mx-bluesky 0.3.1__py3-none-any.whl → 1.2.0__py3-none-any.whl

mx_bluesky/hyperion/experiment_plans/pin_tip_centring_plan.py

@@ -0,0 +1,164 @@
+import dataclasses
+from collections.abc import Generator
+
+import bluesky.plan_stubs as bps
+from blueapi.core import BlueskyContext
+from bluesky.utils import Msg
+from dodal.devices.backlight import Backlight
+from dodal.devices.oav.oav_detector import OAV
+from dodal.devices.oav.oav_parameters import OAV_CONFIG_JSON, OAVParameters
+from dodal.devices.oav.pin_image_recognition import PinTipDetection
+from dodal.devices.oav.utils import (
+    Pixel,
+    get_move_required_so_that_beam_is_at_pixel,
+    wait_for_tip_to_be_found,
+)
+from dodal.devices.smargon import Smargon
+
+from mx_bluesky.hyperion.device_setup_plans.setup_oav import pre_centring_setup_oav
+from mx_bluesky.hyperion.device_setup_plans.smargon import (
+    move_smargon_warn_on_out_of_range,
+)
+from mx_bluesky.hyperion.exceptions import WarningException
+from mx_bluesky.hyperion.log import LOGGER
+from mx_bluesky.hyperion.parameters.constants import CONST
+from mx_bluesky.hyperion.utils.context import device_composite_from_context
+
+DEFAULT_STEP_SIZE = 0.5
+
+
+@dataclasses.dataclass
+class PinTipCentringComposite:
+    """All devices which are directly or indirectly required by this plan"""
+
+    backlight: Backlight
+    oav: OAV
+    smargon: Smargon
+    pin_tip_detection: PinTipDetection
+
+
+def create_devices(context: BlueskyContext) -> PinTipCentringComposite:
+    return device_composite_from_context(context, PinTipCentringComposite)
+
+
+def trigger_and_return_pin_tip(
+    pin_tip: PinTipDetection,
+) -> Generator[Msg, None, Pixel]:
+    yield from bps.trigger(pin_tip, wait=True)
+    tip_x_y_px = yield from bps.rd(pin_tip.triggered_tip)
+    LOGGER.info(f"Pin tip found at {tip_x_y_px}")
+    return tip_x_y_px  # type: ignore
+
+
+def move_pin_into_view(
+    pin_tip_device: PinTipDetection,
+    smargon: Smargon,
+    step_size_mm: float = DEFAULT_STEP_SIZE,
+    max_steps: int = 2,
+) -> Generator[Msg, None, Pixel]:
+    """Attempt to move the pin into view and return the tip location in pixels if found.
+    The gonio x is moved in a number of discrete steps to find the pin. If the move
+    would take it past its limit, it moves to the limit instead.
+
+    Args:
+        pin_tip_device (PinTipDetection): The device being used to detect the pin
+        smargon (Smargon): The gonio to move the tip
+        step_size (float, optional): Distance to move the gonio (in mm) for each
+                                    step of the search. Defaults to 0.5.
+        max_steps (int, optional): The number of steps to search with. Defaults to 2.
+
+    Raises:
+        WarningException: Error if the pin tip is never found
+
+    Returns:
+        Tuple[int, int]: The location of the pin tip in pixels
+    """
+
+    def pin_tip_valid(pin_x: float):
+        return pin_x != 0 and pin_x != pin_tip_device.INVALID_POSITION[0]
+
+    for _ in range(max_steps):
+        tip_x_px, tip_y_px = yield from trigger_and_return_pin_tip(pin_tip_device)
+
+        if pin_tip_valid(tip_x_px):
+            return (tip_x_px, tip_y_px)
+
+        if tip_x_px == 0:
+            # Pin is off in the -ve direction
+            step_size_mm = -step_size_mm
+
+        smargon_x = yield from bps.rd(smargon.x.user_readback)
+        ideal_move_to_find_pin = float(smargon_x) + step_size_mm
+        high_limit = yield from bps.rd(smargon.x.high_limit_travel)
+        low_limit = yield from bps.rd(smargon.x.low_limit_travel)
+        move_within_limits = max(min(ideal_move_to_find_pin, high_limit), low_limit)
+        if move_within_limits != ideal_move_to_find_pin:
+            LOGGER.warning(
+                f"Pin tip is off screen, and moving {step_size_mm} mm would cross limits, "
+                f"moving to {move_within_limits} instead"
+            )
+        yield from bps.mv(smargon.x, move_within_limits)
+
+        # Some time for the view to settle after the move
+        yield from bps.sleep(CONST.HARDWARE.OAV_REFRESH_DELAY)
+
+    tip_x_px, tip_y_px = yield from trigger_and_return_pin_tip(pin_tip_device)
+
+    if not pin_tip_valid(tip_x_px):
+        raise WarningException(
+            "Pin tip centring failed - pin too long/short/bent and out of range"
+        )
+    else:
+        return (tip_x_px, tip_y_px)
+
+
+def pin_tip_centre_plan(
+    composite: PinTipCentringComposite,
+    tip_offset_microns: float,
+    oav_config_file: str = OAV_CONFIG_JSON,
+):
+    """Finds the tip of the pin and moves to roughly the centre based on this tip. Does
+    this at both the current omega angle and +90 deg from this angle so as to get a
+    centre in 3D.
