Merge branch 'main' into 618_aperture_selection_based_on_real_box_size

.gitignore

@@ -172,3 +172,6 @@ edm_serial/
 **/parameters/fixed_target/*/*.map
 # idea project files
 .idea/
+
+# Generated PlantUML diagrams
+docs/developer/hyperion/reference/param_hierarchy.puml

docs/developer/hyperion/reference/param-hierarchy.rst

@@ -1,9 +1,4 @@
 Hyperion Parameter class hierarchy
 ==================================
 
-TODO: automate including the param hierarchy here
-
-How Gridscan Parameters are Obtained
-------------------------------------
-
-.. uml:: gridscan.puml
+.. uml:: param_hierarchy.puml

pyproject.toml

@@ -46,7 +46,7 @@ dependencies = [
     "ophyd == 1.9.0",
     "ophyd-async >= 0.8a5",
     "bluesky >= 1.13.0a4",
-    "dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@00858ea059bb147c04fdc51a478bd2674ca4ea00",
+    "dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@e6ad77ee5aa489d0035918e45a28a0d6f72b19ed",
 ]
 
 
@@ -79,7 +79,6 @@ dev = [
     "ruff",
     "sphinx-autobuild",
     "sphinx-copybutton",
-    "sphinxcontrib-plantuml",
     "sphinx-design",
     "tox-direct",
     "tox",
@@ -181,6 +180,9 @@ commands =
     type-checking: pyright src tests {posargs}
     tests: pytest --cov=mx_bluesky --cov-report term --cov-report xml:cov.xml {posargs}
     docs: sphinx-{posargs:build -EW --keep-going} -T docs build/html
+commands_pre =
+    docs: /usr/bin/bash -c "{toxinidir}/utility_scripts/generate_plantuml.py > \
+        docs/developer/hyperion/reference/param_hierarchy.puml"
 """
 
 [tool.ruff]

src/mx_bluesky/beamlines/i24/serial/extruder/i24ssx_Extruder_Collect_py3v2.py

@@ -16,7 +16,7 @@
 import bluesky.preprocessors as bpp
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
-from dodal.devices.attenuator import ReadOnlyAttenuator
+from dodal.devices.attenuator.attenuator import ReadOnlyAttenuator
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
 from dodal.devices.i24.beam_center import DetectorBeamCenter

src/mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_Collect_py3v1.py

@@ -10,7 +10,7 @@
 import bluesky.preprocessors as bpp
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
-from dodal.devices.attenuator import ReadOnlyAttenuator
+from dodal.devices.attenuator.attenuator import ReadOnlyAttenuator
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
 from dodal.devices.i24.beam_center import DetectorBeamCenter

src/mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_Manager_py3v1.py

@@ -15,7 +15,7 @@
 import numpy as np
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
-from dodal.devices.attenuator import ReadOnlyAttenuator
+from dodal.devices.attenuator.attenuator import ReadOnlyAttenuator
 from dodal.devices.i24.beamstop import Beamstop, BeamstopPositions
 from dodal.devices.i24.dual_backlight import BacklightPositions, DualBacklight
 from dodal.devices.i24.i24_detector_motion import DetectorMotion

src/mx_bluesky/hyperion/device_setup_plans/check_beamstop.py

@@ -0,0 +1,27 @@
+import bluesky.plan_stubs as bps
+from dodal.devices.i03.beamstop import Beamstop, BeamstopPositions
+
+from mx_bluesky.common.utils.log import LOGGER
+
+
+class BeamstopException(Exception):
+    pass
+
+
+def check_beamstop(beamstop: Beamstop):
+    """
+    Check the current position of the beamstop to ensure it is in position for data collection
+    Args:
+        beamstop: The beamstop device
+
+    Raises:
+        BeamstopException: If the beamstop is in any other position than DATA_COLLECTION
+    """
+    current_pos = yield from bps.rd(beamstop.selected_pos)
+    if current_pos != BeamstopPositions.DATA_COLLECTION:
+        LOGGER.info(f"Beamstop check failed: position {current_pos}")
+        raise BeamstopException(
+            f"Beamstop is not DATA_COLLECTION, current state is {current_pos}"
+        )
+
+    LOGGER.info("Beamstop check ok")

src/mx_bluesky/hyperion/device_setup_plans/read_hardware_for_setup.py

@@ -2,7 +2,7 @@
 
 import bluesky.plan_stubs as bps
 from dodal.devices.aperturescatterguard import ApertureScatterguard
-from dodal.devices.attenuator import Attenuator
+from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.dcm import DCM
 from dodal.devices.eiger import EigerDetector
 from dodal.devices.flux import Flux
@@ -39,7 +39,7 @@ def read_hardware_pre_collection(
 
