mx-bluesky 1.5.0__py3-none-any.whl → 1.5.2__py3-none-any.whl

mx_bluesky/hyperion/external_interaction/callbacks/{robot_load → robot_actions}/ispyb_callback.py

@@ -12,6 +12,7 @@ from mx_bluesky.common.external_interaction.ispyb.exp_eye_store import (
     BLSampleStatus,
     ExpeyeInteraction,
     RobotActionID,
+    create_update_data_from_event_doc,
 )
 from mx_bluesky.common.utils.log import ISPYB_ZOCALO_CALLBACK_LOGGER
 from mx_bluesky.hyperion.parameters.constants import CONST
@@ -20,11 +21,21 @@ if TYPE_CHECKING:
     from event_model.documents import Event, EventDescriptor, RunStart, RunStop
 
 
+robot_update_mapping = {
+    "robot-barcode": "sampleBarcode",
+    "robot-current_pin": "containerLocation",
+    "robot-current_puck": "dewarLocation",
+    # I03 uses webcam/oav snapshots in place of before/after snapshots
+    "webcam-last_saved_path": "xtalSnapshotBefore",
+    "oav-snapshot-last_saved_path": "xtalSnapshotAfter",
+}
+
+
 class RobotLoadISPyBCallback(PlanReactiveCallback):
     def __init__(self) -> None:
         ISPYB_ZOCALO_CALLBACK_LOGGER.debug("Initialising ISPyB Robot Load Callback")
         super().__init__(log=ISPYB_ZOCALO_CALLBACK_LOGGER)
-        self._metadata: dict | None = None
+        self._sample_id: int | None = None
 
         self.run_uid: str | None = None
         self.descriptors: dict[str, EventDescriptor] = {}
@@ -35,22 +46,24 @@ class RobotLoadISPyBCallback(PlanReactiveCallback):
         ISPYB_ZOCALO_CALLBACK_LOGGER.debug(
             "ISPyB robot load callback received start document."
         )
-        if doc.get("subplan_name") == CONST.PLAN.ROBOT_LOAD:
+        subplan = doc.get("subplan_name")
+        if subplan == CONST.PLAN.ROBOT_LOAD or subplan == CONST.PLAN.ROBOT_UNLOAD:
             ISPYB_ZOCALO_CALLBACK_LOGGER.debug(
                 f"ISPyB robot load callback received: {doc}"
             )
             self.run_uid = doc.get("uid")
-            self._metadata = doc.get("metadata")
-            assert isinstance(self._metadata, dict)
+            metadata = doc.get("metadata")
+            assert isinstance(metadata, dict)
+            self._sample_id = metadata["sample_id"]
+            assert isinstance(self._sample_id, int)
             proposal, session = get_proposal_and_session_from_visit_string(
-                self._metadata["visit"]
+                metadata["visit"]
             )
-            self.action_id = self.expeye.start_load(
+            self.action_id = self.expeye.start_robot_action(
+                "LOAD" if subplan == CONST.PLAN.ROBOT_LOAD else "UNLOAD",
                 proposal,
                 session,
-                self._metadata["sample_id"],
-                self._metadata["sample_puck"],
-                self._metadata["sample_pin"],
+                self._sample_id,
             )
         return super().activity_gated_start(doc)
 
@@ -62,18 +75,14 @@ class RobotLoadISPyBCallback(PlanReactiveCallback):
         event_descriptor = self.descriptors.get(doc["descriptor"])
         if (
             event_descriptor
-            and event_descriptor.get("name") == CONST.DESCRIPTORS.ROBOT_LOAD
+            and event_descriptor.get("name") == CONST.DESCRIPTORS.ROBOT_UPDATE
         ):
             assert self.action_id is not None, (
                 "ISPyB Robot load callback event called unexpectedly"
             )
-            barcode = doc["data"]["robot-barcode"]
-            oav_snapshot = doc["data"]["oav-snapshot-last_saved_path"]
-            webcam_snapshot = doc["data"]["webcam-last_saved_path"]
             # I03 uses webcam/oav snapshots in place of before/after snapshots
-            self.expeye.update_barcode_and_snapshots(
-                self.action_id, barcode, webcam_snapshot, oav_snapshot
-            )
+            update_data = create_update_data_from_event_doc(robot_update_mapping, doc)
+            self.expeye.update_robot_action(self.action_id, update_data)
 
         return super().activity_gated_event(doc)
 
