Merge branch 'main' into 1266_allow_individual_scatterguard_moves

setup.cfg

@@ -31,6 +31,7 @@ install_requires =
     pyzmq
     scanspec
     scipy
+    semver
     #
     # These dependencies may be issued as pre-release versions and should have a pin constraint
     # as by default pip-install will not upgrade to a pre-release.
@@ -40,7 +41,6 @@ install_requires =
     ophyd-async >= 0.3a5
     bluesky >= 1.13.0a4
     blueapi >= 0.4.3-rc1
-    mx-bluesky @ git+https://github.com/DiamondLightSource/mx-bluesky.git
     dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@5d7ed608fa66d8937c62662633a309f1b345834d
 
 [options.entry_points]

src/hyperion/experiment_plans/oav_snapshot_plan.py

@@ -11,9 +11,9 @@
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.oav_parameters import OAVParameters
 from dodal.devices.smargon import Smargon
-from mx_bluesky.parameters import WithSnapshot
 
 from hyperion.device_setup_plans.setup_oav import setup_general_oav_params
+from hyperion.parameters.components import WithSnapshot
 from hyperion.parameters.constants import DocDescriptorNames
 
 OAV_SNAPSHOT_SETUP_GROUP = "oav_snapshot_setup"

src/hyperion/external_interaction/callbacks/rotation/ispyb_callback.py

@@ -3,8 +3,6 @@
 from collections.abc import Sequence
 from typing import TYPE_CHECKING, Any, Callable, Optional
 
-from mx_bluesky.parameters import IspybExperimentType
-
 from hyperion.external_interaction.callbacks.common.ispyb_mapping import (
     populate_data_collection_group,
     populate_remaining_data_collection_info,
@@ -25,6 +23,7 @@
     StoreInIspyb,
 )
 from hyperion.log import ISPYB_LOGGER, set_dcgid_tag
+from hyperion.parameters.components import IspybExperimentType
 from hyperion.parameters.constants import CONST
 from hyperion.parameters.rotation import RotationScan
 

src/hyperion/parameters/components.py

@@ -3,15 +3,19 @@
 import datetime
 import json
 from abc import abstractmethod
+from enum import StrEnum
 from pathlib import Path
-from typing import TypeVar
+from typing import Sequence, SupportsInt, TypeVar
 
+from dodal.devices.aperturescatterguard import AperturePositionGDANames
 from dodal.devices.detector import (
+    DetectorParams,
     TriggerMode,
 )
-from mx_bluesky.parameters import DiffractionExperiment, ParameterVersion, WithSample
 from numpy.typing import NDArray
-from pydantic import BaseModel, Extra, Field, validator
+from pydantic import BaseModel, Extra, Field, root_validator, validator
+from scanspec.core import AxesPoints
+from semver import Version
 
 from hyperion.external_interaction.config_server import FeatureFlags
 from hyperion.external_interaction.ispyb.ispyb_dataclass import (
@@ -22,9 +26,85 @@
 T = TypeVar("T")
 
 
+class ParameterVersion(Version):
+    @classmethod
+    def _parse(cls, version):
+        if isinstance(version, cls):
+            return version
+        return cls.parse(version)
+
+    @classmethod
+    def __get_validators__(cls):
+        """Return a list of validator methods for pydantic models."""
+        yield cls._parse
+
+    @classmethod
+    def __modify_schema__(cls, field_schema):
+        """Inject/mutate the pydantic field schema in-place."""
+        field_schema.update(examples=["1.0.2", "2.15.3-alpha", "21.3.15-beta+12345"])
+
+
 PARAMETER_VERSION = ParameterVersion.parse("5.0.0")
 
