microeye 2.3.7__tar.gz → 2.3.9__tar.gz

{microeye-2.3.7/src/microeye.egg-info → microeye-2.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: microeye
-Version: 2.3.7
+Version: 2.3.9
 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
@@ -70,6 +70,14 @@ The **`microEye`** is a Python toolkit for fluorescence microscopy that supports
 
 This toolkit is compatible with the [hardware](#hardware) used in our microscope. For further details, refer to the [miEye microscope paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy).
 
+```bash
+ __  __ _            ___               ___   ____ ___ 
+|  \/  (_)__ _ _ ___| __|  _ ___  __ _|_  ) |__ // _ \
+| |\/| | / _| '_/ _ \ _| || / -_) \ V // / _ |_ \\_, /
+|_|  |_|_\__|_| \___/___\_, \___|  \_//___(_)___(_)_/ 
+                        |__/
+```
+
 ![Package Health](https://snyk.io/advisor/python/microEye/badge.svg)
 ![Python Version](https://img.shields.io/badge/Python->=3.9_|_<3.12-blue)
 ![Package Version](https://img.shields.io/pypi/v/microEye.svg)
@@ -94,14 +102,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Forks](https://img.shields.io/github/forks/samhitech/microEye.svg)
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
-```bash
-   __  ____              ____                ___    ____ ____
-  /  |/  (_)__________  / __/_ _____   _  __|_  |  |_  //_  /
- / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __/_ _/_ <_ / / 
-/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)____(_)_/  
-                          /___/
-```
-
 ## Table of Contents
 
 - [The microEye](#the-microeye)

{microeye-2.3.7 → microeye-2.3.9}/README.md

@@ -6,6 +6,14 @@ The **`microEye`** is a Python toolkit for fluorescence microscopy that supports
 
 This toolkit is compatible with the [hardware](#hardware) used in our microscope. For further details, refer to the [miEye microscope paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy).
 
+```bash
+ __  __ _            ___               ___   ____ ___ 
+|  \/  (_)__ _ _ ___| __|  _ ___  __ _|_  ) |__ // _ \
+| |\/| | / _| '_/ _ \ _| || / -_) \ V // / _ |_ \\_, /
+|_|  |_|_\__|_| \___/___\_, \___|  \_//___(_)___(_)_/ 
+                        |__/
+```
+
 ![Package Health](https://snyk.io/advisor/python/microEye/badge.svg)
 ![Python Version](https://img.shields.io/badge/Python->=3.9_|_<3.12-blue)
 ![Package Version](https://img.shields.io/pypi/v/microEye.svg)
@@ -30,14 +38,6 @@ This toolkit is compatible with the [hardware](#hardware) used in our microscope
 ![GitHub Forks](https://img.shields.io/github/forks/samhitech/microEye.svg)
 ![GitHub Stars](https://img.shields.io/github/stars/samhitech/microEye.svg)
 
-```bash
-   __  ____              ____                ___    ____ ____
-  /  |/  (_)__________  / __/_ _____   _  __|_  |  |_  //_  /
- / /|_/ / / __/ __/ _ \/ _// // / -_) | |/ / __/_ _/_ <_ / / 
-/_/  /_/_/\__/_/  \___/___/\_, /\__/  |___/____(_)____(_)_/  
-                          /___/
-```
-
 ## Table of Contents
 
 - [The microEye](#the-microeye)

{microeye-2.3.7 → microeye-2.3.9}/src/microEye/_version.py

@@ -1,2 +1,2 @@
-version_info = (2, 3, 7)
+version_info = (2, 3, 9)
 __version__ = '.'.join(map(str, version_info))

{microeye-2.3.7 → microeye-2.3.9}/src/microEye/analysis/multi_viewer.py

@@ -203,6 +203,10 @@ class multi_viewer(QMainWindow):
         # Connect double-click signal to a method that uses QTimer
         self.tree.doubleClicked.connect(self._open_file)
 
+        # Create Tree view context menu
+        self.tree.setContextMenuPolicy(Qt.CustomContextMenu)
+        self.tree.customContextMenuRequested.connect(self._show_tree_context_menu)
+
         # Add the File system tab contents
         self.imsq_pattern = QtWidgets.QLineEdit('/image_0*.ome.tif')
 
@@ -210,6 +214,66 @@ class multi_viewer(QMainWindow):
         self.file_tree_layout.addWidget(self.imsq_pattern)
         self.file_tree_layout.addWidget(self.tree)
 
