mx-bluesky 1.4.1a0__py3-none-any.whl → 1.4.3__py3-none-any.whl

mx_bluesky/hyperion/parameters/gridscan.py

@@ -7,27 +7,22 @@ from dodal.devices.fast_grid_scan import (
     PandAGridScanParams,
     ZebraGridScanParams,
 )
-from pydantic import Field, PrivateAttr
-from scanspec.core import Path as ScanPath
-from scanspec.specs import Line, Static
-
-from mx_bluesky.common.parameters.components import (
-    SplitScan,
-    WithOptionalEnergyChange,
-    WithPandaGridScan,
-)
+from pydantic import Field
+
+from mx_bluesky.common.parameters.constants import GridscanParamConstants
 from mx_bluesky.common.parameters.gridscan import (
     GridCommon,
-    SpecifiedGrid,
+    SpecifiedThreeDGridScan,
 )
-from mx_bluesky.hyperion.parameters.components import WithHyperionFeatures
+from mx_bluesky.hyperion.parameters.components import WithHyperionUDCFeatures
 from mx_bluesky.hyperion.parameters.constants import CONST, I03Constants
 
 
-class HyperionGridCommon(GridCommon, WithHyperionFeatures):
-    # This class only exists so that we can properly select enable_dev_shm. Remove in
-    # https://github.com/DiamondLightSource/hyperion/issues/1395"""
+class GridCommonWithHyperionDetectorParams(GridCommon, WithHyperionUDCFeatures):
+    """Used by models which require detector parameters but have no specifications of the grid"""
 
+    # These detector params only exist so that we can properly select enable_dev_shm. Remove in
+    # https://github.com/DiamondLightSource/hyperion/issues/1395"""
     @property
     def detector_params(self):
         self.det_dist_to_beam_converter_path = (
@@ -37,9 +32,9 @@ class HyperionGridCommon(GridCommon, WithHyperionFeatures):
         optional_args = {}
         if self.run_number:
             optional_args["run_number"] = self.run_number
-        assert (
-            self.detector_distance_mm is not None
-        ), "Detector distance must be filled before generating DetectorParams"
+        assert self.detector_distance_mm is not None, (
+            "Detector distance must be filled before generating DetectorParams"
+        )
         return DetectorParams(
             detector_size_constants=I03Constants.DETECTOR,
             expected_energy_ev=self.demand_energy_ev,
@@ -59,28 +54,42 @@ class HyperionGridCommon(GridCommon, WithHyperionFeatures):
         )
 
 
-class HyperionThreeDGridScan(
-    HyperionGridCommon,
-    SpecifiedGrid,
-    SplitScan,
-    WithOptionalEnergyChange,
-    WithPandaGridScan,
-):
-    """Parameters representing a so-called 3D grid scan, which consists of doing a
-    gridscan in X and Y, followed by one in X and Z."""
-
-    grid1_omega_deg: float = Field(default=CONST.PARAM.GRIDSCAN.OMEGA_1)  # type: ignore
-    grid2_omega_deg: float = Field(default=CONST.PARAM.GRIDSCAN.OMEGA_2)
-    x_step_size_um: float = Field(default=CONST.PARAM.GRIDSCAN.BOX_WIDTH_UM)
-    y_step_size_um: float = Field(default=CONST.PARAM.GRIDSCAN.BOX_WIDTH_UM)
-    z_step_size_um: float = Field(default=CONST.PARAM.GRIDSCAN.BOX_WIDTH_UM)
-    y2_start_um: float
-    z2_start_um: float
-    x_steps: int = Field(gt=0)
-    y_steps: int = Field(gt=0)
-    z_steps: int = Field(gt=0)
-    _set_stub_offsets: bool = PrivateAttr(default_factory=lambda: False)
+class HyperionSpecifiedThreeDGridScan(SpecifiedThreeDGridScan, WithHyperionUDCFeatures):
+    """Hyperion's 3D grid scan deviates from the common class due to: optionally using a PandA, optionally using dev_shm for GPU analysis, and using a config server for features"""
+
+    # These detector params only exist so that we can properly select enable_dev_shm. Remove in
+    # https://github.com/DiamondLightSource/hyperion/issues/1395"""
+    @property
+    def detector_params(self):
+        self.det_dist_to_beam_converter_path = (
+            self.det_dist_to_beam_converter_path
+            or CONST.PARAM.DETECTOR.BEAM_XY_LUT_PATH
+        )
+        optional_args = {}
+        if self.run_number:
+            optional_args["run_number"] = self.run_number
+        assert self.detector_distance_mm is not None, (
+            "Detector distance must be filled before generating DetectorParams"
+        )
+        return DetectorParams(
+            detector_size_constants=I03Constants.DETECTOR,
+            expected_energy_ev=self.demand_energy_ev,
+            exposure_time=self.exposure_time_s,
+            directory=self.storage_directory,
+            prefix=self.file_name,
+            detector_distance=self.detector_distance_mm,
+            omega_start=self.omega_start_deg or 0,
+            omega_increment=0,
+            num_images_per_trigger=1,
+            num_triggers=self.num_images,
+            use_roi_mode=self.use_roi_mode,
+            det_dist_to_beam_converter_path=self.det_dist_to_beam_converter_path,
+            trigger_mode=self.trigger_mode,
+            enable_dev_shm=self.features.compare_cpu_and_gpu_zocalo,
+            **optional_args,
+        )
 
