pytme 0.2.2__cp311-cp311-macosx_14_0_arm64.whl → 0.2.4__cp311-cp311-macosx_14_0_arm64.whl

{pytme-0.2.2.data → pytme-0.2.4.data}/scripts/preprocessor_gui.py

@@ -132,14 +132,6 @@ def local_gaussian_filter(
     )
 
 
-def ntree(
-    template: NDArray,
-    sigma_range: Tuple[float, float],
-    **kwargs: dict,
-) -> NDArray:
-    return preprocessor.ntree_filter(template=template, sigma_range=sigma_range)
-
-
 def mean(
     template: NDArray,
     width: int,
@@ -155,9 +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)
@@ -169,9 +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)
@@ -185,7 +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)
@@ -197,6 +184,10 @@ def compute_power_spectrum(template: NDArray) -> NDArray:
     return np.fft.fftshift(np.log(np.abs(np.fft.fftn(template))))
 
 
+def invert_contrast(template: NDArray) -> NDArray:
+    return template * -1
+
+
 def widgets_from_function(function: Callable, exclude_params: List = ["self"]):
     """
     Creates list of magicui widgets by inspecting function typing ann
@@ -252,13 +243,13 @@ WRAPPED_FUNCTIONS = {
     "gaussian_filter": gaussian_filter,
     "bandpass_filter": bandpass_filter,
     "edge_gaussian_filter": edge_gaussian_filter,
-    "ntree_filter": ntree,
     "local_gaussian_filter": local_gaussian_filter,
     "difference_of_gaussian_filter": difference_of_gaussian_filter,
     "mean_filter": mean,
     "wedge_filter": wedge,
     "power_spectrum": compute_power_spectrum,
     "ctf": ctf_filter,
+    "invert_contrast": invert_contrast,
 }
 
 EXCLUDED_FUNCTIONS = [
@@ -487,10 +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:
@@ -500,22 +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,
     )
 
@@ -634,6 +625,7 @@ class MaskWidget(widgets.Container):
 
         data = active_layer.data.copy()
         cutoff = np.quantile(data, self.percentile_range_edit.value / 100)
+        cutoff = max(cutoff, np.finfo(np.float32).resolution)
         data[data < cutoff] = 0
 
         center_of_mass = Density.center_of_mass(np.abs(data), 0)

{pytme-0.2.2.dist-info → pytme-0.2.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pytme
-Version: 0.2.2
+Version: 0.2.4
 Summary: Python Template Matching Engine
 Author: Valentin Maurer
 Author-email: Valentin Maurer <valentin.maurer@embl-hamburg.de>
@@ -12,7 +12,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: mrcfile >=1.4.3
-Requires-Dist: numpy >=1.22.2
+Requires-Dist: numpy <2.0,>=1.22.2
 Requires-Dist: pyfftw >=0.13.1
 Requires-Dist: pytest >=6.2.5
 Requires-Dist: PyYAML >=6.0
@@ -30,13 +30,14 @@ Requires-Dist: torch ; extra == 'all'
 Requires-Dist: jax ; extra == 'all'
 Requires-Dist: jaxlib ; extra == 'all'
 Provides-Extra: cupy
-Requires-Dist: cupy ; extra == 'cupy'
+Requires-Dist: cupy-cuda12x ; extra == 'cupy'
 Requires-Dist: voltools ==0.6.0 ; extra == 'cupy'
 Provides-Extra: jax
 Requires-Dist: jax ; extra == 'jax'
 Requires-Dist: jaxlib ; extra == 'jax'
 Provides-Extra: pytorch
 Requires-Dist: torch ; extra == 'pytorch'
+Requires-Dist: torchvision ; extra == 'pytorch'
 
 # Python Template Matching Engine (PyTME)
 
@@ -47,9 +48,9 @@ Requires-Dist: torch ; extra == 'pytorch'
 
 PyTME is a Python library for data-intensive n-dimensional template matching using CPUs and GPUs.
 
