mx-bluesky 1.4.8__py3-none-any.whl → 1.4.9__py3-none-any.whl

mx_bluesky/common/external_interaction/nexus/nexus_utils.py

@@ -158,6 +158,6 @@ def create_beam_and_attenuator_parameters(
         tuple[Beam, Attenuator]: Descriptions of the beam and attenuator for nexgen.
     """
     return (
-        Beam(convert_eV_to_angstrom(energy_kev * 1000), flux),  # pyright: ignore
-        Attenuator(transmission_fraction),  # pyright: ignore
+        Beam(wavelength=convert_eV_to_angstrom(energy_kev * 1000), flux=flux),
+        Attenuator(transmission=transmission_fraction),
     )

mx_bluesky/common/utils/log.py

@@ -66,7 +66,7 @@ def do_default_logging_setup(
     """Configures dodal logger so that separate debug and info log files are created,
     info logs are sent to Graylog, info logs are streamed to sys.sterr, and logs from ophyd
     and bluesky and ophyd-async are optionally included."""
-    logging_path, debug_logging_path = _get_logging_dirs()
+    logging_path, debug_logging_path = _get_logging_dirs(dev_mode)
     handlers = set_up_all_logging_handlers(
         dodal_logger,
         logging_path,
@@ -103,7 +103,7 @@ def flush_debug_handler() -> str:
     return handler.target.baseFilename
 
 
-def _get_logging_dirs() -> tuple[Path, Path]:
+def _get_logging_dirs(dev_mode: bool) -> tuple[Path, Path]:
     """Get the paths to write the mx_bluesky log files to.
 
     Log location can be specified in the LOG_DIR environment variable, otherwise MX bluesky logs are written to 'dls_sw/ixx/logs/bluesky'.
@@ -115,17 +115,18 @@ def _get_logging_dirs() -> tuple[Path, Path]:
         tuple[Path, Path]: Paths to the standard log file and to the debug log file, for the file handlers to write to
     """
 
-    logging_str = environ.get("LOG_DIR")
     beamline = environ.get("BEAMLINE")
-    if logging_str:
-        logging_path = Path(logging_str)
-        debug_logging_path = logging_path
-    elif beamline:
-        logging_path = Path(f"/dls_sw/{beamline}/logs/bluesky/")
-        debug_logging_path = Path(f"/dls/tmp/{beamline}/logs/bluesky/")
+
+    if beamline and not dev_mode:
+        default_logging_str = f"/dls_sw/{beamline}/logs/bluesky/"
+        default_debug_logging_str = f"/dls/tmp/{beamline}/logs/bluesky/"
     else:
-        logging_path = Path("/tmp/logs/bluesky")
-        debug_logging_path = logging_path
+        default_logging_str = "/tmp/logs/bluesky"
+        default_debug_logging_str = default_logging_str
+
+    logging_path = Path(environ.get("LOG_DIR", default_logging_str))
+    debug_logging_path = Path(environ.get("DEBUG_LOG_DIR", default_debug_logging_str))
+
     Path.mkdir(logging_path, exist_ok=True, parents=True)
     Path.mkdir(debug_logging_path, exist_ok=True, parents=True)
     return logging_path, debug_logging_path

mx_bluesky/hyperion/__main__.py

@@ -19,9 +19,6 @@ from pydantic.dataclasses import dataclass
 from mx_bluesky.common.external_interaction.callbacks.common.log_uid_tag_callback import (
     LogUidTaggingCallback,
 )
-from mx_bluesky.common.external_interaction.callbacks.common.logging_callback import (
-    VerbosePlanExecutionLoggingCallback,
-)
 from mx_bluesky.common.parameters.components import MxBlueskyParameters
 from mx_bluesky.common.parameters.constants import Actions, Status
 from mx_bluesky.common.utils.exceptions import WarningException
@@ -41,10 +38,9 @@ from mx_bluesky.hyperion.external_interaction.agamemnon import (
 )
 from mx_bluesky.hyperion.parameters.cli import parse_cli_args
 from mx_bluesky.hyperion.parameters.constants import CONST
+from mx_bluesky.hyperion.parameters.load_centre_collect import LoadCentreCollect
 from mx_bluesky.hyperion.utils.context import setup_context
 
-VERBOSE_EVENT_LOGGING: bool | None = None
-
 
 @dataclass
 class Command:
@@ -97,9 +93,6 @@ class BlueskyRunner:
         self.publisher = Publisher(f"localhost:{CONST.CALLBACK_0MQ_PROXY_PORTS[0]}")
         RE.subscribe(self.publisher)
 
