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Cephla-Lab · Feb 24, 2025 · 3323ab5 · 3323ab5
1 parent 4ba7838
commit 3323ab5
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Showing 8 changed files with 302 additions and 224 deletions.
diff --git a/software/control/_def.py b/software/control/_def.py
@@ -435,6 +435,7 @@ class PLATE_READER:
 ENABLE_TRACKING = False
 TRACKING_SHOW_MICROSCOPE_CONFIGURATIONS = False  # set to true when doing multimodal acquisition
 
+
 class AF:
     STOP_THRESHOLD = 0.85
     CROP_WIDTH = 800

diff --git a/software/control/core/core.py b/software/control/core/core.py
diff --git a/software/control/gui_hcs.py b/software/control/gui_hcs.py
@@ -236,7 +236,9 @@ def loadObjects(self, is_simulation):
             self.laserAFSettingManager = core.LaserAFSettingManager()
         else:
             self.laserAFSettingManager = None
-        self.configurationManager = core.ConfigurationManager(channel_manager=self.channelConfigurationManager, laser_af_manager=self.laserAFSettingManager)
+        self.configurationManager = core.ConfigurationManager(
+            channel_manager=self.channelConfigurationManager, laser_af_manager=self.laserAFSettingManager
+        )
         self.contrastManager = core.ContrastManager()
         self.streamHandler = core.StreamHandler()
 
@@ -309,7 +311,7 @@ def loadObjects(self, is_simulation):
                 self.stage,
                 self.piezo,
                 self.objectiveStore,
-                self.laserAFSettingManager
+                self.laserAFSettingManager,
             )
 
         if USE_SQUID_FILTERWHEEL:
@@ -547,7 +549,9 @@ def waitForMicrocontroller(self, timeout=5.0, error_message=None):
     def loadWidgets(self):
         # Initialize all GUI widgets
         if ENABLE_SPINNING_DISK_CONFOCAL:
-            self.spinningDiskConfocalWidget = widgets.SpinningDiskConfocalWidget(self.xlight, self.channelConfigurationManager)
+            self.spinningDiskConfocalWidget = widgets.SpinningDiskConfocalWidget(
+                self.xlight, self.channelConfigurationManager
+            )
         if ENABLE_NL5:
             import control.NL5Widget as NL5Widget
 
@@ -684,7 +688,9 @@ def loadWidgets(self):
                 show_configurations=TRACKING_SHOW_MICROSCOPE_CONFIGURATIONS,
             )
         if ENABLE_STITCHER:
-            self.stitcherWidget = widgets.StitcherWidget(self.objectiveStore, self.channelConfigurationManager, self.contrastManager)
+            self.stitcherWidget = widgets.StitcherWidget(
+                self.objectiveStore, self.channelConfigurationManager, self.contrastManager
+            )
 
         self.recordTabWidget = QTabWidget()
         self.setupRecordTabWidget()
@@ -978,19 +984,20 @@ def makeConnections(self):
             self.wellSelectionWidget.signal_wellSelected.connect(self.wellplateMultiPointWidget.update_well_coordinates)
             self.objectivesWidget.signal_objective_changed.connect(self.wellplateMultiPointWidget.update_coordinates)
 
-        self.objectivesWidget.signal_objective_changed.connect(lambda: self.liveControlWidget.update_microscope_mode_by_name(
-            self.liveControlWidget.currentConfiguration.name
-            ))
+        self.objectivesWidget.signal_objective_changed.connect(
+            lambda: self.liveControlWidget.update_microscope_mode_by_name(
+                self.liveControlWidget.currentConfiguration.name
+            )
+        )
 
         if SUPPORT_LASER_AUTOFOCUS:
+
             def connect_objective_changed_laser_af():
                 self.laserAutofocusController.on_objective_changed()
                 self.laserAutofocusControlWidget.update_init_state()
                 self.laserAutofocusSettingWidget.update_values()
 
-            self.objectivesWidget.signal_objective_changed.connect(
-                connect_objective_changed_laser_af
-            )
+            self.objectivesWidget.signal_objective_changed.connect(connect_objective_changed_laser_af)
             self.laserAutofocusSettingWidget.signal_newExposureTime.connect(
                 self.cameraSettingWidget_focus_camera.set_exposure_time
             )
@@ -1001,8 +1008,12 @@ def connect_objective_changed_laser_af():
                 self.laserAutofocusControlWidget.update_init_state
             )
 
-            self.laserAutofocusSettingWidget.update_exposure_time(self.laserAutofocusSettingWidget.exposure_spinbox.value())
-            self.laserAutofocusSettingWidget.update_analog_gain(self.laserAutofocusSettingWidget.analog_gain_spinbox.value())
+            self.laserAutofocusSettingWidget.update_exposure_time(
+                self.laserAutofocusSettingWidget.exposure_spinbox.value()
+            )
+            self.laserAutofocusSettingWidget.update_analog_gain(
+                self.laserAutofocusSettingWidget.analog_gain_spinbox.value()
+            )
 
             self.streamHandler_focus_camera.signal_new_frame_received.connect(
                 self.liveController_focus_camera.on_new_frame

diff --git a/software/control/utils.py b/software/control/utils.py
@@ -395,4 +395,4 @@ def get_script_dir(follow_symlinks=True):
         return f"{repo.head.object.hexsha} (dirty={repo.is_dirty()})"
     except git.GitError as e:
         _log.warning(f"Failed to get script git repo info: {e}")
-        return None
+        return None
diff --git a/software/control/utils_channel.py b/software/control/utils_channel.py
@@ -1,5 +1,6 @@
 from control._def import CHANNEL_COLORS_MAP
 
+
 def extract_wavelength_from_config_name(name):
     # Split the string and find the wavelength number immediately after "Fluorescence"
     parts = name.split()
@@ -14,5 +15,7 @@ def extract_wavelength_from_config_name(name):
 
 
 def get_channel_color(channel):
-    channel_info = CHANNEL_COLORS_MAP.get(extract_wavelength_from_config_name(channel), {"hex": 0xFFFFFF, "name": "gray"})
-    return channel_info["hex"]
+    channel_info = CHANNEL_COLORS_MAP.get(
+        extract_wavelength_from_config_name(channel), {"hex": 0xFFFFFF, "name": "gray"}
+    )
+    return channel_info["hex"]