Merge branch 'main' into 158_migrate_to_copier

.pre-commit-config.yaml

@@ -22,3 +22,12 @@ repos:
         entry: ruff format --force-exclude
         types: [python]
         require_serial: true
+
+  # Type checking
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.4.1
+    hooks:
+      - id: mypy
+        files: 'src/.*\.py$'
+        additional_dependencies: [types-requests, types-redis]
+        args: ["--ignore-missing-imports", "--no-strict-optional"]

docs/developer/index.rst

@@ -29,3 +29,15 @@ Documentation is split general and topic-specific sections. Each section is spli
         +++
 
         Documentation relating to serial crystallography on I24
+
+    .. grid-item-card:: :material-regular:`apps;3em`
+
+        .. toctree::
+            :caption: Murko Integration
+            :maxdepth: 1
+
+            murko-integration/index
+
+        +++
+
+        Documentation relating to integrating the murko image recognition system

docs/developer/murko-integration/explanations/architecture.rst

@@ -0,0 +1,18 @@
+Murko Architecture
+------------------
+
+The architecture of how Murko is integrated is still in flux but as of 07/08 the following has been tried on the beamline.
+
+.. image:: ../images/murko_setup.drawio.png
+
+The mx_bluesky code is deployed into the `beamline kubernetes cluster <https://k8s-i04.diamond.ac.uk/>`_ behind a `blueAPI <https://github.com/DiamondLightSource/blueapi>`_ REST interface. Alongside this an instance of murko is also deployed to the k8s cluster.
+
+When GDA reaches a point where it will thaw the pin (usually just after robot load), if the ``gda.mx.bluesky.thaw`` property has been set to True it will instead call out to the thaw_and_center plan inside mx_bluesky.
+
+The thawing plan will first create a ``MurkoCallback`` callback, this will stream metadata into a key in a redis database running on i04-control (this should be moved in `#145 <https://github.com/DiamondLightSource/mx_bluesky/issues/145>`_).
+
+It will then trigger the ``OAVToRedisForwarder`` device in ``dodal`` that will stream image data to redis in the form of pickled RGB numpy arrays. Each image is given a uuid by this device, which is used to correlate the images with the other metadata, which could be streamed with a different frequency.
+
+The image streaming must be done with an ophyd device as there is too much data for it all to be emitted in bluesky documents.
+
+When the data is entered into redis it will publish a message to the redis ``murko`` channel. This will get picked up by the `socket_handler <https://github.com/DiamondLightSource/mx_auto_mjpeg_capture/tree/main/socket_handler>`_, which will forward the data to murko. Currently, during testing the socket_handler is just manually run on a workstation, `#146 <https://github.com/DiamondLightSource/mx_bluesky/issues/146>`_ should fix this.

docs/developer/murko-integration/index.rst

@@ -0,0 +1,22 @@
+Murko Integration
+=================
+
+The `Murko system <https://github.com/MartinSavko/murko>`_ uses ML to analyse images of sample from optical cameras and determine where the sample is.
+
+Its integration at DLS, using Bluesky, is still a work in progress but this documentation aims to give an overview of how it works.
+
+
+.. grid:: 2
+    :gutter: 2
+
+    .. grid-item-card:: :material-regular:`apartment;3em`
+
+        .. toctree::
+            :caption: Explanations
+            :maxdepth: 1
+
+            explanations/architecture
+
+        +++
+
+        Explanations of how and why the architecture is why it is.

src/mx_bluesky/i04/__init__.py

@@ -1,3 +1,3 @@
-from mx_bluesky.i04.thawing_plan import thaw
+from mx_bluesky.i04.thawing_plan import thaw, thaw_and_center
 
