Add plan to do pin tip centring then xray centring

src/artemis/device_setup_plans/unit_tests/test_utils.py

@@ -0,0 +1,56 @@
+from unittest.mock import MagicMock
+
+import pytest
+from bluesky import RunEngine
+from bluesky import plan_stubs as bps
+from bluesky.run_engine import RunEngine
+from dodal.beamlines import i03
+
+from artemis.device_setup_plans.utils import (
+    start_preparing_data_collection_then_do_plan,
+)
+
+
+def test_given_plan_raises_when_exception_raised_then_eiger_disarmed_and_correct_exception_returned():
+    class TestException(Exception):
+        pass
+
+    def my_plan():
+        yield from bps.null()
+        raise TestException()
+
+    eiger = i03.eiger(fake_with_ophyd_sim=True)
+    eiger.detector_params = MagicMock()
+    eiger.async_stage = MagicMock()
+    eiger.disarm_detector = MagicMock()
+
+    RE = RunEngine()
+
+    with pytest.raises(TestException):
+        RE(
+            start_preparing_data_collection_then_do_plan(
+                eiger, MagicMock(), 0.2, my_plan()
+            )
+        )
+
+    # Check detector was armed
+    eiger.async_stage.assert_called_once()
+
+    eiger.disarm_detector.assert_called_once()
+
+
+def test_when_preparing_data_collection_then_transmission_set():
+    def my_plan():
+        yield from bps.null()
+
+    attenuator = MagicMock()
+    RE = RunEngine()
+
+    RE(
+        start_preparing_data_collection_then_do_plan(
+            MagicMock(), attenuator, 0.2, my_plan()
+        )
+    )
+
+    # Check transmission set
+    attenuator.set.assert_called_once_with(0.2)

src/artemis/device_setup_plans/utils.py

@@ -0,0 +1,30 @@
+from typing import Generator
+
+from bluesky import plan_stubs as bps
+from bluesky import preprocessors as bpp
+from bluesky.utils import Msg
+from dodal.devices.attenuator import Attenuator
+from dodal.devices.eiger import EigerDetector
+
+
+def start_preparing_data_collection_then_do_plan(
+    eiger: EigerDetector,
+    attenuator: Attenuator,
+    transmission_fraction: float,
+    plan_to_run: Generator[Msg, None, None],
+    group="ready_for_data_collection",
+) -> Generator[Msg, None, None]:
+    """Starts preparing for the next data collection by arming the eiger and setting the
+    transmission. Then runs the given plan. If the plan fails it will stop disarm the eiger.
+    """
+    yield from bps.abs_set(eiger.do_arm, 1, group=group)
+    yield from bps.abs_set(
+        attenuator,
+        transmission_fraction,
+        group=group,
+    )
+
+    yield from bpp.contingency_wrapper(
+        plan_to_run,
+        except_plan=lambda e: (yield from bps.stop(eiger)),
+    )

src/artemis/experiment_plans/experiment_registry.py

@@ -7,6 +7,7 @@
 from artemis.experiment_plans import (
     fast_grid_scan_plan,
     full_grid_scan_plan,
+    pin_centre_then_xray_centre_plan,
     rotation_scan_plan,
     stepped_grid_scan_plan,
 )
@@ -24,6 +25,10 @@
     GridScanWithEdgeDetectInternalParameters,
     GridScanWithEdgeDetectParams,
 )
+from artemis.parameters.plan_specific.pin_centre_then_xray_centre_params import (
+    PinCentreThenXrayCentreInternalParameters,
+    PinCentreThenXrayCentreParams,
+)
 from artemis.parameters.plan_specific.rotation_scan_internal_params import (
     RotationInternalParameters,
     RotationScanParams,
@@ -62,6 +67,12 @@ def do_nothing():
         "experiment_param_type": RotationScanParams,
         "callback_collection_type": RotationCallbackCollection,
     },
+    "pin_tip_centre_then_xray_centre": {
+        "setup": pin_centre_then_xray_centre_plan.create_devices,
+        "internal_param_type": PinCentreThenXrayCentreInternalParameters,
+        "experiment_param_type": PinCentreThenXrayCentreParams,
+        "callback_collection_type": NullPlanCallbackCollection,
+    },
     "stepped_grid_scan": {
         "setup": stepped_grid_scan_plan.create_devices,
         "run": stepped_grid_scan_plan.get_plan,

src/artemis/experiment_plans/full_grid_scan_plan.py

@@ -15,6 +15,9 @@
 from dodal.devices.eiger import EigerDetector
 from dodal.devices.oav.oav_parameters import OAV_CONFIG_FILE_DEFAULTS, OAVParameters
 
+from artemis.device_setup_plans.utils import (
+    start_preparing_data_collection_then_do_plan,
+)
 from artemis.experiment_plans.fast_grid_scan_plan import (
     create_devices as fgs_create_devices,
 )
@@ -80,35 +83,6 @@ def create_parameters_for_fast_grid_scan(
     return fast_grid_scan_parameters
 
