update_from_main

.gitattributes

@@ -0,0 +1 @@
+* text=auto

.gitignore

@@ -236,5 +236,8 @@ ClAUDE.md
 
 tiled_data/
 outputs/
+output_tango_devices_logs/
 
 .claude/
+
+aws-use/

README.md

@@ -1,7 +1,9 @@
-# Asyncroscopy:
-- Enabling smart microscopy via asynchronous servers
+# Asyncroscopy: Enabling smart microscopy via asynchronous servers
 
-![Schematic of the functional project structure](architecture.png)
+<div class="d-flex justify-content-between">
+  <img src="docs/images/architecturev1.png" width="33.5%" />
+  <img src="docs/images/architecturev2.png" width="57%" />
+</div>
 
 Note: `main` branch now contains the PyTango-based architecture. The previous Twisted-based implementation is preserved in the `twisted-legacy` branch for reference.
 ---
@@ -17,7 +19,7 @@ see: [Tutorial notebook](notebooks/1_Client_tutorial.ipynb)
 ```
 .
 ├── src/
-│   ├── Microscope.py              # Main device — owns AutoScript connection and all acquisition commands
+│   ├── ElectronMicroscope.py      # Electron microscope base device and acquisition commands
 │   ├── detectors/
 │   │   ├── HAADF.py               # HAADF detector settings device
 │   │   ├── EELS.py                # EELS detector settings device (stub)
@@ -30,7 +32,7 @@ see: [Tutorial notebook](notebooks/1_Client_tutorial.ipynb)
 │       └── advanced_acquisition.py  # Multi-detector acquisition helpers (stub)
 ├── tests/
 │   ├── conftest.py                # Shared pytest fixtures (DeviceTestContext proxies)
-│   ├── test_microscope.py         # Microscope device tests
+│   ├── test_microscope.py         # STEMMicroscope device tests
 │   ├── test_acquisition.py        # Acquisition tests
 │   └── detectors/
 │       └── test_HAADF.py          # HAADF device tests

asyncroscopy/JeolMicroscope.py

@@ -0,0 +1,126 @@
+## started on 5th June 2026 --> Aimed for JEM-F200
+
+# Import python internal libraries
+import math
+import time
+from datetime import datetime
+from pathlib import Path
+
+# Import external libraries
+import numpy as np
+import tango
+from tango import AttrWriteType, DevState
+from tango.server import attribute, command, device_property
+
+# Import Asyncroscopy relevant modules
+from asyncroscopy.Microscope import Microscope
+from asyncroscopy.software.DataWriter import DEFAULT_ACQUISITION_DIR, save_acquisition
+
+# Import Manufacturer-specific libraries
+
+
+
+# Define class for Microscope
+
+class JeolMicroscope(Microscope):
+    """
+    Manages the PyJEM connection and exposes acquisition commands.
+    Detector-specific settings (dwell time, resolution) are stored in
+    dedicated detector devices and read via DeviceProxy at acquisition time.
+    """
+
+    # ------------------------------------------------------------------
+    # Device properties — configure in Tango DB per deployment
+    # ------------------------------------------------------------------
+    autoscript_host_ip = device_property(
+        dtype=str,
+        default_value="10.46.217.241",
+        doc="Hostname or IP of the AutoScript microscope server",
+    )
+    autoscript_host_port = device_property(
+        dtype=int,
+        default_value=9095,
+        doc="Hostname or IP of the AutoScript microscope server",
+    )
+    acquisition_save_directory = device_property(
+        dtype=str,
+        default_value=DEFAULT_ACQUISITION_DIR,
+        doc="Directory where AutoScript acquisitions are saved before the Tiled server serves them.",
+    )
+    acquisition_file_format = device_property(
+        dtype=str,
+        default_value="h5",
+        doc="Acquisition file format. HDF5 stores acquisition data and parsed metadata attributes.",
+    )
+    data_device_address = device_property(
+        dtype=str,
+        default_value="",
+        doc="Optional Tango device address for the DATA device, e.g. 'asyncroscopy/data/default'.",
+    )
+    # ------------------------------------------------------------------
+    # Attributes
+    # ------------------------------------------------------------------
+
+    # ------------------------------------------------------------------
+    # Initialisation
+    # ------------------------------------------------------------------
+
+    # ------------------------------------------------------------------
+    # Attribute read methods
+    # ------------------------------------------------------------------
+
+    # ------------------------------------------------------------------
+    # Commands pertaining to setting children attributes, e.g. stage position, scan parameters, EDS settings, etc. --> iuser accesses it in a jupyter notebook using the device proxy
+    # ------------------------------------------------------------------
+
+
+    # ------------------------------------------------------------------
+    # Internal acquisition helpers
+    # ------------------------------------------------------------------
+    def _persist(self, adorned, acquisition_type, detector, data_server, dataset_name="image"):
+        """Save acquired images in the format requested by the SCAN device.
+        """
+        scan = self._detector_proxies.get("scan")
+        fmt = scan.output_format if scan is not None else ".h5"  # ".h5" default
+        if fmt == ".h5":
+            return save_acquisition(self, data_server, acquisition_type, detector, adorned, dataset_name=dataset_name)
+        if fmt != ".tiff":
+            raise ValueError(f"Unsupported output_format {fmt!r}; expected '.h5' or '.tiff'")
+
+        # .tiff → AutoScript native save, one file per detector sharing one stamp
+        images = list(adorned) if isinstance(adorned, (list, tuple)) else [adorned]
+        detectors = list(detector) if isinstance(detector, (list, tuple)) else [detector]
+        if len(images) != len(detectors):
+            raise ValueError(f"Got {len(images)} images for {len(detectors)} detector(s) {detectors}")
+
+        save_dir = data_server.save_path if data_server is not None else DEFAULT_ACQUISITION_DIR
+        directory = Path(save_dir).expanduser()
+        directory.mkdir(parents=True, exist_ok=True)
+        stamp = datetime.now().strftime("%Y%m%dT%H%M%S%f")
+        stem = f"{acquisition_type}_{stamp}"
+        # AutoScript returns images in the requested detector order (assumed; verify on hardware)
+        for img, det in zip(images, detectors):
+            path = directory / f"{stem}_{det}.tiff"
+            img.save(str(path))
+            if data_server is not None:
+                data_server.register_path(str(path))
+        return stem
+
+    def _acquire_scanned_image(
+        self,
+        imsize: int,
+        dwell_time: float,
+        detector_list: list[str] = ["haadf"],
+        scan_region: list[float] = [0.0, 0.0, 1.0, 1.0],
+    ) -> str:
+        """
+        Call AutoScript scanned image acquisition, save one HDF5 file, and return its DATA/Tiled key.
+        """
+        detector_list = [d.upper() for d in detector_list]
+        #settings = StemAcquisitionSettings(dwell_time=dwell_time, detector_types=detector_list, size=imsize, region=Region(RegionCoordinateSystem.RELATIVE, Rectangle(*scan_region)))
+        #adorned = self._microscope.acquisition.acquire_stem_images_advanced(settings)
+        if not isinstance(adorned, list):
+            adorned = [adorned]
+        data_server = self._detector_proxies.get("data")
+        return self._persist(adorned, "stem_image", detector_list, data_server)
+