@@ -87,12 +96,12 @@ class RobotLoadISPyBCallback(PlanReactiveCallback):
             )
             exit_status = doc.get("exit_status")
             assert exit_status, "Exit status not available in stop document!"
-            assert self._metadata, "Metadata not received before stop document."
+            assert self._sample_id is not None, "Stop called before start"
             reason = doc.get("reason") or "OK"
 
-            self.expeye.end_load(self.action_id, exit_status, reason)
+            self.expeye.end_robot_action(self.action_id, exit_status, reason)
             self.expeye.update_sample_status(
-                self._metadata["sample_id"],
+                self._sample_id,
                 BLSampleStatus.LOADED
                 if exit_status == "success"
                 else BLSampleStatus.ERROR_BEAMLINE,

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

@@ -54,6 +54,7 @@ class RotationISPyBCallback(BaseISPyBCallback):
         super().__init__(emit=emit)
         self.last_sample_id: int | None = None
         self.ispyb_ids: IspybIds = IspybIds()
+        self.ispyb = StoreInIspyb(self.ispyb_config)
 
     def activity_gated_start(self, doc: RunStart):
         if doc.get("subplan_name") == CONST.PLAN.ROTATION_OUTER:
@@ -82,7 +83,6 @@ class RotationISPyBCallback(BaseISPyBCallback):
                     f"Collection is {self.params.ispyb_experiment_type} - storing sampleID to bundle images"
                 )
                 self.last_sample_id = self.params.sample_id
-            self.ispyb = StoreInIspyb(self.ispyb_config)
             ISPYB_ZOCALO_CALLBACK_LOGGER.info("Beginning ispyb deposition")
             data_collection_group_info = populate_data_collection_group(self.params)
             data_collection_info = populate_data_collection_info_for_rotation(

mx_bluesky/hyperion/external_interaction/callbacks/snapshot_callback.py

@@ -1,4 +1,5 @@
 import dataclasses
+import os
 import re
 from collections.abc import Iterator
 from datetime import datetime
@@ -172,6 +173,8 @@ class BeamDrawingCallback(PlanReactiveCallback):
                 f"Generating snapshot at {current_sample_pos_mm} from base snapshot {snapshot_info}"
             )
             output_snapshot_directory = data["oav-snapshot-directory"]
+            if not os.path.exists(output_snapshot_directory):
+                os.mkdir(output_snapshot_directory)
             base_file_stem = Path(snapshot_info.snapshot_path).stem
             output_snapshot_filename = _snapshot_filename(base_file_stem)
             output_snapshot_path = (

mx_bluesky/hyperion/external_interaction/config_server.py

@@ -1,7 +1,6 @@
 from functools import cache
 
 from daq_config_server.client import ConfigServer
-from pydantic import model_validator
 
 from mx_bluesky.common.external_interaction.config_server import FeatureFlags
 from mx_bluesky.common.utils.log import LOGGER
@@ -14,8 +13,6 @@ class HyperionFeatureFlags(FeatureFlags):
 
     Attributes:
         use_panda_for_gridscan:         If True then the PandA is used for gridscans, otherwise the zebra is used
-        compare_cpu_and_gpu_zocalo:     If True then GPU result processing is enabled
-            alongside CPU and the results are compared. The CPU result is still take.n
         use_gpu_results:                If True then GPU result processing is enabled
             and the GPU result is taken.
         set_stub_offsets:               If True then set the stub offsets after moving to the crystal (ignored for
@@ -31,15 +28,7 @@ class HyperionFeatureFlags(FeatureFlags):
     def get_config_server() -> ConfigServer:
         return ConfigServer(CONST.CONFIG_SERVER_URL, LOGGER)
 