-        if VERBOSE_EVENT_LOGGING:
-            RE.subscribe(VerbosePlanExecutionLoggingCallback())
-
     def start(
         self,
         experiment: Callable,
@@ -198,7 +191,8 @@ def compose_start_args(context: BlueskyContext, plan_name: str, action: Actions)
     try:
         parameters = experiment_internal_param_type(**json.loads(request.data))
         parameters = update_params_from_agamemnon(parameters)
-        compare_params(parameters)
+        if isinstance(parameters, LoadCentreCollect):
+            compare_params(parameters)
         if parameters.model_extra:
             raise ValueError(f"Extra fields not allowed {parameters.model_extra}")
     except Exception as e:
@@ -271,8 +265,9 @@ class FlushLogs(Resource):
 def create_app(
     test_config=None,
     RE: RunEngine = RunEngine({}),
+    dev_mode: bool = False,
 ) -> tuple[Flask, BlueskyRunner]:
-    context = setup_context()
+    context = setup_context(dev_mode=dev_mode)
     runner = BlueskyRunner(
         RE,
         context=context,
@@ -305,7 +300,7 @@ def create_targets():
         CONST.LOG_FILE_NAME, CONST.GRAYLOG_PORT, dev_mode=args.dev_mode
     )
     LOGGER.info(f"Hyperion launched with args:{argv}")
-    app, runner = create_app()
+    app, runner = create_app(dev_mode=args.dev_mode)
     return app, runner, hyperion_port, args.dev_mode
 
 

mx_bluesky/hyperion/baton_handler.py

@@ -1,3 +1,5 @@
+from collections.abc import Sequence
+
 from bluesky import plan_stubs as bps
 from bluesky import preprocessors as bpp
 from dodal.devices.baton import Baton
@@ -37,9 +39,12 @@ def main_hyperion_loop(baton: Baton, composite: LoadCentreCollectComposite):
     while requested_user == HYPERION_USER:
 
         def inner_loop():
-            parameters: LoadCentreCollect | None = create_parameters_from_agamemnon()  # type: ignore # not complete until https://github.com/DiamondLightSource/mx-bluesky/issues/773
-            if parameters:
-                yield from load_centre_collect_full(composite, parameters)
+            parameter_list: Sequence[LoadCentreCollect] = (
+                create_parameters_from_agamemnon()
+            )
+            if parameter_list:
+                for parameters in parameter_list:
+                    yield from load_centre_collect_full(composite, parameters)
             else:
                 yield from bps.mv(baton.requested_user, NO_USER)
 

mx_bluesky/hyperion/device_setup_plans/smargon.py

@@ -1,6 +1,6 @@
 import numpy as np
 from bluesky import plan_stubs as bps
-from dodal.devices.smargon import Smargon
+from dodal.devices.smargon import CombinedMove, Smargon
 
 from mx_bluesky.common.utils.exceptions import SampleException
 
@@ -16,10 +16,5 @@ def move_smargon_warn_on_out_of_range(
             "Pin tip centring failed - pin too long/short/bent and out of range"
         )
     yield from bps.mv(
-        smargon.x,
-        position[0],
-        smargon.y,
-        position[1],
-        smargon.z,
-        position[2],
+        smargon, CombinedMove(x=position[0], y=position[1], z=position[2])
     )

mx_bluesky/hyperion/device_setup_plans/utils.py

@@ -8,10 +8,9 @@ from dodal.devices.detector import (
 )
 from dodal.devices.detector.detector_motion import DetectorMotion, ShutterState
 from dodal.devices.eiger import EigerDetector
-from dodal.devices.i03 import Beamstop
 from dodal.devices.i03.dcm import DCM
+from dodal.devices.mx_phase1.beamstop import Beamstop, BeamstopPositions
 
-from mx_bluesky.common.device_setup_plans.check_beamstop import check_beamstop
 from mx_bluesky.common.device_setup_plans.position_detector import (
     set_detector_z_position,
     set_shutter,
@@ -45,6 +44,9 @@ def start_preparing_data_collection_then_do_plan(
 
     def wrapped_plan():
         yield from bps.abs_set(eiger.do_arm, 1, group=group)  # type: ignore # Fix types in ophyd-async (https://github.com/DiamondLightSource/mx-bluesky/issues/855)
+        yield from bps.abs_set(
+            beamstop.selected_pos, BeamstopPositions.DATA_COLLECTION, group=group
+        )
         if detector_distance_mm:
             yield from set_detector_z_position(
                 detector_motion, detector_distance_mm, group
@@ -52,7 +54,6 @@ def start_preparing_data_collection_then_do_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 # Fix types in ophyd-async (https://github.com/DiamondLightSource/mx-bluesky/issues/855)

mx_bluesky/hyperion/experiment_plans/__init__.py

@@ -13,12 +13,12 @@ from mx_bluesky.hyperion.experiment_plans.pin_centre_then_xray_centre_plan impor
     pin_tip_centre_then_xray_centre,
 )
 from mx_bluesky.hyperion.experiment_plans.rotation_scan_plan import (
-    multi_rotation_scan,
+    rotation_scan,
 )
 