+    # Relative to common grid scan, stub offsets are defined by config server
     @property
     def FGS_params(self) -> ZebraGridScanParams:
         return ZebraGridScanParams(
@@ -124,59 +133,17 @@ class HyperionThreeDGridScan(
             transmission_fraction=self.transmission_frac,
         )
 
-    def do_set_stub_offsets(self, value: bool):
-        self._set_stub_offsets = value
-
-    @property
-    def grid_1_spec(self):
-        x_end = self.x_start_um + self.x_step_size_um * (self.x_steps - 1)
-        y1_end = self.y_start_um + self.y_step_size_um * (self.y_steps - 1)
-        grid_1_x = Line("sam_x", self.x_start_um, x_end, self.x_steps)
-        grid_1_y = Line("sam_y", self.y_start_um, y1_end, self.y_steps)
-        grid_1_z = Static("sam_z", self.z_start_um)
-        return grid_1_y.zip(grid_1_z) * ~grid_1_x
-
-    @property
-    def grid_2_spec(self):
-        x_end = self.x_start_um + self.x_step_size_um * (self.x_steps - 1)
-        z2_end = self.z2_start_um + self.z_step_size_um * (self.z_steps - 1)
-        grid_2_x = Line("sam_x", self.x_start_um, x_end, self.x_steps)
-        grid_2_z = Line("sam_z", self.z2_start_um, z2_end, self.z_steps)
-        grid_2_y = Static("sam_y", self.y2_start_um)
-        return grid_2_z.zip(grid_2_y) * ~grid_2_x
-
-    @property
-    def scan_indices(self):
-        """The first index of each gridscan, useful for writing nexus files/VDS"""
-        return [
-            0,
-            len(ScanPath(self.grid_1_spec.calculate()).consume().midpoints["sam_x"]),
-        ]
-
-    @property
-    def scan_spec(self):
-        """A fully specified ScanSpec object representing both grids, with x, y, z and
-        omega positions."""
-        return self.grid_1_spec.concat(self.grid_2_spec)
 
-    @property
-    def scan_points(self):
-        """A list of all the points in the scan_spec."""
-        return ScanPath(self.scan_spec.calculate()).consume().midpoints
-
-    @property
-    def scan_points_first_grid(self):
-        """A list of all the points in the first grid scan."""
-        return ScanPath(self.grid_1_spec.calculate()).consume().midpoints
+class OddYStepsException(Exception): ...
 
