mx-bluesky 1.4.7__py3-none-any.whl → 1.4.9__py3-none-any.whl

mx_bluesky/hyperion/experiment_plans/flyscan_xray_centre_plan.py

@@ -1,467 +0,0 @@
-from __future__ import annotations
-
-import dataclasses
-from collections.abc import Callable, Sequence
-from functools import partial
-from pathlib import Path
-from typing import Protocol
-
-import bluesky.plan_stubs as bps
-import bluesky.preprocessors as bpp
-import numpy as np
-from blueapi.core import BlueskyContext
-from bluesky.utils import MsgGenerator
-from dodal.devices.fast_grid_scan import (
-    FastGridScanCommon,
-)
-from dodal.devices.fast_grid_scan import (
-    set_fast_grid_scan_params as set_flyscan_params,
-)
-from dodal.devices.zebra.zebra import Zebra
-from dodal.devices.zocalo.zocalo_results import (
-    ZOCALO_READING_PLAN_NAME,
-    ZOCALO_STAGE_GROUP,
-    XrcResult,
-    get_full_processing_results,
-)
-from dodal.plans.preprocessors.verify_undulator_gap import (
-    verify_undulator_gap_before_run_decorator,
-)
-
-from mx_bluesky.common.external_interaction.callbacks.xray_centre.ispyb_callback import (
-    ispyb_activation_wrapper,
-)
-from mx_bluesky.common.parameters.constants import HardwareConstants
-from mx_bluesky.common.plans.do_fgs import kickoff_and_complete_gridscan
-from mx_bluesky.common.plans.read_hardware import (
-    standard_read_hardware_during_collection,
-    standard_read_hardware_pre_collection,
-)
-from mx_bluesky.common.preprocessors.preprocessors import (
-    transmission_and_xbpm_feedback_for_collection_decorator,
-)
-from mx_bluesky.common.utils.context import device_composite_from_context
-from mx_bluesky.common.utils.exceptions import (
-    CrystalNotFoundException,
-    SampleException,
-)
-from mx_bluesky.common.utils.log import LOGGER
-from mx_bluesky.common.utils.tracing import TRACER
-from mx_bluesky.common.xrc_result import XRayCentreEventHandler, XRayCentreResult
-from mx_bluesky.hyperion.device_setup_plans.setup_panda import (
-    disarm_panda_for_gridscan,
-    set_panda_directory,
-    setup_panda_for_flyscan,
-)
-from mx_bluesky.hyperion.device_setup_plans.setup_zebra import (
-    setup_zebra_for_gridscan,
-    setup_zebra_for_panda_flyscan,
-    tidy_up_zebra_after_gridscan,
-)
-from mx_bluesky.hyperion.experiment_plans.change_aperture_then_move_plan import (
-    change_aperture_then_move_to_xtal,
-)
-from mx_bluesky.hyperion.parameters.constants import CONST
-from mx_bluesky.hyperion.parameters.device_composites import (
-    HyperionFlyScanXRayCentreComposite,
-)
-from mx_bluesky.hyperion.parameters.gridscan import HyperionSpecifiedThreeDGridScan
-
-ZOCALO_MIN_TOTAL_COUNT_THRESHOLD = 3
-
-
-class SmargonSpeedException(Exception):
-    pass
-
-
-def create_devices(context: BlueskyContext) -> HyperionFlyScanXRayCentreComposite:
-    """Creates the devices required for the plan and connect to them"""
-    return device_composite_from_context(context, HyperionFlyScanXRayCentreComposite)
-
-
-def flyscan_xray_centre_no_move(
-    composite: HyperionFlyScanXRayCentreComposite,
-    parameters: HyperionSpecifiedThreeDGridScan,
-) -> MsgGenerator:
-    """Perform a flyscan and determine the centres of interest"""
-
-    composite.eiger.set_detector_parameters(parameters.detector_params)
-    composite.zocalo.zocalo_environment = CONST.ZOCALO_ENV
-
-    parameters.features.update_self_from_server()
-    composite.zocalo.use_cpu_and_gpu = parameters.features.compare_cpu_and_gpu_zocalo
-    composite.zocalo.use_gpu = parameters.features.use_gpu_results
