[feat] add system fingerprint based configuration

fibsem/configuration.py

@@ -3,6 +3,132 @@
 import os
 from fibsem.config import CONFIG_PATH, DEFAULT_CONFIGURATION_VALUES
 
+# TODO: 
+# eucentric heights -> requires taking an image?
+# reference rotation -> how to get this without having the user move to position?
+
+def system_fingerprint(ip_address: str = "192.168.0.1", manufactuer: str = "Thermo") -> dict:
+    """Automatically configure system based on microscope fingerprinting."""
+
+    # load default configuration
+    with open(os.path.join(CONFIG_PATH, "microscope-configuration.yaml"), "r") as f:
+        config = yaml.safe_load(f)
+
+    if manufactuer != "Thermo":
+        raise ValueError("Only Thermo Fisher microscopes are currently supported for fingerprinting.")
+
+    # ip,  manufacturer
+    config["info"]["ip"] = ip_address               # default ip (support pc -> microscope pc)
+    config["info"]["manufacturer"] = manufactuer    # default manufacturer
+
+    from fibsem.microscope import ThermoMicroscope
+    from fibsem.structures import SystemSettings, BeamSystemSettings, StageSystemSettings, FibsemDetectorSettings
+
+    microscope = ThermoMicroscope()
+    microscope.connect_to_microscope(config["info"]["ip"])
+
+    # get name of system
+    system_name = microscope.connection.service.system.name
+    serial_number = microscope.connection.service.system.serial_number
+    config["info"]["name"] = f"{system_name}-{serial_number}-configuration" 
+
+    # stage
+    # enabled, compustage, rotation, tilt
+    stage_enabled = microscope.connection.specimen.stage.is_installed
+    compustage_enabled = microscope.connection.specimen.compustage.is_installed
+    config["stage"]["enabled"] = stage_enabled or compustage_enabled
+    config["stage"]["rotation"] = stage_enabled and not compustage_enabled
+    config["stage"]["tilt"] = stage_enabled or compustage_enabled
+
+    # rotation reference, rotation_180
+    if compustage_enabled: # TODO: check if this is accurate
+        config["stage"]["rotation_reference"] = 0
+        config["stage"]["rotation_180"] = 0
+
+    # otherwise? I think need to get this manually?
+    # TODO: get the user to move the stage to this position?
+    # tilt = 0, rotation = same as when loading?
+
+    # eucentric height map, [electron, ion] (otherwise we need to take an image to get this?)
+    eucentric_height_map = {
+        "Aquilios": [7e-3, 16.5e-3],
+        "Helios": [4e-3, 16.5e-3],
+        "Artcis": [4e-3, 16.5e-3],
+        "Scios": [4e-3, 10.0e-3]
+    }
+
+    # check if any key in system_name
+    for model in eucentric_height_map:
+        if model in system_name:
+            system_model = model
+
+    # electron beam
+    config["electron"]["enabled"] = microscope.connection.beams.electron_beam.is_installed
+    config["electron"]["column_tilt"] = get_column_tilt(config["info"]["manufacturer"], "electron")
+    config["electron"]["eucentric_height"] = eucentric_height_map[system_model][0]
+
+    # ion beam
+    # is_installed, column tilt, eucentric_height (req taking image), plasma, plasma gas
+    config["ion"]["enabled"] = microscope.connection.beams.ion_beam.is_installed
+    config["ion"]["column_tilt"] = get_column_tilt(config["info"]["manufacturer"], "ion")
+    config["ion"]["eucentric_height"] = eucentric_height_map[system_model][1]
+
+    # plasma enabled
+    ion_plasma_enabled = False
+
+    if config["ion"]["enabled"]:
+
+        try:
+            # throws an 
+            ion_plasma_gas = microscope.connection.beams.ion_beam.source.plasma_gas.value
+            ion_plasma_enabled = True
+            print(f"Ion Plasma Available, Plasma Gas: {ion_plasma_gas}")
+        except Exception as e:
+            print(f"Exception: {e}")
+            ion_plasma_gas = "None"
+            ion_plasma_enabled = False
+
+    config["ion"]["plasma"] = ion_plasma_enabled
+    config["ion"]["plasma_gas"] = ion_plasma_gas
+
+    # manipulator
+    config["manipulator"]["enabled"] = microscope.connection.specimen.manipulator.is_installed
+    config["manipulator"]["rotation"] = False   # always?
+    config["manipulator"]["tilt"] = False       # always?
+
+    # gis
+    gis_enabled = len(microscope.connection.gas.list_all_gis_ports())
+    multichem_enabled = len(microscope.connection.gas.list_all_multichem_ports())
+    sputter_coater_enabled = microscope.connection.specimen.sputter_coater.is_installed
+
+    config["gis"]["enabled"] = bool(gis_enabled)
+    config["gis"]["multichem"] = bool(multichem_enabled)
+    config["gis"]["sputter_coater"] = sputter_coater_enabled
+
+    print(f"""System Fingerprint:
+    Electron Beam: 
+        Enabled: {config["electron"]["enabled"]}
+        Column Tilt: {config["electron"]["column_tilt"]}
+    Ion Beam:
+        Enabled: {config["ion"]["enabled"]}
+        Column Tilt: {config["ion"]["column_tilt"]}
+        Plasma: {config["ion"]["plasma"]}
+        Plasma Gas: {config["ion"]["plasma_gas"]}
+    Stage: 
+        Enabled: {config["stage"]["enabled"]}
+        Rotation: {config["stage"]["rotation"]}
+        Tilt: {config["stage"]["tilt"]}
+        Rotation Reference: {config["stage"]["rotation_reference"]}
+        Rotation 180: {config["stage"]["rotation_180"]}
+    Manipulator:
+        Enabled: {config["manipulator"]["enabled"]}
+    GIS: 
+        Enabled: {config["gis"]["enabled"]}
+        Multichem: {config["gis"]["multichem"]}
+        Sputter Coater: {config["gis"]["sputter_coater"]}
+    """)
+
+    return config
 
