Merge pull request #976 from annie-xd-wang/973-expansion-microscope

973 expansion microscope

Author: AdvancedImagingUTSW

src/navigate/config/config.py

@@ -360,6 +360,7 @@ def verify_experiment_config(manager, configuration):
         "is_centered": True,
         "center_x": 1024,
         "center_y": 1024,
+        "readout_time": 0,
     }
     if (
         "CameraParameters" not in configuration["experiment"]
@@ -371,58 +372,73 @@ def verify_experiment_config(manager, configuration):
             "CameraParameters",
             camera_parameters_dict_sample,
         )
-    camera_setting_dict = configuration["experiment"]["CameraParameters"]
-    for k in camera_parameters_dict_sample:
-        if k not in camera_setting_dict.keys():
-            camera_setting_dict[k] = camera_parameters_dict_sample[k]
-    # binning
-    if camera_setting_dict["binning"] not in ["1x1", "2x2", "4x4"]:
-        camera_setting_dict["binning"] = "1x1"
-    # x_pixels and y_pixels
-    try:
-        camera_setting_dict["x_pixels"] = int(camera_setting_dict["x_pixels"])
-    except ValueError:
-        camera_setting_dict["x_pixels"] = camera_parameters_dict_sample["x_pixels"]
-
-    try:
-        camera_setting_dict["y_pixels"] = int(camera_setting_dict["y_pixels"])
-    except ValueError:
-        camera_setting_dict["y_pixels"] = camera_parameters_dict_sample["y_pixels"]
-
-    # image width and height
-    if camera_setting_dict["x_pixels"] <= 0:
-        camera_setting_dict["x_pixels"] = camera_parameters_dict_sample["x_pixels"]
-    if camera_setting_dict["y_pixels"] <= 0:
-        camera_setting_dict["y_pixels"] = camera_parameters_dict_sample["y_pixels"]
-    x_binning = int(camera_setting_dict["binning"][0])
-    y_binning = int(camera_setting_dict["binning"][2])
-    img_x_pixels = camera_setting_dict["x_pixels"] // x_binning
-    img_y_pixels = camera_setting_dict["y_pixels"] // y_binning
-    camera_setting_dict["img_x_pixels"] = img_x_pixels
-    camera_setting_dict["img_y_pixels"] = img_y_pixels
-    if camera_setting_dict["is_centered"]:
-        camera_setting_dict["center_x"] = camera_setting_dict["x_pixels"] // 2
-        camera_setting_dict["center_y"] = camera_setting_dict["y_pixels"] // 2
-
-    # sensor mode
-    if camera_setting_dict["sensor_mode"] not in ["Normal", "Light-Sheet"]:
-        camera_setting_dict["sensor_mode"] = "Normal"
-    if camera_setting_dict["readout_direction"] not in [
-        "Top-to-Bottom",
-        "Bottom-to-Top",
-        "Bidirectional",
-        "Rev. Bidirectional",
-    ]:
-        camera_setting_dict["readout_direction"] = "Top-to-Bottom"
-
-    # databuffer_size, number_of_pixels
-    for k in ["databuffer_size", "number_of_pixels", "frames_to_average"]:
+    microscope_names = [""] + list(configuration["configuration"]["microscopes"].keys())
+    for microscope_name in microscope_names:
+        camera_setting_dict = configuration["experiment"]["CameraParameters"]
+        if microscope_name:
+            if (
+                microscope_name not in camera_setting_dict
+                or type(camera_setting_dict[microscope_name]) is not DictProxy
+            ):
+                update_config_dict(
+                    manager,
+                    camera_setting_dict,
+                    microscope_name,
+                    camera_parameters_dict_sample,
+                )
+            camera_setting_dict = camera_setting_dict[microscope_name]
+
+        for k in camera_parameters_dict_sample:
+            if k not in camera_setting_dict.keys():
+                camera_setting_dict[k] = camera_parameters_dict_sample[k]
+        # binning
+        if camera_setting_dict["binning"] not in ["1x1", "2x2", "4x4"]:
+            camera_setting_dict["binning"] = "1x1"
+        # x_pixels and y_pixels
         try:
-            camera_setting_dict[k] = int(camera_setting_dict[k])
+            camera_setting_dict["x_pixels"] = int(camera_setting_dict["x_pixels"])
         except ValueError:
-            camera_setting_dict[k] = camera_parameters_dict_sample[k]
-        if camera_setting_dict[k] < 1:
-            camera_setting_dict[k] = camera_parameters_dict_sample[k]
+            camera_setting_dict["x_pixels"] = camera_parameters_dict_sample["x_pixels"]
+
+        try:
+            camera_setting_dict["y_pixels"] = int(camera_setting_dict["y_pixels"])
+        except ValueError:
+            camera_setting_dict["y_pixels"] = camera_parameters_dict_sample["y_pixels"]
+
+        # image width and height
+        if camera_setting_dict["x_pixels"] <= 0:
+            camera_setting_dict["x_pixels"] = camera_parameters_dict_sample["x_pixels"]
+        if camera_setting_dict["y_pixels"] <= 0:
+            camera_setting_dict["y_pixels"] = camera_parameters_dict_sample["y_pixels"]
+        x_binning = int(camera_setting_dict["binning"][0])
+        y_binning = int(camera_setting_dict["binning"][2])
+        img_x_pixels = camera_setting_dict["x_pixels"] // x_binning
+        img_y_pixels = camera_setting_dict["y_pixels"] // y_binning
+        camera_setting_dict["img_x_pixels"] = img_x_pixels
+        camera_setting_dict["img_y_pixels"] = img_y_pixels
+        if camera_setting_dict["is_centered"]:
+            camera_setting_dict["center_x"] = camera_setting_dict["x_pixels"] // 2
+            camera_setting_dict["center_y"] = camera_setting_dict["y_pixels"] // 2
+
+        # sensor mode
+        if camera_setting_dict["sensor_mode"] not in ["Normal", "Light-Sheet"]:
+            camera_setting_dict["sensor_mode"] = "Normal"
+        if camera_setting_dict["readout_direction"] not in [
+            "Top-to-Bottom",
+            "Bottom-to-Top",
+            "Bidirectional",
+            "Rev. Bidirectional",
+        ]:
+            camera_setting_dict["readout_direction"] = "Top-to-Bottom"
+
+        # databuffer_size, number_of_pixels
+        for k in ["databuffer_size", "number_of_pixels", "frames_to_average"]:
+            try:
+                camera_setting_dict[k] = int(camera_setting_dict[k])
+            except ValueError:
+                camera_setting_dict[k] = camera_parameters_dict_sample[k]
+            if camera_setting_dict[k] < 1:
+                camera_setting_dict[k] = camera_parameters_dict_sample[k]
 