 def read_hardware_during_collection(
     aperture_scatterguard: ApertureScatterguard,
-    attenuator: Attenuator,
+    attenuator: BinaryFilterAttenuator,
     flux: Flux,
     dcm: DCM,
     detector: EigerDetector,

src/mx_bluesky/hyperion/device_setup_plans/utils.py

@@ -9,7 +9,9 @@
 )
 from dodal.devices.detector.detector_motion import DetectorMotion, ShutterState
 from dodal.devices.eiger import EigerDetector
+from dodal.devices.i03.beamstop import Beamstop
 
+from mx_bluesky.hyperion.device_setup_plans.check_beamstop import check_beamstop
 from mx_bluesky.hyperion.device_setup_plans.position_detector import (
     set_detector_z_position,
     set_shutter,
@@ -24,6 +26,7 @@ def fill_in_energy_if_not_supplied(dcm: DCM, detector_params: DetectorParams):
 
 
 def start_preparing_data_collection_then_do_plan(
+    beamstop: Beamstop,
     eiger: EigerDetector,
     detector_motion: DetectorMotion,
     detector_distance_mm: float | None,
@@ -49,6 +52,7 @@ def wrapped_plan():
         yield from set_shutter(detector_motion, ShutterState.OPEN, group)
         yield from plan_to_run
 
+    yield from check_beamstop(beamstop)
     yield from bpp.contingency_wrapper(
         wrapped_plan(),
         except_plan=lambda e: (yield from bps.stop(eiger)),  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809

src/mx_bluesky/hyperion/device_setup_plans/xbpm_feedback.py

@@ -1,15 +1,15 @@
 from bluesky import plan_stubs as bps
 from bluesky.preprocessors import finalize_wrapper
 from bluesky.utils import make_decorator
-from dodal.devices.attenuator import Attenuator
+from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.xbpm_feedback import Pause, XBPMFeedback
 
 from mx_bluesky.common.utils.log import LOGGER
 
 
 def _check_and_pause_feedback(
     xbpm_feedback: XBPMFeedback,
-    attenuator: Attenuator,
+    attenuator: BinaryFilterAttenuator,
     desired_transmission_fraction: float,
 ):
     """Checks that the xbpm is in position before then turning it off and setting a new
@@ -18,7 +18,7 @@ def _check_and_pause_feedback(
     Args:
         xbpm_feedback (XBPMFeedback): The XBPM device that is responsible for keeping
                                       the beam in position
-        attenuator (Attenuator): The attenuator used to set transmission
+        attenuator (BinaryFilterAttenuator): The attenuator used to set transmission
         desired_transmission_fraction (float): The desired transmission to set after
                                                turning XBPM feedback off.
 
@@ -34,23 +34,23 @@ def _check_and_pause_feedback(
 
 
 def _unpause_xbpm_feedback_and_set_transmission_to_1(
-    xbpm_feedback: XBPMFeedback, attenuator: Attenuator
+    xbpm_feedback: XBPMFeedback, attenuator: BinaryFilterAttenuator
 ):
     """Turns the XBPM feedback back on and sets transmission to 1 so that it keeps the
     beam aligned whilst not collecting.
 
     Args:
         xbpm_feedback (XBPMFeedback): The XBPM device that is responsible for keeping
                                       the beam in position
-        attenuator (Attenuator): The attenuator used to set transmission
+        attenuator (BinaryFilterAttenuator): The attenuator used to set transmission
     """
     yield from bps.mv(xbpm_feedback.pause_feedback, Pause.RUN, attenuator, 1.0)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
 
 
 def transmission_and_xbpm_feedback_for_collection_wrapper(
     plan,
     xbpm_feedback: XBPMFeedback,
-    attenuator: Attenuator,
+    attenuator: BinaryFilterAttenuator,
     desired_transmission_fraction: float,
 ):
     """Sets the transmission for the data collection, ensuring the xbpm feedback is valid
@@ -70,7 +70,7 @@ def transmission_and_xbpm_feedback_for_collection_wrapper(
         plan: The plan performing the data collection
         xbpm_feedback (XBPMFeedback): The XBPM device that is responsible for keeping
                                       the beam in position
-        attenuator (Attenuator): The attenuator used to set transmission
+        attenuator (BinaryFilterAttenuator): The attenuator used to set transmission
         desired_transmission_fraction (float): The desired transmission for the collection
     """
 