-
-    feature_controlled = _get_feature_controlled(composite, parameters)
-
-    @bpp.set_run_key_decorator(CONST.PLAN.GRIDSCAN_OUTER)
-    @bpp.run_decorator(  # attach experiment metadata to the start document
-        md={
-            "subplan_name": CONST.PLAN.GRIDSCAN_OUTER,
-            "mx_bluesky_parameters": parameters.model_dump_json(),
-            "activate_callbacks": [
-                "GridscanNexusFileCallback",
-            ],
-        }
-    )
-    @bpp.finalize_decorator(lambda: feature_controlled.tidy_plan(composite))
-    def run_gridscan_and_fetch_and_tidy(
-        fgs_composite: HyperionFlyScanXRayCentreComposite,
-        params: HyperionSpecifiedThreeDGridScan,
-        feature_controlled: _FeatureControlled,
-    ) -> MsgGenerator:
-        yield from run_gridscan_and_fetch_results(
-            fgs_composite, params, feature_controlled
-        )
-
-    yield from run_gridscan_and_fetch_and_tidy(
-        composite, parameters, feature_controlled
-    )
-
-
-def flyscan_xray_centre(
-    composite: HyperionFlyScanXRayCentreComposite,
-    parameters: HyperionSpecifiedThreeDGridScan,
-) -> MsgGenerator:
-    """Create the plan to run the grid scan based on provided parameters.
-
-    The ispyb handler should be added to the whole gridscan as we want to capture errors
-    at any point in it.
-
-    Args:
-        parameters (HyperionSpecifiedThreeDGridScan): The parameters to run the scan.
-
-    Returns:
-        Generator: The plan for the gridscan
-    """
-    xrc_event_handler = XRayCentreEventHandler()
-
-    @transmission_and_xbpm_feedback_for_collection_decorator(
-        composite,
-        parameters.transmission_frac,
-    )
-    @verify_undulator_gap_before_run_decorator(composite)
-    @bpp.subs_decorator(xrc_event_handler)
-    def flyscan_and_fetch_results() -> MsgGenerator:
-        yield from ispyb_activation_wrapper(
-            flyscan_xray_centre_no_move(composite, parameters), parameters
-        )
-
-    yield from flyscan_and_fetch_results()
-
-    xray_centre_results = xrc_event_handler.xray_centre_results
-    assert xray_centre_results, (
-        "Flyscan result event not received or no crystal found and exception not raised"
-    )
-    yield from change_aperture_then_move_to_xtal(
-        xray_centre_results[0],
-        composite.smargon,
-        composite.aperture_scatterguard,
-        parameters,
-    )
-
-
-@bpp.set_run_key_decorator(CONST.PLAN.GRIDSCAN_AND_MOVE)
-@bpp.run_decorator(md={"subplan_name": CONST.PLAN.GRIDSCAN_AND_MOVE})
-def run_gridscan_and_fetch_results(
-    fgs_composite: HyperionFlyScanXRayCentreComposite,
-    parameters: HyperionSpecifiedThreeDGridScan,
-    feature_controlled: _FeatureControlled,
-) -> MsgGenerator:
-    """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"""
-
-    yield from feature_controlled.setup_trigger(fgs_composite, parameters)
-
-    LOGGER.info("Starting grid scan")
-    yield from bps.stage(
-        fgs_composite.zocalo, group=ZOCALO_STAGE_GROUP
-    )  # connect to zocalo and make sure the queue is clear
-    yield from run_gridscan(fgs_composite, parameters, feature_controlled)
-
-    LOGGER.info("Grid scan finished, getting results.")
-
-    try:
-        with TRACER.start_span("wait_for_zocalo"):
-            yield from bps.trigger_and_read(
-                [fgs_composite.zocalo], name=ZOCALO_READING_PLAN_NAME
-            )
-            LOGGER.info("Zocalo triggered and read, interpreting results.")