     # stage parameters
     stage_dict_sample = {}

src/navigate/controller/controller.py

@@ -312,11 +312,18 @@ def update_buffer(self):
             Size dictated by x_pixels, y_pixels, an number_of_frames in
             configuration file.
         """
+        microscope_name = self.configuration["experiment"]["MicroscopeState"][
+            "microscope_name"
+        ]
         img_width = int(
-            self.configuration["experiment"]["CameraParameters"]["img_x_pixels"]
+            self.configuration["experiment"]["CameraParameters"][microscope_name][
+                "img_x_pixels"
+            ]
         )
         img_height = int(
-            self.configuration["experiment"]["CameraParameters"]["img_y_pixels"]
+            self.configuration["experiment"]["CameraParameters"][microscope_name][
+                "img_y_pixels"
+            ]
         )
         if img_width == self.img_width and img_height == self.img_height:
             return
@@ -325,11 +332,6 @@ def update_buffer(self):
         self.img_width = img_width
         self.img_height = img_height
 
-        # virtual microscopes
-        for microscope_name in list(self.additional_microscopes.keys()):
-            self.destroy_virtual_microscope(microscope_name)
-        self.additional_microscopes = {}
-
     def update_acquire_control(self):
         """Update the acquire control based on the current experiment parameters."""
         self.view.acqbar.stop_stage.config(
@@ -356,6 +358,7 @@ def change_microscope(self, microscope_name, zoom=None):
             self.stage_controller.initialize()
             self.channels_tab_controller.initialize()
             self.camera_setting_controller.update_camera_device_related_setting()
+            self.camera_setting_controller.populate_experiment_values()
             self.camera_setting_controller.calculate_physical_dimensions()
             self.camera_view_controller.update_snr()
 
