microeye 2.3.3__tar.gz → 2.3.5__tar.gz

{microeye-2.3.3/src/microeye.egg-info → microeye-2.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: microeye
-Version: 2.3.3
+Version: 2.3.5
 Summary: A python toolkit for fluorescence microscopy         that features hardware control, data analysis and vizualization         for super-resolution single-molecule localization microscopy and         single-partical tracking.
 Home-page: https://github.com/samhitech/microEye
 Author: Mohammad Nour Alsamsam
@@ -49,8 +49,7 @@ Requires-Dist: tables==3.9.1
 Requires-Dist: tabulate==0.9.0
 Requires-Dist: tqdm==4.66.4
 Requires-Dist: tifffile==2024.8.10
-Requires-Dist: vispy==0.14.2
-Requires-Dist: zarr==2.18.2
+Requires-Dist: zarr>=2.18.2
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -96,11 +95,11 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
 ```bash
-   __  ____              ____                ___    ____   ____
-  /  |/  (_)__________  / __/_ _____   _  __|_  |  |_  /  |_  /
- / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __/_ _/_ <_ _/_ <
-/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)____(_)____/
-                          /___/
+ __  __ _            ___               ___   ____  ___ 
+|  \/  (_)__ _ _ ___| __|  _ ___  __ _|_  ) |__ / | __|
+| |\/| | / _| '_/ _ \ _| || / -_) \ V // / _ |_ \_|__ \
+|_|  |_|_\__|_| \___/___\_, \___|  \_//___(_)___(_)___/
+                        |__/
 ```
 
 ## Table of Contents
@@ -281,18 +280,21 @@ microEye --module viewer
 
 The `microEye` uses the following Python packages:
 
-| Data Analysis and Visualization | GUI and UI Development | Code Quality and Formatting | Image and Video Processing | File and Data Storage | Other Utilities |
-| ------------------------------- | ---------------------- | --------------------------- | -------------------------- | --------------------- | --------------- |
-| dask                            | PySide6                | autopep8                    | opencv-python              | ome-types             | hidapi          |
-| matplotlib                      | pyqtdarktheme          | pyflakes                    |                            | tables                | pyfiglet        |
-| numba                           | pyqtgraph              |                             |                            | zarr                  | pyserial        |
-| numpy                           | QDarkStyle             |                             |                            |                       | pyjokes         |
-| pandas                          | QScintilla             |                             |                            |                       | setuptools      |
-| scikit-image                    | PyQt5 (optional)       |                             |                            |                       | tabulate        |
-| scikit_learn                    | PyQt6 (optional)       |                             |                            |                       | pyueye          |
-| scipy                           |                        |                             |                            |                       |                 |
-| tifffile                        |                        |                             |                            |                       |                 |
-| vispy                           |                        |                             |                            |                       |                 |
+| Data Analysis and Visualization | GUI and UI Development | Code Quality and Formatting | Image and Video Processing | File and Data Storage | Other Utilities |  Microscopy  |
+| :-----------------------------: | :--------------------: | :-------------------------: | :------------------------: | :-------------------: | :-------------: | :----------: |
+|              dask               |        PySide6         |          autopep8           |       opencv-python        |       ome-types       |     hidapi      | pycromanager |
+|           matplotlib            |     pyqtdarktheme      |          pyflakes           |                            |        tables         |    pyfiglet     |              |
+|              numba              |       pyqtgraph        |                             |                            |         zarr          |    pyserial     |              |
+|              numpy              |       QDarkStyle       |                             |                            |                       |     pyjokes     |              |
+|             pandas              |       QScintilla       |                             |                            |                       |   setuptools    |              |
+|          scikit-image           |    PyQt5 (optional)    |                             |                            |                       |    tabulate     |              |
+|          scikit_learn           |    PyQt6 (optional)    |                             |                            |                       |     pyueye      |              |
+|              scipy              |                        |                             |                            |                       |      tqdm       |              |
+|            tifffile             |                        |                             |                            |                       |                 |              |
+|              h5py               |                        |                             |                            |                       |                 |              |
+|               pco               |                        |                             |                            |                       |                 |              |
+|                                 |                        |                             |                            |                       |                 |              |
+|            PyOpenGL             |                        |                             |                            |                       |                 |              |
 
 Note: VimbaPython is included in Vimba SDK and needs to be installed manually.
 

{microeye-2.3.3 → microeye-2.3.5}/README.md

@@ -31,11 +31,11 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
 ```bash
-   __  ____              ____                ___    ____   ____
-  /  |/  (_)__________  / __/_ _____   _  __|_  |  |_  /  |_  /
- / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __/_ _/_ <_ _/_ <
-/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)____(_)____/
-                          /___/
+ __  __ _            ___               ___   ____  ___ 
+|  \/  (_)__ _ _ ___| __|  _ ___  __ _|_  ) |__ / | __|
+| |\/| | / _| '_/ _ \ _| || / -_) \ V // / _ |_ \_|__ \
+|_|  |_|_\__|_| \___/___\_, \___|  \_//___(_)___(_)___/
+                        |__/
 ```
 
 ## Table of Contents
@@ -216,18 +216,21 @@ microEye --module viewer
 
 The `microEye` uses the following Python packages:
 