+    def _show_tree_context_menu(self, position):
+        index = self.tree.indexAt(position)
+        if not index.isValid():
+            return
+
+        menu = QtWidgets.QMenu()
+        reveal_action = menu.addAction('Reveal in Explorer')
+        new_folder_action = menu.addAction('New Folder')
+        menu.addSeparator()
+
+        # Root path shortcuts
+        root_action = menu.addAction('This PC (Root Path)')
+        home_action = menu.addAction('Home (User Directory)')
+        desktop_action = menu.addAction('Desktop')
+        initial_action = menu.addAction('Initial Path')
+        working_dir_action = menu.addAction('Working Directory')
+
+        action = menu.exec(self.tree.viewport().mapToGlobal(position))
+        if action == reveal_action:
+            path = self.model.filePath(index)
+            folder = path if os.path.isdir(path) else os.path.dirname(path)
+            os.startfile(folder)
+        elif action == new_folder_action:
+            self._create_new_folder()
+        elif action == home_action:
+            home = os.path.expanduser('~')
+            self.tree.setRootIndex(self.model.index(home))
+        elif action == desktop_action:
+            desktop = os.path.join(os.path.expanduser('~'), 'Desktop')
+            self.tree.setRootIndex(self.model.index(desktop))
+        elif action == root_action:
+            self.tree.setRootIndex(self.model.index(''))
+        elif action == initial_action:
+            self.tree.setRootIndex(self.model.index(self.path))
+        elif action == working_dir_action:
+            self.tree.setRootIndex(
+                self.model.index(os.path.dirname(os.path.abspath(__package__)))
+            )
+
+    def _create_new_folder(self):
+        index = self.tree.currentIndex()
+        if not index.isValid():
+            return
+
+        path = self.model.filePath(index)
+        if not os.path.isdir(path):
+            path = os.path.dirname(path)
+
+        new_folder_name, ok = QtWidgets.QInputDialog.getText(
+            self, 'New Folder', 'Enter folder name:'
+        )
+        if ok and new_folder_name:
+            new_folder_path = os.path.join(path, new_folder_name)
+            try:
+                os.makedirs(new_folder_path)
+            except OSError as e:
+                QtWidgets.QMessageBox.critical(
+                    self, 'Error', f'Could not create folder: {e}'
+                )
+
     def tabifyDocks(self):
         # Tabify docks
         pass

{microeye-2.3.7 → microeye-2.3.9}/src/microEye/analysis/viewer/localizations.py

@@ -285,23 +285,25 @@ class LocalizationsView(QtWidgets.QWidget):
         ndarray or None
             Rendered super-res image or None.
         '''
-        for idx, localizations in enumerate(self.fittingResults):
-            if localizations is None:
-                continue
+        if not self.fittingResults:
+            return
 
-            if len(localizations) <= 0:
-                continue
+        images = [None] * len(self.fittingResults)
 
-            render_idx = self.render_cbox.currentData()
-            projection = self.projection_cbox.currentData()
+        render_idx = self.render_cbox.currentData()
+        projection = self.projection_cbox.currentData()
+        xy_bin = self.xy_binsize.value()
+        z_bin = self.z_binsize.value()
+        auto_levels = self.auto_level.isChecked()
+
+        renderer = BaseRenderer(xy_bin, z_bin, RenderModes(render_idx))
+
+        for idx, localizations in enumerate(self.fittingResults):
+            if not localizations or len(localizations) <= 0:
+                continue
 
-            renderClass = BaseRenderer(
-                self.xy_binsize.value(),
-                self.z_binsize.value(),
-                RenderModes(render_idx),
-            )
             if 0 <= projection < 3:
-                img = renderClass.render(
+                rendered_img = renderer.render(
                     Projection(projection),
                     localizations.data[DataColumns.X],
                     localizations.data[DataColumns.Y],
@@ -309,29 +311,15 @@ class LocalizationsView(QtWidgets.QWidget):
                     localizations.data[DataColumns.INTENSITY],
                 )
 
-                self.setImage(
-                    img, index=idx, autoLevels=self.auto_level.isChecked()
-                )
-
-                if projection == 0:
-                    self.view_box.setAspectLocked(True, 1)
-                else:
-                    self.view_box.setAspectLocked(
-                        True, self.xy_binsize.value() / self.z_binsize.value()
-                    )
+                aspect = 1 if projection == 0 else xy_bin / z_bin
+                self.view_box.setAspectLocked(True, aspect)
             elif 3 <= projection < 6:
-                projection -= 3
-
-                if projection == 0:
-                    self.view_box.setAspectLocked(True, 1)
-                    width = self.z_binsize.value()
-                else:
-                    self.view_box.setAspectLocked(
-                        True, self.xy_binsize.value() / self.z_binsize.value()
-                    )
-                    width = self.xy_binsize.value()
+                slice_proj = projection - 3
+                aspect = 1 if slice_proj == 0 else xy_bin / z_bin
+                self.view_box.setAspectLocked(True, aspect)
+                width = z_bin if slice_proj == 0 else xy_bin
 