@@ -451,10 +454,15 @@ def update_experiment_setting(self):
 
         """
         warning_message = self.camera_setting_controller.update_experiment_values()
+        microscope_name = self.configuration["experiment"]["MicroscopeState"][
+            "microscope_name"
+        ]
 
         # set waveform template
         if self.acquire_bar_controller.mode in ["live", "single", "z-stack"]:
-            camera_setting = self.configuration["experiment"]["CameraParameters"]
+            camera_setting = self.configuration["experiment"]["CameraParameters"][
+                microscope_name
+            ]
             if camera_setting["sensor_mode"] == "Light-Sheet" and camera_setting[
                 "readout_direction"
             ] in ["Bidirectional", "Rev. Bidirectional"]:
@@ -482,6 +490,13 @@ def update_experiment_setting(self):
         # TODO: validate experiment dict
 
         warning_message += self.channels_tab_controller.verify_experiment_values()
+
+        # additional microscopes
+        for microscope_name in self.additional_microscopes_configs:
+            if hasattr(self, f"{microscope_name.lower()}_camera_setting_controller"):
+                getattr(
+                    self, f"{microscope_name.lower()}_camera_setting_controller"
+                ).update_experiment_values()
         if warning_message:
             return warning_message
         return ""
@@ -557,6 +572,14 @@ def set_mode_of_sub(self, mode):
         self.camera_setting_controller.set_mode(mode)
         self.mip_setting_controller.set_mode(mode)
         self.waveform_tab_controller.set_mode(mode)
+
+        # additional microscopes
+        for microscope_name in self.additional_microscopes_configs:
+            if hasattr(self, f"{microscope_name.lower()}_camera_setting_controller"):
+                getattr(
+                    self, f"{microscope_name.lower()}_camera_setting_controller"
+                ).set_mode(mode)
+
         if mode == "stop":
             # GUI Failsafe
             self.acquire_bar_controller.stop_acquire()
@@ -987,15 +1010,18 @@ def capture_image(self, command, mode, *args):
             return
         self.acquire_bar_controller.view.acquire_btn.configure(text="Stop")
         self.acquire_bar_controller.view.acquire_btn.configure(state="normal")
+        microscope_name = self.configuration["experiment"]["MicroscopeState"][
+            "microscope_name"
+        ]
 
         self.camera_view_controller.initialize_non_live_display(
             self.configuration["experiment"]["MicroscopeState"],
-            self.configuration["experiment"]["CameraParameters"],
+            self.configuration["experiment"]["CameraParameters"][microscope_name],
         )
 
         self.mip_setting_controller.initialize_non_live_display(
             self.configuration["experiment"]["MicroscopeState"],
-            self.configuration["experiment"]["CameraParameters"],
+            self.configuration["experiment"]["CameraParameters"][microscope_name],
         )
 
         self.stop_acquisition_flag = False
@@ -1076,11 +1102,15 @@ def capture_image(self, command, mode, *args):
     def launch_additional_microscopes(self):
         """Launch additional microscopes."""
 
-        def display_images(camera_view_controller, show_img_pipe, data_buffer):
+        def display_images(
+            microscope_name, camera_view_controller, show_img_pipe, data_buffer
+        ):
             """Display images from additional microscopes.
 