+
+    Args:
+        tip_offset_microns (float): The x offset from the tip where the centre is assumed
+                                    to be.
+    """
+    oav: OAV = composite.oav
+    smargon: Smargon = composite.smargon
+    oav_params = OAVParameters("pinTipCentring", oav_config_file)
+
+    pin_tip_setup = composite.pin_tip_detection
+    pin_tip_detect = composite.pin_tip_detection
+
+    assert oav.parameters.micronsPerXPixel is not None
+    tip_offset_px = int(tip_offset_microns / oav.parameters.micronsPerXPixel)
+
+    def offset_and_move(tip: Pixel):
+        pixel_to_move_to = (tip[0] + tip_offset_px, tip[1])
+        position_mm = yield from get_move_required_so_that_beam_is_at_pixel(
+            smargon, pixel_to_move_to, oav.parameters
+        )
+        LOGGER.info(f"Tip centring moving to : {position_mm}")
+        yield from move_smargon_warn_on_out_of_range(smargon, position_mm)
+
+    LOGGER.info(f"Tip offset in pixels: {tip_offset_px}")
+
+    # need to wait for the OAV image to update
+    # See #673 for improvements
+    yield from bps.sleep(0.3)
+
+    yield from pre_centring_setup_oav(oav, oav_params, pin_tip_setup)
+
+    tip = yield from move_pin_into_view(pin_tip_detect, smargon)
+    yield from offset_and_move(tip)
+
+    yield from bps.mvr(smargon.omega, 90)
+
+    # need to wait for the OAV image to update
+    # See #673 for improvements
+    yield from bps.sleep(0.3)
+
+    tip = yield from wait_for_tip_to_be_found(pin_tip_detect)
+    yield from offset_and_move(tip)

mx_bluesky/hyperion/experiment_plans/robot_load_and_change_energy.py

@@ -0,0 +1,237 @@
+from __future__ import annotations
+
+import dataclasses
+from collections.abc import Generator
+from datetime import datetime
+from pathlib import Path
+from typing import cast
+
+import bluesky.plan_stubs as bps
+import bluesky.preprocessors as bpp
+from blueapi.core import BlueskyContext
+from bluesky.utils import Msg
+from dodal.devices.aperturescatterguard import ApertureScatterguard, ApertureValue
+from dodal.devices.attenuator import Attenuator
+from dodal.devices.dcm import DCM
+from dodal.devices.focusing_mirror import FocusingMirrorWithStripes, VFMMirrorVoltages
+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.thawer import Thawer
+from dodal.devices.undulator_dcm import UndulatorDCM
+from dodal.devices.webcam import Webcam
+from dodal.devices.xbpm_feedback import XBPMFeedback
+from dodal.plans.motor_util_plans import MoveTooLarge, home_and_reset_wrapper
+
+from mx_bluesky.hyperion.experiment_plans.set_energy_plan import (
+    SetEnergyComposite,
+    set_energy_plan,
+)
+from mx_bluesky.hyperion.log import LOGGER
+from mx_bluesky.hyperion.parameters.constants import CONST
+from mx_bluesky.hyperion.parameters.robot_load import RobotLoadAndEnergyChange
+
+
+@dataclasses.dataclass
+class RobotLoadAndEnergyChangeComposite:
+    # SetEnergyComposite fields
+    vfm: FocusingMirrorWithStripes
+    vfm_mirror_voltages: VFMMirrorVoltages
+    dcm: DCM
+    undulator_dcm: UndulatorDCM
+    xbpm_feedback: XBPMFeedback
+    attenuator: Attenuator
+
+    # RobotLoad fields
+    robot: BartRobot
+    webcam: Webcam
+    lower_gonio: XYZPositioner
+    thawer: Thawer
+    oav: OAV
+    smargon: Smargon
+    aperture_scatterguard: ApertureScatterguard
+
+
+def create_devices(context: BlueskyContext) -> RobotLoadAndEnergyChangeComposite:
+    from mx_bluesky.hyperion.utils.context import device_composite_from_context
+
+    return device_composite_from_context(context, RobotLoadAndEnergyChangeComposite)
+
+
+def wait_for_smargon_not_disabled(smargon: Smargon, timeout=60):
+    """Waits for the smargon disabled flag to go low. The robot hardware is responsible
+    for setting this to low when it is safe to move. It does this through a physical
+    connection between the robot and the smargon.
