Merge branch 'develop' into pr/896

Author: AdvancedImagingUTSW

src/navigate/controller/controller.py

@@ -415,6 +415,9 @@ def populate_experiment_setting(self, file_name=None, in_initialize=False):
         )
         self.channels_tab_controller.populate_experiment_values()
         self.camera_setting_controller.populate_experiment_values()
+        self.waveform_tab_controller.set_waveform_template(
+            self.configuration["experiment"]["MicroscopeState"]["waveform_template"]
+        )
 
         # autofocus popup
         if hasattr(self, "af_popup_controller"):

src/navigate/controller/sub_controllers/plugins_controller.py

@@ -95,10 +95,11 @@ def load_plugins(self):
         plugins_config_path = os.path.join(
             get_navigate_path(), "config", "plugins_config.yml"
         )
-        if not os.path.exists(plugins_config_path):
+        plugins_config = load_yaml_file(plugins_config_path)
+        if plugins_config is None:
+            plugins_config = {}
             save_yaml_file(get_navigate_path(), {}, "plugins_config.yml")
         else:
-            plugins_config = load_yaml_file(plugins_config_path)
             for plugin_name, plugin_path in plugins_config.items():
                 if plugin_path and os.path.exists(plugin_path):
                     installed_plugins[plugin_name] = plugin_path

src/navigate/model/device_startup_functions.py

@@ -1368,26 +1368,22 @@ def load_devices(configuration, is_synthetic=False, plugin_devices={}) -> dict:
                     camera = plugin_devices["camera"]["load_device"](
                         configuration, id, is_synthetic
                     )
+                else:
+                    raise e
 
             if (not is_synthetic) and device["type"].startswith("Hamamatsu"):
                 camera_serial_number = str(camera._serial_number)
-                device_ref_name = build_ref_name(
-                    "_", device["type"], camera_serial_number
-                )
+                device_ref_name = camera_serial_number
                 # if the serial number has leading zeros,
                 # the yaml reader will convert it to an octal number
                 if camera_serial_number.startswith("0"):
                     try:
                         oct_num = int(camera_serial_number, 8)
-                        devices["camera"][
-                            build_ref_name("_", device["type"], oct_num)
-                        ] = camera
+                        device_ref_name = str(oct_num)
                     except ValueError:
                         pass
             else:
-                device_ref_name = build_ref_name(
-                    "_", device["type"], device["serial_number"]
-                )
+                device_ref_name = str(device["serial_number"])
             devices["camera"][device_ref_name] = camera
 
     # load mirror

src/navigate/model/microscope.py

@@ -115,7 +115,7 @@ def __init__(
             return
 
         device_ref_dict = {
-            "camera": ["type", "serial_number"],
+            "camera": ["serial_number"],
             "filter_wheel": ["type"],
             "zoom": ["type", "servo_id"],
             "shutter": ["type", "channel"],

src/navigate/model/model.py

@@ -1424,11 +1424,9 @@ def load_feature_records(self):
             os.makedirs(feature_lists_path)
             return
         # get __sequence.yml
-        if not os.path.exists(f"{feature_lists_path}/__sequence.yml"):
+        feature_records = load_yaml_file(f"{feature_lists_path}/__sequence.yml")
+        if feature_records is None:
             feature_records = []
-        else:
-            feature_records = load_yaml_file(f"{feature_lists_path}/__sequence.yml")
-
         # add non added feature lists
         feature_list_files = [
             temp
@@ -1440,6 +1438,8 @@ def load_feature_records(self):
             if item == "__sequence.yml":
                 continue
             temp = load_yaml_file(f"{feature_lists_path}/{item}")
+            if temp is None:
+                continue
             add_flag = True
             for feature in feature_records:
                 if feature["feature_list_name"] == temp["feature_list_name"]:
@@ -1460,6 +1460,9 @@ def load_feature_records(self):
                 del feature_records[i]
                 continue
             item = load_yaml_file(f"{feature_lists_path}/{temp['yaml_file_name']}")
+            if item is None:
+                i += 1
+                continue
 
             if item["module_name"]:
                 try:

src/navigate/model/plugins_model.py

@@ -81,12 +81,13 @@ def load_plugins(self):
         plugins_config_path = os.path.join(
             get_navigate_path(), "config", "plugins_config.yml"
         )
-        if not os.path.exists(plugins_config_path):
+        plugins_config = load_yaml_file(plugins_config_path)
+        if plugins_config is None:
+            plugins_config = {}
             save_yaml_file(
                 os.path.join(get_navigate_path(), "config"), {}, "plugins_config.yml"
             )
         else:
-            plugins_config = load_yaml_file(plugins_config_path)
             verified_plugins_config = {}
             for plugin_name, plugin_path in plugins_config.items():
                 if not plugin_path: