Merge branch 'main' into 770_correct_upper_left

setup.cfg

@@ -36,7 +36,7 @@ install_requires =
     xarray
     doct
     databroker
-    dodal @ git+https://github.com/DiamondLightSource/python-dodal.git@b78af4a9927e3b525cbb15cabaae0271cbc06fa0
+    dodal @ git+https://github.com/DiamondLightSource/python-dodal.git@ea49bf7453a0959a48904698182b7c920a0d5fbd
     pydantic<2.0 # See https://github.com/DiamondLightSource/python-artemis/issues/774
 
 

src/artemis/device_setup_plans/setup_oav.py

@@ -76,13 +76,15 @@ def pre_centring_setup_oav(oav: OAV, parameters: OAVParameters):
         parameters.minimum_height,
     )
 
-    # Connect MXSC output to MJPG input
     yield from start_mxsc(
         oav,
         parameters.min_callback_time,
         parameters.detection_script_filename,
     )
 
+    # Connect MXSC output to MJPG input for debugging
+    yield from bps.abs_set(oav.snapshot.input_plugin, "OAV.MXSC")
+
     zoom_level_str = f"{float(parameters.zoom)}x"
     if zoom_level_str not in oav.zoom_controller.allowed_zoom_levels:
         raise OAVError_ZoomLevelNotFound(

src/artemis/experiment_plans/fast_grid_scan_plan.py

@@ -224,24 +224,21 @@ def run_gridscan(
 
     @bpp.set_run_key_decorator("do_fgs")
     @bpp.run_decorator(md={"subplan_name": "do_fgs"})
+    @bpp.contingency_decorator(
+        except_plan=lambda e: (yield from bps.stop(fgs_composite.eiger)),
+        else_plan=lambda: (yield from bps.unstage(fgs_composite.eiger)),
+    )
     def do_fgs():
-        try:
-            yield from bps.wait()  # Wait for all moves to complete
-            yield from bps.kickoff(fgs_motors)
-            yield from bps.complete(fgs_motors, wait=True)
-        finally:
-            yield from bps.unstage(fgs_composite.eiger)
-
-    # Wait for arming to finish
-    artemis.log.LOGGER.info("Waiting for arming...")
-    yield from bps.wait("arming")
-    artemis.log.LOGGER.info("Arming finished")
+        yield from bps.wait()  # Wait for all moves to complete
+        yield from bps.kickoff(fgs_motors)
+        yield from bps.complete(fgs_motors, wait=True)
+
+    yield from bps.stage(fgs_composite.eiger)
 
     with TRACER.start_span("do_fgs"):
         yield from do_fgs()
 
-    with TRACER.start_span("move_to_z_0"):
-        yield from bps.abs_set(fgs_motors.z_steps, 0, wait=False)
+    yield from bps.abs_set(fgs_motors.z_steps, 0, wait=False)
 
 
 @bpp.set_run_key_decorator("run_gridscan_and_move")

src/artemis/experiment_plans/full_grid_scan.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
 
+import json
 from typing import TYPE_CHECKING, Callable
 
+import numpy as np
 from bluesky import plan_stubs as bps
 from bluesky import preprocessors as bpp
 from dodal.beamlines import i03
@@ -19,15 +21,15 @@
     create_devices as oav_create_devices,
 )
 from artemis.experiment_plans.oav_grid_detection_plan import grid_detection_plan
-from artemis.external_interaction.callbacks.fgs.fgs_callback_collection import (
-    FGSCallbackCollection,
-)
 from artemis.external_interaction.callbacks.oav_snapshot_callback import (
     OavSnapshotCallback,
 )
 from artemis.log import LOGGER
 from artemis.parameters.beamline_parameters import get_beamline_parameters
-from artemis.parameters.plan_specific.fgs_internal_params import GridScanParams
+from artemis.parameters.plan_specific.fgs_internal_params import (
+    FGSInternalParameters,
+    GridScanParams,
+)
 
 if TYPE_CHECKING:
     from artemis.parameters.plan_specific.grid_scan_with_edge_detect_params import (
@@ -65,6 +67,17 @@ def wait_for_det_to_finish_moving(detector: DetectorMotion, timeout=120):
     raise TimeoutError("Detector not finished moving")
 