 
+class RotationAxis(StrEnum):
+    OMEGA = "omega"
+    PHI = "phi"
+    CHI = "chi"
+    KAPPA = "kappa"
+
+
+class XyzAxis(StrEnum):
+    X = "sam_x"
+    Y = "sam_y"
+    Z = "sam_z"
+
+
+class IspybExperimentType(StrEnum):
+    # Enum values from ispyb column data type
+    SAD = "SAD"  # at or slightly above the peak
+    SAD_INVERSE_BEAM = "SAD - Inverse Beam"
+    OSC = "OSC"  # "native" (in the absence of a heavy atom)
+    COLLECT_MULTIWEDGE = (
+        "Collect - Multiwedge"  # "poorly determined" ~ EDNA complex strategy???
+    )
+    MAD = "MAD"
+    HELICAL = "Helical"
+    MULTI_POSITIONAL = "Multi-positional"
+    MESH = "Mesh"
+    BURN = "Burn"
+    MAD_INVERSE_BEAM = "MAD - Inverse Beam"
+    CHARACTERIZATION = "Characterization"
+    DEHYDRATION = "Dehydration"
+    TOMO = "tomo"
+    EXPERIMENT = "experiment"
+    EM = "EM"
+    PDF = "PDF"
+    PDF_BRAGG = "PDF+Bragg"
+    BRAGG = "Bragg"
+    SINGLE_PARTICLE = "single particle"
+    SERIAL_FIXED = "Serial Fixed"
+    SERIAL_JET = "Serial Jet"
+    STANDARD = "Standard"  # Routine structure determination experiment
+    TIME_RESOLVED = "Time Resolved"  # Investigate the change of a system over time
+    DLS_ANVIL_HP = "Diamond Anvil High Pressure"  # HP sample environment pressure cell
+    CUSTOM = "Custom"  # Special or non-standard data collection
+    XRF_MAP = "XRF map"
+    ENERGY_SCAN = "Energy scan"
+    XRF_SPECTRUM = "XRF spectrum"
+    XRF_MAP_XAS = "XRF map xas"
+    MESH_3D = "Mesh3D"
+    SCREENING = "Screening"
+    STILL = "Still"
+    SSX_CHIP = "SSX-Chip"
+    SSX_JET = "SSX-Jet"
+
+    # Aliases for historic hyperion experiment type mapping
+    ROTATION = "SAD"
+    GRIDSCAN_2D = "mesh"
+    GRIDSCAN_3D = "Mesh3D"
+
+
 class HyperionParameters(BaseModel):
     class Config:
         arbitrary_types_allowed = True
@@ -60,32 +140,128 @@ def from_json(cls, input: str | None, *, allow_extras: bool = False):
         return params
 
 
-class HyperionDiffractionExperiment(DiffractionExperiment, HyperionParameters):
+class WithSnapshot(BaseModel):
+    snapshot_directory: Path
+    snapshot_omegas_deg: list[float] | None
+
+    @property
+    def take_snapshots(self) -> bool:
+        return bool(self.snapshot_omegas_deg)
+
+
+class DiffractionExperiment(HyperionParameters, WithSnapshot):
     """For all experiments which use beam"""
 
-    beamline: str = Field(default=CONST.I03.BEAMLINE, regex=r"BL\d{2}[BIJS]")
+    visit: str = Field(min_length=1)
+    file_name: str = Field(pattern=r"[\w]{2}[\d]+-[\d]+")
+    exposure_time_s: float = Field(gt=0)
+    comment: str = Field(default="")
+    beamline: str = Field(default=CONST.I03.BEAMLINE, pattern=r"BL\d{2}[BIJS]")
     insertion_prefix: str = Field(
-        default=CONST.I03.INSERTION_PREFIX, regex=r"SR\d{2}[BIJS]"
+        default=CONST.I03.INSERTION_PREFIX, pattern=r"SR\d{2}[BIJS]"
     )
     det_dist_to_beam_converter_path: str = Field(
         default=CONST.PARAM.DETECTOR.BEAM_XY_LUT_PATH
     )
     zocalo_environment: str = Field(default=CONST.ZOCALO_ENV)
     trigger_mode: TriggerMode = Field(default=TriggerMode.FREE_RUN)
+    detector_distance_mm: float | None = Field(default=None, gt=0)
+    demand_energy_ev: float | None = Field(default=None, gt=0)
+    run_number: int | None = Field(default=None, ge=0)
+    selected_aperture: AperturePositionGDANames | None = Field(default=None)
+    transmission_frac: float = Field(default=0.1)
+    ispyb_experiment_type: IspybExperimentType
+    storage_directory: str
+
+    @root_validator(pre=True)
+    def validate_snapshot_directory(cls, values):
+        snapshot_dir = values.get(
+            "snapshot_directory", Path(values["storage_directory"], "snapshots")
+        )
+        values["snapshot_directory"] = (
+            snapshot_dir if isinstance(snapshot_dir, Path) else Path(snapshot_dir)
+        )
+        return values
 
     @property
     def visit_directory(self) -> Path:
         return (
             Path(CONST.I03.BASE_DATA_DIR) / str(datetime.date.today().year) / self.visit
         )
 
+    @property
+    def num_images(self) -> int:
+        return 0
+
+    @property
+    @abstractmethod
+    def detector_params(self) -> DetectorParams: ...
+
     @property
     @abstractmethod
     def ispyb_params(self) -> IspybParams:  # Soon to remove
         ...
 
