pytme 0.2.3__cp311-cp311-macosx_14_0_arm64.whl → 0.2.4__cp311-cp311-macosx_14_0_arm64.whl

{pytme-0.2.3.data → pytme-0.2.4.data}/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.data → pytme-0.2.4.data}/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.data → pytme-0.2.4.data}/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-0.2.3.dist-info → pytme-0.2.4.dist-info}/METADATA

@@ -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-0.2.4.dist-info/RECORD

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+tme/preprocessing/__init__.py,sha256=7O3vDzJcIfxovJkf7avWSPtzaIVlTbmsW7egQFukC_s,98
+tme/preprocessing/_utils.py,sha256=1K8xPquM0v1MASwsMpIc3ZWxxpUFt69LezVZY5QcJnY,6179
+tme/preprocessing/composable_filter.py,sha256=zmXN_NcuvvtstFdU6yYQ09z-XJFE4Y-kkMCL4vHy-jc,778
+tme/preprocessing/compose.py,sha256=NFB6oUQOwn8foy82i3Lm5DeZUd_5dmcKdhuwX8E6wpo,1454
+tme/preprocessing/frequency_filters.py,sha256=XPG6zRF_VSPH4CWFj1BLICm3_jNrzmiHaln0JZR7CrU,12755
+tme/preprocessing/tilt_series.py,sha256=6OptAfqISxzZOtHIx5MdSaJf7VGFeDntz2jWekpZMus,37307
+pytme-0.2.4.dist-info/LICENSE,sha256=K1IUNSVAz8BXbpH5EA8y5FpaHdvFXnAF2zeK95Lr2bY,18467
+pytme-0.2.4.dist-info/METADATA,sha256=fq2oJEwpG-N_8XYERPQwaBD-IbXySwuJ75BG8NP0WtQ,5278
+pytme-0.2.4.dist-info/WHEEL,sha256=uY16WuvBs6SVLr1w0jr9fTUdSkt0n_9cWxlDSGwcm3o,109
+pytme-0.2.4.dist-info/entry_points.txt,sha256=ff3LQL3FCWfCYOwFiP9zatm7laUbnwCkuPELkQVyUO4,241
+pytme-0.2.4.dist-info/top_level.txt,sha256=ovCUR7UXXouH3zYt_fJLoqr_vtjp1wudFgjVAnztQLE,18
+pytme-0.2.4.dist-info/RECORD,,

{pytme-0.2.3.dist-info → pytme-0.2.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (72.1.0)
+Generator: setuptools (73.0.1)
 Root-Is-Purelib: false
 Tag: cp311-cp311-macosx_14_0_arm64
 

{pytme-0.2.3.dist-info → pytme-0.2.4.dist-info}/top_level.txt

@@ -1,2 +1,3 @@
 scripts
+tests
 tme

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
 

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()

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,
     )
 

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