Merge pull request #135 from Alpaca233/save_merged_image

bug fix: channel colormap and configuration manager connections

software/control/_def.py

@@ -74,15 +74,6 @@ class Acquisition:
     NUMBER_OF_FOVS_PER_AF = 3
     IMAGE_FORMAT = "bmp"
     IMAGE_DISPLAY_SCALING_FACTOR = 0.3
-    PSEUDO_COLOR = False
-    MERGE_CHANNELS = False
-    PSEUDO_COLOR_MAP = {
-        "405": {"hex": 0x0000FF},  # blue
-        "488": {"hex": 0x00FF00},  # green
-        "561": {"hex": 0xFFCF00},  # yellow
-        "638": {"hex": 0xFF0000},  # red
-        "730": {"hex": 0x770000},  # dark red
-    }
     DX = 0.9
     DY = 0.9
     DZ = 1.5
@@ -657,8 +648,10 @@ class SOFTWARE_POS_LIMIT:
 IS_HCS = False
 DYNAMIC_REGISTRATION = False
 STITCH_COMPLETE_ACQUISITION = False
+
+# Pseudo color settings
 CHANNEL_COLORS_MAP = {
-    "405": {"hex": 0x3300FF, "name": "blue"},
+    "405": {"hex": 0x20ADF8, "name": "bop blue"},
     "488": {"hex": 0x1FFF00, "name": "green"},
     "561": {"hex": 0xFFCF00, "name": "yellow"},
     "638": {"hex": 0xFF0000, "name": "red"},
@@ -667,6 +660,8 @@ class SOFTWARE_POS_LIMIT:
     "G": {"hex": 0x1FFF00, "name": "green"},
     "B": {"hex": 0x3300FF, "name": "blue"},
 }
+SAVE_IN_PSEUDO_COLOR = False
+MERGE_CHANNELS = False
 
 # Emission filter wheel
 USE_ZABER_EMISSION_FILTER_WHEEL = False

software/control/core/core.py

@@ -1908,20 +1908,21 @@ def save_image(self, image, file_ID, config, current_path):
                 elif MULTIPOINT_BF_SAVING_OPTION == "Green Channel Only":
                     image = image[:, :, 1]
 
-        if Acquisition.PSEUDO_COLOR:
+        if SAVE_IN_PSEUDO_COLOR:
             image = self.return_pseudo_colored_image(image, config)
 
-        if Acquisition.MERGE_CHANNELS:
+        if MERGE_CHANNELS:
             self._save_merged_image(image, file_ID, current_path)
 
         iio.imwrite(saving_path, image)
 
     def _save_merged_image(self, image, file_ID, current_path):
         self.image_count += 1
+
         if self.image_count == 1:
             self.merged_image = image
         else:
-            self.merged_image += image
+            self.merged_image = np.maximum(self.merged_image, image)
 
             if self.image_count == len(self.selected_configurations):
                 if image.dtype == np.uint16:
@@ -1931,19 +1932,22 @@ def _save_merged_image(self, image, file_ID, current_path):
 
                 iio.imwrite(saving_path, self.merged_image)
                 self.image_count = 0
+
         return
 
     def return_pseudo_colored_image(self, image, config):
         if "405 nm" in config.name:
-            image = self.grayscale_to_rgb(image, Acquisition.PSEUDO_COLOR_MAP["405"]["hex"])
+            image = self.grayscale_to_rgb(image, CHANNEL_COLORS_MAP["405"]["hex"])
         elif "488 nm" in config.name:
-            image = self.grayscale_to_rgb(image, Acquisition.PSEUDO_COLOR_MAP["488"]["hex"])
+            image = self.grayscale_to_rgb(image, CHANNEL_COLORS_MAP["488"]["hex"])
         elif "561 nm" in config.name:
-            image = self.grayscale_to_rgb(image, Acquisition.PSEUDO_COLOR_MAP["561"]["hex"])
+            image = self.grayscale_to_rgb(image, CHANNEL_COLORS_MAP["561"]["hex"])
         elif "638 nm" in config.name:
-            image = self.grayscale_to_rgb(image, Acquisition.PSEUDO_COLOR_MAP["638"]["hex"])
+            image = self.grayscale_to_rgb(image, CHANNEL_COLORS_MAP["638"]["hex"])
         elif "730 nm" in config.name:
-            image = self.grayscale_to_rgb(image, Acquisition.PSEUDO_COLOR_MAP["730"]["hex"])
+            image = self.grayscale_to_rgb(image, CHANNEL_COLORS_MAP["730"]["hex"])
+        else:
+            image = np.stack([image] * 3, axis=-1)
 
         return image
 
@@ -1961,7 +1965,7 @@ def update_napari(self, image, config_name, k):
                 self.napari_layers_init.emit(image.shape[0], image.shape[1], image.dtype)
             pos = self.stage.get_pos()
             objective_magnification = str(int(self.objectiveStore.get_current_objective_info()["magnification"]))
-            self.napari_layers_update.emit(image, pos.x_mm, pos.y_mm, k, objective_magnification + "x_" + config_name)
+            self.napari_layers_update.emit(image, pos.x_mm, pos.y_mm, k, objective_magnification + "x " + config_name)
 
     def handle_dpc_generation(self, current_round_images):
         keys_to_check = [
@@ -3767,11 +3771,9 @@ def update_laser_af_settings(
             self.autofocus_configurations[objective].set_reference_image(crop_image)
 
 
-class ConfigurationManager(QObject):
+class ConfigurationManager:
     """Main configuration manager that coordinates channel and autofocus configurations."""
 