 
-class DiffractionExperimentWithSample(HyperionDiffractionExperiment, WithSample): ...
+class WithScan(BaseModel):
+    """For experiments where the scan is known"""
+
+    @property
+    @abstractmethod
+    def scan_points(self) -> AxesPoints: ...
+
+    @property
+    @abstractmethod
+    def num_images(self) -> int: ...
+
+
+class SplitScan(BaseModel):
+    @property
+    @abstractmethod
+    def scan_indices(self) -> Sequence[SupportsInt]:
+        """Should return the first index of each scan (i.e. for each nexus file)"""
+        ...
+
+
+class WithSample(BaseModel):
+    sample_id: int
+    sample_puck: int | None = None
+    sample_pin: int | None = None
+
+
+class DiffractionExperimentWithSample(DiffractionExperiment, WithSample): ...
+
+
+class WithOavCentring(BaseModel):
+    oav_centring_file: str = Field(default=CONST.I03.OAV_CENTRING_FILE)
+
+
+class OptionalXyzStarts(BaseModel):
+    x_start_um: float | None = None
+    y_start_um: float | None = None
+    z_start_um: float | None = None
+
+
+class XyzStarts(BaseModel):
+    x_start_um: float
+    y_start_um: float
+    z_start_um: float
+
+    def _start_for_axis(self, axis: XyzAxis) -> float:
+        match axis:
+            case XyzAxis.X:
+                return self.x_start_um
+            case XyzAxis.Y:
+                return self.y_start_um
+            case XyzAxis.Z:
+                return self.z_start_um
+
+
+class OptionalGonioAngleStarts(BaseModel):
+    omega_start_deg: float | None = None
+    phi_start_deg: float | None = None
+    chi_start_deg: float | None = None
+    kappa_start_deg: float | None = None
 
 
 class TemporaryIspybExtras(BaseModel):

src/hyperion/parameters/gridscan.py

@@ -11,29 +11,28 @@
     PandAGridScanParams,
     ZebraGridScanParams,
 )
-from mx_bluesky.parameters import (
-    IspybExperimentType,
-    OptionalGonioAngleStarts,
-    SplitScan,
-    WithOavCentring,
-    WithScan,
-    XyzStarts,
-)
 from pydantic import Field, PrivateAttr
 from scanspec.core import Path as ScanPath
 from scanspec.specs import Line, Static
 
 from hyperion.external_interaction.ispyb.ispyb_dataclass import (
     GridscanIspybParams,
 )
-from hyperion.parameters.components import DiffractionExperimentWithSample
+from hyperion.parameters.components import (
+    DiffractionExperimentWithSample,
+    IspybExperimentType,
+    OptionalGonioAngleStarts,
+    SplitScan,
+    WithOavCentring,
+    WithScan,
+    XyzStarts,
+)
 from hyperion.parameters.constants import CONST, I03Constants
 
 
 class GridCommon(
     DiffractionExperimentWithSample, OptionalGonioAngleStarts, WithOavCentring
 ):
-    oav_centring_file: str = Field(default=CONST.I03.OAV_CENTRING_FILE)
     grid_width_um: float = Field(default=CONST.PARAM.GRIDSCAN.WIDTH_UM)
     exposure_time_s: float = Field(default=CONST.PARAM.GRIDSCAN.EXPOSURE_TIME_S)
     use_roi_mode: bool = Field(default=CONST.PARAM.GRIDSCAN.USE_ROI)

src/hyperion/parameters/rotation.py

@@ -13,14 +13,6 @@
 from dodal.devices.zebra import (
     RotationDirection,
 )
-from mx_bluesky.parameters import (
-    IspybExperimentType,
-    OptionalGonioAngleStarts,
-    OptionalXyzStarts,
-    RotationAxis,
-    SplitScan,
-    WithScan,
-)
 from pydantic import Field, root_validator
 from scanspec.core import AxesPoints
 from scanspec.core import Path as ScanPath
@@ -29,7 +21,13 @@
 from hyperion.external_interaction.ispyb.ispyb_dataclass import RotationIspybParams
 from hyperion.parameters.components import (
     DiffractionExperimentWithSample,
+    IspybExperimentType,
+    OptionalGonioAngleStarts,
+    OptionalXyzStarts,
+    RotationAxis,
+    SplitScan,
     TemporaryIspybExtras,
+    WithScan,
 )
 from hyperion.parameters.constants import CONST, I03Constants