-| Data Analysis and Visualization | GUI and UI Development | Code Quality and Formatting | Image and Video Processing | File and Data Storage | Other Utilities |
-| ------------------------------- | ---------------------- | --------------------------- | -------------------------- | --------------------- | --------------- |
-| dask                            | PySide6                | autopep8                    | opencv-python              | ome-types             | hidapi          |
-| matplotlib                      | pyqtdarktheme          | pyflakes                    |                            | tables                | pyfiglet        |
-| numba                           | pyqtgraph              |                             |                            | zarr                  | pyserial        |
-| numpy                           | QDarkStyle             |                             |                            |                       | pyjokes         |
-| pandas                          | QScintilla             |                             |                            |                       | setuptools      |
-| scikit-image                    | PyQt5 (optional)       |                             |                            |                       | tabulate        |
-| scikit_learn                    | PyQt6 (optional)       |                             |                            |                       | pyueye          |
-| scipy                           |                        |                             |                            |                       |                 |
-| tifffile                        |                        |                             |                            |                       |                 |
-| vispy                           |                        |                             |                            |                       |                 |
+| Data Analysis and Visualization | GUI and UI Development | Code Quality and Formatting | Image and Video Processing | File and Data Storage | Other Utilities |  Microscopy  |
+| :-----------------------------: | :--------------------: | :-------------------------: | :------------------------: | :-------------------: | :-------------: | :----------: |
+|              dask               |        PySide6         |          autopep8           |       opencv-python        |       ome-types       |     hidapi      | pycromanager |
+|           matplotlib            |     pyqtdarktheme      |          pyflakes           |                            |        tables         |    pyfiglet     |              |
+|              numba              |       pyqtgraph        |                             |                            |         zarr          |    pyserial     |              |
+|              numpy              |       QDarkStyle       |                             |                            |                       |     pyjokes     |              |
+|             pandas              |       QScintilla       |                             |                            |                       |   setuptools    |              |
+|          scikit-image           |    PyQt5 (optional)    |                             |                            |                       |    tabulate     |              |
+|          scikit_learn           |    PyQt6 (optional)    |                             |                            |                       |     pyueye      |              |
+|              scipy              |                        |                             |                            |                       |      tqdm       |              |
+|            tifffile             |                        |                             |                            |                       |                 |              |
+|              h5py               |                        |                             |                            |                       |                 |              |
+|               pco               |                        |                             |                            |                       |                 |              |
+|                                 |                        |                             |                            |                       |                 |              |
+|            PyOpenGL             |                        |                             |                            |                       |                 |              |
 
 Note: VimbaPython is included in Vimba SDK and needs to be installed manually.
 

{microeye-2.3.3 → microeye-2.3.5}/src/microEye/_version.py

@@ -1,2 +1,2 @@
-version_info = (2, 3, 3)
+version_info = (2, 3, 5)
 __version__ = '.'.join(map(str, version_info))

{microeye-2.3.3 → microeye-2.3.5}/src/microEye/analysis/filters/__init__.py

@@ -1,9 +1,8 @@
-from microEye.analysis.filters.base import AbstractFilter
+from microEye.analysis.filters.base import AbstractFilter, SpatialFilter, TemporalFilter
 from microEye.analysis.filters.spatial import (
-    BANDPASS_TYPES,
-    BandpassFilter,
+    BackgroundReduction,
     DoG_Filter,
-    GaussFilter,
+    FourierFilter,
     PassFilter,
 )
 from microEye.analysis.filters.temporal import TemporalMedianFilter

microeye-2.3.5/src/microEye/analysis/filters/base.py

@@ -0,0 +1,62 @@
+from abc import ABC, abstractmethod
+from typing import Optional
+
+import numpy as np
+from PyQt5 import QtWidgets
+
+
+class AbstractFilter(ABC):
+    def __init__(self, name: str = 'Abstract Base Filter', parameters: dict = None):
+        self._name = name
+        self._parameters = parameters or {}
+        self._show_filter = False
+
+    @abstractmethod
+    def run(self, image: np.ndarray) -> np.ndarray:
+        '''Apply the filter to the input image.'''
+        pass
+
+    def getWidget(self):
+        '''Return the QWidget for configuring the filter.'''
+        return QtWidgets.QWidget()
+
+    def get_metadata(self) -> dict:
+        '''Return metadata about the filter.'''
+        return {
+            'name': self.name,
+            'parameters': self._parameters,
+        }
+
+    @classmethod
+    def get_tree_parameters(cls) -> dict:
+        '''Return the parameters for the pyqtgraph tree view.'''
+        return None
+
+    @property
+    def name(self):
+        return self._name
+
+    @property
+    def parameters(self) -> Optional[dict]:
+        return self._parameters
+
+class SpatialFilter(AbstractFilter):
+    '''Base class for spatial filters.'''
+    def __init__(self, name: str = 'Spatial Filter', parameters: dict = None):
+        super().__init__(name=name, parameters=parameters)
+
+    @abstractmethod
+    def run(self, image: np.ndarray) -> np.ndarray:
+        '''Apply the spatial filter to the input image.'''
+        pass
+
+
+class TemporalFilter(AbstractFilter):
+    '''Base class for temporal filters.'''
+    def __init__(self, name: str = 'Temporal Filter', parameters: dict = None):
+        super().__init__(name=name, parameters=parameters)
+
+    @abstractmethod
+    def run(self, image: np.ndarray) -> np.ndarray:
+        '''Apply the temporal filter to the input image.'''
+        pass