 
-def start_arming_then_do_grid(
-    parameters: GridScanWithEdgeDetectInternalParameters,
-    attenuator: Attenuator,
-    backlight: Backlight,
-    eiger: EigerDetector,
-    aperture_scatterguard: ApertureScatterguard,
-    detector_motion: DetectorMotion,
-    oav_params: OAVParameters,
-):
-    # Start stage with asynchronous arming here
-    yield from bps.abs_set(eiger.do_arm, 1, group="ready_for_data_collection")
-    yield from bps.abs_set(
-        attenuator,
-        parameters.artemis_params.ispyb_params.transmission_fraction,
-        group="ready_for_data_collection",
-    )
-
-    yield from bpp.contingency_wrapper(
-        detect_grid_and_do_gridscan(
-            parameters,
-            backlight,
-            aperture_scatterguard,
-            detector_motion,
-            oav_params,
-        ),
-        except_plan=lambda e: (yield from bps.stop(eiger)),
-    )
-
-
 def detect_grid_and_do_gridscan(
     parameters: GridScanWithEdgeDetectInternalParameters,
     backlight: Backlight,
@@ -196,12 +170,13 @@ def full_grid_scan(
 
     oav_params = OAVParameters("xrayCentring", **oav_param_files)
 
-    return start_arming_then_do_grid(
-        parameters,
-        attenuator,
-        backlight,
+    plan_to_perform = detect_grid_and_do_gridscan(
+        parameters, backlight, aperture_scatterguard, detector_motion, oav_params
+    )
+
+    return start_preparing_data_collection_then_do_plan(
         eiger,
-        aperture_scatterguard,
-        detector_motion,
-        oav_params,
+        attenuator,
+        parameters.artemis_params.ispyb_params.transmission_fraction,
+        plan_to_perform,
     )

src/artemis/experiment_plans/pin_centre_then_xray_centre_plan.py

@@ -0,0 +1,89 @@
+import json
+
+from blueapi.core import MsgGenerator
+from dodal.beamlines import i03
+from dodal.devices.attenuator import Attenuator
+from dodal.devices.eiger import EigerDetector
+from dodal.devices.oav.oav_parameters import OAV_CONFIG_FILE_DEFAULTS, OAVParameters
+
+from artemis.device_setup_plans.utils import (
+    start_preparing_data_collection_then_do_plan,
+)
+from artemis.experiment_plans.full_grid_scan_plan import (
+    create_devices as full_grid_create_devices,
+)
+from artemis.experiment_plans.full_grid_scan_plan import detect_grid_and_do_gridscan
+from artemis.experiment_plans.pin_tip_centring_plan import (
+    create_devices as pin_tip_create_devices,
+)
+from artemis.experiment_plans.pin_tip_centring_plan import pin_tip_centre_plan
+from artemis.log import LOGGER
+from artemis.parameters.plan_specific.grid_scan_with_edge_detect_params import (
+    GridScanWithEdgeDetectInternalParameters,
+)
+from artemis.parameters.plan_specific.pin_centre_then_xray_centre_params import (
+    PinCentreThenXrayCentreInternalParameters,
+)
+
+
+def create_devices():
+    full_grid_create_devices()
+    pin_tip_create_devices()
+
+
+def create_parameters_for_grid_detection(
+    pin_centre_parameters: PinCentreThenXrayCentreInternalParameters,
+) -> GridScanWithEdgeDetectInternalParameters:
+    params_json = json.loads(pin_centre_parameters.json())
+    grid_detect_and_xray_centre = GridScanWithEdgeDetectInternalParameters(
+        **params_json
+    )
+    LOGGER.info(
+        f"Parameters for grid detect and xray centre: {grid_detect_and_xray_centre}"
+    )
+    return grid_detect_and_xray_centre
+
+
+def pin_centre_then_xray_centre_plan(
+    parameters: PinCentreThenXrayCentreInternalParameters,
+    oav_config_files=OAV_CONFIG_FILE_DEFAULTS,
+):
+    """Plan that perfoms a pin tip centre followed by an xray centre to completely
+    centre the sample"""
+    oav_config_files["oav_config_json"] = parameters.experiment_params.oav_centring_file
+
+    yield from pin_tip_centre_plan(
+        parameters.experiment_params.tip_offset_microns, oav_config_files
+    )
+    grid_detect_params = create_parameters_for_grid_detection(parameters)
+
+    backlight = i03.backlight()
+    aperture_scattergaurd = i03.aperture_scatterguard()
+    detector_motion = i03.detector_motion()
+    oav_params = OAVParameters("xrayCentring", **oav_config_files)
+
+    yield from detect_grid_and_do_gridscan(
+        grid_detect_params,
+        backlight,
+        aperture_scattergaurd,
+        detector_motion,
+        oav_params,
+    )
+
+
+def pin_tip_centre_then_xray_centre(
+    parameters: PinCentreThenXrayCentreInternalParameters,
+) -> MsgGenerator:
+    """Starts preparing for collection then performs the pin tip centre and xray centre"""
+
+    eiger: EigerDetector = i03.eiger()
+    attenuator: Attenuator = i03.attenuator()
+
+    eiger.set_detector_parameters(parameters.artemis_params.detector_params)
+
+    return start_preparing_data_collection_then_do_plan(
+        eiger,
+        attenuator,
+        parameters.artemis_params.ispyb_params.transmission_fraction,
+        pin_centre_then_xray_centre_plan(parameters),
+    )