-__all__ = ["thaw"]
+__all__ = ["thaw", "thaw_and_center"]

src/mx_bluesky/i04/callbacks/murko_callback.py

@@ -0,0 +1,46 @@
+import copy
+import json
+from typing import Optional
+
+from bluesky.callbacks import CallbackBase
+from dodal.log import LOGGER
+from event_model.documents import Event, RunStart
+from redis import StrictRedis
+
+
+class MurkoCallback(CallbackBase):
+    def __init__(self, redis_host: str, redis_password: str, redis_db: int = 0):
+        self.redis_client = StrictRedis(
+            host=redis_host, password=redis_password, db=redis_db
+        )
+        self.last_uuid = None
+
+    def start(self, doc: RunStart) -> Optional[RunStart]:
+        self.murko_metadata = {
+            "zoom_percentage": doc.get("zoom_percentage"),
+            "microns_per_x_pixel": doc.get("microns_per_x_pixel"),
+            "microns_per_y_pixel": doc.get("microns_per_y_pixel"),
+            "beam_centre_i": doc.get("beam_centre_i"),
+            "beam_centre_j": doc.get("beam_centre_j"),
+            "sample_id": doc.get("sample_id"),
+        }
+        self.last_uuid = None
+        return doc
+
+    def event(self, doc: Event) -> Event:
+        if latest_omega := doc["data"].get("smargon-omega"):
+            if self.last_uuid is not None:
+                self.call_murko(self.last_uuid, latest_omega)
+        elif (uuid := doc["data"].get("oav_to_redis_forwarder-uuid")) is not None:
+            self.last_uuid = uuid
+        return doc
+
+    def call_murko(self, uuid: str, omega: float):
+        metadata = copy.deepcopy(self.murko_metadata)
+        metadata["omega_angle"] = omega
+        metadata["uuid"] = uuid
+
+        # Send metadata to REDIS and trigger murko
+        self.redis_client.hset("test-metadata", uuid, json.dumps(metadata))
+        self.redis_client.publish("murko", json.dumps(metadata))
+        LOGGER.info("Metadata sent to redis")

src/mx_bluesky/i04/thawing_plan.py

@@ -1,16 +1,58 @@
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
+from bluesky.preprocessors import run_decorator, subs_decorator
 from dls_bluesky_core.core import MsgGenerator
+from dodal.beamlines.i04 import MURKO_REDIS_DB, REDIS_HOST, REDIS_PASSWORD
 from dodal.common import inject
+from dodal.devices.oav.oav_detector import OAV
+from dodal.devices.oav.oav_to_redis_forwarder import OAVToRedisForwarder
+from dodal.devices.robot import BartRobot
 from dodal.devices.smargon import Smargon
 from dodal.devices.thawer import Thawer, ThawerStates
 
+from mx_bluesky.i04.callbacks.murko_callback import MurkoCallback
+
+
+def thaw_and_center(
+    time_to_thaw: float,
+    rotation: float = 360,
+    robot: BartRobot = inject("robot"),
+    thawer: Thawer = inject("thawer"),
+    smargon: Smargon = inject("smargon"),
+    oav: OAV = inject("oav"),
+    oav_to_redis_forwarder: OAVToRedisForwarder = inject("oav_to_redis_forwarder"),
+) -> MsgGenerator:
+    zoom_percentage = yield from bps.rd(oav.zoom_controller.percentage)
+    sample_id = yield from bps.rd(robot.sample_id)
+
+    yield from bps.abs_set(oav.zoom_controller.level, "1.0x", wait=True)
+
+    @subs_decorator(MurkoCallback(REDIS_HOST, REDIS_PASSWORD, MURKO_REDIS_DB))
+    @run_decorator(
+        md={
+            "microns_per_x_pixel": oav.parameters.micronsPerXPixel,
+            "microns_per_y_pixel": oav.parameters.micronsPerYPixel,
+            "beam_centre_i": oav.parameters.beam_centre_i,
+            "beam_centre_j": oav.parameters.beam_centre_j,
+            "zoom_percentage": zoom_percentage,
+            "sample_id": sample_id,
+        }
+    )
+    def _thaw_and_center():
+        yield from bps.kickoff(oav_to_redis_forwarder, wait=True)
+        yield from bps.monitor(smargon.omega.user_readback, name="smargon")
+        yield from bps.monitor(oav_to_redis_forwarder.uuid, name="oav")
+        yield from thaw(time_to_thaw, rotation, thawer, smargon)
+        yield from bps.complete(oav_to_redis_forwarder)
+
+    yield from _thaw_and_center()
+
 
 def thaw(
     time_to_thaw: float,
     rotation: float = 360,
-    thawer: Thawer = inject("thawer"),  # type: ignore
-    smargon: Smargon = inject("smargon"),  # type: ignore
+    thawer: Thawer = inject("thawer"),
+    smargon: Smargon = inject("smargon"),
 ) -> MsgGenerator:
     """Rotates the sample and thaws it at the same time.
 

