add camera images by AustinHouston · Pull Request #70 · pycroscopy/asyncroscopy

AustinHouston · 2026-04-22T13:34:50Z

camera images now, done with advanced acquisition settings

Copilot

Pull request overview

This PR extends the Tango device stack to support acquiring camera images using “advanced acquisition settings”, wiring a CAMERA settings device into registration and the microscope acquisition path, and updating an aberrations notebook to use the DB-registered devices.

Changes:

Register and link a new CAMERA device (and CORRECTOR) in the Tango DB registration script.
Add a readout_area setting to the CAMERA settings device and implement a get_camera_image microscope command.
Add an AutoScript advanced camera acquisition helper to ThermoMicroscope and update the aberrations notebook setup/connection flow.

Reviewed changes

Copilot reviewed 5 out of 10 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
scripts/2_register_devices.py	Registers CAMERA/CORRECTOR devices and sets microscope device-address properties.
notebooks/2_Aberrations.ipynb	Adds setup/launch logic for Tango DB + servers; updates device addressing and shows new runtime output.
asyncroscopy/detectors/CAMERA.py	Adds `readout_area` acquisition preset as a read/write attribute with defaults.
asyncroscopy/ThermoMicroscope.py	Connects a camera proxy and adds AutoScript “advanced” camera acquisition helper; adjusts stage move and shift behavior.
asyncroscopy/Microscope.py	Adds `camera_device_address` property and implements `get_camera_image` command + updated metadata for `get_scanned_image`.

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Copilot · 2026-04-24T16:16:00Z

+     "ename": "KeyError",
+     "evalue": "'result'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mKeyError\u001b[39m                                  Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[7]\u001b[39m\u001b[32m, line 2\u001b[39m\n\u001b[32m      1\u001b[39m ab_msg = corrector_proxy.acquire_tableau(\u001b[33m'Enhanced 40'\u001b[39m)\n\u001b[32m----> \u001b[39m\u001b[32m2\u001b[39m ab = json.loads(ab_msg)[\u001b[33m'result'\u001b[39m][\u001b[33m'aberrations'\u001b[39m]\n\u001b[32m      3\u001b[39m \n\u001b[32m      4\u001b[39m ab[\u001b[33m'acceleration_voltage'\u001b[39m] = \u001b[32m60e3\u001b[39m \u001b[38;5;66;03m# eV\u001b[39;00m\n\u001b[32m      5\u001b[39m ab[\u001b[33m'FOV'\u001b[39m] = \u001b[32m100\u001b[39m /\u001b[32m10\u001b[39m \u001b[38;5;66;03m# nm\u001b[39;00m\n",
+      "\u001b[31mKeyError\u001b[39m: 'result'"
     ]


The notebook output shows KeyError: 'result' when doing json.loads(ab_msg)['result']['aberrations'], which suggests the acquire_tableau() response schema doesn't match what this cell expects. Please adjust the parsing (or add a schema check with a clearer error) so the cell can run successfully without raising.

Copilot · 2026-04-24T16:16:01Z

+        this is the advanced version
+        """
+
+        detector = 'BM-Ceta' # or "Flucam"


_acquire_camera_image ignores the detector argument by overwriting it with a hard-coded value ('BM-Ceta'). This makes the method signature misleading and prevents selecting other camera detectors. Either remove the parameter and document the fixed detector, or use the passed-in detector value (ideally validating it against supported detectors).

Suggested change

detector = 'BM-Ceta' # or "Flucam"

detector = detector or 'BM-Ceta' # default to BM-Ceta if no detector is provided

Copilot · 2026-04-24T16:16:01Z

+
+        detector = 'BM-Ceta' # or "Flucam"
+
+        settings = CameraAcquisitionSettings(camera_detector=detector, size=imsize,
+            exposure_time=exposure_time, fixed_readout_area=readout_area, frame_combining=1)
+        adorned = self._microscope.acquisition.acquire_camera_image_advanced(settings)
+        image = adorned.data
+        return image
+



_acquire_camera_image uses self._microscope.acquisition... without checking self._microscope is not None (unlike _acquire_stem_image). In testing mode / when AutoScript is unavailable, this will raise an AttributeError instead of falling back or returning a controlled Tango error. Please add the same guard and either simulate a camera image or throw a Tango exception with a clear message.

Suggested change

detector = 'BM-Ceta' # or "Flucam"

settings = CameraAcquisitionSettings(camera_detector=detector, size=imsize,

exposure_time=exposure_time, fixed_readout_area=readout_area, frame_combining=1)

adorned = self._microscope.acquisition.acquire_camera_image_advanced(settings)

image = adorned.data

return image

if self._microscope is not None:

detector = 'BM-Ceta' # or "Flucam"

settings = CameraAcquisitionSettings(camera_detector=detector, size=imsize,

exposure_time=exposure_time, fixed_readout_area=readout_area, frame_combining=1)

adorned = self._microscope.acquisition.acquire_camera_image_advanced(settings)

image = adorned.data

return image

# Simulation fallback

self.warn_stream(

f"Simulating camera acquisition for detector={detector}, "

f"readout_area={readout_area}, size={imsize}"

)

rng = np.random.default_rng()

return rng.integers(0, 65535, size=(imsize, imsize), dtype=np.uint16)

Copilot · 2026-04-24T16:16:01Z

        """Apply image shift in meters."""
        x_shift = float(shift[0])
        y_shift = float(shift[1])
+        print(shift)


print(shift) is left in _set_image_shift, which will spam stdout in a running Tango server. Please remove it or replace it with self.debug_stream(...)/info_stream(...) depending on desired verbosity.

