Stage limits popup

src/navigate/config/config.py

@@ -208,8 +208,7 @@ def update_config_dict(
     config_name : str
         Name of dictionary to replace
     new_config : dict or str
-        Dictionary values or
-        yaml file name
+        Dictionary values or yaml file name
 
     Returns
     -------
@@ -751,16 +750,16 @@ def verify_waveform_constants(manager, configuration):
                         # "delay",
                     ]:
                         if k not in waveform_dict[microscope_name][zoom][laser].keys():
-                            waveform_dict[microscope_name][zoom][laser][
-                                k
-                            ] = config_dict["remote_focus"].get(k, "0")
+                            waveform_dict[microscope_name][zoom][laser][k] = (
+                                config_dict["remote_focus"].get(k, "0")
+                            )
                         else:
                             try:
                                 float(waveform_dict[microscope_name][zoom][laser][k])
                             except ValueError:
-                                waveform_dict[microscope_name][zoom][laser][
-                                    k
-                                ] = config_dict["remote_focus"].get(k, "0")
+                                waveform_dict[microscope_name][zoom][laser][k] = (
+                                    config_dict["remote_focus"].get(k, "0")
+                                )
 
             # delete non-exist lasers
             for k in waveform_dict[microscope_name][zoom].keys():
@@ -1004,24 +1003,16 @@ def verify_configuration(manager, configuration):
                 laser_hardware_config = {"type": "Synthetic"}
             laser_hardware_config["wavelength"] = laser_config["wavelength"]
 
-            update_config_dict(
-                manager,
-                laser_config,
-                "hardware",
-                laser_hardware_config
-            )
+            update_config_dict(manager, laser_config, "hardware", laser_hardware_config)
 
         # zoom
         zoom_config = device_config[microscope_name]["zoom"]
         if "hardware" not in zoom_config:
             update_config_dict(
-                manager,
-                zoom_config,
-                "hardware",
-                {"type": "Synthetic", "servo_id": 0}
+                manager, zoom_config, "hardware", {"type": "Synthetic", "servo_id": 0}
             )
         elif "type" not in zoom_config["hardware"]:
-                zoom_config["hardware"]["type"] = "Synthetic"
+            zoom_config["hardware"]["type"] = "Synthetic"
 
         filter_wheel_config = device_config[microscope_name]["filter_wheel"]
         if type(filter_wheel_config) == DictProxy:
@@ -1034,7 +1025,6 @@ def verify_configuration(manager, configuration):
                 [filter_wheel_config],
             )
 
-
         temp_config = device_config[microscope_name]["filter_wheel"]
         for _, filter_wheel_config in enumerate(temp_config):
             filter_wheel_idx = build_ref_name(
@@ -1091,7 +1081,7 @@ def verify_positions_config(positions):
         return []
 
     position_num = len(positions)
-    for i in range(position_num - 1, start_index-1, -1):
+    for i in range(position_num - 1, start_index - 1, -1):
         position = positions[i]
         try:
             for j in range(len(position)):
@@ -1101,6 +1091,7 @@ def verify_positions_config(positions):
 
     return positions
 
+
 def support_deceased_configuration(configuration):
     """Support old version of configurations.
 
@@ -1120,7 +1111,9 @@ def support_deceased_configuration(configuration):
     for microscope_name in device_config.keys():
         microscope_config = device_config[microscope_name]
         if "remote_focus_device" in microscope_config.keys():
-            microscope_config["remote_focus"] = microscope_config.pop("remote_focus_device")
+            microscope_config["remote_focus"] = microscope_config.pop(
+                "remote_focus_device"
+            )
             is_updated = True
         if "lasers" in microscope_config.keys():
             microscope_config["laser"] = microscope_config.pop("lasers")
@@ -1136,4 +1129,3 @@ def support_deceased_configuration(configuration):
                 if stage["type"] in deceased_device_type_names:
                     stage["type"] = deceased_device_type_names[stage["type"]]
                     is_updated = True
-

src/navigate/controller/configuration_controller.py

@@ -77,7 +77,14 @@ def __init__(self, configuration):
             )
         )
 
-    def change_microscope(self) -> bool:
+    def update_configuration(self) -> None:
+        """Update the microscope configuration to reflect any changes made to it."""
+
+        self.microscope_config = self.configuration["configuration"]["microscopes"][
+            self.microscope_name
+        ]
+
+    def change_microscope(self, microscope_name=None) -> bool:
         """Get the new microscope configuration dict according to the name.
 