 
+def create_parameters_for_fast_grid_scan(
+    grid_scan_with_edge_params: GridScanWithEdgeDetectInternalParameters,
+    grid_parameters: GridScanParams,
+) -> FGSInternalParameters:
+    params_json = json.loads(grid_scan_with_edge_params.json())
+    params_json["experiment_params"] = json.loads(grid_parameters.json())
+    fast_grid_scan_parameters = FGSInternalParameters(**params_json)
+    LOGGER.info(f"Parameters for FGS: {fast_grid_scan_parameters}")
+    return fast_grid_scan_parameters
+
+
 def start_arming_then_do_grid(
     parameters: GridScanWithEdgeDetectInternalParameters,
     backlight: Backlight,
@@ -76,15 +89,15 @@ def start_arming_then_do_grid(
     # Start stage with asynchronous arming here
     yield from bps.abs_set(eiger.do_arm, 1, group="arming")
 
-    yield from bpp.finalize_wrapper(
+    yield from bpp.contingency_wrapper(
         detect_grid_and_do_gridscan(
             parameters,
             backlight,
             aperture_scatterguard,
             detector_motion,
             oav_params,
         ),
-        bps.unstage(eiger),
+        except_plan=lambda e: (yield from bps.stop(eiger)),
     )
 
 
@@ -96,7 +109,7 @@ def detect_grid_and_do_gridscan(
     oav_params: OAVParameters,
 ):
     experiment_params: GridScanWithEdgeDetectParams = parameters.experiment_params
-    fgs_params = GridScanParams(dwell_time=experiment_params.exposure_time * 1000)
+    grid_params = GridScanParams(dwell_time=experiment_params.exposure_time * 1000)
 
     detector_params = parameters.artemis_params.detector_params
     snapshot_template = (
@@ -121,15 +134,15 @@ def run_grid_detection_plan(
 
     yield from run_grid_detection_plan(
         oav_params,
-        fgs_params,
+        grid_params,
         snapshot_template,
         experiment_params.snapshot_dir,
     )
 
     # Hack because GDA only passes 3 values to ispyb
-    out_upper_left = oav_callback.out_upper_left[0] + [
-        oav_callback.out_upper_left[1][1]
-    ]
+    out_upper_left = np.array(
+        oav_callback.out_upper_left[0] + [oav_callback.out_upper_left[1][1]]
+    )
 
     # Hack because the callback returns the list in inverted order
     parameters.artemis_params.ispyb_params.xtal_snapshots_omega_start = (
@@ -140,12 +153,9 @@ def run_grid_detection_plan(
     )
     parameters.artemis_params.ispyb_params.upper_left = out_upper_left
 
-    parameters.experiment_params = fgs_params
-
-    parameters.artemis_params.detector_params.num_triggers = fgs_params.get_num_images()
-
-    LOGGER.info(f"Parameters for FGS: {parameters}")
-    subscriptions = FGSCallbackCollection.from_params(parameters)
+    fast_grid_scan_parameters = create_parameters_for_fast_grid_scan(
+        parameters, grid_params
+    )
 
     yield from bps.abs_set(backlight.pos, Backlight.OUT)
     LOGGER.info(
@@ -156,7 +166,7 @@ def run_grid_detection_plan(
     )
     yield from wait_for_det_to_finish_moving(detector_motion)
 
-    yield from fgs_get_plan(parameters, subscriptions)
+    yield from fgs_get_plan(fast_grid_scan_parameters)
 
 
 def get_plan(

src/artemis/experiment_plans/oav_grid_detection_plan.py

@@ -8,10 +8,9 @@
 import numpy as np
 from bluesky.preprocessors import finalize_wrapper
 from dodal.beamlines import i03
-from dodal.devices.areadetector.plugins.MXSC import PinTipDetect
 from dodal.devices.fast_grid_scan import GridScanParams
 from dodal.devices.oav.oav_calculations import camera_coordinates_to_xyz
-from dodal.devices.oav.oav_detector import OAV
+from dodal.devices.oav.oav_detector import MXSC, OAV
 from dodal.devices.smargon import Smargon
 
 from artemis.device_setup_plans.setup_oav import pre_centring_setup_oav
@@ -49,10 +48,16 @@ def grid_detection_plan(
     )
 
