Dev ach

asyncroscopy/instruments/electron_microscope/auto_script.py

@@ -54,15 +54,20 @@ class AutoScriptMicroscope(ElectronMicroscope):
     # ------------------------------------------------------------------
     # Device properties — configure in Tango DB per deployment
     # ------------------------------------------------------------------
-    autoscript_host_ip = device_property(
+    hardware_host = device_property(
         dtype=str,
         default_value="10.46.217.241",
         doc="Hostname or IP of the AutoScript microscope server",
     )
-    autoscript_host_port = device_property(
+    hardware_port = device_property(
         dtype=int,
         default_value=9095,
-        doc="Hostname or IP of the AutoScript microscope server",
+        doc="Port of the AutoScript microscope server",
+    )
+    hardware_timeout_seconds = device_property(
+        dtype=int,
+        default_value=120,
+        doc="Hardware connection timeout in seconds.",
     )
     acquisition_save_directory = device_property(
         dtype=str,
@@ -156,8 +161,8 @@ def _connect_hardware(self) -> None:
             return
         try:
             self._microscope = TemMicroscopeClient()
-            self._microscope.connect(self.autoscript_host_ip, self.autoscript_host_port)
-            self.info_stream(f"Connected to AutoScript at {self.autoscript_host_ip}:{self.autoscript_host_port}")
+            self._microscope.connect(self.hardware_host, self.hardware_port)
+            self.info_stream(f"Connected to AutoScript at {self.hardware_host}:{self.hardware_port}")
             self.is_autoscript = True
         except Exception as e:
             self.error_stream(f"AutoScript connection failed: {e}")

asyncroscopy/instruments/electron_microscope/jeol.py

@@ -24,16 +24,21 @@ class JeolMicroscope(ElectronMicroscope):
     dedicated detector devices and read via DeviceProxy at acquisition time.
     """
 
-    pyjem_host_ip = device_property(
+    hardware_host = device_property(
         dtype=str,
         default_value='10.46.217.241',
         doc='Hostname or IP of the JEOL microscope control server.',
     )
-    pyjem_host_port = device_property(
+    hardware_port = device_property(
         dtype=int,
         default_value=9095,
         doc='Port of the JEOL microscope control server.',
     )
+    hardware_timeout_seconds = device_property(
+        dtype=int,
+        default_value=120,
+        doc='Hardware connection timeout in seconds.',
+    )
     acquisition_save_directory = device_property(
         dtype=str,
         default_value=DEFAULT_ACQUISITION_DIR,

configs/hackathon.yaml

@@ -24,9 +24,10 @@ devices:
 tango:
   host: 127.0.0.1
   port: 9094
+  reset_database_file: true
 tiled:
   host: 127.0.0.1
   port: 9091
-  acquisition_dir: /Users/austin/Downloads/18167694/hackathon_data
+  acquisition_dir: /Users/austin/Desktop/18167694/hackathon_data
   autostart: true
 device_timeout_seconds: 120

docs/MCP/mcp_server.md

@@ -1,16 +1,16 @@
 # Asyncroscopy MCP Server
 
 The MCP server is a FastMCP HTTP bridge over the live Tango database. It should
-start after the Tango database, support devices, Tiled, and microscope or
-digital twin are ready.
+start after the Tango database, support devices, Tiled, and selected instrument
+are ready.
 
 ## Start It
 
 Start the device stack first:
 
 ```bash
 uv run startup_scripts/run_servers.py --yaml configs/Spectra300.yaml
-uv run startup_scripts/run_servers.py --yaml configs/Spectra300.yaml --microscope dt
+uv run startup_scripts/run_servers.py --yaml configs/STEMDigitalTwin.yaml
 ```
 
 Then start MCP in another terminal or on the MCP computer:

docs/Operation/run-servers.md

@@ -3,7 +3,7 @@
 `startup_scripts/run_servers.py` starts the Tango/device side of asyncroscopy. It
 clears stale processes, starts the Tango database, registers devices, launches
 device servers, starts the DATA-managed Tiled HTTP server, and starts the
-microscope or digital twin last.
+selected instrument last.
 