-    signal_profile_loaded = Signal()
-
     def __init__(
         self,
         channel_manager: ChannelConfigurationManager,
@@ -3821,8 +3823,6 @@ def load_profile(self, profile_name: str) -> None:
             if self.laser_af_manager:
                 self.laser_af_manager.load_configurations(objective)
 
-        self.signal_profile_loaded.emit()
-
     def create_new_profile(self, profile_name: str) -> None:
         """Create a new profile using current configurations."""
         new_profile_path = self.base_config_path / profile_name

software/control/gui_hcs.py

@@ -572,9 +572,7 @@ 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)
         if ENABLE_NL5:
             import control.NL5Widget as NL5Widget
 
@@ -1022,7 +1020,7 @@ def makeConnections(self):
             self.wellSelectionWidget.signal_wellSelected.connect(self.wellplateMultiPointWidget.update_well_coordinates)
             self.objectivesWidget.signal_objective_changed.connect(self.wellplateMultiPointWidget.update_coordinates)
 
-        self.configurationManager.signal_profile_loaded.connect(
+        self.profileWidget.signal_profile_changed.connect(
             lambda: self.liveControlWidget.update_microscope_mode_by_name(
                 self.liveControlWidget.currentConfiguration.name
             )
@@ -1040,7 +1038,7 @@ def slot_settings_changed_laser_af():
                 self.laserAutofocusControlWidget.update_init_state()
                 self.laserAutofocusSettingWidget.update_values()
 
-            self.configurationManager.signal_profile_loaded.connect(slot_settings_changed_laser_af)
+            self.profileWidget.signal_profile_changed.connect(slot_settings_changed_laser_af)
             self.objectivesWidget.signal_objective_changed.connect(slot_settings_changed_laser_af)
             self.laserAutofocusSettingWidget.signal_newExposureTime.connect(
                 self.cameraSettingWidget_focus_camera.set_exposure_time
@@ -1082,6 +1080,16 @@ def slot_settings_changed_laser_af():
                     self.piezoWidget.update_displacement_um_display
                 )
 
+        if ENABLE_SPINNING_DISK_CONFOCAL:
+            self.spinningDiskConfocalWidget.signal_toggle_confocal_widefield.connect(
+                self.channelConfigurationManager.toggle_confocal_widefield
+            )
+            self.spinningDiskConfocalWidget.signal_toggle_confocal_widefield.connect(
+                lambda: self.liveControlWidget.update_microscope_mode_by_name(
+                    self.liveControlWidget.currentConfiguration.name
+                )
+            )
+
         self.camera.set_callback(self.streamHandler.on_new_frame)
 
     def setup_movement_updater(self):

software/control/widgets.py

@@ -643,10 +643,11 @@ def show_cross_correlation_result(self, value):
 
 
 class SpinningDiskConfocalWidget(QWidget):
-    def __init__(self, xlight, config_manager=None):
-        super(SpinningDiskConfocalWidget, self).__init__()
 
-        self.config_manager = config_manager
+    signal_toggle_confocal_widefield = Signal(bool)
+
+    def __init__(self, xlight):
+        super(SpinningDiskConfocalWidget, self).__init__()
 
         self.xlight = xlight
 
@@ -660,8 +661,7 @@ def __init__(self, xlight, config_manager=None):
 
         self.disk_position_state = self.xlight.get_disk_position()
 
-        if self.config_manager:
-            self.config_manager.toggle_confocal_widefield(self.disk_position_state)
+        self.signal_toggle_confocal_widefield.emit(self.disk_position_state)  # signal initial state
 
         if self.disk_position_state == 1:
             self.btn_toggle_widefield.setText("Switch to Widefield")
@@ -780,9 +780,8 @@ def toggle_disk_position(self):
         else:
             self.disk_position_state = self.xlight.set_disk_position(1)
             self.btn_toggle_widefield.setText("Switch to Widefield")
-        if self.config_manager is not None:
-            self.config_manager.toggle_confocal_widefield(self.disk_position_state)
         self.enable_all_buttons()
+        self.signal_toggle_confocal_widefield.emit(self.disk_position_state)
 
     def toggle_motor(self):
         self.disable_all_buttons()
@@ -5271,6 +5270,7 @@ def finishedSaving(self, output_path, dtype):
         self.output_path = output_path
 
     def extractWavelength(self, name):
+        # TODO: Use the 'color' attribute of the ChannelMode object
         # Split the string and find the wavelength number immediately after "Fluorescence"
         parts = name.split()
         if "Fluorescence" in parts: