pytme 0.1.6__cp311-cp311-macosx_14_0_arm64.whl → 0.1.8__cp311-cp311-macosx_14_0_arm64.whl

{pytme-0.1.6.data → pytme-0.1.8.data}/scripts/preprocessor_gui.py

@@ -29,17 +29,17 @@ preprocessor = Preprocessor()
 SLIDER_MIN, SLIDER_MAX = 0, 25
 
 
-def gaussian_filter(template, sigma: float, **kwargs: dict):
+def gaussian_filter(template: NDArray, sigma: float, **kwargs: dict) -> NDArray:
     return preprocessor.gaussian_filter(template=template, sigma=sigma, **kwargs)
 
 
 def bandpass_filter(
-    template,
+    template: NDArray,
     minimum_frequency: float,
     maximum_frequency: float,
     gaussian_sigma: float,
     **kwargs: dict,
-):
+) -> NDArray:
     return preprocessor.bandpass_filter(
         template=template,
         minimum_frequency=minimum_frequency,
@@ -51,8 +51,8 @@ def bandpass_filter(
 
 
 def difference_of_gaussian_filter(
-    template, sigmas: Tuple[float, float], **kwargs: dict
-):
+    template: NDArray, sigmas: Tuple[float, float], **kwargs: dict
+) -> NDArray:
     low_sigma, high_sigma = sigmas
     return preprocessor.difference_of_gaussian_filter(
         template=template, low_sigma=low_sigma, high_sigma=high_sigma, **kwargs
@@ -60,7 +60,7 @@ def difference_of_gaussian_filter(
 
 
 def edge_gaussian_filter(
-    template,
+    template: NDArray,
     sigma: float,
     edge_algorithm: Annotated[
         str,
@@ -68,7 +68,7 @@ def edge_gaussian_filter(
     ],
     reverse: bool = False,
     **kwargs: dict,
-):
+) -> NDArray:
     return preprocessor.edge_gaussian_filter(
         template=template,
         sigma=sigma,
@@ -78,13 +78,13 @@ def edge_gaussian_filter(
 
 
 def local_gaussian_filter(
-    template,
+    template: NDArray,
     lbd: float,
     sigma_range: Tuple[float, float],
     gaussian_sigma: float,
     reverse: bool = False,
     **kwargs: dict,
-):
+) -> NDArray:
     return preprocessor.local_gaussian_filter(
         template=template,
         lbd=lbd,
@@ -94,21 +94,76 @@ def local_gaussian_filter(
 
 
 def ntree(
-    template,
+    template: NDArray,
     sigma_range: Tuple[float, float],
     **kwargs: dict,
-):
+) -> NDArray:
     return preprocessor.ntree_filter(template=template, sigma_range=sigma_range)
 
 
 def mean(
-    template,
+    template: NDArray,
     width: int,
     **kwargs: dict,
-):
+) -> NDArray:
     return preprocessor.mean_filter(template=template, width=width)
 
 
+def resolution_sphere(
+    template: NDArray,
+    cutoff_angstrom: float,
+    highpass: bool = False,
+    sampling_rate=None,
+) -> NDArray:
+    if cutoff_angstrom == 0:
+        return template
+
+    cutoff_frequency = np.max(2 * sampling_rate / cutoff_angstrom)
+
+    min_freq, max_freq = 0, cutoff_frequency
+    if highpass:
+        min_freq, max_freq = cutoff_frequency, 1e10
+
+    mask = preprocessor.bandpass_mask(
+        shape=template.shape,
+        minimum_frequency=min_freq,
+        maximum_frequency=max_freq,
+        omit_negative_frequencies=False,
+    )
+
+    template_ft = np.fft.fftn(template)
+    np.multiply(template_ft, mask, out=template_ft)
+    return np.fft.ifftn(template_ft).real
+
+
+def resolution_gaussian(
+    template: NDArray,
+    cutoff_angstrom: float,
+    highpass: bool = False,
+    sampling_rate=None,
+) -> NDArray:
+    if cutoff_angstrom == 0:
+        return template
+
+    grid = preprocessor.fftfreqn(
+        shape=template.shape, sampling_rate=sampling_rate / sampling_rate.max()
+    )
+
+    sigma_fourier = np.divide(
+        np.max(2 * sampling_rate / cutoff_angstrom), np.sqrt(2 * np.log(2))
+    )
+
+    mask = np.exp(-(grid**2) / (2 * sigma_fourier**2))
+    if highpass:
+        mask = 1 - mask
+
+    mask = np.fft.ifftshift(mask)
+
+    template_ft = np.fft.fftn(template)
+    np.multiply(template_ft, mask, out=template_ft)
+    return np.fft.ifftn(template_ft).real
+
+
 def wedge(
     template: NDArray,
     tilt_start: float,
@@ -120,7 +175,7 @@ def wedge(
     omit_negative_frequencies: bool = True,
     extrude_plane: bool = True,
     infinite_plane: bool = True,
-):
+) -> NDArray:
     template_ft = np.fft.rfftn(template)
 