 MCP is started separately with `startup_scripts/run_mcp.py`; see
 [mcp_server.md](../MCP/mcp_server.md).
@@ -12,10 +12,9 @@ MCP is started separately with `startup_scripts/run_mcp.py`; see
 
 ```bash
 uv run startup_scripts/run_servers.py
-uv run startup_scripts/run_servers.py --microscope dt
 
 uv run startup_scripts/run_servers.py --yaml configs/Spectra300.yaml
-uv run startup_scripts/run_servers.py --yaml configs/Spectra300.yaml --microscope dt
+uv run startup_scripts/run_servers.py --yaml configs/STEMDigitalTwin.yaml
 uv run startup_scripts/run_servers.py --yaml configs/ThinkPad-utkarsh-covalent-setup.yaml
 ```
 
@@ -40,11 +39,11 @@ uv run startup_scripts/run_mcp.py --yaml configs/mcp.yaml
 |-------|-----------|------------|
 | 1 | support devices | `asyncroscopy/{camera,corrector,data,eds,flucam,scan,stage}/default` |
 | 2 | Tiled HTTP server | started through the `data` device |
-| 3 | microscope or digital twin | `asyncroscopy/microscope/default` |
+| 3 | instrument | `asyncroscopy/instrument/default` |
 
-The microscope starts last because it depends on the support devices. The runner
-writes support-device addresses into Tango database properties before the
-microscope starts. In `real` mode it also writes the AutoScript host and port.
+The instrument starts last because it depends on the support devices. The runner
+writes support-device addresses and hardware connection values into Tango
+database properties before the instrument starts.
 
 ## Server GUI
 
@@ -53,7 +52,7 @@ does not start servers directly. It formats the current selections into YAML,
 writes that YAML to `outputs/startup_configs/server_gui.yaml`, and runs:
 
 ```bash
-uv run python startup_scripts/run_servers.py --yaml outputs/startup_configs/server_gui.yaml --microscope <real-or-dt>
+uv run python startup_scripts/run_servers.py --yaml outputs/startup_configs/server_gui.yaml
 ```
 
 The GUI includes:
@@ -74,16 +73,15 @@ Server startup configs live in [configs/](../../configs):
 
 Each server config has:
 
-- `microscope:` for the real microscope.
-- `digital_twin:` for `--microscope dt`.
+- `instrument:` for the selected instrument class, Python file, and hardware connection values.
 - `devices:` for support device modules.
 - `tango:` for the Tango database host, port, and optional database-file reset.
 - `tiled:` for the DATA-managed Tiled HTTP server.
 - `device_timeout_seconds:` for device readiness waits.
 
 Device `class_name` defaults to the upper-cased key (`scan` becomes `SCAN`).
-`microscope.host` and `microscope.port` become the microscope device's
-`autoscript_host_ip` and `autoscript_host_port` properties.
+`instrument.hardware_host`, `instrument.hardware_port`, and
+`instrument.timeout_seconds` become instrument device properties.
 
 Set `tango.reset_database_file: true` to delete a stale local
 `tango_database.db` / `Tango_database.db` before starting the Tango database.
@@ -118,18 +116,18 @@ Interactive mode is used only when `--yaml` is omitted. The defaults come from
 | Start Tiled HTTP server | Whether DATA starts its managed Tiled server. |
 | Clear old processes first | Frees stale Tango/Tiled ports and old device servers. |
 | Start Tango database | Starts the DB or waits for an existing one. |
-| Register devices | Adds device entries and microscope properties to the DB. |
+| Register devices | Adds device entries and instrument properties to the DB. |
 | Device startup timeout seconds | How long to wait for each device to answer `ping()`. |
-| AutoScript host IP / port | Real microscope mode only. |
+| Hardware host / port / timeout seconds | Connection values for the selected instrument. |
 
 ## Startup Stages
 
 1. **Clearing old processes** frees the database/Tiled ports and kills old device
    server process groups.
 2. **Starting Tango database** starts or waits for the database server.
-3. **Registering devices** writes device entries and microscope properties.
+3. **Registering devices** writes device entries and instrument properties.
 4. **Starting device servers** starts support devices, Tiled, and then the
-   microscope or digital twin.
+   selected instrument.
 5. **Startup summary** prints `TANGO_HOST`, PIDs, ready times, and the Tiled URI.
 
 ## Manual Fallback
@@ -141,7 +139,7 @@ TANGO_HOST=localhost:9094 uv run python -m tango.databaseds.database 2
 
 export TANGO_HOST=localhost:9094
 uv run python -m asyncroscopy.instruments.electron_microscope.hardware.scan scan_instance
-uv run python -m asyncroscopy.instruments.electron_microscope.auto_script microscope_instance
+uv run python -m asyncroscopy.instruments.electron_microscope.auto_script instrument_instance
 ```
 
 Manual device startup requires the devices to already be registered in Tango.