-    @property
-    def scan_points_second_grid(self):
-        """A list of all the points in the second grid scan."""
-        return ScanPath(self.grid_2_spec.calculate()).consume().midpoints
 
-    @property
-    def num_images(self) -> int:
-        return len(self.scan_points["sam_x"])
+class PinTipCentreThenXrayCentre(
+    GridCommonWithHyperionDetectorParams, WithHyperionUDCFeatures
+):
+    tip_offset_um: float = 0
 
 
-class OddYStepsException(Exception): ...
+class GridScanWithEdgeDetect(
+    GridCommonWithHyperionDetectorParams, WithHyperionUDCFeatures
+):
+    box_size_um: float = Field(default=GridscanParamConstants.BOX_WIDTH_UM)

mx_bluesky/hyperion/parameters/load_centre_collect.py

@@ -1,4 +1,4 @@
-from typing import TypeVar
+from typing import Self, TypeVar
 
 from pydantic import BaseModel, model_validator
 
@@ -8,7 +8,8 @@ from mx_bluesky.common.parameters.components import (
     WithSample,
     WithVisit,
 )
-from mx_bluesky.common.parameters.gridscan import (
+from mx_bluesky.hyperion.parameters.components import WithHyperionUDCFeatures
+from mx_bluesky.hyperion.parameters.robot_load import (
     RobotLoadThenCentre,
 )
 from mx_bluesky.hyperion.parameters.rotation import MultiRotationScan
@@ -23,7 +24,11 @@ def construct_from_values(parent_context: dict, child_dict: dict, t: type[T]) ->
 
 
 class LoadCentreCollect(
-    MxBlueskyParameters, WithVisit, WithSample, WithCentreSelection
+    MxBlueskyParameters,
+    WithVisit,
+    WithSample,
+    WithCentreSelection,
+    WithHyperionUDCFeatures,
 ):
     """Experiment parameters to perform the combined robot load,
     pin-tip centre and rotation scan operations."""
@@ -39,10 +44,31 @@ class LoadCentreCollect(
             | RobotLoadThenCentre.model_fields.keys()
             | MultiRotationScan.model_fields.keys()
         )
+
         disallowed_keys = values.keys() - allowed_keys
-        assert (
-            disallowed_keys == set()
-        ), f"Unexpected fields found in LoadCentreCollect {disallowed_keys}"
+        assert disallowed_keys == set(), (
+            f"Unexpected fields found in LoadCentreCollect {disallowed_keys}"
+        )
+
+        keys_from_outer_load_centre_collect = (
+            MxBlueskyParameters.model_fields.keys()
+            | WithSample.model_fields.keys()
+            | WithVisit.model_fields.keys()
+        )
+        duplicated_robot_load_then_centre_keys = (
+            keys_from_outer_load_centre_collect
+            & values["robot_load_then_centre"].keys()
+        )
+        assert not (duplicated_robot_load_then_centre_keys), (
+            f"Unexpected keys in robot_load_then_centre: {', '.join(duplicated_robot_load_then_centre_keys)}"
+        )
+
+        duplicated_multi_rotation_scan_keys = (
+            keys_from_outer_load_centre_collect & values["multi_rotation_scan"].keys()
+        )
+        assert not (duplicated_multi_rotation_scan_keys), (
+            f"Unexpected keys in multi_rotation_scan: {', '.join(duplicated_multi_rotation_scan_keys)}"
+        )
 
         new_robot_load_then_centre_params = construct_from_values(
             values, values["robot_load_then_centre"], RobotLoadThenCentre
@@ -53,3 +79,22 @@ class LoadCentreCollect(
         values["multi_rotation_scan"] = new_multi_rotation_scan_params
         values["robot_load_then_centre"] = new_robot_load_then_centre_params
         return values
+
+    @model_validator(mode="after")
+    def _check_rotation_start_xyz_is_not_specified(self) -> Self:
+        for scan in self.multi_rotation_scan.single_rotation_scans:
+            assert (
+                not scan.x_start_um and not scan.y_start_um and not scan.z_start_um
+            ), (
+                "Specifying start xyz for sweeps is not supported in combination with centring."
+            )
+        return self
+
+    @model_validator(mode="after")
+    def _check_different_gridscan_and_rotation_energy_not_specified(self) -> Self:
+        assert (
+            self.multi_rotation_scan.demand_energy_ev is None
+            or self.multi_rotation_scan.demand_energy_ev
+            == self.robot_load_then_centre.demand_energy_ev
+        ), "Setting a different energy for gridscan and rotation is not supported."
+        return self

