mx-bluesky 1.5.8__py3-none-any.whl → 1.5.10__py3-none-any.whl

mx_bluesky/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.5.8'
-__version_tuple__ = version_tuple = (1, 5, 8)
+__version__ = version = '1.5.10'
+__version_tuple__ = version_tuple = (1, 5, 10)
 
 __commit_id__ = commit_id = None

mx_bluesky/beamlines/i04/experiment_plans/i04_grid_detect_then_xray_centre_plan.py

@@ -6,10 +6,10 @@ import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
-from dodal.devices.aperturescatterguard import ApertureScatterguard
+from dodal.devices.aperturescatterguard import ApertureScatterguard, ApertureValue
 from dodal.devices.attenuator.attenuator import BinaryFilterAttenuator
 from dodal.devices.backlight import Backlight
-from dodal.devices.common_dcm import BaseDCM
+from dodal.devices.common_dcm import DoubleCrystalMonochromator
 from dodal.devices.detector.detector_motion import DetectorMotion
 from dodal.devices.eiger import EigerDetector
 from dodal.devices.fast_grid_scan import (
@@ -17,6 +17,7 @@ from dodal.devices.fast_grid_scan import (
     set_fast_grid_scan_params,
 )
 from dodal.devices.flux import Flux
+from dodal.devices.i04.transfocator import Transfocator
 from dodal.devices.mx_phase1.beamstop import Beamstop
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.pin_image_recognition import PinTipDetection
@@ -33,6 +34,10 @@ from dodal.plans.preprocessors.verify_undulator_gap import (
     verify_undulator_gap_before_run_decorator,
 )
 
+from mx_bluesky.common.device_setup_plans.setup_zebra_and_shutter import (
+    setup_zebra_for_gridscan,
+    tidy_up_zebra_after_gridscan,
+)
 from mx_bluesky.common.experiment_plans.common_flyscan_xray_centre_plan import (
     BeamlineSpecificFGSFeatures,
     construct_beamline_specific_FGS_features,
@@ -67,10 +72,22 @@ from mx_bluesky.common.preprocessors.preprocessors import (
     transmission_and_xbpm_feedback_for_collection_decorator,
 )
 from mx_bluesky.common.utils.log import LOGGER
-from mx_bluesky.phase1_zebra.device_setup_plans.setup_zebra import (
-    setup_zebra_for_gridscan,
-    tidy_up_zebra_after_gridscan,
-)
+
+DEFAULT_BEAMSIZE_MICRONS = 20
+
+
+def _change_beamsize(
+    transfocator: Transfocator, beamsize: float, parameters: GridCommon
+):
+    """i04 always uses the large aperture and changes beamsize with the transfocator.
+
+    An aperture is needed to reduce scatter but the transfocator is best used for beamsize
+    changes as it gives more flux compared to a bigger beam with a small aperture.
+    """
+    parameters.selected_aperture = ApertureValue.LARGE
+    yield from bps.abs_set(
+        transfocator, beamsize, group=PlanGroupCheckpointConstants.GRID_READY_FOR_DC
+    )
 
 
 # See https://github.com/DiamondLightSource/blueapi/issues/506 for using device composites
@@ -80,7 +97,7 @@ def i04_grid_detect_then_xray_centre(
     attenuator: BinaryFilterAttenuator = inject("attenuator"),
     backlight: Backlight = inject("backlight"),
     beamstop: Beamstop = inject("beamstop"),
-    dcm: BaseDCM = inject("dcm"),
+    dcm: DoubleCrystalMonochromator = inject("dcm"),
     zebra_fast_grid_scan: ZebraFastGridScanThreeD = inject("zebra_fast_grid_scan"),
     flux: Flux = inject("flux"),
     oav: OAV = inject("oav"),
@@ -96,6 +113,7 @@ def i04_grid_detect_then_xray_centre(
     zocalo: ZocaloResults = inject("zocalo"),
     smargon: Smargon = inject("smargon"),
     detector_motion: DetectorMotion = inject("detector_motion"),
+    transfocator: Transfocator = inject("transfocator"),
     oav_config: str = OavConstants.OAV_CONFIG_JSON,
     udc: bool = False,
 ) -> MsgGenerator:
@@ -108,7 +126,7 @@ def i04_grid_detect_then_xray_centre(
 
 
     i04's implementation of this plan is very similar to Hyperion. However, since i04
-    isn't running in a continious Bluesky UDC loop, we take additional steps in beamline
+    isn't running in a continuous Bluesky UDC loop, we take additional steps in beamline
     tidy-up.
     """
 
