From 59ad13dd59ed90f71dd4957aa41f7bd1cd88b55d Mon Sep 17 00:00:00 2001 From: Patrick Cleeve Date: Thu, 27 Jul 2023 22:02:23 +1000 Subject: [PATCH] add SYSTEM_PATH, fix auto-connect --- fibsem/config.py | 1 + fibsem/ui/FibsemSystemSetupWidget.py | 5 ++--- fibsem/ui/FibsemUI.py | 9 ++------- 3 files changed, 5 insertions(+), 10 deletions(-) diff --git a/fibsem/config.py b/fibsem/config.py index 96acd794..d2ecff8d 100644 --- 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 index 8b17a8ac..515cc915 100644 --- 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 index a0f54b6a..7c58aa49 100644 --- 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()