-            xrc_results = yield from get_full_processing_results(fgs_composite.zocalo)
-            LOGGER.info(f"Got xray centres, top 5: {xrc_results[:5]}")
-            filtered_results = [
-                result
-                for result in xrc_results
-                if result["total_count"] >= ZOCALO_MIN_TOTAL_COUNT_THRESHOLD
-            ]
-            discarded_count = len(xrc_results) - len(filtered_results)
-            if discarded_count > 0:
-                LOGGER.info(
-                    f"Removed {discarded_count} results because below threshold"
-                )
-            if filtered_results:
-                flyscan_results = [
-                    _xrc_result_in_boxes_to_result_in_mm(xr, parameters)
-                    for xr in filtered_results
-                ]
-            else:
-                LOGGER.warning("No X-ray centre received")
-                raise CrystalNotFoundException()
-            yield from _fire_xray_centre_result_event(flyscan_results)
-
-    finally:
-        # Turn off dev/shm streaming to avoid filling disk, see https://github.com/DiamondLightSource/hyperion/issues/1395
-        LOGGER.info("Turning off Eiger dev/shm streaming")
-        yield from bps.abs_set(fgs_composite.eiger.odin.fan.dev_shm_enable, 0)  # type: ignore # Fix types in ophyd-async (https://github.com/DiamondLightSource/mx-bluesky/issues/855)
-
-        # Wait on everything before returning to GDA (particularly apertures), can be removed
-        # when we do not return to GDA here
-        yield from bps.wait()
-
-
-def _xrc_result_in_boxes_to_result_in_mm(
-    xrc_result: XrcResult, parameters: HyperionSpecifiedThreeDGridScan
-) -> XRayCentreResult:
-    fgs_params = parameters.FGS_params
-    xray_centre = fgs_params.grid_position_to_motor_position(
-        np.array(xrc_result["centre_of_mass"])
-    )
-    # A correction is applied to the bounding box to map discrete grid coordinates to
-    # the corners of the box in motor-space; we do not apply this correction
-    # to the xray-centre as it is already in continuous space and the conversion has
-    # been performed already
-    # In other words, xrc_result["bounding_box"] contains the position of the box centre,
-    # so we subtract half a box to get the corner of the box
-    return XRayCentreResult(
-        centre_of_mass_mm=xray_centre,
-        bounding_box_mm=(
-            fgs_params.grid_position_to_motor_position(
-                np.array(xrc_result["bounding_box"][0]) - 0.5
-            ),
-            fgs_params.grid_position_to_motor_position(
-                np.array(xrc_result["bounding_box"][1]) - 0.5
-            ),
-        ),
-        max_count=xrc_result["max_count"],
-        total_count=xrc_result["total_count"],
-    )
-
-
-@bpp.set_run_key_decorator(CONST.PLAN.FLYSCAN_RESULTS)
-def _fire_xray_centre_result_event(results: Sequence[XRayCentreResult]):
-    def empty_plan():
-        return iter([])
-
-    yield from bpp.run_wrapper(
-        empty_plan(),
-        md={CONST.PLAN.FLYSCAN_RESULTS: [dataclasses.asdict(r) for r in results]},
-    )
-
-