@@ -134,8 +152,9 @@ def i04_grid_detect_then_xray_centre(
         robot,
         sample_shutter,
     )
+    initial_beamsize = yield from bps.rd(transfocator.beamsize_set_microns)
 
-    def tidy_beamline_if_not_udc():
+    def tidy_beamline():
         if not udc:
             yield from get_ready_for_oav_and_close_shutter(
                 composite.smargon,
@@ -143,8 +162,9 @@ def i04_grid_detect_then_xray_centre(
                 composite.aperture_scatterguard,
                 composite.detector_motion,
             )
+        yield from bps.mv(transfocator, initial_beamsize)
 
-    @bpp.finalize_decorator(tidy_beamline_if_not_udc)
+    @bpp.finalize_decorator(tidy_beamline)
     def _inner_grid_detect_then_xrc():
         # These callbacks let us talk to ISPyB and Nexgen. They aren't included in the common plan because
         # Hyperion handles its callbacks differently to BlueAPI-managed plans, see
@@ -167,6 +187,7 @@ def i04_grid_detect_then_xray_centre(
 
         yield from grid_detect_then_xray_centre_with_callbacks()
 
+    yield from _change_beamsize(transfocator, DEFAULT_BEAMSIZE_MICRONS, parameters)
     yield from _inner_grid_detect_then_xrc()
 
 
@@ -178,7 +199,7 @@ def get_ready_for_oav_and_close_shutter(
 ):
     yield from bps.wait(PlanGroupCheckpointConstants.GRID_READY_FOR_DC)
     group = "get_ready_for_oav_and_close_shutter"
-    LOGGER.info("Non-udc tidy: Seting up beamline for OAV")
+    LOGGER.info("Non-udc tidy: Setting up beamline for OAV")
     yield from setup_beamline_for_OAV(
         smargon, backlight, aperture_scatterguard, group=group
     )
@@ -247,7 +268,9 @@ def construct_i04_specific_features(
     )
     fgs_motors = xrc_composite.zebra_fast_grid_scan
     return construct_beamline_specific_FGS_features(
-        setup_zebra_for_gridscan,
+        partial(
+            setup_zebra_for_gridscan,
+        ),
         tidy_plan,
         set_flyscan_params_plan,
         fgs_motors,