src/artemis/experiment_plans/pin_tip_centring_plan.py

@@ -89,7 +89,7 @@ def move_smargon_warn_on_out_of_range(smargon: Smargon, position: np.ndarray):
 
 
 def pin_tip_centre_plan(
-    tip_offset_microns: float = 900,
+    tip_offset_microns: float,
     oav_config_files: Dict[str, str] = OAV_CONFIG_FILE_DEFAULTS,
 ):
     """Finds the tip of the pin and moves to roughly the centre based on this tip. Does
@@ -116,6 +116,10 @@ def offset_and_move(tip: Pixel):
 
     LOGGER.info(f"Tip offset in pixels: {tip_offset_px}")
 
+    # need to wait for the OAV image to update
+    # See #673 for improvements
+    yield from bps.sleep(0.3)
+
     yield from pre_centring_setup_oav(oav, oav_params)
 
     tip = yield from move_pin_into_view(oav, smargon)

src/artemis/experiment_plans/tests/test_full_grid_scan_plan.py

@@ -2,7 +2,7 @@
 from unittest.mock import ANY, MagicMock, patch
 
 import pytest
-from bluesky import RunEngine
+from bluesky.run_engine import RunEngine
 from dodal.beamlines.i03 import detector_motion
 from dodal.devices.aperturescatterguard import AperturePositions, ApertureScatterguard
 from dodal.devices.backlight import Backlight
@@ -15,7 +15,6 @@
     create_devices,
     detect_grid_and_do_gridscan,
     full_grid_scan,
-    start_arming_then_do_grid,
     wait_for_det_to_finish_moving,
 )
 from artemis.external_interaction.callbacks.oav_snapshot_callback import (
@@ -222,78 +221,3 @@ def test_when_full_grid_scan_run_then_parameters_sent_to_fgs_as_expected(
 
         # Parameters can be serialized
         params.json()
-
-
-@patch(
-    "artemis.experiment_plans.full_grid_scan_plan.grid_detection_plan", autospec=True
-)
-@patch(
-    "artemis.experiment_plans.full_grid_scan_plan.OavSnapshotCallback",
-    autospec=True,
-    spec_set=True,
-)
-def test_grid_detection_running_when_exception_raised_then_eiger_disarmed_and_correct_exception_returned(
-    mock_oav_callback: MagicMock,
-    mock_grid_detection_plan: MagicMock,
-    eiger: EigerDetector,
-    RE: RunEngine,
-    test_full_grid_scan_params: GridScanWithEdgeDetectInternalParameters,
-    mock_subscriptions: MagicMock,
-    test_config_files: Dict,
-):
-    class DetectException(Exception):
-        pass
-
-    mock_grid_detection_plan.side_effect = DetectException()
-    eiger.detector_params = MagicMock()
-    eiger.async_stage = MagicMock()
-    eiger.disarm_detector = MagicMock()
-
-    with patch(
-        "artemis.external_interaction.callbacks.fgs.fgs_callback_collection.FGSCallbackCollection.from_params",
-        return_value=mock_subscriptions,
-        autospec=True,
-    ):
-        with pytest.raises(DetectException):
-            RE(
-                start_arming_then_do_grid(
-                    parameters=test_full_grid_scan_params,
-                    attenuator=MagicMock(),
-                    backlight=MagicMock(),
-                    eiger=eiger,
-                    aperture_scatterguard=MagicMock(),
-                    detector_motion=MagicMock(),
-                    oav_params=OAVParameters("xrayCentring", **test_config_files),
-                )
-            )
-
-        # Check detector was armed
-        eiger.async_stage.assert_called_once()
-
-        eiger.disarm_detector.assert_called_once()
-
-
-@patch("artemis.experiment_plans.full_grid_scan_plan.detect_grid_and_do_gridscan")
-def test_when_start_arming_then_transmission_set(
-    mock_grid_detection_plan: MagicMock,
-    RE: RunEngine,
-    test_full_grid_scan_params: GridScanWithEdgeDetectInternalParameters,
-    test_config_files: Dict,
-):
-    attenuator = MagicMock()
-    RE(
-        start_arming_then_do_grid(
-            parameters=test_full_grid_scan_params,
-            attenuator=attenuator,
-            backlight=MagicMock(),
-            eiger=MagicMock(),
-            aperture_scatterguard=MagicMock(),
-            detector_motion=MagicMock(),
-            oav_params=OAVParameters("xrayCentring", **test_config_files),
-        )
-    )
-
-    # Check transmission set
-    attenuator.set.assert_called_once_with(
-        test_full_grid_scan_params.artemis_params.ispyb_params.transmission_fraction
-    )