Merge pull request #699 from TheDeanLab/adaptive-optics+develop-20231128

Adaptive Optics final merge (at the buzzer)

Author: AdvancedImagingUTSW

.gitignore

@@ -295,3 +295,4 @@ src/aslm/log_files/LOGS
 test.n5
 test_dir
 test.xml
+*_log.txt

src/aslm/controller/configuration_controller.py

@@ -374,3 +374,26 @@ def number_of_channels(self):
         if self.microscope_config is not None:
             return self.configuration["configuration"]["gui"]["channels"]["count"]
         return 5
+
+    @property
+    def microscope_list(self):
+        """Return a list of microscope names
+
+        Returns
+        -------
+        microscope_list : list
+            List of microscope names.
+        """
+        return list(self.configuration["configuration"]["microscopes"].keys())
+
+    def get_zoom_value_list(self, microscope_name):
+        """Return a list of zoom values
+
+        Returns
+        -------
+        zoom_value_list : list
+            List of zoom values.
+        """
+        return self.configuration["waveform_constants"]["remote_focus_constants"][
+            microscope_name
+        ].keys()

src/aslm/controller/controller.py

@@ -61,6 +61,8 @@
     AcquireBarController,
     FeaturePopupController,
     MenuController,
+    # MicroscopePopupController,
+    # AdaptiveOpticsPopupController,
 )
 
 from aslm.controller.thread_pool import SynchronizedThreadPool
@@ -298,30 +300,35 @@ def update_acquire_control(self):
             command=self.stage_controller.stop_button_handler
         )
 
-    def change_microscope(self, microscope_name):
+    def change_microscope(self, microscope_name, zoom=None):
         """Change the microscope configuration.
 
         Parameters
         ----------
         microscope_name : string
             Name of the microscope to change to.
+        zoom : string
+            Name of the zoom value to change to.
         """
         self.configuration["experiment"]["MicroscopeState"][
             "microscope_name"
         ] = microscope_name
+        if zoom:
+            self.configuration["experiment"]["MicroscopeState"]["zoom"] = zoom
         if self.configuration_controller.change_microscope():
             # update widgets
             self.stage_controller.initialize()
             self.channels_tab_controller.initialize()
             self.camera_setting_controller.update_camera_device_related_setting()
             self.camera_setting_controller.calculate_physical_dimensions()
-            if (
-                hasattr(self, "waveform_popup_controller")
-                and self.waveform_popup_controller
-            ):
-                self.waveform_popup_controller.populate_experiment_values()
             self.camera_view_controller.update_snr()
 
+        if (
+            hasattr(self, "waveform_popup_controller")
+            and self.waveform_popup_controller
+        ):
+            self.waveform_popup_controller.populate_experiment_values()
+
     def initialize_cam_view(self):
         """Populate view tab.
 
@@ -590,22 +597,28 @@ def execute(self, command, *args):
 
             Parameters
             ----------
-            args : dict
-                dict = {'resolution_mode': self.resolution,
-                'zoom': self.mag,
-                'laser_info': self.resolution_info[
-                'remote_focus_constants'][self.resolution][self.mag]
-                }
+            args : str
+                "microscope_name zoom_value", "microscope_name", or "zoom_value"
             """
-            microscope_name, zoom = self.menu_controller.resolution_value.get().split()
-            self.configuration["experiment"]["MicroscopeState"]["zoom"] = zoom
-            if (
-                microscope_name
-                != self.configuration["experiment"]["MicroscopeState"][
-                    "microscope_name"
-                ]
-            ):
-                self.change_microscope(microscope_name)
+            # get microscope name and zoom value from args[0]
+            temp = args[0].split()
+            if len(temp) == 1:
+                # microscope name is given
+                if temp[0] in self.configuration_controller.microscope_list:
+                    temp.append(
+                        self.configuration_controller.get_zoom_value_list(temp[0])[0]
+                    )
+                elif temp[0] in self.configuration_controller.get_zoom_value_list(
+                    self.configuration_controller.microscope_name
+                ):
+                    temp = [self.configuration_controller.microscope_name, temp[0]]
+                else:
+                    return
+            resolution_value = " ".join(temp)
+            if resolution_value != self.menu_controller.resolution_value.get():
+                self.menu_controller.resolution_value.set(resolution_value)
+                return
+            self.change_microscope(temp[0], temp[1])
             work_thread = self.threads_pool.createThread(
                 "model", lambda: self.model.run_command("update_setting", "resolution")
             )
@@ -647,6 +660,30 @@ def execute(self, command, *args):
                 "model", lambda: self.model.run_command("stage_limits", *args)
             )
 
+        # mirror commands:
+        elif command == "flatten_mirror":
+            self.model.run_command("flatten_mirror", *args)
+        elif command == "zero_mirror":
+            self.model.run_command("zero_mirror", *args)
+        elif command == "set_mirror":
+            self.model.run_command("set_mirror", *args)
+        elif command == "set_mirror_from_wcs":
+            self.model.run_command("set_mirror_from_wcs", *args)
+        elif command == "save_wcs_file":
+            self.model.run_command("save_wcs_file", *args)
+        elif command == "tony_wilson":
+            self.threads_pool.createThread(
+                "camera",
+                self.capture_image,
+                args=(
+                    "tony_wilson",
+                    "live",
+                ),
+            )
+
+        # elif command == "change_camera":
+        #     self.model.run_command("change_camera", *args)
+
         elif command == "autofocus":
             """Execute autofocus routine."""
             self.threads_pool.createThread(
@@ -1091,6 +1128,18 @@ def update_event(self):
                         data=value[0], line_plot=value[1], clear_data=value[2]
                     )
 
+            elif event == "tonywilson":
+                if hasattr(self, "ao_popup_controller"):
+                    # self.ao_popup_controller.set_widgets_from_coef(value['coefs'])
+                    self.ao_popup_controller.plot_tonywilson(value)
+                    # self.ao_popup_controller.plot_mirror(value)
+                    if value["done"]:
+                        print("Tony Wilson done! Updating expt...")
+                        self.ao_popup_controller.update_experiment_values()
+            elif event == "mirror_update":
+                if hasattr(self, "ao_popup_controller"):
+                    self.ao_popup_controller.set_widgets_from_coef(value["coefs"])
+                    self.ao_popup_controller.plot_mirror(value)
             elif event == "stop":
                 # Stop the software
                 break

src/aslm/controller/sub_controllers/__init__.py

@@ -6,12 +6,15 @@
 from .waveform_tab_controller import WaveformTabController  # noqa
 from .waveform_popup_controller import WaveformPopupController  # noqa
 from .autofocus_popup_controller import AutofocusPopupController  # noqa
-from .features_popup_controller import FeaturePopupController #noqa
-from .feature_advanced_setting_controller import FeatureAdvancedSettingController #noqa
+from .features_popup_controller import FeaturePopupController  # noqa
+from .feature_advanced_setting_controller import (
+    FeatureAdvancedSettingController,  # noqa
+)
 from .keystroke_controller import KeystrokeController  # noqa
 from .multi_position_controller import MultiPositionController  # noqa
 from .ilastik_popup_controller import IlastikPopupController  # noqa
 from .camera_map_setting_popup_controller import CameraMapSettingPopupController  # noqa
 from .microscope_popup_controller import MicroscopePopupController  # noqa
-from .help_popup_controller import HelpPopupController #noqa
-from .menu_controller import MenuController  # noqa
+from .help_popup_controller import HelpPopupController  # noqa
+from .adaptiveoptics_popup_controller import AdaptiveOpticsPopupController  # noqa
+from .menu_controller import MenuController  # noqa