         Gets the name of the microscope, retrieves its configuration, and updates the
@@ -87,9 +94,11 @@ def change_microscope(self) -> bool:
         -------
         result: bool
         """
-        microscope_name = self.configuration["experiment"]["MicroscopeState"][
-            "microscope_name"
-        ]
+        if microscope_name is None:
+            microscope_name = self.configuration["experiment"]["MicroscopeState"][
+                "microscope_name"
+            ]
+
         assert (
             microscope_name in self.configuration["configuration"]["microscopes"].keys()
         )
@@ -255,7 +264,9 @@ def get_stage_position_limits(self, suffix):
         if self.microscope_config is not None:
             stage_dict = self.microscope_config["stage"]
             for a in axes:
-                position_limits[a] = stage_dict.get(a + suffix, 0 if suffix == "_min" else 100)
+                position_limits[a] = stage_dict.get(
+                    a + suffix, 0 if suffix == "_min" else 100
+                )
         else:
             for a in axes:
                 position_limits[a] = 0 if suffix == "_min" else 100
@@ -279,7 +290,7 @@ def stage_flip_flags(self):
         for axis in self.stage_axes:
             flip_flags[axis] = stage_dict.get(f"flip_{axis}", False)
         return flip_flags
-    
+
     @property
     def stage_axes(self):
         """Return the axes of the stage
@@ -298,9 +309,9 @@ def stage_axes(self):
             else:
                 axes = list(stage_config["axes"])
             return axes
-        
+
         return ["x", "y"]
-    
+
     @property
     def all_stage_axes(self):
         """Return all the axes of the stage
@@ -411,6 +422,20 @@ def stage_setting_dict(self):
             return self.microscope_config["stage"]
         return None
 
+    @property
+    def has_analog_stage(self):
+        """Check to see if the has_ni_galvo_stage flag is set in the configuration.
+
+        Returns
+        -------
+        has_ni_galvo_stage : bool
+            True if the microscope has an NI galvo stage, False otherwise.
+        """
+
+        if self.microscope_config is not None:
+            return self.microscope_config["stage"].get("has_ni_galvo_stage", False)
+        return False
+
     def get_stages_by_axis(self, axis_prefix="z"):
         """Return a list of all stage names.
 
@@ -430,7 +455,12 @@ def get_stages_by_axis(self, axis_prefix="z"):
                 stages = list(stages)
             else:
                 stages = [stages]
-            return [f"{stage['type']} - {axis}" for stage in stages for axis in stage["axes"] if axis.startswith(axis_prefix)]
+            return [
+                f"{stage['type']} - {axis}"
+                for stage in stages
+                for axis in stage["axes"]
+                if axis.startswith(axis_prefix)
+            ]
         return []
 
     @property

src/navigate/controller/sub_controllers/__init__.py

@@ -19,6 +19,7 @@
 from .microscope_popup import MicroscopePopupController  # noqa
 from .adaptive_optics import AdaptiveOpticsPopupController  # noqa
 from .histogram import HistogramController  # noqa
+from .stages_advanced import AdvancedStageParametersController  # noqa
 
 # from .uninstall_plugin_controller import UninstallPluginController  # noqa
 from .plugins import PluginsController, UninstallPluginController  # noqa

src/navigate/controller/sub_controllers/menus.py

@@ -43,7 +43,7 @@
 
 # Third Party Imports
 
-# Local Imports
+# Local View Imports
 from navigate.view.popups.ilastik_setting_popup import ilastik_setting_popup
 from navigate.view.popups.autofocus_setting_popup import AutofocusPopup
 from navigate.view.popups.adaptiveoptics_popup import AdaptiveOpticsPopup
@@ -53,6 +53,9 @@
 )
 from navigate.view.popups.feature_list_popup import FeatureListPopup
 from navigate.view.popups.camera_setting_popup import CameraSettingPopup
+from navigate.view.popups.stages_advanced_popup import AdvancedStageParametersPopup
+
+# Local Controller Imports
 from navigate.controller.sub_controllers.gui import GUIController
 from navigate.controller.sub_controllers import (
     AutofocusPopupController,
@@ -65,7 +68,10 @@
     FeatureAdvancedSettingController,
     AdaptiveOpticsPopupController,
     UninstallPluginController,
+    AdvancedStageParametersController,
 )
+
+# Local Tools Imports
 from navigate.tools.file_functions import save_yaml_file, load_yaml_file
 from navigate.tools.decorators import FeatureList
 from navigate.tools.common_functions import load_module_from_file, combine_funcs
@@ -359,6 +365,14 @@ def initialize_menus(self):
                     None,
                 ],
                 "add_separator_1": [None, None, None, None, None],
+                "Advanced Stage Parameters": [
+                    "standard",
+                    self.stage_limits_popup,
+                    None,
+                    None,
+                    None,
+                ],
+                "add_separator_2": [None, None, None, None, None],
             },
         }
         self.populate_menu(stage_control_menu)
@@ -1002,17 +1016,25 @@ def popup_help(self) -> None:
     def toggle_stage_limits(self, *args) -> None:
         """Toggle stage limits."""
         if self.disable_stage_limits.get() == 1:
+            limits_enabled = False
             self.parent_controller.configuration["experiment"]["StageParameters"][
                 "limits"
-            ] = False
+            ] = limits_enabled
             logger.debug("Disabling stage limits")
-            self.parent_controller.execute("stage_limits", False)
+            self.parent_controller.execute("stage_limits", limits_enabled)
         else:
+            limits_enabled = True
             self.parent_controller.configuration["experiment"]["StageParameters"][
                 "limits"
-            ] = True
+            ] = limits_enabled
             logger.debug("Enabling stage limits")
-            self.parent_controller.execute("stage_limits", True)
+            self.parent_controller.execute("stage_limits", limits_enabled)
+
+        # If the stage limits popup is open, update it.
+        if hasattr(self.parent_controller, "stage_limits_popup_controller"):
+            self.parent_controller.stage_limits_popup_controller.view.enable_stage_limits_var.set(
+                limits_enabled
+            )
 