     if tilt_step <= 0:
@@ -139,15 +194,14 @@ def wedge(
         template = np.real(np.fft.irfftn(template_ft))
         return template
 
-    tilt_angles = np.arange(-tilt_start, tilt_stop, tilt_step)
-    angles = np.zeros((template.ndim, tilt_angles.size))
-    angles[tilt_axis, :] = tilt_angles
-
-    wedge_mask = preprocessor.wedge_mask(
-        tilt_angles=angles,
+    wedge_mask = preprocessor.step_wedge_mask(
+        start_tilt=tilt_start,
+        stop_tilt=tilt_stop,
+        tilt_axis=tilt_axis,
+        tilt_step=tilt_step,
+        opening_axis=opening_axis,
         shape=template.shape,
         sigma=gaussian_sigma,
-        opening_axes=opening_axis,
         omit_negative_frequencies=omit_negative_frequencies,
     )
     np.multiply(template_ft, wedge_mask, out=template_ft)
@@ -155,7 +209,7 @@ def wedge(
     return template
 
 
-def compute_power_spectrum(template: NDArray):
+def compute_power_spectrum(template: NDArray) -> NDArray:
     return np.fft.fftshift(np.log(np.abs(np.fft.fftn(template))))
 
 
@@ -220,6 +274,8 @@ WRAPPED_FUNCTIONS = {
     "mean_filter": mean,
     "wedge_filter": wedge,
     "power_spectrum": compute_power_spectrum,
+    "resolution_gaussian": resolution_gaussian,
+    "resolution_sphere": resolution_sphere,
 }
 
 EXCLUDED_FUNCTIONS = [
@@ -332,6 +388,9 @@ class FilterWidget(widgets.Container):
         function_name = self.name_mapping.get(self.method_dropdown.value)
         function = self._get_function(function_name)
 
+        if "sampling_rate" in inspect.getfullargspec(function).args:
+            kwargs["sampling_rate"] = selected_layer_metadata["sampling_rate"]
+
         processed_data = function(selected_layer.data, **kwargs)
 
         new_layer_name = f"{selected_layer.name} ({self.method_dropdown.value})"
@@ -358,7 +417,7 @@ class FilterWidget(widgets.Container):
 
 def sphere_mask(
     template: NDArray, center_x: float, center_y: float, center_z: float, radius: float
-):
+) -> NDArray:
     return create_mask(
         mask_type="ellipse",
         shape=template.shape,
@@ -375,7 +434,7 @@ def ellipsod_mask(
     radius_x: float,
     radius_y: float,
     radius_z: float,
-):
+) -> NDArray:
     return create_mask(
         mask_type="ellipse",
         shape=template.shape,
@@ -392,7 +451,7 @@ def box_mask(
     height_x: int,
     height_y: int,
     height_z: int,
-):
+) -> NDArray:
     return create_mask(
         mask_type="box",
         shape=template.shape,
@@ -410,7 +469,7 @@ def tube_mask(
     inner_radius: float,
     outer_radius: float,
     height: int,
-):
+) -> NDArray:
     return create_mask(
         mask_type="tube",
         shape=template.shape,
@@ -433,7 +492,7 @@ def wedge_mask(
     omit_negative_frequencies: bool = False,
     extrude_plane: bool = True,
     infinite_plane: bool = True,
-):
+) -> NDArray:
     if tilt_step <= 0:
         wedge_mask = preprocessor.continuous_wedge_mask(
             start_tilt=tilt_start,
@@ -449,25 +508,24 @@ def wedge_mask(
         wedge_mask = np.fft.fftshift(wedge_mask)
         return wedge_mask
 
