microeye 2.3.4__tar.gz → 2.3.5__tar.gz

{microeye-2.3.4/src/microeye.egg-info → microeye-2.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: microeye
-Version: 2.3.4
+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-2.3.4 → 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-2.3.4 → microeye-2.3.5}/src/microEye/_version.py

@@ -1,2 +1,2 @@
-version_info = (2, 3, 4)
+version_info = (2, 3, 5)
 __version__ = '.'.join(map(str, version_info))

{microeye-2.3.4 → microeye-2.3.5}/src/microEye/analysis/tools/roi_selectors.py

@@ -403,19 +403,19 @@ class MultiRectangularROISelector:
             elif key == 3014656:  # Delete
                 if self.active_roi_idx != -1:
                     self.delete_active()
-            elif key == ord('a'):
+            elif key in [ord('a'), ord('A')]:
                 while self.current_mode != 'Add':
                     self.cycle_mode()
-            elif key == ord('e'):
+            elif key in [ord('e'), ord('E')]:
                 while self.current_mode != 'Edit':
                     self.cycle_mode()
-            elif key == ord('i'):
+            elif key in [ord('i'), ord('I')]:
                 while self.current_mode != 'Insert':
                     self.cycle_mode()
-            elif key == ord('m'):
+            elif key in [ord('m'), ord('M')]:
                 while self.current_mode != 'Move':
                     self.cycle_mode()
-            elif key == ord('r'):
+            elif key in [ord('r'), ord('R')]:
                 while self.current_mode != 'Remove':
                     self.cycle_mode()
 

{microeye-2.3.4 → microeye-2.3.5}/src/microEye/hardware/cams/camera_options.py

@@ -50,11 +50,15 @@ class CamParams(Enum):
     PREVIEW = 'Display.Preview'
     DISPLAY_STATS_OPTION = 'Display.Display Stats'
     AUTO_STRETCH = 'Display.Auto Stretch'
+    PLOT_TYPE = 'Display.Plot Type'
     VIEW_OPTIONS = 'Display.View Options'
     SINGLE_VIEW = 'Display.View Options.Single View'
-    DUAL_SIDE = 'Display.View Options.Dual Channel (Side by Side)'
-    DUAL_OVERLAID = 'Display.View Options.Dual Channel (Overlapped)'
+    DUAL_VIEW = 'Display.View Options.Dual Channel'
+    DUAL_OVERLAID = 'Display.View Options.Dual Channel (Overlaid)'
     ROIS_VIEW = 'Display.View Options.Export ROIs'
+    ROIS_VIEW_OVERLAID = 'Display.View Options.Export ROIs (Overlaid)'
+    # add colors for dual view RG, GB, GR, BR, BG, etc.
+    DUAL_VIEW_COLORS = 'Display.Dual View Colors'
     LINE_PROFILER = 'Display.Line Profiler'
     LUT = 'Display.LUT'
     LUT_NUMPY = 'Display.LUT Numpy (12bit)'
@@ -208,20 +212,36 @@ class CameraOptions(Tree):
                         'value': True,
                     },
                     {
-                        'name': str(CamParams.LUT),
+                        'name': str(CamParams.PLOT_TYPE),
                         'type': 'list',
-                        'limits': [str(CamParams.LUT_NUMPY), str(CamParams.LUT_OPENCV)],
+                        'limits': ['Histogram', 'Cumulative'],
                     },
                     {
                         'name': str(CamParams.VIEW_OPTIONS),
                         'type': 'list',
                         'limits': [
                             str(CamParams.SINGLE_VIEW),
-                            str(CamParams.DUAL_SIDE),
+                            str(CamParams.DUAL_VIEW),
                             str(CamParams.DUAL_OVERLAID),
                             str(CamParams.ROIS_VIEW),
+                            str(CamParams.ROIS_VIEW_OVERLAID),
                         ],
                     },
+                    {
+                        'name': str(CamParams.DUAL_VIEW_COLORS),
+                        'type': 'list',
+                        'limits': [
+                            'RG',
+                            'GB',
+                            'GR',
+                            'BR',
+                            'BG',
+                            'RB',
+                            'GB',
+                            'RG',
+                        ],
+                        'value': 'GB',
+                    },
                     {
                         'name': str(CamParams.LINE_PROFILER),
                         'type': 'bool',
@@ -501,8 +521,7 @@ class CameraOptions(Tree):
         for p, _, data in changes:
             path = self.param_tree.childPath(p)
 
-            self.paramsChanged.emit(
-                p, data)
+            self.paramsChanged.emit(p, data)
 
     @property
     def isTiff(self):
@@ -558,9 +577,17 @@ class CameraOptions(Tree):
             True if the view option is set to export ROIs view, False otherwise.
         '''
         return self.get_param_value(CamParams.VIEW_OPTIONS) in [
-            str(CamParams.ROIS_VIEW)
+            str(CamParams.ROIS_VIEW),
+            str(CamParams.ROIS_VIEW_OVERLAID),
         ]
 
+    @property
+    def isFlippedROIsView(self) -> bool:
+        '''
+        Check if the view option is set to export ROIs view with flipped ROIs.
+        '''
+        return self.get_param_value(CamParams.EXPORT_ROIS_FLIPPED)
+
     @property
     def isOverlaidView(self):
         '''
@@ -572,7 +599,8 @@ class CameraOptions(Tree):
             True if the view option is set to overlaid view, False otherwise.
         '''
         return self.get_param_value(CamParams.VIEW_OPTIONS) in [
-            str(CamParams.DUAL_OVERLAID)
+            str(CamParams.DUAL_OVERLAID),
+            str(CamParams.ROIS_VIEW_OVERLAID),
         ]
 
     @property
@@ -680,7 +708,7 @@ class CameraOptions(Tree):
         return self.get_param_value(CamParams.LINE_PROFILER)
 
     @property
-    def isNumpyLUT(self):
+    def isHistogramPlot(self):
         '''
         Check if the LUT option is set to numpy lut.
 
@@ -689,7 +717,24 @@ class CameraOptions(Tree):
         bool
             True if the LUT option is set to numpy lut, False otherwise.
         '''
-        return self.get_param_value(CamParams.LUT) in [str(CamParams.LUT_NUMPY)]
+        return self.get_param_value(CamParams.PLOT_TYPE) == 'Histogram'
+
+    @property
+    def dualViewColors(self):
+        '''
+        Get the dual view colors as channel indices.
+
+        Returns
+        -------
+        str
+            The selected dual view colors.
+        '''
+        # get the selected dual view colors from the parameter tree e.g. 'RG', 'GB', etc.
+        scheme = self.get_param_value(CamParams.DUAL_VIEW_COLORS)
+
+        indices = {'R': 0, 'G': 1, 'B': 2}
+
+        return [indices[c] for c in scheme]
 
 
 if __name__ == '__main__':