-@bpp.set_run_key_decorator(CONST.PLAN.GRIDSCAN_MAIN)
-@bpp.run_decorator(md={"subplan_name": CONST.PLAN.GRIDSCAN_MAIN})
-def run_gridscan(
-    fgs_composite: HyperionFlyScanXRayCentreComposite,
-    parameters: HyperionSpecifiedThreeDGridScan,
-    feature_controlled: _FeatureControlled,
-    md={  # noqa
-        "plan_name": CONST.PLAN.GRIDSCAN_MAIN,
-    },
-):
-    # Currently gridscan only works for omega 0, see #
-    with TRACER.start_span("moving_omega_to_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
-    # ispyb deposition
-    with TRACER.start_span("ispyb_hardware_readings"):
-        yield from standard_read_hardware_pre_collection(
-            fgs_composite.undulator,
-            fgs_composite.synchrotron,
-            fgs_composite.s4_slit_gaps,
-            fgs_composite.dcm,
-            fgs_composite.smargon,
-        )
-
-    read_during_collection = partial(
-        standard_read_hardware_during_collection,
-        fgs_composite.aperture_scatterguard,
-        fgs_composite.attenuator,
-        fgs_composite.flux,
-        fgs_composite.dcm,
-        fgs_composite.eiger,
-    )
-
-    LOGGER.info("Setting fgs params")
-    yield from feature_controlled.set_flyscan_params()
-
-    LOGGER.info("Waiting for gridscan validity check")
-    yield from wait_for_gridscan_valid(feature_controlled.fgs_motors)
-
-    LOGGER.info("Waiting for arming to finish")
-    yield from bps.wait(CONST.WAIT.GRID_READY_FOR_DC)
-    yield from bps.stage(fgs_composite.eiger)
-
-    yield from kickoff_and_complete_gridscan(
-        feature_controlled.fgs_motors,
-        fgs_composite.eiger,
-        fgs_composite.synchrotron,
-        [parameters.scan_points_first_grid, parameters.scan_points_second_grid],
-        parameters.scan_indices,
-        plan_during_collection=read_during_collection,
-    )
-    yield from bps.abs_set(feature_controlled.fgs_motors.z_steps, 0, wait=False)
-
-
-def wait_for_gridscan_valid(fgs_motors: FastGridScanCommon, timeout=0.5):
-    LOGGER.info("Waiting for valid fgs_params")
-    SLEEP_PER_CHECK = 0.1
-    times_to_check = int(timeout / SLEEP_PER_CHECK)
-    for _ in range(times_to_check):
-        scan_invalid = yield from bps.rd(fgs_motors.scan_invalid)
-        pos_counter = yield from bps.rd(fgs_motors.position_counter)
-        LOGGER.debug(
-            f"Scan invalid: {scan_invalid} and position counter: {pos_counter}"
-        )
-        if not scan_invalid and pos_counter == 0:
-            LOGGER.info("Gridscan scan valid and position counter reset")
-            return
-        yield from bps.sleep(SLEEP_PER_CHECK)
-    raise SampleException("Scan invalid - pin too long/short/bent and out of range")
-
-
-@dataclasses.dataclass
-class _FeatureControlled:
-    class _ZebraSetup(Protocol):
-        def __call__(
-            self, zebra: Zebra, group="setup_zebra_for_gridscan", wait=True
-        ) -> MsgGenerator: ...
-
-    class _ExtraSetup(Protocol):
-        def __call__(
-            self,
-            fgs_composite: HyperionFlyScanXRayCentreComposite,
-            parameters: HyperionSpecifiedThreeDGridScan,
-        ) -> MsgGenerator: ...