mx_bluesky/beamlines/i24/jungfrau_commissioning/experiment_plans/do_darks.py

@@ -0,0 +1,78 @@
+import bluesky.preprocessors as bpp
+from bluesky import plan_stubs as bps
+from bluesky.utils import MsgGenerator
+from dodal.common import inject
+from dodal.devices.i24.commissioning_jungfrau import CommissioningJungfrau
+from ophyd_async.core import WatchableAsyncStatus
+from ophyd_async.fastcs.jungfrau import (
+    AcquisitionType,
+    GainMode,
+    create_jungfrau_pedestal_triggering_info,
+)
+from pydantic import PositiveInt
+
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_stubs.plan_utils import (
+    fly_jungfrau,
+    override_file_path,
+)
+from mx_bluesky.common.utils.log import LOGGER
+
+PEDESTAL_DARKS_RUN = "PEDESTAL DARKS RUN"
+
+
+def do_pedestal_darks(
+    exp_time_s: float = 0.001,
+    pedestal_frames: PositiveInt = 20,
+    pedestal_loops: PositiveInt = 200,
+    jungfrau: CommissioningJungfrau = inject("jungfrau"),
+    path_of_output_file: str | None = None,
+) -> MsgGenerator[WatchableAsyncStatus]:
+    """Acquire darks in pedestal mode, using dynamic gain mode. This calibrates the offsets
+    for the jungfrau, and must be performed before acquiring real data in dynamic gain mode.
+
+    When Bluesky triggers the detector in pedestal mode, with pedestal frames F and pedestal loops L,
+    the acquisition is managed at the driver level to:
+    1. Acquire F-1 frames in dynamic gain mode
+    2. Acquire 1 frame in ForceSwitchG1 gain mode
+    3. Repeat steps 1-2 L times
+    4. Do the first three steps a second time, except use ForceSwitchG2 instead of ForceSwitchG1
+    during step 2.
+
+    Args:
+        exp_time_s: Length of detector exposure for each frame.
+        pedestal_frames: Number of frames acquired per pedestal loop.
+        pedestal_loops: Number of times to acquire a set of pedestal_frames
+        jungfrau: Jungfrau device
+        path_of_output_file: Absolute path of the detector file output, including file name. If None, then use the PathProvider
+            set during Jungfrau device instantiation
+    """
+
+    @bpp.set_run_key_decorator(PEDESTAL_DARKS_RUN)
+    @bpp.run_decorator(md={"subplan_name": PEDESTAL_DARKS_RUN})
+    @bpp.stage_decorator([jungfrau])
+    def _do_decorated_plan():
+        if path_of_output_file:
+            override_file_path(jungfrau, path_of_output_file)
+
+        trigger_info = create_jungfrau_pedestal_triggering_info(
+            exp_time_s, pedestal_frames, pedestal_loops
+        )
+        LOGGER.info(
+            "Jungfrau will be triggered in pedestal mode and in dynamic gain mode"
+        )
+        yield from bps.mv(
+            jungfrau.drv.acquisition_type,
+            AcquisitionType.PEDESTAL,
+            jungfrau.drv.gain_mode,
+            GainMode.DYNAMIC,
+        )
+        return (
+            yield from fly_jungfrau(
+                jungfrau,
+                trigger_info,
+                wait=True,
+                log_on_percentage_prefix="Jungfrau pedestal dynamic gain mode darks triggers recieved",
+            )
+        )
+
+    return (yield from _do_decorated_plan())

mx_bluesky/beamlines/i24/jungfrau_commissioning/plan_stubs/__init__.py

@@ -0,0 +1 @@
+"""Jungfrau plan stubs should be used as part of Jungfrau experiment plans, and should not be run in isolation."""

mx_bluesky/beamlines/i24/jungfrau_commissioning/{do_external_acquisition.py → plan_stubs/do_external_acquisition.py}

@@ -9,7 +9,7 @@ from ophyd_async.fastcs.jungfrau import (
 )
 from pydantic import PositiveInt
 
-from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_utils import (
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_stubs.plan_utils import (
     fly_jungfrau,
     override_file_path,
 )
@@ -18,14 +18,15 @@ from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_utils import (
 def do_external_acquisition(
     exp_time_s: float,
     total_triggers: PositiveInt = 1,
-    output_file_name: str | None = None,
+    output_file_path: str | None = None,
     wait: bool = False,
     jungfrau: CommissioningJungfrau = inject("commissioning_jungfrau"),
 ) -> MsgGenerator[WatchableAsyncStatus]:
     """
     Kickoff external triggering on the Jungfrau, and optionally wait for completion.
 
-    Must be used within an open Bluesky run.
+    Any plan using this stub MUST stage the Jungfrau with the stage_decorator and open a run,
+    ideally using the run_decorator.
 
     Args:
         exp_time_s: Length of detector exposure for each frame.
@@ -36,9 +37,9 @@ def do_external_acquisition(
         wait: Optionally block until data collection is complete.
     """
 
-    if output_file_name:
-        override_file_path(jungfrau, output_file_name)
+    if output_file_path:
+        override_file_path(jungfrau, output_file_path)
 
     trigger_info = create_jungfrau_external_triggering_info(total_triggers, exp_time_s)
-    status = yield from fly_jungfrau(jungfrau, trigger_info, wait)
+    status = yield from fly_jungfrau(jungfrau, trigger_info, wait=wait)
     return status

mx_bluesky/beamlines/i24/jungfrau_commissioning/{do_internal_acquisition.py → plan_stubs/do_internal_acquisition.py}

@@ -9,7 +9,7 @@ from ophyd_async.fastcs.jungfrau import (
 )
 from pydantic import PositiveInt
 
-from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_utils import (
+from mx_bluesky.beamlines.i24.jungfrau_commissioning.plan_stubs.plan_utils import (
     fly_jungfrau,
     override_file_path,
 )
@@ -26,7 +26,8 @@ def do_internal_acquisition(
     Kickoff internal triggering on the Jungfrau, and optionally wait for completion. Frames
     per trigger will trigger as rapidly as possible according to the Jungfrau deadtime.
 
