add SYSTEM_PATH, fix auto-connect

DeMarcoLab · Jul 27, 2023 · 59ad13d · 59ad13d
1 parent 43233e5
commit 59ad13d
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Showing 3 changed files with 5 additions and 10 deletions.
diff --git a/fibsem/config.py b/fibsem/config.py
@@ -41,6 +41,7 @@
 
 BASE_PATH = os.path.dirname(fibsem.__path__[0]) # TODO: figure out a more stable way to do this
 CONFIG_PATH = os.path.join(BASE_PATH, "fibsem", "config")
+SYSTEM_PATH = os.path.join(CONFIG_PATH, "system.yaml")
 PROTOCOL_PATH = os.path.join(CONFIG_PATH, "protocol.yaml")
 LOG_PATH = os.path.join(BASE_PATH, "fibsem", "log")
 DATA_PATH = os.path.join(BASE_PATH, "fibsem", "log", "data")

diff --git a/fibsem/ui/FibsemSystemSetupWidget.py b/fibsem/ui/FibsemSystemSetupWidget.py
@@ -14,7 +14,6 @@
 from fibsem.structures import MicroscopeSettings, StageSettings, FibsemHardware, BeamSystemSettings, BeamType, ImageSettings, FibsemMillingSettings, SystemSettings
 from fibsem.ui.qtdesigner_files import FibsemSystemSetupWidget
 from fibsem.ui.utils import _get_file_ui, _get_save_file_ui
-from fibsem.utils import load_yaml
 
 def log_status_message(step: str):
     logging.debug(
@@ -45,7 +44,7 @@ def __init__(
         self.viewer = viewer
         self.config_path = config_path  # TODO: allow user to set this
 
-        settings_dict = load_yaml(os.path.join(self.config_path))
+        settings_dict = utils.load_yaml(os.path.join(self.config_path))
 
         self.auto_connect = False
         self.apply_settings = False
@@ -329,7 +328,7 @@ def get_model_from_ui(self) -> FibsemHardware:
 
     def connect(self, ip_address: str = None, manufacturer: str = None) -> None:
 
-        if ip_address is not str:
+        if not isinstance(ip_address, str):
             if self.lineEdit_ipadress.text() == "":
                 napari.utils.notifications.show_error(
                     f"IP address not set. Please enter an IP address before connecting to microscope."

diff --git a/fibsem/ui/FibsemUI.py b/fibsem/ui/FibsemUI.py
@@ -11,12 +11,9 @@
 from fibsem.ui.FibsemManipulatorWidget import FibsemManipulatorWidget
 from fibsem.ui.FibsemGISWidget import FibsemGISWidget
 from fibsem.ui.FibsemSystemSetupWidget import FibsemSystemSetupWidget
-from fibsem.ui.FibsemPositionsWidget import FibsemPositionsWidget
 
 from napari.qt.threading import thread_worker
 from PyQt5 import QtWidgets
-from PyQt5 import QtCore
-from PyQt5.QtWidgets import QMessageBox
 from fibsem import config as cfg
 
 
@@ -45,13 +42,11 @@ def __init__(self, viewer: napari.Viewer):
         self.alignment_widget: FibsemAlignmentWidget = None
         self.manipulator_widget: FibsemManipulatorWidget = None
 
-
-        CONFIG_PATH = os.path.join(cfg.CONFIG_PATH, "system.yaml")
         self.system_widget = FibsemSystemSetupWidget(
                 microscope=self.microscope,
                 settings=self.settings,
                 viewer=self.viewer,
-                config_path = CONFIG_PATH,
+                config_path = cfg.SYSTEM_PATH,
             )
 
         self.tabWidget.addTab(self.system_widget, "System")
@@ -69,7 +64,7 @@ def setup_connections(self):
         self.actionManipulator_Positions_Calibration.triggered.connect(self.calibrate_manipulator_positions)
         if self.system_widget.microscope is not None:
             self.connect_to_microscope()
-            settings_dict = load_yaml(os.path.join(cfg.CONFIG_PATH, "system.yaml"))
+            settings_dict = utils.load_yaml(cfg.SYSTEM_PATH)
             if bool(settings_dict["apply_settings_on_startup"]):
                 self.system_widget.apply_settings = True
                 self.system_widget.apply_defaults_settings()