mx_bluesky/hyperion/parameters/robot_load.py

@@ -0,0 +1,40 @@
+from pydantic import Field
+
+from mx_bluesky.common.parameters.components import (
+    MxBlueskyParameters,
+    WithOptionalEnergyChange,
+    WithSample,
+    WithSnapshot,
+    WithVisit,
+)
+from mx_bluesky.common.parameters.constants import (
+    HardwareConstants,
+)
+from mx_bluesky.hyperion.parameters.components import WithHyperionUDCFeatures
+from mx_bluesky.hyperion.parameters.gridscan import (
+    GridCommonWithHyperionDetectorParams,
+    PinTipCentreThenXrayCentre,
+)
+
+
+class RobotLoadAndEnergyChange(
+    MxBlueskyParameters, WithSample, WithSnapshot, WithOptionalEnergyChange, WithVisit
+):
+    thawing_time: float = Field(default=HardwareConstants.THAWING_TIME)
+
+
+class RobotLoadThenCentre(
+    GridCommonWithHyperionDetectorParams, WithHyperionUDCFeatures
+):
+    thawing_time: float = Field(default=HardwareConstants.THAWING_TIME)
+
+    @property
+    def robot_load_params(self) -> RobotLoadAndEnergyChange:
+        my_params = self.model_dump()
+        return RobotLoadAndEnergyChange(**my_params)
+
+    @property
+    def pin_centre_then_xray_centre_params(self) -> PinTipCentreThenXrayCentre:
+        my_params = self.model_dump()
+        del my_params["thawing_time"]
+        return PinTipCentreThenXrayCentre(**my_params)

mx_bluesky/hyperion/parameters/rotation.py

@@ -3,12 +3,12 @@ from __future__ import annotations
 import os
 from collections.abc import Iterator
 from itertools import accumulate
-from typing import Annotated, Any
+from typing import Annotated, Any, Self
 
 from annotated_types import Len
 from dodal.devices.aperturescatterguard import ApertureValue
 from dodal.devices.detector import DetectorParams
-from dodal.devices.zebra import (
+from dodal.devices.zebra.zebra import (
     RotationDirection,
 )
 from dodal.log import LOGGER
@@ -26,6 +26,7 @@ from mx_bluesky.common.parameters.components import (
     SplitScan,
     WithScan,
 )
+from mx_bluesky.hyperion.parameters.components import WithHyperionUDCFeatures
 from mx_bluesky.hyperion.parameters.constants import (
     CONST,
     I03Constants,
@@ -33,6 +34,18 @@ from mx_bluesky.hyperion.parameters.constants import (
 
 
 class RotationScanPerSweep(OptionalGonioAngleStarts, OptionalXyzStarts):
+    """
+    Describes a rotation scan about the specified axis.
+
+    Attributes:
+        rotation_axis: The rotation axis, by default this is the omega axis
+        omega_start_deg: The initial angle of the rotation in degrees (default 0)
+        scan_width_deg: The sweep of the rotation in degrees, this must be positive (default 360)
+        rotation_direction: Indicates the direction of rotation, if RotationDirection.POSITIVE
+            the final angle is obtained by adding scan_width_deg, otherwise by subtraction (default NEGATIVE)
+        nexus_vds_start_img: The frame number of the first frame captured during the rotation
+    """
+
     omega_start_deg: float = Field(default=0)  # type: ignore
     rotation_axis: RotationAxis = Field(default=RotationAxis.OMEGA)
     scan_width_deg: float = Field(default=360, gt=0)
@@ -40,7 +53,7 @@ class RotationScanPerSweep(OptionalGonioAngleStarts, OptionalXyzStarts):
     nexus_vds_start_img: int = Field(default=0, ge=0)
 
 
-class RotationExperiment(DiffractionExperimentWithSample):
+class RotationExperiment(DiffractionExperimentWithSample, WithHyperionUDCFeatures):
     shutter_opening_time_s: float = Field(default=CONST.I03.SHUTTER_TIME_S)
     rotation_increment_deg: float = Field(default=0.1, gt=0)
     ispyb_experiment_type: IspybExperimentType = Field(
@@ -98,6 +111,7 @@ class RotationScan(WithScan, RotationScanPerSweep, RotationExperiment):
 