 __all__ = [
     "grid_detect_then_xray_centre",
     "pin_tip_centre_then_xray_centre",
-    "multi_rotation_scan",
+    "rotation_scan",
     "load_centre_collect_full",
 ]

mx_bluesky/hyperion/experiment_plans/experiment_registry.py

@@ -15,7 +15,7 @@ from mx_bluesky.hyperion.parameters.gridscan import (
     PinTipCentreThenXrayCentre,
 )
 from mx_bluesky.hyperion.parameters.load_centre_collect import LoadCentreCollect
-from mx_bluesky.hyperion.parameters.rotation import MultiRotationScan, RotationScan
+from mx_bluesky.hyperion.parameters.rotation import RotationScan
 
 
 def not_implemented():
@@ -32,7 +32,6 @@ class ExperimentRegistryEntry(TypedDict):
         HyperionSpecifiedThreeDGridScan
         | GridScanWithEdgeDetect
         | RotationScan
-        | MultiRotationScan
         | PinTipCentreThenXrayCentre
         | LoadCentreCollect
     ]
@@ -47,9 +46,9 @@ PLAN_REGISTRY: dict[str, ExperimentRegistryEntry] = {
         "setup": pin_centre_then_xray_centre_plan.create_devices,
         "param_type": PinTipCentreThenXrayCentre,
     },
-    "multi_rotation_scan": {
+    "rotation_scan": {
         "setup": rotation_scan_plan.create_devices,
-        "param_type": MultiRotationScan,
+        "param_type": RotationScan,
     },
     "load_centre_collect_full": {
         "setup": load_centre_collect_full_plan.create_devices,

mx_bluesky/hyperion/experiment_plans/grid_detect_then_xray_centre_plan.py

@@ -49,6 +49,9 @@ from mx_bluesky.hyperion.device_setup_plans.utils import (
 from mx_bluesky.hyperion.experiment_plans.hyperion_flyscan_xray_centre_plan import (
     construct_hyperion_specific_features,
 )
+from mx_bluesky.hyperion.experiment_plans.oav_snapshot_plan import (
+    setup_beamline_for_OAV,
+)
 from mx_bluesky.hyperion.parameters.constants import CONST
 from mx_bluesky.hyperion.parameters.device_composites import (
     GridDetectThenXRayCentreComposite,
@@ -106,6 +109,13 @@ def detect_grid_and_do_gridscan(
             parameters.box_size_um,
         )
 
+    yield from setup_beamline_for_OAV(
+        composite.smargon,
+        composite.backlight,
+        composite.aperture_scatterguard,
+        wait=True,
+    )
+
     if parameters.selected_aperture:
         # Start moving the aperture/scatterguard into position without moving it in
         yield from bps.prepare(

mx_bluesky/hyperion/experiment_plans/load_centre_collect_full_plan.py

@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from collections.abc import Generator
+
 import bluesky.plan_stubs as bps
 import numpy as np
 import pydantic
@@ -18,12 +20,13 @@ from mx_bluesky.hyperion.experiment_plans.robot_load_then_centre_plan import (
     robot_load_then_xray_centre,
 )
 from mx_bluesky.hyperion.experiment_plans.rotation_scan_plan import (
-    MultiRotationScan,
+    RotationScan,
     RotationScanComposite,
-    multi_rotation_scan_internal,
+    rotation_scan_internal,
 )
 from mx_bluesky.hyperion.parameters.constants import CONST
 from mx_bluesky.hyperion.parameters.load_centre_collect import LoadCentreCollect
+from mx_bluesky.hyperion.parameters.rotation import RotationScanPerSweep
 
 
 @pydantic.dataclasses.dataclass(config={"arbitrary_types_allowed": True})
@@ -48,6 +51,8 @@ def load_centre_collect_full(
     * If X-ray centring finds a diffracting centre then move to that centre and
     * do a collection with the specified parameters.
     """
+    parameters.features.update_self_from_server()
+
     if not oav_params:
         oav_params = OAVParameters(context="xrayCentring")
     oav_config_file = oav_params.oav_config_json
@@ -99,21 +104,46 @@ def load_centre_collect_full(
 
         multi_rotation.rotation_scans.clear()
 