 
 def get_column_tilt(manufacturer: str, beam: str) -> int:

fibsem/microscope.py

@@ -764,7 +764,10 @@ def __init__(self, system_settings: SystemSettings = None):
         self.experiment = FibsemExperiment()
 
         # logging
-        logging.debug({"msg": "create_microscope_client", "system_settings": system_settings.to_dict()})
+        if system_settings is not None:
+            system_settings = system_settings.to_dict()
+        logging.debug({"msg": "create_microscope_client", "system_settings": system_settings})
+
 
     def reconnect(self):
         if not hasattr(self, "system"):
@@ -808,18 +811,20 @@ def connect_to_microscope(self, ip_address: str, port: int = 7520) -> None:
         logging.info(f"Microscope client connected to [{ip_address}:{port}]")
 
         # system information
-        self.system.info.model = self.connection.service.system.name
-        self.system.info.serial_number = self.connection.service.system.serial_number
-        self.system.info.hardware_version = self.connection.service.system.version
-        self.system.info.software_version = self.connection.service.autoscript.client.version
-        info = self.system.info
-        logging.info(f"Microscope client connected to model {info.model} with serial number {info.serial_number} and software version {info.software_version}.")
+        if self.system is not None:
+            self.system.info.model = self.connection.service.system.name
+            self.system.info.serial_number = self.connection.service.system.serial_number
+            self.system.info.hardware_version = self.connection.service.system.version
+            self.system.info.software_version = self.connection.service.autoscript.client.version
+            info = self.system.info
+            logging.info(f"Microscope client connected to model {info.model} with serial number {info.serial_number} and software version {info.software_version}.")
 
         # autoscript information
         logging.info(f"Autoscript Client: {self.connection.service.autoscript.client.version}")
         logging.info(f"Autoscript Server: {self.connection.service.autoscript.server.version}")
 
-        self.reset_beam_shifts()
+        if self.system is not None: # tmp
+            self.reset_beam_shifts()
 
     def acquire_image(self, image_settings:ImageSettings) -> FibsemImage:
         """