src/mx_bluesky/hyperion/experiment_plans/flyscan_xray_centre_plan.py

@@ -16,7 +16,7 @@
 from dodal.devices.aperturescatterguard import (
     ApertureScatterguard,
 )
-from dodal.devices.attenuator import Attenuator
+from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.backlight import Backlight
 from dodal.devices.dcm import DCM
 from dodal.devices.eiger import EigerDetector
@@ -94,7 +94,7 @@ class FlyScanXRayCentreComposite:
     """All devices which are directly or indirectly required by this plan"""
 
     aperture_scatterguard: ApertureScatterguard
-    attenuator: Attenuator
+    attenuator: BinaryFilterAttenuator
     backlight: Backlight
     dcm: DCM
     eiger: EigerDetector
@@ -112,11 +112,6 @@ class FlyScanXRayCentreComposite:
     robot: BartRobot
     sample_shutter: ZebraShutter
 
-    @property
-    def sample_motors(self) -> Smargon:
-        """Convenience alias with a more user-friendly name"""
-        return self.smargon
-
 
 class XRayCentreEventHandler(CallbackBase):
     def __init__(self):
@@ -225,16 +220,7 @@ def run_gridscan_and_fetch_results(
     """A multi-run plan which runs a gridscan, gets the results from zocalo
     and fires an event with the centres of mass determined by zocalo"""
 
-    # We get the initial motor positions so we can return to them on zocalo failure
-    initial_xyz = np.array(
-        [
-            (yield from bps.rd(fgs_composite.sample_motors.x)),
-            (yield from bps.rd(fgs_composite.sample_motors.y)),
-            (yield from bps.rd(fgs_composite.sample_motors.z)),
-        ]
-    )
-
-    yield from feature_controlled.setup_trigger(fgs_composite, parameters, initial_xyz)
+    yield from feature_controlled.setup_trigger(fgs_composite, parameters)
 
     LOGGER.info("Starting grid scan")
     yield from bps.stage(
@@ -331,11 +317,9 @@ def run_gridscan(
         "plan_name": CONST.PLAN.GRIDSCAN_MAIN,
     },
 ):
-    sample_motors = fgs_composite.sample_motors
-
     # Currently gridscan only works for omega 0, see #
     with TRACER.start_span("moving_omega_to_0"):
-        yield from bps.abs_set(sample_motors.omega, 0)
+        yield from bps.abs_set(fgs_composite.smargon.omega, 0)
 
     # We only subscribe to the communicator callback for run_gridscan, so this is where
     # we should generate an event reading the values which need to be included in the
@@ -408,7 +392,6 @@ def __call__(
             self,
             fgs_composite: FlyScanXRayCentreComposite,
             parameters: HyperionThreeDGridScan,
-            initial_xyz: np.ndarray,
         ) -> MsgGenerator: ...
 
     setup_trigger: _ExtraSetup
@@ -469,7 +452,6 @@ def _panda_tidy(fgs_composite: FlyScanXRayCentreComposite):
 def _zebra_triggering_setup(
     fgs_composite: FlyScanXRayCentreComposite,
     parameters: HyperionThreeDGridScan,
-    initial_xyz: np.ndarray,
 ):
     yield from setup_zebra_for_gridscan(
         fgs_composite.zebra, fgs_composite.sample_shutter, wait=True
@@ -479,7 +461,6 @@ def _zebra_triggering_setup(
 def _panda_triggering_setup(
     fgs_composite: FlyScanXRayCentreComposite,
     parameters: HyperionThreeDGridScan,
-    initial_xyz: np.ndarray,
 ):
     LOGGER.info("Setting up Panda for flyscan")
 
@@ -492,6 +473,8 @@ def _panda_triggering_setup(
 
     time_between_x_steps_ms = (DEADTIME_S + parameters.exposure_time_s) * 1e3
 
+    current_x = yield from bps.rd(fgs_composite.smargon.x.user_readback)
+
     smargon_speed_limit_mm_per_s = yield from bps.rd(
         fgs_composite.smargon.x.max_velocity
     )
@@ -524,7 +507,7 @@ def _panda_triggering_setup(
     yield from setup_panda_for_flyscan(
         fgs_composite.panda,
         parameters.panda_FGS_params,
-        initial_xyz[0],
+        current_x,
         parameters.exposure_time_s,
         time_between_x_steps_ms,
         sample_velocity_mm_per_s,