+        is_alternating = parameters.features.alternate_rotation_direction
+
+        generator = rotation_scan_generator(is_alternating)
+        next(generator)
         for location in locations_to_collect_um:
             for rot in rotation_template:
-                combination = rot.model_copy()
-                (
-                    combination.x_start_um,
-                    combination.y_start_um,
-                    combination.z_start_um,
-                ) = location
+                combination = generator.send((rot, location))
                 multi_rotation.rotation_scans.append(combination)
-        multi_rotation = MultiRotationScan.model_validate(multi_rotation)
+        multi_rotation = RotationScan.model_validate(multi_rotation)
 
         assert (
             multi_rotation.demand_energy_ev
             == parameters.robot_load_then_centre.demand_energy_ev
         ), "Setting a different energy for gridscan and rotation is not supported"
-        yield from multi_rotation_scan_internal(composite, multi_rotation, oav_params)
+        yield from rotation_scan_internal(composite, multi_rotation, oav_params)
 
     yield from plan_with_callback_subs()
+
+
+def rotation_scan_generator(
+    is_alternating: bool,
+) -> Generator[RotationScanPerSweep, tuple[RotationScanPerSweep, np.ndarray], None]:
+    scan_template, location = yield  # type: ignore
+    next_rotation_direction = scan_template.rotation_direction
+    while True:
+        scan = scan_template.model_copy()
+        (
+            scan.x_start_um,
+            scan.y_start_um,
+            scan.z_start_um,
+        ) = location
+        if is_alternating:
+            if next_rotation_direction != scan.rotation_direction:
+                # If originally specified direction of the current scan is different
+                # from that required, swap the start and ends.
+                start = scan.omega_start_deg
+                rotation_sign = scan.rotation_direction.multiplier
+                end = start + rotation_sign * scan.scan_width_deg
+                scan.omega_start_deg = end
+                scan.rotation_direction = next_rotation_direction
+            next_rotation_direction = next_rotation_direction.opposite
+
+        scan_template, location = yield scan

mx_bluesky/hyperion/experiment_plans/oav_snapshot_plan.py

@@ -29,6 +29,7 @@ def setup_beamline_for_OAV(
     backlight: Backlight,
     aperture_scatterguard: ApertureScatterguard,
     group=CONST.WAIT.READY_FOR_OAV,
+    wait=False,
 ):
     max_vel = yield from bps.rd(smargon.omega.max_velocity)
     yield from bps.abs_set(smargon.omega.velocity, max_vel, group=group)
@@ -36,6 +37,8 @@ def setup_beamline_for_OAV(
     yield from bps.abs_set(
         aperture_scatterguard.selected_aperture, ApertureValue.OUT_OF_BEAM, group=group
     )
+    if wait:
+        yield from bps.wait(group)
 
 
 def oav_snapshot_plan(

mx_bluesky/hyperion/experiment_plans/robot_load_and_change_energy.py

@@ -19,7 +19,7 @@ from dodal.devices.i03.undulator_dcm import UndulatorDCM
 from dodal.devices.motors import XYZPositioner
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.robot import BartRobot, SampleLocation
-from dodal.devices.smargon import Smargon, StubPosition
+from dodal.devices.smargon import CombinedMove, Smargon, StubPosition
 from dodal.devices.thawer import Thawer
 from dodal.devices.webcam import Webcam
 from dodal.devices.xbpm_feedback import XBPMFeedback
@@ -104,16 +104,7 @@ def prepare_for_robot_load(
 
     yield from bps.mv(smargon.stub_offsets, StubPosition.RESET_TO_ROBOT_LOAD)
 
-    # fmt: off
-    yield from bps.mv(
-        smargon.x, 0,
-        smargon.y, 0,
-        smargon.z, 0,
-        smargon.omega, 0,
-        smargon.chi, 0,
-        smargon.phi, 0
-    )
-    # fmt: on
+    yield from bps.mv(smargon, CombinedMove(x=0, y=0, z=0, chi=0, phi=0, omega=0))
 
     yield from bps.wait("prepare_robot_load")
 

mx_bluesky/hyperion/experiment_plans/rotation_scan_plan.py

@@ -19,7 +19,7 @@ from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.oav_parameters import OAVParameters
 from dodal.devices.robot import BartRobot
 from dodal.devices.s4_slit_gaps import S4SlitGaps
-from dodal.devices.smargon import Smargon
+from dodal.devices.smargon import CombinedMove, Smargon
 from dodal.devices.synchrotron import Synchrotron
 from dodal.devices.undulator import Undulator
 from dodal.devices.xbpm_feedback import XBPMFeedback
@@ -32,8 +32,6 @@ from dodal.plans.preprocessors.verify_undulator_gap import (
 
