resolved: merge conflict with main

Author: utkarshp1161

.DS_Store

@@ -0,0 +1,43 @@
+name: Deploy MyST Site
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+      - name: Setup MyST
+        run: npm install -g mystmd
+      - name: Build site
+        env:
+          BASE_URL: /asyncroscopy
+        run: |
+          cd docs
+          myst build --html
+          touch _build/html/.nojekyll
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/_build/html'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/deploy.yml

@@ -206,5 +206,11 @@ marimo/_static/
 marimo/_lsp/
 __marimo__/
 
+.DS_Store
+
 PythonPackages-AS-1.15/
-llm-context/
+llm-context/
+# MyST build outputs
+_build
+
+extra-notebooks-debug/

.gitignore

@@ -1,6 +1,8 @@
 # Asyncroscopy:
 - Enabling smart microscopy via asynchronous servers
 
+![Schematic of the functional project structure](architecture.png)
+
 Note: `main` branch now contains the PyTango-based architecture. The previous Twisted-based implementation is preserved in the `twisted-legacy` branch for reference.
 ---
 
@@ -47,7 +49,7 @@ See - docs/dev_guide.md
 ### Core installation (simulation mode)
 
 ```bash
-pip install .
+pip install --find-links ./stubs -e .
 ```
 
 or with `uv`:

README.md

@@ -44,7 +44,6 @@ class Microscope(Device, metaclass=CombinedMeta):
     # Device properties — configure in Tango DB per deployment
     # ------------------------------------------------------------------
 
-
     scan_device_address = device_property(
         dtype=str,
         doc="Tango device address for the SCAN settings device. "
@@ -66,14 +65,12 @@ class Microscope(Device, metaclass=CombinedMeta):
             "No-DB mode: 'tango://127.0.0.1:8888/test/nodb/stage#dbase=no'",
     )
 
-
-    corrector_device_address = device_property(
+    camera_device_address = device_property(
         dtype=str,
-        doc="Tango device address for the aberration corrector settings device. "
-            "DB mode: 'test/hardware/corrector' "
-            "No-DB mode: 'tango://127.0.0.1:8888/test/nodb/corrector#dbase=no'",
+        doc="Tango device address for the CAMERA settings . "
+            "DB mode: 'test/detector/camera' "
+            "No-DB mode: 'tango://127.0.0.1:8888/test/nodb/camera#dbase=no'",
     )
-    
     testing_mode_bool = device_property(dtype=bool, 
                                         default_value=False,
                                         doc="When True - used for running tests, passed in conftest.py")
@@ -198,6 +195,14 @@ def get_spectrum(self, detector_name: str) -> tuple[str, bytes]:
 
         return json.dumps(metadata), raw_bytes
 
+    @command(dtype_out=DevEncoded)
+    def get_camera_image(self) -> tuple[str, bytes]:
+        """
+        get image on the camera
+        """
+
+        camera = self._detector_proxies.get("camera")
+        # use this to get params
 
     @command(dtype_out=DevEncoded)#In PyTango, DevEncoded is a special Tango data type designed to send binary data + a small description string together as a single return value.
     def get_scanned_image(self) -> tuple[str, bytes]:
@@ -224,18 +229,63 @@ def get_scanned_image(self) -> tuple[str, bytes]:
         dwell_time=scan.dwell_time
         imsize=scan.imsize
 
-        adorned_image = self._acquire_stem_image(imsize, dwell_time, ['haadf'])
+        image = self._acquire_stem_image(imsize, dwell_time, ['haadf'])
 
         metadata = {
             "detector": 'haadf',
             "shape": [imsize, imsize],
-            "dtype": str(adorned_image.dtype),
+            "dtype": str(image.dtype),
             "dwell_time": dwell_time,
             "timestamp": time.time(),
             # TODO: add metadata from adorned_image.metadata when using real AutoScript
         }
 
