Merge pull request #753 from DiamondLightSource/716_full_grid_scan_se…

…ts_transmission_first

Full grid scan sets transmission, transmission sent to ispbyb

src/artemis/experiment_plans/fast_grid_scan_plan.py

@@ -11,6 +11,7 @@
 from dodal.beamlines import i03
 from dodal.beamlines.i03 import (
     ApertureScatterguard,
+    Attenuator,
     Backlight,
     EigerDetector,
     FastGridScan,
@@ -61,6 +62,7 @@ class FGSComposite:
     synchrotron: Synchrotron
     undulator: Undulator
     zebra: Zebra
+    attenuator: Attenuator
 
     def __init__(
         self,
@@ -82,6 +84,7 @@ def __init__(
         self.undulator = i03.undulator(fake_with_ophyd_sim=fake)
         self.synchrotron = i03.synchrotron(fake_with_ophyd_sim=fake)
         self.zebra = i03.zebra(fake_with_ophyd_sim=fake)
+        self.attenuator = i03.attenuator(fake_with_ophyd_sim=fake)
 
 
 fast_grid_scan_composite: FGSComposite | None = None
@@ -131,6 +134,7 @@ def read_hardware_for_ispyb(
     undulator: Undulator,
     synchrotron: Synchrotron,
     s4_slit_gaps: S4SlitGaps,
+    attenuator: Attenuator,
     flux: Flux,
 ):
     artemis.log.LOGGER.info(
@@ -143,6 +147,7 @@ def read_hardware_for_ispyb(
     yield from bps.read(synchrotron.machine_status.synchrotron_mode)
     yield from bps.read(s4_slit_gaps.xgap)
     yield from bps.read(s4_slit_gaps.ygap)
+    yield from bps.read(attenuator.actual_transmission)
     yield from bps.read(flux.flux_reading)
     yield from bps.save()
 
@@ -213,6 +218,7 @@ def run_gridscan(
             fgs_composite.undulator,
             fgs_composite.synchrotron,
             fgs_composite.s4_slit_gaps,
+            fgs_composite.attenuator,
             fgs_composite.flux,
         )
 
@@ -233,6 +239,8 @@ def do_fgs():
         yield from bps.kickoff(fgs_motors)
         yield from bps.complete(fgs_motors, wait=True)
 
+    # Wait for arming to finish
+    yield from bps.wait("ready_for_data_collection")
     yield from bps.stage(fgs_composite.eiger)
 
     with TRACER.start_span("do_fgs"):

src/artemis/experiment_plans/full_grid_scan.py

@@ -8,6 +8,7 @@
 from bluesky import preprocessors as bpp
 from dodal.beamlines import i03
 from dodal.devices.aperturescatterguard import AperturePositions, ApertureScatterguard
+from dodal.devices.attenuator import Attenuator
 from dodal.devices.backlight import Backlight
 from dodal.devices.detector_motion import DetectorMotion
 from dodal.devices.eiger import EigerDetector
@@ -80,14 +81,20 @@ def create_parameters_for_fast_grid_scan(
 
 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="arming")
+    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,
+        group="ready_for_data_collection",
+    )
 
     yield from bpp.contingency_wrapper(
         detect_grid_and_do_gridscan(
@@ -181,13 +188,15 @@ def get_plan(
     eiger: EigerDetector = i03.eiger()
     aperture_scatterguard: ApertureScatterguard = i03.aperture_scatterguard()
     detector_motion: DetectorMotion = i03.detector_motion()
+    attenuator: Attenuator = i03.attenuator()
 
     eiger.set_detector_parameters(parameters.artemis_params.detector_params)
 
     oav_params = OAVParameters("xrayCentring", **oav_param_files)
 
     return start_arming_then_do_grid(
         parameters,
+        attenuator,
         backlight,
         eiger,
         aperture_scatterguard,

src/artemis/experiment_plans/tests/test_fast_grid_scan_plan.py

@@ -79,6 +79,9 @@ def test_read_hardware_for_ispyb_updates_from_ophyd_devices(
         synchrotron_test_value
     )
 