-    tilt_angles = np.arange(-tilt_start, tilt_stop + tilt_step, tilt_step)
-    angles = np.zeros((template.ndim, tilt_angles.size))
-
-    angles[tilt_axis, :] = tilt_angles
-
-    wedge_mask = preprocessor.wedge_mask(
-        tilt_angles=angles,
+    wedge_mask = preprocessor.step_wedge_mask(
+        start_tilt=tilt_start,
+        stop_tilt=tilt_stop,
+        tilt_axis=tilt_axis,
+        tilt_step=tilt_step,
+        opening_axis=opening_axis,
         shape=template.shape,
         sigma=gaussian_sigma,
-        opening_axes=opening_axis,
         omit_negative_frequencies=omit_negative_frequencies,
     )
+
     wedge_mask = np.fft.fftshift(wedge_mask)
     return wedge_mask
 
 
 def threshold_mask(
     template: NDArray, standard_deviation: float = 5.0, invert: bool = False
-):
+) -> NDArray:
     template_mean = template.mean()
     template_deviation = standard_deviation * template.std()
     upper = template_mean + template_deviation
@@ -479,6 +537,15 @@ def threshold_mask(
     return mask
 
 
+def lowpass_mask(template: NDArray, sigma: float = 1.0):
+    template = template / template.max()
+    template = (template > np.exp(-2)) * 128.0
+    template = preprocessor.gaussian_filter(template=template, sigma=sigma)
+    mask = template > np.exp(-2)
+
+    return mask
+
+
 class MaskWidget(widgets.Container):
     def __init__(self, viewer):
         super().__init__(layout="vertical")
@@ -496,6 +563,7 @@ class MaskWidget(widgets.Container):
             "Box": box_mask,
             "Wedge": wedge_mask,
             "Threshold": threshold_mask,
+            "Lowpass": lowpass_mask,
         }
 
         self.method_dropdown = widgets.ComboBox(
@@ -509,7 +577,6 @@ class MaskWidget(widgets.Container):
 
         self.adapt_button = widgets.PushButton(text="Adapt to layer", enabled=False)
         self.adapt_button.changed.connect(self._update_initial_values)
-
         self.viewer.layers.selection.events.active.connect(
             self._update_action_button_state
         )
@@ -520,8 +587,9 @@ class MaskWidget(widgets.Container):
         # self.density_field.value = f"Positive Density in Mask: {0:.2f}%"
 
         self.append(self.method_dropdown)
-        self.append(self.percentile_range_edit)
         self.append(self.adapt_button)
+        self.append(self.percentile_range_edit)
+
         self.append(self.align_button)
         self.append(self.action_button)
         self.append(self.density_field)
@@ -559,6 +627,7 @@ class MaskWidget(widgets.Container):
             arr=active_layer.data,
             rotation_matrix=rotation_matrix,
             use_geometric_center=False,
+            order=1,
         )
         eps = np.finfo(rotated_data.dtype).eps
         rotated_data[rotated_data < eps] = 0
@@ -589,10 +658,10 @@ class MaskWidget(widgets.Container):
             dict(zip(["height_x", "height_y", "height_z"], coordinates_heights))
         )
 
-        defaults["radius"] = np.min(coordinate_radius)
+        defaults["radius"] = np.max(coordinate_radius)
         defaults["inner_radius"] = np.min(coordinate_radius)
         defaults["outer_radius"] = np.max(coordinate_radius)
-        defaults["height"] = defaults["radius"]
+        defaults["height"] = np.max(coordinates_heights)
 
         for widget in self.action_widgets:
             if widget.name in defaults:
@@ -804,6 +873,7 @@ def parse_args():
     args = parser.parse_args()
     return args
 
+
 if __name__ == "__main__":
     parse_args()
     main()

{pytme-0.1.6.dist-info → pytme-0.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pytme
-Version: 0.1.6
+Version: 0.1.8
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
@@ -31,7 +31,7 @@ A software for template matching on electron microscopy data.
 
