topleft_pad(matching_data.template, fastt_shape)
-        )
-        matching_data.template_mask = be.reverse(
-            be.topleft_pad(matching_data.template_mask, fastt_shape)
-        )
+        # matching_data.template = be.reverse(
+        #     be.topleft_pad(matching_data.template, fastt_shape)
+        # )
+        # matching_data.template_mask = be.reverse(
+        #     be.topleft_pad(matching_data.template_mask, fastt_shape)
+        # )
         matching_data._set_matching_dimension(
             target_dims=matching_data._target_dims,
             template_dims=matching_data._template_dims,
@@ -208,7 +208,7 @@ def scan(
 
     Examples
     --------
-    Schematically, using :py:meth:`scan` is similar to :py:meth:`scan_subsets`,
+    Schematically, :py:meth:`scan` is identical to :py:meth:`scan_subsets`,
     with the distinction that the objects contained in ``matching_data`` are not
     split and the search is only parallelized over angles.
     Assuming you have followed the example in :py:meth:`scan_subsets`, :py:meth:`scan`