 
-def wait_for_tip_to_be_found(pin_tip: PinTipDetect):
+def wait_for_tip_to_be_found(mxsc: MXSC):
+    pin_tip = mxsc.pin_tip
     yield from bps.trigger(pin_tip, wait=True)
     found_tip = yield from bps.rd(pin_tip)
     if found_tip == pin_tip.INVALID_POSITION:
+        top_edge = yield from bps.rd(mxsc.top)
+        bottom_edge = yield from bps.rd(mxsc.bottom)
+        LOGGER.info(
+            f"No tip found with top/bottom of {list(top_edge), list(bottom_edge)}"
+        )
         raise WarningException(
             f"No pin found after {pin_tip.validity_timeout.get()} seconds"
         )
@@ -104,7 +109,7 @@ def grid_detection_main_plan(
         # See #673 for improvements
         yield from bps.sleep(0.3)
 
-        tip_x_px, tip_y_px = yield from wait_for_tip_to_be_found(oav.mxsc.pin_tip)
+        tip_x_px, tip_y_px = yield from wait_for_tip_to_be_found(oav.mxsc)
 
         LOGGER.info(f"Tip is at x,y: {tip_x_px},{tip_y_px}")
 
@@ -212,5 +217,7 @@ def grid_detection_main_plan(
 
 
 def reset_oav():
+    """Changes the MJPG stream to look at the camera without the edge detection and turns off the edge detcetion plugin."""
     oav = i03.oav()
+    yield from bps.abs_set(oav.snapshot.input_plugin, "OAV.CAM")
     yield from bps.abs_set(oav.mxsc.enable_callbacks, 0)

src/artemis/experiment_plans/tests/conftest.py

@@ -4,6 +4,7 @@
 from bluesky.run_engine import RunEngine
 from dodal.beamlines import i03
 from dodal.devices.aperturescatterguard import AperturePositions
+from dodal.devices.smargon import Smargon
 from ophyd.status import Status
 
 from artemis.experiment_plans.fast_grid_scan_plan import FGSComposite
@@ -45,7 +46,7 @@ def eiger():
 
 
 @pytest.fixture
-def smargon():
+def smargon() -> Smargon:
     smargon = i03.smargon(fake_with_ophyd_sim=True)
     smargon.x.user_setpoint._use_limits = False
     smargon.y.user_setpoint._use_limits = False
@@ -111,7 +112,7 @@ def test_full_grid_scan_params():
 
 
 @pytest.fixture
-def fake_fgs_composite(test_fgs_params: InternalParameters):
+def fake_fgs_composite(smargon: Smargon, test_fgs_params: InternalParameters):
     fake_composite = FGSComposite(
         aperture_positions=AperturePositions(
             LARGE=(1, 2, 3, 4, 5),
@@ -135,6 +136,8 @@ def fake_fgs_composite(test_fgs_params: InternalParameters):
     fake_composite.fast_grid_scan.scan_invalid.sim_put(False)
     fake_composite.fast_grid_scan.position_counter.sim_put(0)
 
+    fake_composite.sample_motors = smargon
+
     return fake_composite
 
 

src/artemis/experiment_plans/tests/test_fast_grid_scan_plan.py

@@ -337,71 +337,52 @@ def test_when_grid_scan_ran_then_eiger_disarmed_before_zocalo_end(
     mock_parent.assert_has_calls([call.disarm(), call.run_end(0), call.run_end(0)])
 
 
-@patch("artemis.experiment_plans.fast_grid_scan_plan.bps.abs_set")
-@patch("artemis.experiment_plans.fast_grid_scan_plan.bps.kickoff")
+@patch("artemis.experiment_plans.fast_grid_scan_plan.bps.wait")
 @patch("artemis.experiment_plans.fast_grid_scan_plan.bps.complete")
-@patch("artemis.experiment_plans.fast_grid_scan_plan.bps.mv")
-@patch("artemis.experiment_plans.fast_grid_scan_plan.wait_for_fgs_valid")
-def test_when_exception_occurs_during_running_then_eiger_disarmed(
-    wait_for_valid,
-    mock_mv,
+def test_fgs_arms_eiger_without_grid_detect(
     mock_complete,
-    mock_kickoff,
-    mock_abs_set,
+    mock_wait,
     fake_fgs_composite: FGSComposite,
     test_fgs_params: FGSInternalParameters,
-    mock_subscriptions: FGSCallbackCollection,
     RE: RunEngine,
 ):
-    fake_fgs_composite.eiger.disarm_detector = MagicMock()
+    fake_fgs_composite.eiger.stage = MagicMock()
+    fake_fgs_composite.eiger.unstage = MagicMock()
 