-
-    setup_trigger: _ExtraSetup
-    tidy_plan: Callable[[HyperionFlyScanXRayCentreComposite], MsgGenerator]
-    set_flyscan_params: Callable[[], MsgGenerator]
-    fgs_motors: FastGridScanCommon
-
-
-def _get_feature_controlled(
-    fgs_composite: HyperionFlyScanXRayCentreComposite,
-    parameters: HyperionSpecifiedThreeDGridScan,
-):
-    if parameters.features.use_panda_for_gridscan:
-        return _FeatureControlled(
-            setup_trigger=_panda_triggering_setup,
-            tidy_plan=_panda_tidy,
-            set_flyscan_params=partial(
-                set_flyscan_params,
-                fgs_composite.panda_fast_grid_scan,
-                parameters.panda_FGS_params,
-            ),
-            fgs_motors=fgs_composite.panda_fast_grid_scan,
-        )
-    else:
-        return _FeatureControlled(
-            setup_trigger=_zebra_triggering_setup,
-            tidy_plan=partial(_generic_tidy, group="flyscan_zebra_tidy", wait=True),
-            set_flyscan_params=partial(
-                set_flyscan_params,
-                fgs_composite.zebra_fast_grid_scan,
-                parameters.FGS_params,
-            ),
-            fgs_motors=fgs_composite.zebra_fast_grid_scan,
-        )
-
-
-def _generic_tidy(
-    fgs_composite: HyperionFlyScanXRayCentreComposite, group, wait=True
-) -> MsgGenerator:
-    LOGGER.info("Tidying up Zebra")
-    yield from tidy_up_zebra_after_gridscan(
-        fgs_composite.zebra, fgs_composite.sample_shutter, group=group, wait=wait
-    )
-    LOGGER.info("Tidying up Zocalo")
-    # make sure we don't consume any other results
-    yield from bps.unstage(fgs_composite.zocalo, group=group, wait=wait)
-
-
-def _panda_tidy(fgs_composite: HyperionFlyScanXRayCentreComposite):
-    group = "panda_flyscan_tidy"
-    LOGGER.info("Disabling panda blocks")
-    yield from disarm_panda_for_gridscan(fgs_composite.panda, group)
-    yield from _generic_tidy(fgs_composite, group, False)
-    yield from bps.wait(group, timeout=10)
-    yield from bps.unstage(fgs_composite.panda)
-
-
-def _zebra_triggering_setup(
-    fgs_composite: HyperionFlyScanXRayCentreComposite,
-    parameters: HyperionSpecifiedThreeDGridScan,
-):
-    yield from setup_zebra_for_gridscan(
-        fgs_composite.zebra, fgs_composite.sample_shutter, wait=True
-    )
-
-
-def _panda_triggering_setup(
-    fgs_composite: HyperionFlyScanXRayCentreComposite,
-    parameters: HyperionSpecifiedThreeDGridScan,
-):
-    LOGGER.info("Setting up Panda for flyscan")
-
-    run_up_distance_mm = yield from bps.rd(
-        fgs_composite.panda_fast_grid_scan.run_up_distance_mm
-    )
-
-    time_between_x_steps_ms = (
-        HardwareConstants.PANDA_FGS_EIGER_DEADTIME_S + parameters.exposure_time_s
-    ) * 1e3
-
-    smargon_speed_limit_mm_per_s = yield from bps.rd(
-        fgs_composite.smargon.x.max_velocity
-    )
-
-    sample_velocity_mm_per_s = (
-        parameters.panda_FGS_params.x_step_size_mm * 1e3 / time_between_x_steps_ms
-    )
-    if sample_velocity_mm_per_s > smargon_speed_limit_mm_per_s:
-        raise SmargonSpeedException(
-            f"Smargon speed was calculated from x step size\
-            {parameters.panda_FGS_params.x_step_size_mm}mm and\
-            time_between_x_steps_ms {time_between_x_steps_ms} as\
-            {sample_velocity_mm_per_s}mm/s. The smargon's speed limit is\
-            {smargon_speed_limit_mm_per_s}mm/s."
-        )
-    else:
-        LOGGER.info(
-            f"Panda grid scan: Smargon speed set to {sample_velocity_mm_per_s} mm/s"
-            f" and using a run-up distance of {run_up_distance_mm}"
-        )
-
-    yield from bps.mv(
-        fgs_composite.panda_fast_grid_scan.time_between_x_steps_ms,
-        time_between_x_steps_ms,
-    )
-
-    directory_provider_root = Path(parameters.storage_directory)
-    yield from set_panda_directory(directory_provider_root)
-
-    yield from setup_panda_for_flyscan(
-        fgs_composite.panda,
-        parameters.panda_FGS_params,
-        fgs_composite.smargon,
-        parameters.exposure_time_s,
-        time_between_x_steps_ms,
-        sample_velocity_mm_per_s,
-    )
-
-    LOGGER.info("Setting up Zebra for panda flyscan")
-    yield from setup_zebra_for_panda_flyscan(
-        fgs_composite.zebra, fgs_composite.sample_shutter, wait=True
-    )