tests/i04/callbacks/test_murko_callback.py

@@ -0,0 +1,107 @@
+import json
+from unittest.mock import MagicMock
+
+import pytest
+from event_model import Event
+
+from mx_bluesky.i04.callbacks.murko_callback import MurkoCallback
+
+test_oav_uuid = "UUID"
+test_smargon_data = 90
+
+
+def event_template(data_key, data_value) -> Event:
+    return {
+        "descriptor": "bd45c2e5-2b85-4280-95d7-a9a15800a78b",
+        "time": 1666604299.828203,
+        "data": {data_key: data_value},
+        "timestamps": {data_key: 1666604299.8220396},
+        "seq_num": 1,
+        "uid": "29033ecf-e052-43dd-98af-c7cdd62e8173",
+        "filled": {},
+    }
+
+
+test_oav_event = event_template("oav_to_redis_forwarder-uuid", test_oav_uuid)
+test_smargon_event = event_template("smargon-omega", test_smargon_data)
+
+test_start_document = {
+    "uid": "event_uuid",
+    "zoom_percentage": 80,
+    "microns_per_x_pixel": 1.2,
+    "microns_per_y_pixel": 2.5,
+    "beam_centre_i": 158,
+    "beam_centre_j": 452,
+    "sample_id": 12345,
+}
+
+
+@pytest.fixture
+def murko_callback() -> MurkoCallback:
+    callback = MurkoCallback("", "")
+    callback.redis_client = MagicMock()
+    return callback
+
+
+@pytest.fixture
+def murko_with_mock_call(murko_callback) -> MurkoCallback:
+    murko_callback.call_murko = MagicMock()
+    return murko_callback
+
+
+def test_when_oav_data_arrives_then_murko_not_called(
+    murko_with_mock_call: MurkoCallback,
+):
+    murko_with_mock_call.event(test_oav_event)
+    murko_with_mock_call.call_murko.assert_not_called()  # type: ignore
+
+
+def test_when_smargon_data_arrives_then_murko_not_called(
+    murko_with_mock_call: MurkoCallback,
+):
+    murko_with_mock_call.event(test_smargon_event)
+    murko_with_mock_call.call_murko.assert_not_called()  # type: ignore
+
+
+def test_when_smargon_data_arrives_before_oav_data_then_murko_not_called(
+    murko_with_mock_call: MurkoCallback,
+):
+    murko_with_mock_call.event(test_smargon_event)
+    murko_with_mock_call.event(test_oav_event)
+    murko_with_mock_call.call_murko.assert_not_called()  # type: ignore
+
+
+def test_when_smargon_data_arrives_before_oav_data_then_murko_called_with_smargon_data(
+    murko_with_mock_call: MurkoCallback,
+):
+    murko_with_mock_call.event(test_oav_event)
+    murko_with_mock_call.event(test_smargon_event)
+    murko_with_mock_call.call_murko.assert_called_once_with(  # type: ignore
+        test_oav_uuid, test_smargon_data
+    )
+
+
+def test_when_murko_called_with_event_data_then_meta_data_put_in_redis(
+    murko_callback: MurkoCallback,
+):
+    murko_callback.start(test_start_document)  # type: ignore
+    murko_callback.event(test_oav_event)
+    murko_callback.event(test_smargon_event)
+
+    expected_metadata = {
+        "zoom_percentage": 80,
+        "microns_per_x_pixel": 1.2,
+        "microns_per_y_pixel": 2.5,
+        "beam_centre_i": 158,
+        "beam_centre_j": 452,
+        "sample_id": 12345,
+        "omega_angle": test_smargon_data,
+        "uuid": test_oav_uuid,
+    }
+
+    murko_callback.redis_client.hset.assert_called_once_with(  # type: ignore
+        "test-metadata", test_oav_uuid, json.dumps(expected_metadata)
+    )
+    murko_callback.redis_client.publish.assert_called_once_with(  # type: ignore
+        "murko", json.dumps(expected_metadata)
+    )