+    """
+    LOGGER.info("Waiting for smargon enabled")
+    SLEEP_PER_CHECK = 0.1
+    times_to_check = int(timeout / SLEEP_PER_CHECK)
+    for _ in range(times_to_check):
+        smargon_disabled = yield from bps.rd(smargon.disabled)
+        if not smargon_disabled:
+            LOGGER.info("Smargon now enabled")
+            return
+        yield from bps.sleep(SLEEP_PER_CHECK)
+    raise TimeoutError(
+        "Timed out waiting for smargon to become enabled after robot load"
+    )
+
+
+def take_robot_snapshots(oav: OAV, webcam: Webcam, directory: Path):
+    time_now = datetime.now()
+    snapshot_format = f"{time_now.strftime('%H%M%S')}_{{device}}_after_load"
+    for device in [oav.snapshot, webcam]:
+        yield from bps.abs_set(
+            device.filename, snapshot_format.format(device=device.name)
+        )
+        yield from bps.abs_set(device.directory, str(directory))
+        # Note: should be able to use `wait=True` after https://github.com/bluesky/bluesky/issues/1795
+        yield from bps.trigger(device, group="snapshots")
+        yield from bps.wait("snapshots")
+
+
+def prepare_for_robot_load(
+    aperture_scatterguard: ApertureScatterguard, smargon: Smargon
+):
+    yield from bps.abs_set(
+        aperture_scatterguard,
+        ApertureValue.ROBOT_LOAD,
+        group="prepare_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.wait("prepare_robot_load")
+
+
+def do_robot_load(
+    composite: RobotLoadAndEnergyChangeComposite,
+    sample_location: SampleLocation,
+    demand_energy_ev: float | None,
+    thawing_time: float,
+):
+    yield from bps.abs_set(
+        composite.robot,
+        sample_location,
+        group="robot_load",
+    )
+
+    if demand_energy_ev:
+        yield from set_energy_plan(
+            demand_energy_ev / 1000,
+            cast(SetEnergyComposite, composite),
+        )
+
+    yield from bps.wait("robot_load")
+
+    yield from bps.abs_set(
+        composite.thawer.thaw_for_time_s, thawing_time, group="thawing_finished"
+    )
+    yield from wait_for_smargon_not_disabled(composite.smargon)
+
+
+def raise_exception_if_moved_out_of_cryojet(exception):
+    yield from bps.null()
+    if isinstance(exception, MoveTooLarge):
+        raise Exception(
+            f"Moving {exception.axis} back to {exception.position} after \
+                        robot load would move it out of the cryojet. The max safe \
+                        distance is {exception.maximum_move}"
+        )
+
+
+def pin_already_loaded(
+    robot: BartRobot, sample_location: SampleLocation
+) -> Generator[Msg, None, bool]:
+    current_puck = yield from bps.rd(robot.current_puck)
+    current_pin = yield from bps.rd(robot.current_pin)
+    return (
+        int(current_puck) == sample_location.puck
+        and int(current_pin) == sample_location.pin
+    )
+
+
+def robot_load_and_snapshots(
+    composite: RobotLoadAndEnergyChangeComposite,
+    location: SampleLocation,
+    snapshot_directory: Path,
+    thawing_time: float,
+    demand_energy_ev: float | None,
+):
+    robot_load_plan = do_robot_load(
+        composite,
+        location,
+        demand_energy_ev,
+        thawing_time,
+    )
+
+    # The lower gonio must be in the correct position for the robot load and we
+    # want to put it back afterwards. Note we don't wait the robot is interlocked
+    # to the lower gonio and the  move is quicker than the robot takes to get to the
+    # load position.