 from mx_bluesky.common.device_setup_plans.manipulate_sample import (
     cleanup_sample_environment,
-    move_phi_chi_omega,
-    move_x_y_z,
     setup_sample_environment,
 )
 from mx_bluesky.common.parameters.components import WithSnapshot
@@ -62,8 +60,8 @@ from mx_bluesky.hyperion.experiment_plans.oav_snapshot_plan import (
 )
 from mx_bluesky.hyperion.parameters.constants import CONST
 from mx_bluesky.hyperion.parameters.rotation import (
-    MultiRotationScan,
     RotationScan,
+    SingleRotationScan,
 )
 
 
@@ -118,7 +116,7 @@ class RotationMotionProfile:
 
 
 def calculate_motion_profile(
-    params: RotationScan,
+    params: SingleRotationScan,
     motor_time_to_speed_s: float,
     max_velocity_deg_s: float,
 ) -> RotationMotionProfile:
@@ -212,7 +210,7 @@ def calculate_motion_profile(
 
 def rotation_scan_plan(
     composite: RotationScanComposite,
-    params: RotationScan,
+    params: SingleRotationScan,
     motion_values: RotationMotionProfile,
 ):
     """A stub plan to collect diffraction images from a sample continuously rotating
@@ -319,7 +317,7 @@ def _cleanup_plan(composite: RotationScanComposite, **kwargs):
 
 def _move_and_rotation(
     composite: RotationScanComposite,
-    params: RotationScan,
+    params: SingleRotationScan,
     oav_params: OAVParameters,
 ):
     motor_time_to_speed = yield from bps.rd(composite.smargon.omega.acceleration_time)
@@ -330,19 +328,18 @@ def _move_and_rotation(
         return num / 1000 if num else num
 
     LOGGER.info("moving to position (if specified)")
-    yield from move_x_y_z(
+    yield from bps.abs_set(
         composite.smargon,
-        _div_by_1000_if_not_none(params.x_start_um),
-        _div_by_1000_if_not_none(params.y_start_um),
-        _div_by_1000_if_not_none(params.z_start_um),
-        group=CONST.WAIT.MOVE_GONIO_TO_START,
-    )
-    yield from move_phi_chi_omega(
-        composite.smargon,
-        params.phi_start_deg,
-        params.chi_start_deg,
+        CombinedMove(
+            x=_div_by_1000_if_not_none(params.x_start_um),
+            y=_div_by_1000_if_not_none(params.y_start_um),
+            z=_div_by_1000_if_not_none(params.z_start_um),
+            phi=params.phi_start_deg,
+            chi=params.chi_start_deg,
+        ),
         group=CONST.WAIT.MOVE_GONIO_TO_START,
     )
+
     if params.take_snapshots:
         yield from bps.wait(CONST.WAIT.MOVE_GONIO_TO_START)
         yield from setup_beamline_for_OAV(
@@ -359,9 +356,9 @@ def _move_and_rotation(
     yield from rotation_scan_plan(composite, params, motion_values)
 
 
-def multi_rotation_scan(
+def rotation_scan(
     composite: RotationScanComposite,
-    parameters: MultiRotationScan,
+    parameters: RotationScan,
     oav_params: OAVParameters | None = None,
 ) -> MsgGenerator:
     @bpp.set_run_key_decorator(CONST.PLAN.ROTATION_MULTI_OUTER)
@@ -373,15 +370,15 @@ def multi_rotation_scan(
             ),
         }
     )
-    def _wrapped_multi_rotation_scan():
-        yield from multi_rotation_scan_internal(composite, parameters, oav_params)
+    def _wrapped_rotation_scan():
+        yield from rotation_scan_internal(composite, parameters, oav_params)
 
-    yield from _wrapped_multi_rotation_scan()
+    yield from _wrapped_rotation_scan()
 
 
-def multi_rotation_scan_internal(
+def rotation_scan_internal(
     composite: RotationScanComposite,
-    parameters: MultiRotationScan,
+    parameters: RotationScan,
     oav_params: OAVParameters | None = None,
 ) -> MsgGenerator:
     parameters.features.update_self_from_server()
@@ -419,7 +416,7 @@ def multi_rotation_scan_internal(
                 }
             )
             def rotation_scan_core(
-                params: RotationScan,
+                params: SingleRotationScan,
             ):
                 yield from _move_and_rotation(composite, params, oav_params)