-    Must be used within an open Bluesky run.
+    Any plan using this stub MUST stage the Jungfrau with the stage_decorator and open a run,
+    ideally using the run_decorator.
 
     Args:
         exp_time_s: Length of detector exposure for each frame.
@@ -42,5 +43,5 @@ def do_internal_acquisition(
         override_file_path(jungfrau, path_of_output_file)
 
     trigger_info = create_jungfrau_internal_triggering_info(total_frames, exp_time_s)
-    status = yield from fly_jungfrau(jungfrau, trigger_info, wait)
+    status = yield from fly_jungfrau(jungfrau, trigger_info, wait=wait)
     return status

mx_bluesky/beamlines/i24/jungfrau_commissioning/{plan_utils.py → plan_stubs/plan_utils.py}

@@ -2,7 +2,6 @@ from pathlib import PurePath
 from typing import cast
 
 import bluesky.plan_stubs as bps
-import bluesky.preprocessors as bpp
 from bluesky.utils import MsgGenerator
 from dodal.common.watcher_utils import log_on_percentage_complete
 from dodal.devices.i24.commissioning_jungfrau import CommissioningJungfrau
@@ -19,44 +18,38 @@ JF_COMPLETE_GROUP = "JF complete"
 
 
 def fly_jungfrau(
-    jungfrau: CommissioningJungfrau, trigger_info: TriggerInfo, wait: bool = False
+    jungfrau: CommissioningJungfrau,
+    trigger_info: TriggerInfo,
+    wait: bool = False,
+    log_on_percentage_prefix="Jungfrau data collection triggers recieved",
 ) -> MsgGenerator[WatchableAsyncStatus]:
     """Stage, prepare, and kickoff Jungfrau with a configured TriggerInfo. Optionally wait
     for completion.
 
-    Note that this plan doesn't include unstaging of the Jungfrau, and a run must be open
-    before this plan is called.
+    Any plan using this stub MUST stage the Jungfrau with the stage_decorator and open a run,
+    ideally using the run_decorator.
 
     Args:
     jungfrau: Jungfrau device.
-    trigger_info: TriggerInfo which should be acquired using jungfrau util functions create_jungfrau_internal_triggering_info
-        or create_jungfrau_external_triggering_info.
+    trigger_info: TriggerInfo which should be acquired using jungfrau util functions.
     wait: Optionally block until data collection is complete.
+    log_on_percentage_prefix: String that will be appended to the "percentage completion" logging message.
     """
 
-    @bpp.contingency_decorator(
-        except_plan=lambda _: (yield from bps.unstage(jungfrau, wait=True))
-    )
-    def _fly_with_unstage_contingency():
-        yield from bps.stage(jungfrau)
-        LOGGER.info("Setting up detector...")
-        yield from bps.prepare(jungfrau, trigger_info, wait=True)
-        LOGGER.info("Detector prepared. Starting acquisition")
-        yield from bps.kickoff(jungfrau, wait=True)
-        LOGGER.info("Waiting for acquisition to complete...")
-        status = yield from bps.complete(jungfrau, group=JF_COMPLETE_GROUP)
-
-        # StandardDetector.complete converts regular status to watchable status,
-        # but bluesky plan stubs can't see this currently
-        status = cast(WatchableAsyncStatus, status)
-        log_on_percentage_complete(
-            status, "Jungfrau data collection triggers recieved", 10
-        )
-        if wait:
-            yield from bps.wait(JF_COMPLETE_GROUP)
-        return status
+    LOGGER.info("Preparing detector...")
+    yield from bps.prepare(jungfrau, trigger_info, wait=True)
+    LOGGER.info("Detector prepared. Starting acquisition")
+    yield from bps.kickoff(jungfrau, wait=True)
+    LOGGER.info("Waiting for acquisition to complete...")
+    status = yield from bps.complete(jungfrau, group=JF_COMPLETE_GROUP)
 