-        return json.dumps(metadata), adorned_image.tobytes()
+        return json.dumps(metadata), image.tobytes()
+    
+
+    @command(dtype_out=DevEncoded)
+    def get_camera_image(self) -> tuple[str, bytes]:
+        """
+        Acquire a single camera image from the named detector.
+
+        Parameters
+        ----------
+        detector_name:
+            Name of the detector, e.g. "BM-Ceta". Must match a key in
+            self._detector_proxies.
+
+        Returns
+        -------
+        DevEncoded = (json_metadata, raw_bytes)
+            json_metadata includes: shape, dtype, dwell_time, detector,
+            timestamp, and any other relevant metadata.
+            raw_bytes is the flat numpy array bytes; reshape using shape from metadata.
+        """
+
+        # check active detectors
+        camera = self._detector_proxies.get("camera")
+
+        # Read settings from the detector
+        exposure_time=camera.exposure_time
+        imsize=camera.imsize
+        readout_area=camera.readout_area
+
+        image = self._acquire_camera_image(imsize=imsize, exposure_time=exposure_time,
+                                           detector='BM-Ceta', readout_area=readout_area)
+
+        metadata = {
+            "detector": 'Ceta',
+            "shape": [imsize, imsize],
+            "dtype": str(image.dtype),
+            "exposure_time": exposure_time,
+            "timestamp": time.time(),
+            "readout_area": readout_area,
+            # TODO: move this metadata packing into the _acquire_camera_image method
+            # when usingreal AutoScript,to include metadata from adorned_image.metadata
+        }
+
+        return json.dumps(metadata), image.tobytes()
+
 
     @command(dtype_in=('str',), dtype_out=str)
     def get_images(self, detector_names: list[str]) -> str:
@@ -328,11 +378,32 @@ def unblank_beam(self) -> None:
     @command(dtype_in=DevFloat)
     def set_fov(self, fov):
         """
-        set the field of view for the next acquisition, [0:1]
+        set the field of view for the next acquisition
         """
         print(fov)
         self._set_fov(fov)
 
+    @command(dtype_out=DevFloat)
+    def get_fov(self):
+        """
+        read the field of view for the next acquisition
+        """
+        return self._get_fov()
+    
+    @command(dtype_in=DevFloat)
+    def set_screen_current(self, current):
+        """
+        set the screen current in pA
+        """
+        self._set_screen_current(current)
+
+    @command(dtype_out=DevFloat)
+    def get_screen_current(self):
+        """
+        get the screen current in pA
+        """
+        return self._get_screen_current()
+
     @command(dtype_out=DevVarFloatArray)
     def get_stage(self):
         """
@@ -359,6 +430,23 @@ def move_stage(self, position):
         """
         self._move_stage(position)
 
+    @command()
+    def auto_focus(self):
+        """
+        Run the microscope's autofocus routine.
+        """
+        self._auto_focus()
+
+    @command(dtype_in=DevVarFloatArray)
+    def set_image_shift(self, shift):
+        """
+        Set the image shift to the specified values [x_shift, y_shift].
+
+        Parameters
+        ----------
+        shift: list of two floats [x_shift, y_shift] specifying the desired image shift in meters.
+        """
+        self._set_image_shift(shift)
     # ------------------------------------------------------------------
     # Internal acquisition helpers
     # ------------------------------------------------------------------
@@ -371,6 +459,9 @@ def _acquire_stem_image():
     def _acquire_stem_image_advanced():
         print("Get image with more flexible settings")
         pass
+    def _acquire_camera_image():
+        # define in the inherit class
+        pass
 
     def _place_beam():
         # define in the inherit class
@@ -384,6 +475,15 @@ def _unblank_beam():
         # define in the inherit class
         pass
 
+    @abstractmethod
+    def _set_screen_current():
+        # define in the inherit class
+        pass
+
+    @abstractmethod
+    def _get_screen_current():
+        pass
+
     @abstractmethod
     def _move_stage():
         # define in the inherit class
@@ -396,6 +496,18 @@ def _get_stage():
     @abstractmethod
     def _set_fov():
         pass
+
+    @abstractmethod
+    def _get_fov():
+        pass
+
+    @abstractmethod
+    def _auto_focus():
+        pass
+
+    @abstractmethod
+    def _set_image_shift():
+        pass
 # ----------------------------------------------------------------------
 # Server entry point
 # ----------------------------------------------------------------------