 ### Installation
 
-There are three ways to get PyTME up and running:
+There are three ways to get pyTME up and running:
 
 1. **Install from Source:**
 ```bash
@@ -44,7 +44,7 @@ pip install pytme
 ```
 
 3. **Docker Container:**
-Build and use the PyTME container from Docker. This assumes a linux/amd64 platform.
+Build and use the pyTME container from Docker. This assumes a linux/amd64 platform.
 ```bash
 docker build \
 	-t pytme \
@@ -58,12 +58,14 @@ docker build \
 
 ### Publication
 
-The pyTME publication is available on [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.10.23.563472v1).
+The pyTME publication is available on [SoftwareX](https://www.sciencedirect.com/science/article/pii/S2352711024000074).
 
 ```
-@article{Maurer2023.10.23.563472,
-	author = {Valentin J. Maurer and Marc Siggel and Jan Kosinski},
-	journal = {bioRxiv},
+@article{Maurer:2024aa,
+	author = {Maurer, Valentin J. and Siggel, Marc and Kosinski, Jan},
+	journal = {SoftwareX},
+	pages = {101636},
 	title = {PyTME (Python Template Matching Engine): A fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data},
-	year = {2023}}
+	volume = {25},
+	year = {2024}}
 ```

{pytme-0.1.6.dist-info → pytme-0.1.8.dist-info}/RECORD

@@ -1,34 +1,35 @@
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 scripts/preprocess.py,sha256=ebJVLxbRlB6TI5YHNr0VavZ4lmaRdf8QVafyiDhh_oU,2528
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 tme/__init__.py,sha256=NiPnYfrwb8e04ETubqwd3yzCGBliLBXRvCylD-T59jY,212
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 tme/extensions.cpython-311-darwin.so,sha256=vSNHvFMev0jvKCEwE4lzqgg9520Ucxf27gy3qqixYns,395056
 tme/helpers.py,sha256=TMtBuJoZk6q4M_rfkr8yPpGzJD74ycqyN3yXMuU9mr4,23625
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 tme/matching_memory.py,sha256=GB71b7m-h0fF1A5HCUlAYQh62-Aq2lHgIoRGPYEzZrU,11245
 tme/matching_optimization.py,sha256=oo9HJV65Ji1oL2JumxgmtrHSMUQsKrpDhdOO5o-fAdM,37388
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 tme/structure.py,sha256=AKGZML8bnsqZOpAOQADU1XDXZ-ITPhr3Dc0udQUMP6E,54134
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-tme/backends/npfftw_backend.py,sha256=XexwAwRUZXQiwZOPeq6lOLkJlSInEL6CGyKrR-dRMbU,26232
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 tme/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tme/data/c48n309.npy,sha256=NwH64mOEbm3tStq5c98o81fY1vMOoq4nvXDAh7Z7iZg,296768
 tme/data/c48n527.npy,sha256=saSUMTa1R0MisPvgFL02a7IHQSwEZ-mJu0v3qJjg5AU,506048
@@ -52,9 +53,9 @@ tme/data/c600v.npy,sha256=JqSu3ALoL1A9iguehc0YGUMFPsh2fprHHp76VXeFXIw,2528
 tme/data/c600vc.npy,sha256=Yht-GFXDSjjGvsjFBvyxxEZAI-ODADPd5gEgFNZQVTA,14528
 tme/data/metadata.yaml,sha256=fAgX-mEzB0QMHTEtYDG4cSMbJhYxBbDJH3sdvJvL7a8,750
 tme/data/quat_to_numpy.py,sha256=-gkDZb10fKBxwfYrSLCUWvMB76TzZWELCeKsYProwws,1333
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-pytme-0.1.6.dist-info/RECORD,,
+pytme-0.1.8.dist-info/LICENSE,sha256=K1IUNSVAz8BXbpH5EA8y5FpaHdvFXnAF2zeK95Lr2bY,18467
+pytme-0.1.8.dist-info/METADATA,sha256=zG0llsYOJsC3hU1UCPwepti-FJg1O8VPn1ovO-j4MNE,2121
+pytme-0.1.8.dist-info/WHEEL,sha256=-A_a4qtPtE7THspi2apYwdQWhv5IW90gRqlNhh7cwR4,110
+pytme-0.1.8.dist-info/entry_points.txt,sha256=ff3LQL3FCWfCYOwFiP9zatm7laUbnwCkuPELkQVyUO4,241
+pytme-0.1.8.dist-info/top_level.txt,sha256=J8FUkazOb2fZ0n_KexnqCGyNOtie2bwisFSUBiM5-0w,12
+pytme-0.1.8.dist-info/RECORD,,

scripts/estimate_ram_usage.py

@@ -88,7 +88,7 @@ def main():
         shape2=template_box,
         matching_method=args.score,
         ncores=args.ncores,
-        analyzer_method="MaxScoreOverRotations"
+        analyzer_method="MaxScoreOverRotations",
     )
     print(result)
 

scripts/match_template.py

@@ -252,7 +252,7 @@ def parse_args():
         type=check_positive,
         default=40.0,