+    transmission_test_value = 0.5
+    fake_fgs_composite.attenuator.actual_transmission.sim_put(transmission_test_value)
+
     xgap_test_value = 0.1234
     ygap_test_value = 0.2345
     fake_fgs_composite.s4_slit_gaps.xgap.user_readback.sim_put(xgap_test_value)
@@ -91,16 +94,17 @@ def test_read_hardware_for_ispyb_updates_from_ophyd_devices(
     test_ispyb_callback.ispyb = MagicMock()
     RE.subscribe(test_ispyb_callback)
 
-    def standalone_read_hardware_for_ispyb(und, syn, slits, fl):
+    def standalone_read_hardware_for_ispyb(und, syn, slits, attn, fl):
         yield from bps.open_run()
-        yield from read_hardware_for_ispyb(und, syn, slits, fl)
+        yield from read_hardware_for_ispyb(und, syn, slits, attn, fl)
         yield from bps.close_run()
 
     RE(
         standalone_read_hardware_for_ispyb(
             fake_fgs_composite.undulator,
             fake_fgs_composite.synchrotron,
             fake_fgs_composite.s4_slit_gaps,
+            fake_fgs_composite.attenuator,
             fake_fgs_composite.flux,
         )
     )
@@ -110,6 +114,8 @@ def standalone_read_hardware_for_ispyb(und, syn, slits, fl):
     assert params.artemis_params.ispyb_params.synchrotron_mode == synchrotron_test_value
     assert params.artemis_params.ispyb_params.slit_gap_size_x == xgap_test_value
     assert params.artemis_params.ispyb_params.slit_gap_size_y == ygap_test_value
+    assert params.artemis_params.ispyb_params.transmission == transmission_test_value
+    assert params.artemis_params.ispyb_params.flux == flux_test_value
 
 
 @patch(

src/artemis/experiment_plans/tests/test_full_grid_scan_plan.py

@@ -242,6 +242,7 @@ class DetectException(Exception):
             RE(
                 start_arming_then_do_grid(
                     parameters=test_full_grid_scan_params,
+                    attenuator=MagicMock(),
                     backlight=MagicMock(),
                     eiger=eiger,
                     aperture_scatterguard=MagicMock(),
@@ -254,3 +255,29 @@ class DetectException(Exception):
         eiger.async_stage.assert_called_once()
 
         eiger.disarm_detector.assert_called_once()
+
+
+@patch("artemis.experiment_plans.full_grid_scan.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
+    )

src/artemis/external_interaction/callbacks/fgs/ispyb_callback.py

@@ -81,6 +81,9 @@ def event(self, doc: dict):
             self.params.artemis_params.ispyb_params.slit_gap_size_y = doc["data"][
                 "s4_slit_gaps_ygap"
             ]
+            self.params.artemis_params.ispyb_params.transmission = doc["data"][
+                "attenuator_actual_transmission"
+            ]
 
             LOGGER.info("Creating ispyb entry.")
             self.ispyb_ids = self.ispyb.begin_deposition()

src/artemis/external_interaction/callbacks/fgs/tests/conftest.py

@@ -96,6 +96,7 @@ class TestData:
             "s4_slit_gaps_ygap": 0.2345,
             "synchrotron_machine_status_synchrotron_mode": "test",
             "undulator_gap": 1.234,
+            "attenuator_actual_transmission": 1,
         },
         "timestamps": {"det1": 1666604299.8220396, "det2": 1666604299.8235943},
         "seq_num": 1,

src/artemis/system_tests/test_main_system.py

@@ -300,6 +300,7 @@ def test_cli_args_parse():
     assert test_args == ("DEBUG", True, True, True)
 
 
+@patch("dodal.beamlines.i03.Attenuator")
 @patch("dodal.beamlines.i03.Flux")
 @patch("dodal.beamlines.i03.DetectorMotion")
 @patch("dodal.beamlines.i03.OAV")
@@ -328,6 +329,7 @@ def test_when_blueskyrunner_initiated_then_plans_are_setup_and_devices_connected
     aperture_scatterguard,
     oav,
     detector_motion,
+    attenuator,
     flux,
 ):
     type_comparison.return_value = True
@@ -343,6 +345,7 @@ def test_when_blueskyrunner_initiated_then_plans_are_setup_and_devices_connected
     aperture_scatterguard.return_value.wait_for_connection.assert_called()
     oav.return_value.wait_for_connection.assert_called()
     detector_motion.return_value.wait_for_connection.assert_called()
+    attenuator.return_value.wait_for_connection.assert_called()
     flux.return_value.wait_for_connection.assert_called()