Suggested change

print(shift)

self.debug_stream(f"Applying image shift: {shift}")

Copilot · 2026-04-24T16:16:02Z

+        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(),
+            "fov": self._get_fov(),
            # TODO: add metadata from adorned_image.metadata when using real AutoScript
        }

-        return json.dumps(metadata), adorned_image.tobytes()
+        return json.dumps(metadata), image.tobytes()


get_scanned_image now unconditionally adds "fov": self._get_fov(). In ThermoMicroscope testing mode / when AutoScript is unavailable, _microscope stays None and _get_fov() currently dereferences self._microscope, which will raise and break existing tests/CI. Please guard this (e.g., only include fov when connected, or have _get_fov() return a safe default in simulation/testing mode).

Copilot · 2026-04-24T16:16:03Z

+    @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],


get_camera_image's docstring describes a detector_name parameter, but the command signature takes no inputs and hard-codes the detector ('BM-Ceta' / 'Ceta'). This is confusing for API consumers; either accept a detector name as dtype_in (and pass it through to acquisition + metadata) or update the docstring/metadata to reflect the fixed detector behavior.

Copilot · 2026-04-24T16:16:03Z

+        camera = self._detector_proxies.get("camera")
+
+        # Read settings from the detector
+        exposure_time=camera.exposure_time
+        imsize=camera.imsize
+        readout_area=camera.readout_area


get_camera_image assumes the camera settings proxy exists and immediately reads camera.exposure_time/imsize/readout_area. If camera_device_address isn't configured or the proxy connection failed, this will raise an AttributeError instead of a controlled Tango error. Please add a None check (similar to get_spectrum) and throw a tango.Except.throw_exception(...) with available detectors / configuration hints.

Suggested change

camera = self._detector_proxies.get("camera")

# Read settings from the detector

exposure_time=camera.exposure_time

imsize=camera.imsize

readout_area=camera.readout_area

detector_proxies = getattr(self, "_detector_proxies", {}) or {}

camera = detector_proxies.get("camera")

if camera is None:

available_detectors = ", ".join(sorted(detector_proxies.keys())) or "none"

tango.Except.throw_exception(

"Detector unavailable",

"Camera detector proxy is not configured or could not be connected. "

f"Available detectors: {available_detectors}. "

"Please configure 'camera_device_address' and ensure the camera "

"device proxy can be created successfully.",

"Microscope.get_camera_image",

)

# Read settings from the detector

exposure_time = camera.exposure_time

imsize = camera.imsize

readout_area = camera.readout_area

Copilot · 2026-04-24T16:16:03Z

+    @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(),
+            "fov": self._get_fov(),
+            "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()
+


New camera acquisition behavior is introduced via get_camera_image, but there are existing tests for get_scanned_image in tests/test_thermo_microscope.py and no corresponding coverage for get_camera_image. Adding a test that provisions a CAMERA settings device in MultiDeviceTestContext and patches _acquire_camera_image (similar to patched_single_image) would help prevent regressions in metadata packing and settings propagation.

Copilot · 2026-04-24T16:16:04Z

    def _acquire_stem_image_advanced():
        print("Get image with more flexible settings")
        pass
+    def _acquire_camera_image():


The base Microscope class adds a _acquire_camera_image hook, but it is missing a self parameter and isn't marked @abstractmethod like the other acquisition helpers. This makes it easy for subclasses to accidentally not override it (or to mismatch signatures). Consider defining it as @abstractmethod def _acquire_camera_image(self, ...): ... with the expected parameters.

Suggested change

def _acquire_camera_image():

@abstractmethod

def _acquire_camera_image(self):

Copilot · 2026-04-24T16:16:04Z

+    "import os\n",
+    "import tango\n",
+    "import json\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt"


The imports cell now includes several duplicate imports (tango, json, numpy, matplotlib.pyplot). This makes the notebook harder to maintain and can mask version/namespace issues; please de-duplicate the imports in this cell.

Suggested change

"import os\n",

"import tango\n",

"import json\n",

"import numpy as np\n",

"import matplotlib.pyplot as plt"

"import os"

AustinHouston added 3 commits April 22, 2026 09:32

add camera images

5a277a9

added camera

c6a0132

abb notebook on database mode

992a4ba

whittlegears requested a review from Copilot April 24, 2026 16:09

Copilot started reviewing on behalf of whittlegears April 24, 2026 16:10 View session

Copilot AI reviewed Apr 24, 2026

View reviewed changes

fixing tests

0e7d16b

AustinHouston merged commit 9bb0c5d into main Apr 29, 2026
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add camera images#70

add camera images#70
AustinHouston merged 4 commits intomainfrom
PyTango-dev-ACH

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	detector = 'BM-Ceta' # or "Flucam"
	detector = detector or 'BM-Ceta' # default to BM-Ceta if no detector is provided

	print(shift)
	self.debug_stream(f"Applying image shift: {shift}")

-        camera = self._detector_proxies.get("camera")
-        # Read settings from the detector
-        exposure_time=camera.exposure_time
-        imsize=camera.imsize
-        readout_area=camera.readout_area
+        detector_proxies = getattr(self, "_detector_proxies", {}) or {}
+        camera = detector_proxies.get("camera")
+        if camera is None:
+            available_detectors = ", ".join(sorted(detector_proxies.keys())) or "none"
+            tango.Except.throw_exception(
+                "Detector unavailable",
+                "Camera detector proxy is not configured or could not be connected. "
+                f"Available detectors: {available_detectors}. "
+                "Please configure 'camera_device_address' and ensure the camera "
+                "device proxy can be created successfully.",
+                "Microscope.get_camera_image",
+            )
+        # Read settings from the detector
+        exposure_time = camera.exposure_time
+        imsize = camera.imsize
+        readout_area = camera.readout_area

-    def _acquire_camera_image():
+    @abstractmethod
+    def _acquire_camera_image(self):

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