-                img = renderClass.render_slice(
+                rendered_img = renderer.render_slice(
                     Projection(projection),
                     localizations.data[DataColumns.X],
                     localizations.data[DataColumns.Y],
@@ -340,10 +328,13 @@ class LocalizationsView(QtWidgets.QWidget):
                     self.position.value(),
                     width,
                 )
+            else:
+                continue
 
-                self.setImage(
-                    img, index=idx, autoLevels=self.auto_level.isChecked()
-                )
+            self.setImage(rendered_img, index=idx, autoLevels=auto_levels)
+            images[idx] = rendered_img
+
+        return images
 
     def extract_z(self):
         '''Extract Z values from the fitting results.'''
@@ -1276,7 +1267,7 @@ class LocalizationsView(QtWidgets.QWidget):
                     )
 
             if 'Super-res image' in options:
-                sres_img = self.render_loc()
+                sres_img = self.render_loc()[self.image_layers.currentIndex]
                 tf.imwrite(
                     re.sub(r'(\.h5|\.tsv)$', '_super_res.tif', filename),
                     sres_img,

{microeye-2.3.7 → microeye-2.3.9}/src/microEye/hardware/lasers/io_matchbox.py

@@ -74,7 +74,7 @@ class io_combiner(QtCore.QObject):
     '''TBA
     '''
 
-    DataReady = Signal(str, bytes)
+    DataReady = Signal(object, bytes)
 
     Max_Power = 0.0
 
@@ -133,10 +133,8 @@ class io_combiner(QtCore.QObject):
 
         self.ser = serial.Serial(
             baudrate=kwargs.get('baudrate', 115200),  # Default baudrate
-            port=kwargs.get('port', 'COM1'),  # Default port
             timeout=kwargs.get('timeout', 0.5),  # Default timeout
             write_timeout=kwargs.get('write_timeout', 0.5),  # Default write timeout
-            open=False,  # Start with the port closed
         )
 
         self._lock = threading.Lock()  # Add this line
@@ -740,6 +738,8 @@ class CombinerLaserWidget(Tree):
         self.set_param_value(MB_Params.FIRMWARE, self.Laser.Firmware)
         self.set_param_value(MB_Params.SERIAL, self.Laser.Serial)
 
+        self.timer.start()  # Start the timer to update stats
+
         if not self._laserSwitches:
             for idx in range(len(self.Laser.Wavelengths)):
                 if self.Laser.Wavelengths[idx] > 0:
@@ -778,7 +778,7 @@ class CombinerLaserWidget(Tree):
         '''
         if self.Laser.isOpen():
 
-            def fetch_stats():
+            def fetch_stats(event):
                 '''
                 Fetches the current readings and settings from the laser device.
                 '''
@@ -793,10 +793,11 @@ class CombinerLaserWidget(Tree):
 
                 return {}, {}
 
-            def done(readings: dict, settings: dict):
+            def done(result: tuple[dict, dict]):
                 '''
                 Updates the parameter tree with the fetched readings and settings.
                 '''
+                readings, settings = result
                 if readings:
                     for key, value in readings.items():
                         if isinstance(value, (int, float)):

{microeye-2.3.7 → microeye-2.3.9}/src/microEye/hardware/lasers/io_single_laser.py

@@ -103,10 +103,8 @@ class io_single_laser(QtCore.QObject):
 
         self.ser = serial.Serial(
             baudrate=kwargs.get('baudrate', 115200),  # Default baudrate
-            port=kwargs.get('port', 'COM1'),  # Default port
             timeout=kwargs.get('timeout', 0.5),  # Default timeout
             write_timeout=kwargs.get('write_timeout', 0.5),  # Default write timeout
-            open=False,  # Start with the port closed
         )
 
         self._lock = threading.Lock()  # Add this line
@@ -718,6 +716,8 @@ class SingleMatchBox(Tree):
         self.set_param_value(MB_Params.FIRMWARE, self.Laser.Firmware)
         self.set_param_value(MB_Params.SERIAL, self.Laser.Serial)
 
+        self.timer.start()
+
     def update_stats(self):
         '''
         Updates the statistics displayed in the MatchBox GUI.
@@ -732,7 +732,7 @@ class SingleMatchBox(Tree):
         '''
         if self.Laser.isOpen():
 
-            def fetch_stats():
+            def fetch_stats(event):
                 '''
                 Fetches the current readings and settings from the laser device.
                 '''
@@ -746,10 +746,11 @@ class SingleMatchBox(Tree):
 
                 return {}, {}
 
-            def done(readings: dict, settings: dict):
+            def done(result: tuple[dict, dict]):
                 '''
                 Updates the parameter tree with the fetched readings and settings.
                 '''
+                readings, settings = result
                 if readings:
                     for key, value in readings.items():
                         if isinstance(value, (int, float)):