-With its [backend-agnostic design](https://kosinskilab.github.io/pyTME/reference/backends.html), the same code can be run on diverse hardware platforms using a best-of-breed approach. The underyling abstract backend specification allows for adding new backends to benefit from gains in performance and capabilities without modifying the library's core routines. The implementation of template matching scores is modular and provides developers with a flexible framework for rapid prototyping. Furthermore, pyTME supports a unique callback capability through [analyzers](https://kosinskilab.github.io/pyTME/reference/analyzer.html), which allows for injection of custom code, enabling real-time processing and manipulation of results
+With its [backend-agnostic design](https://kosinskilab.github.io/pyTME/reference/backends.html), the same code can be run on diverse hardware platforms using a best-of-breed approach. The underyling abstract backend specification allows for adding new backends to benefit from gains in performance and capabilities without modifying the library's core routines. The implementation of template matching scores is modular and provides developers with a flexible framework for rapid prototyping. Furthermore, pyTME supports a unique callback capability through [analyzers](https://kosinskilab.github.io/pyTME/reference/analyzer.html), which allows for injection of custom code, enabling real-time processing and manipulation of results.
 
-PyTME includes a [graphical user interface](https://kosinskilab.github.io/pyTME/quickstart/preprocessing.html#practical-example) that provides simplified mask creation, interactive filter exploration, result visualization, and manual refinement capabilities. This GUI serves as an accessible entry point to the library's core functionalities, allowing users to efficiently interact with and analyze their data.
+PyTME includes a [graphical user interface](https://kosinskilab.github.io/pyTME/preprocessing/gui_example.html) that provides simplified mask creation, interactive filter exploration, result visualization, and manual refinement capabilities. This GUI serves as an accessible entry point to the library's core functionalities, allowing users to efficiently interact with and analyze their data.
 
 Finally, pyTME offers specialized tools for cryogenic electron microscopy data, such as wedge masks, CTF correction, as well as [means for handling structural data](https://kosinskilab.github.io/pyTME/reference/data_structure.html). Through dedicated [integrations](https://kosinskilab.github.io/pyTME/quickstart/integrations.html), the output of pyTME seamlessly integrates with commonly used cryogenic electron microscopy software such as RELION, Dynamo and IMOD.
 
@@ -68,17 +69,17 @@ We recommend installation using one of the following methods
 You can find alternative installation methods in the [documentation](https://kosinskilab.github.io/pyTME/quickstart/installation.html).
 
 
-## Quickstart
+## User Guide
 
 Learn how to get started with
 
-- [Preprocessing:](https://kosinskilab.github.io/pyTME/quickstart/preprocessing.html) Picking the right mask and filter for template matching.
-- [Template matching:](https://kosinskilab.github.io/pyTME/quickstart/match_template.html) Find your template of interest.
-- [Postprocessing](https://kosinskilab.github.io/pyTME/quickstart/postprocessing.html) Analyze template matching results and downstream integrations.
+- [Preprocessing:](https://kosinskilab.github.io/pyTME/quickstart/preprocessing/motivation.html) Picking the right mask and filter for template matching.
+- [Template matching:](https://kosinskilab.github.io/pyTME/quickstart/matching/motivation.html) Find your template of interest.
+- [Postprocessing](https://kosinskilab.github.io/pyTME/quickstart/postprocessing/motivation.html) Analyze template matching results and downstream integrations.
 
 ## How to Cite
 
-If PyTME contributed significantly to your research, please cite the corresponding publication on [SoftwareX](https://www.sciencedirect.com/science/article/pii/S2352711024000074).
+If pyTME contributed significantly to your research, please cite the corresponding publication on [SoftwareX](https://www.sciencedirect.com/science/article/pii/S2352711024000074).
 
 ```bibtex
 @article{Maurer:2024aa,

pytme-0.2.4.dist-info/RECORD

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{pytme-0.2.2.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-0.2.2.dist-info → pytme-0.2.4.dist-info}/top_level.txt

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

pytme-0.2.2.data/scripts/preprocess.py → scripts/eval.py

@@ -1,4 +1,4 @@
-#!python
+#!python3
 """ Apply tme.preprocessor.Preprocessor methods to an input file based
     on a provided yaml configuration obtaiend from preprocessor_gui.py.