     @property
     def scan_points(self) -> AxesPoints:
+        """The scan points are defined in application space"""
         scan_spec = Line(
             axis="omega",
             start=self.omega_start_deg,
@@ -141,6 +155,17 @@ class MultiRotationScan(RotationExperiment, SplitScan):
             start_img += scan.scan_width_deg / values.rotation_increment_deg
         return values
 
+    @model_validator(mode="after")
+    def _check_valid_for_single_arm_multiple_sweep(self) -> Self:
+        if len(self.rotation_scans) > 0:
+            scan_width = self.rotation_scans[0].scan_width_deg
+            for scan in self.rotation_scans[1:]:
+                assert scan.scan_width_deg == scan_width, (
+                    "Sweeps with different numbers of frames are not supported."
+                )
+
+        return self
+
     @property
     def single_rotation_scans(self) -> Iterator[RotationScan]:
         for scan in self.rotation_scans:

mx_bluesky/hyperion/utils/context.py

@@ -6,7 +6,7 @@ from blueapi.core.bluesky_types import Device
 from dodal.utils import get_beamline_based_on_environment_variable
 
 import mx_bluesky.hyperion.experiment_plans as hyperion_plans
-from mx_bluesky.hyperion.log import LOGGER
+from mx_bluesky.common.utils.log import LOGGER
 
 T = TypeVar("T", bound=Device)
 

mx_bluesky/hyperion/utils/validation.py

@@ -9,7 +9,7 @@ import bluesky.preprocessors as bpp
 from bluesky.run_engine import RunEngine
 from dodal.beamlines import i03
 from dodal.devices.oav.oav_parameters import OAVConfig
-from ophyd_async.core import set_mock_value
+from ophyd_async.testing import set_mock_value
 
 from mx_bluesky.hyperion.device_setup_plans.read_hardware_for_setup import (
     read_hardware_during_collection,
@@ -62,7 +62,7 @@ def fake_rotation_scan(
     @bpp.run_decorator(  # attach experiment metadata to the start document
         md={
             "subplan_name": CONST.PLAN.ROTATION_OUTER,
-            "hyperion_parameters": parameters.model_dump_json(),
+            "mx_bluesky_parameters": parameters.model_dump_json(),
             "activate_callbacks": "RotationNexusFileCallback",
         }
     )
@@ -79,6 +79,7 @@ def fake_rotation_scan(
 
 
 def fake_create_rotation_devices():
+    beamstop = i03.beamstop(fake_with_ophyd_sim=True)
     eiger = i03.eiger(fake_with_ophyd_sim=True)
     smargon = i03.smargon(fake_with_ophyd_sim=True)
     zebra = i03.zebra(fake_with_ophyd_sim=True)
@@ -106,6 +107,7 @@ def fake_create_rotation_devices():
     return RotationScanComposite(
         attenuator=attenuator,
         backlight=backlight,
+        beamstop=beamstop,
         dcm=dcm,
         detector_motion=detector_motion,
         eiger=eiger,
@@ -135,7 +137,7 @@ def sim_rotation_scan_to_create_nexus(
     fake_create_rotation_devices.eiger.bit_depth.sim_put(32)  # type: ignore
 
     with patch(
-        "mx_bluesky.hyperion.external_interaction.nexus.write_nexus.get_start_and_predicted_end_time",
+        "mx_bluesky.common.external_interaction.nexus.write_nexus.get_start_and_predicted_end_time",
         return_value=("test_time", "test_time"),
     ):
         RE(