             Parameters
             ----------
+            microscope_name : str
+                Microscope name
             camera_view_controller : CameraViewController
                 Camera View Controller object.
             show_img_pipe : multiprocessing.Pipe
@@ -1091,9 +1121,8 @@ def display_images(camera_view_controller, show_img_pipe, data_buffer):
                 configuration file.
             """
             camera_view_controller.initialize_non_live_display(
-                data_buffer,
                 self.configuration["experiment"]["MicroscopeState"],
-                self.configuration["experiment"]["CameraParameters"],
+                self.configuration["experiment"]["CameraParameters"][microscope_name],
             )
             images_received = 0
             while True:
@@ -1122,72 +1151,51 @@ def display_images(camera_view_controller, show_img_pipe, data_buffer):
                     break
                 images_received += 1
 
-        # destroy unnecessary additional microscopes
-        temp = []
-        for microscope_name in self.additional_microscopes:
-            if microscope_name not in self.additional_microscopes_configs:
-                temp.append(microscope_name)
-        for microscope_name in temp:
+        # destroy all additional microscopes
+        for microscope_name in list(self.additional_microscopes.keys()):
             self.destroy_virtual_microscope(microscope_name)
+        self.additional_microscopes = {}
 
         # show additional camera view popup
         for microscope_name in self.additional_microscopes_configs:
-            if microscope_name not in self.additional_microscopes:
-                show_img_pipe = self.model.create_pipe(
-                    f"{microscope_name}_show_img_pipe"
-                )
-                data_buffer = self.model.launch_virtual_microscope(
-                    microscope_name,
-                    self.additional_microscopes_configs[microscope_name],
-                )
+            show_img_pipe = self.model.create_pipe(f"{microscope_name}_show_img_pipe")
+            data_buffer = self.model.launch_virtual_microscope(
+                microscope_name,
+                self.additional_microscopes_configs[microscope_name],
+            )
 
-                self.additional_microscopes[microscope_name] = {
-                    "show_img_pipe": show_img_pipe,
-                    "data_buffer": data_buffer,
-                }
-            if (
-                self.additional_microscopes[microscope_name].get(
-                    "camera_view_controller", None
-                )
-                is None
-            ):
-                popup_window = CameraViewPopupWindow(self.view, microscope_name)
-                camera_view_controller = CameraViewController(
-                    popup_window.camera_view, self
-                )
-                camera_view_controller.data_buffer = self.additional_microscopes[
-                    microscope_name
-                ]["data_buffer"]
-                popup_window.popup.bind("<Configure>", camera_view_controller.resize)
-                self.additional_microscopes[microscope_name][
-                    "popup_window"
-                ] = popup_window
-                self.additional_microscopes[microscope_name][
-                    "camera_view_controller"
-                ] = camera_view_controller
-                popup_window.popup.protocol(
-                    "WM_DELETE_WINDOW",
-                    combine_funcs(
-                        popup_window.popup.dismiss,
-                        lambda: self.additional_microscopes[microscope_name].pop(
-                            "camera_view_controller"
-                        ),
+            self.additional_microscopes[microscope_name] = {
+                "show_img_pipe": show_img_pipe,
+                "data_buffer": data_buffer,
+            }
+            popup_window = CameraViewPopupWindow(self.view, microscope_name)
+            camera_view_controller = CameraViewController(
+                popup_window.camera_view, self
+            )
+            camera_view_controller.data_buffer = self.additional_microscopes[
+                microscope_name
+            ]["data_buffer"]
+            camera_view_controller.microscope_name = microscope_name
+            popup_window.popup.bind("<Configure>", camera_view_controller.resize)
+            self.additional_microscopes[microscope_name]["popup_window"] = popup_window
+            self.additional_microscopes[microscope_name][
+                "camera_view_controller"
+            ] = camera_view_controller
+            popup_window.popup.protocol(
+                "WM_DELETE_WINDOW",
+                combine_funcs(
+                    popup_window.popup.dismiss,
+                    lambda: self.additional_microscopes[microscope_name].pop(
+                        "camera_view_controller"
                     ),
-                )
-
-            # clear show_img_pipe
-            show_img_pipe = self.additional_microscopes[microscope_name][
-                "show_img_pipe"
-            ]
-            while show_img_pipe.poll():
-                image_id = show_img_pipe.recv()
-                if image_id == "stop":
-                    break
+                ),
+            )
 
             # start thread
             capture_img_thread = threading.Thread(
                 target=display_images,
                 args=(
+                    microscope_name,
                     self.additional_microscopes[microscope_name][
                         "camera_view_controller"
                     ],