         help="Angular sampling rate for template matching. "
-        "A lower number yields more rotations.",
+        "A lower number yields more rotations. Values >= 180 sample only the identity.",
     )
     parser.add_argument(
         "-p",
@@ -380,8 +380,8 @@ def parse_args():
         type=float,
         required=False,
         default=None,
-        help="Step size between tilts, e.g. '5'. When set a more accurate"
-        " wedge mask will be computed.",
+        help="Step size between tilts, e.g. '5'. When set the wedge mask"
+        " reflects the individual tilts, otherwise a continuous mask is used.",
     )
     parser.add_argument(
         "--wedge_axes",
@@ -488,14 +488,16 @@ def main():
         if target_mask:
             args.target_mask = generate_tempfile_name(suffix=".mrc")
             target_mask.to_file(args.target_mask)
-            print_block(
-                name="Target Mask",
-                data={
-                    "Initial Shape": initial_shape,
-                    "Sampling Rate": tuple(np.round(target_mask.sampling_rate, 2)),
-                    "Final Shape": target_mask.shape,
-                },
-            )
+
+    if target_mask:
+        print_block(
+            name="Target Mask",
+            data={
+                "Initial Shape": initial_shape,
+                "Sampling Rate": tuple(np.round(target_mask.sampling_rate, 2)),
+                "Final Shape": target_mask.shape,
+            },
+        )
 
     initial_shape = template.shape
     _ = crop_data(data=template, data_mask=template_mask, cutoff=args.cutoff_template)
@@ -537,15 +539,14 @@ def main():
         opening_axis, tilt_axis = [int(x) for x in args.wedge_axes.split(",")]
 
         if args.tilt_step is not None:
-            tilt_angles = np.arange(
-                -tilt_start, tilt_stop + args.tilt_step, args.tilt_step
-            )
-            angles = np.zeros((template.data.ndim, tilt_angles.size))
-            angles[tilt_axis, :] = tilt_angles
-            template_filter["wedge_mask"] = {
-                "tilt_angles": angles,
+            template_filter["step_wedge_mask"] = {
+                "start_tilt": tilt_start,
+                "stop_tilt": tilt_stop,
+                "tilt_step": args.tilt_step,
                 "sigma": args.wedge_smooth,
-                "opening_axes": opening_axis,
+                "opening_axis": opening_axis,
+                "tilt_axis": tilt_axis,
+                "omit_negative_frequencies": True,
             }
         else:
             template_filter["continuous_wedge_mask"] = {
@@ -555,6 +556,7 @@ def main():
                 "opening_axis": opening_axis,
                 "infinite_plane": True,
                 "sigma": args.wedge_smooth,
+                "omit_negative_frequencies": True,
             }
 
     if template_mask is None:
@@ -577,8 +579,9 @@ def main():
     template_mask = template_mask.rigid_transform(
         rotation_matrix=np.eye(template_mask.data.ndim),
         translation=-translation,
+        order=1,
     )
-
+    template_mask.origin = template.origin.copy()
     print_block(
         name="Template Mask",
         data={
@@ -590,7 +593,9 @@ def main():
     print("\n" + "-" * 80)
 
     if args.scramble_phases:
-        template.data = scramble_phases(template.data, noise_proportion=1.0)
+        template.data = scramble_phases(
+            template.data, noise_proportion=1.0, normalize_power=True
+        )
 
     available_memory = backend.get_available_memory()
     if args.use_gpu:
@@ -668,7 +673,7 @@ def main():
         exit(-1)
 
     analyzer_args = {
-        "score_threshold": 0.0,
+        "score_threshold": 0,
         "number_of_peaks": 1000,
         "convolution_mode": "valid",
         "use_memmap": args.use_memmap,