-    return (yield from _fly_with_unstage_contingency())
+    # StandardDetector.complete converts regular status to watchable status,
+    # but bluesky plan stubs can't see this currently
+    status = cast(WatchableAsyncStatus, status)
+    log_on_percentage_complete(status, log_on_percentage_prefix, 10)
+    if wait:
+        yield from bps.wait(JF_COMPLETE_GROUP)
+    return status
 
 
 def override_file_path(jungfrau: CommissioningJungfrau, path_of_output_file: str):

mx_bluesky/common/device_setup_plans/manipulate_sample.py

@@ -9,8 +9,8 @@ from dodal.devices.backlight import Backlight, InOut
 from dodal.devices.detector.detector_motion import DetectorMotion
 from dodal.devices.smargon import CombinedMove, Smargon
 
+from mx_bluesky.common.parameters.constants import PlanGroupCheckpointConstants
 from mx_bluesky.common.utils.log import LOGGER
-from mx_bluesky.hyperion.parameters.constants import CONST
 
 LOWER_DETECTOR_SHUTTER_AFTER_SCAN = True
 
@@ -48,7 +48,7 @@ def move_aperture_if_required(
 
     else:
         LOGGER.info(f"Setting aperture position to {aperture_value}")
-        yield from bps.wait(CONST.WAIT.PREPARE_APERTURE)
+        yield from bps.wait(PlanGroupCheckpointConstants.PREPARE_APERTURE)
         yield from bps.abs_set(
             aperture_scatterguard.selected_aperture,
             aperture_value,

mx_bluesky/common/device_setup_plans/robot_load_unload.py

@@ -7,10 +7,14 @@ from dodal.devices.aperturescatterguard import ApertureScatterguard, ApertureVal
 from dodal.devices.motors import XYZStage
 from dodal.devices.robot import BartRobot
 from dodal.devices.smargon import CombinedMove, Smargon, StubPosition
-from dodal.plan_stubs.motor_utils import MoveTooLarge, home_and_reset_wrapper
+from dodal.plan_stubs.motor_utils import MoveTooLargeError, home_and_reset_wrapper
 
+from mx_bluesky.common.parameters.constants import (
+    DocDescriptorNames,
+    HardwareConstants,
+    PlanNameConstants,
+)
 from mx_bluesky.common.utils.log import LOGGER
-from mx_bluesky.hyperion.parameters.constants import CONST
 
 SLEEP_PER_CHECK = 0.1
 
@@ -35,7 +39,7 @@ def wait_for_smargon_not_disabled(smargon: Smargon, timeout=60):
 
 def _raise_exception_if_moved_out_of_cryojet(exception):
     yield from bps.null()
-    if isinstance(exception, MoveTooLarge):
+    if isinstance(exception, MoveTooLargeError):
         raise Exception(
             f"Moving {exception.axis} back to {exception.position} after \
                         robot load would move it out of the cryojet. The max safe \
@@ -60,7 +64,7 @@ def do_plan_while_lower_gonio_at_home(plan: MsgGenerator, lower_gonio: XYZStage)
             plan,
             lower_gonio,
             BartRobot.LOAD_TOLERANCE_MM,
-            CONST.HARDWARE.CRYOJET_MARGIN_MM,
+            HardwareConstants.CRYOJET_MARGIN_MM,
             "lower_gonio",
             wait_for_all=False,
         ),
@@ -100,7 +104,7 @@ def robot_unload(
 
     @bpp.run_decorator(
         md={
-            "subplan_name": CONST.PLAN.ROBOT_UNLOAD,
+            "subplan_name": PlanNameConstants.ROBOT_UNLOAD,
             "metadata": {"visit": visit, "sample_id": sample_id},
             "activate_callbacks": [
                 "RobotLoadISPyBCallback",
@@ -108,7 +112,7 @@ def robot_unload(
         },
     )
     def do_robot_unload_and_send_to_ispyb():
-        yield from bps.create(name=CONST.DESCRIPTORS.ROBOT_UPDATE)
+        yield from bps.create(name=DocDescriptorNames.ROBOT_UPDATE)
         yield from bps.read(robot)
         yield from bps.save()
 

mx_bluesky/common/device_setup_plans/setup_oav.py

@@ -1,7 +1,7 @@
 from functools import partial
 
 import bluesky.plan_stubs as bps
-from dodal.devices.areadetector.plugins.CAM import ColorMode
+from dodal.devices.areadetector.plugins.cam import ColorMode
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.oav_parameters import OAVParameters
 from dodal.devices.oav.pin_image_recognition import PinTipDetection