+    yield from bpp.contingency_wrapper(
+        home_and_reset_wrapper(
+            robot_load_plan,
+            composite.lower_gonio,
+            BartRobot.LOAD_TOLERANCE_MM,
+            CONST.HARDWARE.CRYOJET_MARGIN_MM,
+            "lower_gonio",
+            wait_for_all=False,
+        ),
+        except_plan=raise_exception_if_moved_out_of_cryojet,
+    )
+
+    yield from take_robot_snapshots(composite.oav, composite.webcam, snapshot_directory)
+
+    yield from bps.create(name=CONST.DESCRIPTORS.ROBOT_LOAD)
+    yield from bps.read(composite.robot.barcode)
+    yield from bps.read(composite.oav.snapshot)
+    yield from bps.read(composite.webcam)
+    yield from bps.save()
+
+    yield from bps.wait("reset-lower_gonio")
+
+
+def robot_load_and_change_energy_plan(
+    composite: RobotLoadAndEnergyChangeComposite,
+    params: RobotLoadAndEnergyChange,
+):
+    assert params.sample_puck is not None
+    assert params.sample_pin is not None
+
+    sample_location = SampleLocation(params.sample_puck, params.sample_pin)
+
+    yield from prepare_for_robot_load(
+        composite.aperture_scatterguard, composite.smargon
+    )
+    yield from bpp.run_wrapper(
+        robot_load_and_snapshots(
+            composite,
+            sample_location,
+            params.snapshot_directory,
+            params.thawing_time,
+            params.demand_energy_ev,
+        ),
+        md={
+            "subplan_name": CONST.PLAN.ROBOT_LOAD,
+            "metadata": {
+                "visit": params.visit,
+                "sample_id": params.sample_id,
+                "sample_puck": sample_location.puck,
+                "sample_pin": sample_location.pin,
+            },
+            "activate_callbacks": [
+                "RobotLoadISPyBCallback",
+            ],
+        },
+    )

mx_bluesky/hyperion/experiment_plans/robot_load_then_centre_plan.py

@@ -0,0 +1,162 @@
+from __future__ import annotations
+
+import dataclasses
+from typing import cast
+
+from blueapi.core import BlueskyContext, MsgGenerator
+from dodal.devices.aperturescatterguard import ApertureScatterguard
+from dodal.devices.attenuator import Attenuator
+from dodal.devices.backlight import Backlight
+from dodal.devices.dcm import DCM
+from dodal.devices.detector.detector_motion import DetectorMotion
+from dodal.devices.eiger import EigerDetector
+from dodal.devices.fast_grid_scan import PandAFastGridScan, ZebraFastGridScan
+from dodal.devices.flux import Flux
+from dodal.devices.focusing_mirror import FocusingMirrorWithStripes, VFMMirrorVoltages
+from dodal.devices.motors import XYZPositioner
+from dodal.devices.oav.oav_detector import OAV
+from dodal.devices.oav.pin_image_recognition import PinTipDetection
+from dodal.devices.robot import BartRobot, SampleLocation
+from dodal.devices.s4_slit_gaps import S4SlitGaps
+from dodal.devices.smargon import Smargon
+from dodal.devices.synchrotron import Synchrotron
+from dodal.devices.thawer import Thawer
+from dodal.devices.undulator import Undulator
+from dodal.devices.undulator_dcm import UndulatorDCM
+from dodal.devices.webcam import Webcam
+from dodal.devices.xbpm_feedback import XBPMFeedback
+from dodal.devices.zebra import Zebra
+from dodal.devices.zebra_controlled_shutter import ZebraShutter
+from dodal.devices.zocalo import ZocaloResults
+from dodal.log import LOGGER
+from ophyd_async.fastcs.panda import HDFPanda
+
+from mx_bluesky.hyperion.device_setup_plans.utils import (
+    fill_in_energy_if_not_supplied,
+    start_preparing_data_collection_then_do_plan,
+)
+from mx_bluesky.hyperion.experiment_plans.grid_detect_then_xray_centre_plan import (
+    GridDetectThenXRayCentreComposite,
+)
+from mx_bluesky.hyperion.experiment_plans.pin_centre_then_xray_centre_plan import (