{mx_bluesky-1.4.1a0.dist-info → mx_bluesky-1.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: mx-bluesky
-Version: 1.4.1a0
+Version: 1.4.3
 Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -226,7 +226,7 @@ Requires-Dist: opencv-python
 Requires-Dist: opentelemetry-distro
 Requires-Dist: opentelemetry-exporter-otlp
 Requires-Dist: pydantic
-Requires-Dist: pydantic-extra-types
+Requires-Dist: pydantic-extra-types>=2.10.1
 Requires-Dist: pyepics
 Requires-Dist: pyzmq
 Requires-Dist: requests
@@ -238,8 +238,8 @@ Requires-Dist: blueapi>=0.5.0
 Requires-Dist: daq-config-server>=0.1.1
 Requires-Dist: ophyd==1.9.0
 Requires-Dist: ophyd-async>=0.8a5
-Requires-Dist: bluesky>=1.13.0a4
-Requires-Dist: dls-dodal==1.36.1a
+Requires-Dist: bluesky>=1.13
+Requires-Dist: dls-dodal==1.38.0
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: build; extra == "dev"
@@ -250,6 +250,7 @@ Requires-Dist: ipython; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: myst-parser; extra == "dev"
 Requires-Dist: pipdeptree; extra == "dev"
+Requires-Dist: plantweb; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: pydata-sphinx-theme>=0.12; extra == "dev"
 Requires-Dist: pyright; extra == "dev"
@@ -260,7 +261,6 @@ Requires-Dist: pytest; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: sphinx-autobuild; extra == "dev"
 Requires-Dist: sphinx-copybutton; extra == "dev"
-Requires-Dist: sphinxcontrib-plantuml; extra == "dev"
 Requires-Dist: sphinx-design; extra == "dev"
 Requires-Dist: tox-direct; extra == "dev"
 Requires-Dist: tox; extra == "dev"

mx_bluesky-1.4.3.dist-info/RECORD

@@ -0,0 +1,155 @@
+mx_bluesky/__init__.py,sha256=Ksms_WJF8LTkbm38gEpm1jBpGqcQ8NGvmb2ZJlOE1j8,198
+mx_bluesky/__main__.py,sha256=RVqPnxDisFMIn_aoEi0drlThNHgKTJULnSrotouIKI0,480
+mx_bluesky/_version.py,sha256=cUUlK35wR7qLNaS4SMOrkRP_HG0nSHq0YEIezhPHr3c,411
+mx_bluesky/jupyter_example.ipynb,sha256=wpwvPrBvwtRMS5AIFk8F54cIlUoD0o4ji8tKK5cZHA4,1672
+mx_bluesky/beamlines/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mx_bluesky/beamlines/i04/__init__.py,sha256=jZjAMN5_oOEjQoR3iTrnMFW3ElxlHhQ7pEQZIv21Y4I,129
+mx_bluesky/beamlines/i04/redis_to_murko_forwarder.py,sha256=10PKvDRKaaTtlOCfRG8T00XwpIFR9m8jk96QES13LpQ,5894
+mx_bluesky/beamlines/i04/thawing_plan.py,sha256=YykXHXINBDnQ0wJ577v4XrXwcqlRRgoUSbaNuOKd1bc,5464
+mx_bluesky/beamlines/i04/callbacks/murko_callback.py,sha256=ZIwkY6gdcmIE-aMBvehN8DVcjGRtb9wwzpgHJNMZ39Q,2125
+mx_bluesky/beamlines/i24/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+mx_bluesky/beamlines/i24/serial/__init__.py,sha256=gSP8Vu9PMDeIgzge48XS3bOdmvb_a9k8RQP98BNcdZg,1080
+mx_bluesky/beamlines/i24/serial/blueapi_config.yaml,sha256=gwOfjzZMbcvpVH71CCyHaxr8hgPYCJIWWWfg1zErtmM,245
+mx_bluesky/beamlines/i24/serial/dcid.py,sha256=iT2mXcS7bG1rQ1l_VlENNh47vsB0CwxRar8I_BHD4AA,14486
+mx_bluesky/beamlines/i24/serial/log.py,sha256=oK7HHjIeuiWdy1vNZL6p-mU8Y3kzeCAgsifCxhAYqOQ,4799
+mx_bluesky/beamlines/i24/serial/run_extruder.sh,sha256=FXYsqdTpVgxB1-QrY4Tg5pl5Ex7PgUoXnuAcr9iDZTE,1078
+mx_bluesky/beamlines/i24/serial/run_fixed_target.sh,sha256=ZzxcVFoitBRvcqsJaBxjtepgkG-ZCGBW6X9xuV_Y478,1229
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