-    fake_fgs_composite.eiger.filewriters_finished = Status()
-    fake_fgs_composite.eiger.filewriters_finished.set_finished()
-    fake_fgs_composite.eiger.odin.check_odin_state = MagicMock(return_value=True)
-    fake_fgs_composite.eiger.odin.file_writer.num_captured.sim_put(1200)
-    fake_fgs_composite.eiger.filewriters_finished = Status()
-    fake_fgs_composite.eiger.filewriters_finished.set_finished()
+    RE(run_gridscan(fake_fgs_composite, test_fgs_params))
+    fake_fgs_composite.eiger.stage.assert_called_once()
+    fake_fgs_composite.eiger.unstage.assert_called_once()
 
-    fake_fgs_composite.eiger.stage = MagicMock(
-        return_value=Status(None, None, 0, True, True)
-    )
 
-    mock_complete.side_effect = Exception()
-
-    with pytest.raises(Exception):
-        RE(
-            run_gridscan_and_move(
-                fake_fgs_composite,
-                test_fgs_params,
-                mock_subscriptions,
-            )
-        )
-
-    fake_fgs_composite.eiger.disarm_detector.assert_called_once()
-
-
-# Eiger is armed if eiger.armed_status is complete and fan ready is called. This test is very slow - could mocking more functions could speed it up
-def test_fgs_arms_eiger_without_grid_detect(
+@patch("artemis.experiment_plans.fast_grid_scan_plan.bps.wait")
+@patch("artemis.experiment_plans.fast_grid_scan_plan.bps.complete")
+def test_when_grid_scan_fails_then_detector_disarmed_and_correct_exception_returned(
+    mock_complete,
+    mock_wait,
     fake_fgs_composite: FGSComposite,
     test_fgs_params: FGSInternalParameters,
-    mock_subscriptions: FGSCallbackCollection,
     RE: RunEngine,
 ):
-    def get_good_status():
-        status = Status()
-        status.set_finished()
-        return status
+    class CompleteException(Exception):
+        pass
 
-    fake_fgs_composite.eiger.odin.check_odin_state = MagicMock(return_value=True)
-    fake_fgs_composite.eiger.odin.check_odin_initialised = MagicMock(
-        return_value=[True, True]
-    )
-    fake_fgs_composite.eiger.set_odin_pvs = MagicMock(return_value=get_good_status())
-    fake_fgs_composite.eiger.stale_params.sim_put(0)
-    fake_fgs_composite.eiger._wait_fan_ready = MagicMock(return_value=get_good_status())
-    fake_fgs_composite.eiger._wait_for_odin_status = MagicMock(
-        return_value=get_good_status()
+    mock_complete.side_effect = CompleteException()
+
+    fake_fgs_composite.eiger.stage = MagicMock(
+        return_value=Status(None, None, 0, True, True)
     )
 
-    RE(bps.stage(fake_fgs_composite.eiger))
-    fake_fgs_composite.eiger._wait_fan_ready.assert_called_once()
+    fake_fgs_composite.eiger.odin.check_odin_state = MagicMock()
+
+    fake_fgs_composite.eiger.disarm_detector = MagicMock()
+    fake_fgs_composite.eiger.disable_roi_mode = MagicMock()
+
+    # Without the complete finishing we will not get all the images
+    fake_fgs_composite.eiger.ALL_FRAMES_TIMEOUT = 0.1
+
+    # Want to get the underlying completion error, not the one raised from unstage
+    with pytest.raises(CompleteException):
+        RE(run_gridscan(fake_fgs_composite, test_fgs_params))
+
+    fake_fgs_composite.eiger.disable_roi_mode.assert_called()
+    fake_fgs_composite.eiger.disarm_detector.assert_called()