     @log_function_call
     def popup_autofocus_setting(self, *args) -> None:
@@ -1422,3 +1444,18 @@ def func(*args):
                 )
 
         return func
+
+    def stage_limits_popup(self, *args, **kwargs) -> None:
+        """Pop up the Stage Limits setting window."""
+        if hasattr(self.parent_controller, "stage_limits_popup_controller"):
+            self.parent_controller.stage_limits_popup_controller.showup()
+            return
+        popup = AdvancedStageParametersPopup(self.view)
+        stage_limits_controller = AdvancedStageParametersController(
+            popup, self.parent_controller
+        )
+        setattr(
+            self.parent_controller,
+            "stage_limits_popup_controller",
+            stage_limits_controller,
+        )

src/navigate/controller/sub_controllers/stages.py

@@ -179,8 +179,6 @@ def __init__(
             command=self.parent_controller.channels_tab_controller.update_end_position
         )
 
-
-
     def stage_key_press(self, event: tk.Event) -> None:
         """The stage key press.
 
@@ -210,6 +208,7 @@ def initialize(self) -> None:
         """Initialize the Stage limits of steps and positions."""
         config = self.parent_controller.configuration_controller
         self.stage_axes = config.stage_axes
+
         # disable stages not available for the current microscope
         for axis in set(config.all_stage_axes) - set(self.stage_axes):
             stage_frame = getattr(self.view, f"{axis}_frame")
@@ -310,7 +309,7 @@ def disable_synthetic_stages(self, config: ConfigurationController) -> None:
                 elif axis == "y":
                     self.view.xy_frame.toggle_button_states(flag, ["y"])
                     self.view.position_frame.inputs["y"].widget.config(state=state)
-                
+
                 else:
                     stage_frame = getattr(self.view, f"{axis}_frame")
                     stage_frame.toggle_button_states(flag, [axis])
@@ -621,6 +620,7 @@ def update_step_size_handler(self, axis: str) -> Callable[[], None]:
         handler : Callable[[], None]
             Function to update step size in experiment.yml.
         """
+
         def func(*args):
             """Callback functions bind to step size variables."""
             microscope_name = self.parent_controller.configuration["experiment"][
@@ -659,15 +659,19 @@ def set_hover_descriptions(self) -> None:
                 description = f"\N{GREEK SMALL LETTER MU}m in {axis.upper()}."
 
             for i in range(len(btn_prefix)):
-                exec(f"self.view.{frame_prefix}_frame.{btn_prefix[i]}_{btn_suffix}.hover."
-                     f"setdescription('Move {step_multiple[i] * step_value} {description}')")
+                exec(
+                    f"self.view.{frame_prefix}_frame.{btn_prefix[i]}_{btn_suffix}.hover."
+                    f"setdescription('Move {step_multiple[i] * step_value} {description}')"
+                )
 
         # Position Frame
         for axis in self.stage_axes:
             if axis == "theta":
                 description = "Theta stage position in degrees."
             else:
-                description = f"{axis.upper()} stage position in \N{GREEK SMALL LETTER MU}m."
+                description = (
+                    f"{axis.upper()} stage position in \N{GREEK SMALL LETTER MU}m."
+                )
             self.view.position_frame.inputs[axis].widget.hover.setdescription(
                 description
             )