+    pin_centre_then_xray_centre_plan,
+)
+from mx_bluesky.hyperion.experiment_plans.robot_load_and_change_energy import (
+    RobotLoadAndEnergyChangeComposite,
+    pin_already_loaded,
+    robot_load_and_change_energy_plan,
+)
+from mx_bluesky.hyperion.parameters.constants import CONST
+from mx_bluesky.hyperion.parameters.gridscan import RobotLoadThenCentre
+
+
+@dataclasses.dataclass
+class RobotLoadThenCentreComposite:
+    # common fields
+    xbpm_feedback: XBPMFeedback
+    attenuator: Attenuator
+
+    # GridDetectThenXRayCentreComposite fields
+    aperture_scatterguard: ApertureScatterguard
+    backlight: Backlight
+    detector_motion: DetectorMotion
+    eiger: EigerDetector
+    zebra_fast_grid_scan: ZebraFastGridScan
+    flux: Flux
+    oav: OAV
+    pin_tip_detection: PinTipDetection
+    smargon: Smargon
+    synchrotron: Synchrotron
+    s4_slit_gaps: S4SlitGaps
+    undulator: Undulator
+    zebra: Zebra
+    zocalo: ZocaloResults
+    panda: HDFPanda
+    panda_fast_grid_scan: PandAFastGridScan
+    thawer: Thawer
+    sample_shutter: ZebraShutter
+
+    # SetEnergyComposite fields
+    vfm: FocusingMirrorWithStripes
+    vfm_mirror_voltages: VFMMirrorVoltages
+    dcm: DCM
+    undulator_dcm: UndulatorDCM
+
+    # RobotLoad fields
+    robot: BartRobot
+    webcam: Webcam
+    lower_gonio: XYZPositioner
+
+
+def create_devices(context: BlueskyContext) -> RobotLoadThenCentreComposite:
+    from mx_bluesky.hyperion.utils.context import device_composite_from_context
+
+    return device_composite_from_context(context, RobotLoadThenCentreComposite)
+
+
+def centring_plan_from_robot_load_params(
+    composite: RobotLoadThenCentreComposite,
+    params: RobotLoadThenCentre,
+):
+    yield from pin_centre_then_xray_centre_plan(
+        cast(GridDetectThenXRayCentreComposite, composite),
+        params.pin_centre_then_xray_centre_params(),
+    )
+
+
+def robot_load_then_centre_plan(
+    composite: RobotLoadThenCentreComposite,
+    params: RobotLoadThenCentre,
+):
+    yield from robot_load_and_change_energy_plan(
+        cast(RobotLoadAndEnergyChangeComposite, composite),
+        params.robot_load_params(),
+    )
+
+    yield from centring_plan_from_robot_load_params(composite, params)
+
+
+def robot_load_then_centre(
+    composite: RobotLoadThenCentreComposite,
+    parameters: RobotLoadThenCentre,
+) -> MsgGenerator:
+    eiger: EigerDetector = composite.eiger
+
+    # TODO: get these from one source of truth #254
+    assert parameters.sample_puck is not None
+    assert parameters.sample_pin is not None
+
+    sample_location = SampleLocation(parameters.sample_puck, parameters.sample_pin)
+
+    doing_sample_load = not (
+        yield from pin_already_loaded(composite.robot, sample_location)
+    )
+
+    doing_chi_change = parameters.chi_start_deg is not None
+
+    if doing_sample_load:
+        plan = robot_load_then_centre_plan(
+            composite,
+            parameters,
+        )
+        LOGGER.info("Pin not loaded, loading and centring")
+    elif doing_chi_change:
+        plan = centring_plan_from_robot_load_params(composite, parameters)
+        LOGGER.info("Pin already loaded but chi changed so centring")
+    else:
+        LOGGER.info("Pin already loaded and chi not changed so doing nothing")
+        return
+
+    detector_params = yield from fill_in_energy_if_not_supplied(
+        composite.dcm, parameters.detector_params
+    )
+
+    eiger.set_detector_parameters(detector_params)
+
+    yield from start_preparing_data_collection_then_do_plan(
+        eiger,
+        composite.detector_motion,
+        parameters.detector_distance_mm,
+        plan,
+        group=CONST.WAIT.GRID_READY_FOR_DC,
+    )