-    @model_validator(mode="after")
-    def use_gpu_and_compare_cannot_both_be_true(self):
-        assert not (self.use_gpu_results and self.compare_cpu_and_gpu_zocalo), (
-            "Cannot both use GPU results and compare them to CPU"
-        )
-        return self
-
     use_panda_for_gridscan: bool = CONST.I03.USE_PANDA_FOR_GRIDSCAN
-    compare_cpu_and_gpu_zocalo: bool = CONST.I03.COMPARE_CPU_AND_GPU_ZOCALO
     use_gpu_results: bool = CONST.I03.USE_GPU_RESULTS
     set_stub_offsets: bool = CONST.I03.SET_STUB_OFFSETS
     omega_flip: bool = CONST.I03.OMEGA_FLIP

mx_bluesky/hyperion/parameters/constants.py

@@ -29,17 +29,12 @@ class I03Constants:
     OMEGA_FLIP = True
     ALTERNATE_ROTATION_DIRECTION = True
 
-    # Turns on GPU processing for zocalo and logs a comparison between GPU and CPU-
-    # processed results.
-    COMPARE_CPU_AND_GPU_ZOCALO = False
-
     # Turns on GPU processing for zocalo and uses the results that come back
-    USE_GPU_RESULTS = False
+    USE_GPU_RESULTS = True
 
 
 @dataclass(frozen=True)
 class HyperionConstants:
-    DESCRIPTORS = DocDescriptorNames()
     ZOCALO_ENV = EnvironmentConstants.ZOCALO_ENV
     HARDWARE = HardwareConstants()
     I03 = I03Constants()
@@ -53,7 +48,7 @@ class HyperionConstants:
         if TEST_MODE
         else "https://daq-config.diamond.ac.uk/api"
     )
-    GRAYLOG_PORT = 12232
+    GRAYLOG_PORT = 12232  # Hyperion stream
     PARAMETER_SCHEMA_DIRECTORY = "src/hyperion/parameters/schemas/"
     LOG_FILE_NAME = "hyperion.log"
     DEVICE_SETTINGS_CONSTANTS = DeviceSettingsConstants()

mx_bluesky/hyperion/parameters/gridscan.py

@@ -20,9 +20,7 @@ class GridCommonWithHyperionDetectorParams(GridCommon, WithHyperionUDCFeatures):
     @property
     def detector_params(self):
         params = super().detector_params
-        params.enable_dev_shm = (
-            self.features.compare_cpu_and_gpu_zocalo or self.features.use_gpu_results
-        )
+        params.enable_dev_shm = self.features.use_gpu_results
         return params
 
 
@@ -35,9 +33,7 @@ class HyperionSpecifiedThreeDGridScan(WithHyperionUDCFeatures, SpecifiedThreeDGr
     @property
     def detector_params(self):
         params = super().detector_params
-        params.enable_dev_shm = (
-            self.features.compare_cpu_and_gpu_zocalo or self.features.use_gpu_results
-        )
+        params.enable_dev_shm = self.features.use_gpu_results
         return params
 
     # Relative to common grid scan, stub offsets are defined by config server

mx_bluesky/hyperion/parameters/load_centre_collect.py

@@ -50,6 +50,12 @@ class LoadCentreCollect(
             f"Unexpected fields found in LoadCentreCollect {disallowed_keys}"
         )
 
+        assert "features" not in values["robot_load_then_centre"], (
+            "Features flags must be specified at top-level in LoadCentreCollect"
+        )
+        assert "features" not in values["multi_rotation_scan"], (
+            "Features flags must be specified at top-level in LoadCentreCollect"
+        )
         keys_from_outer_load_centre_collect = (
             MxBlueskyParameters.model_fields.keys()
             | WithSample.model_fields.keys()
@@ -70,6 +76,9 @@ class LoadCentreCollect(
             f"Unexpected keys in multi_rotation_scan: {', '.join(duplicated_multi_rotation_scan_keys)}"
         )
 
+        for rotation in values["multi_rotation_scan"]["rotation_scans"]:
+            rotation["sample_id"] = values["sample_id"]
+
         new_robot_load_then_centre_params = construct_from_values(
             values, values["robot_load_then_centre"], RobotLoadThenCentre
         )
@@ -80,6 +89,12 @@ class LoadCentreCollect(
         values["robot_load_then_centre"] = new_robot_load_then_centre_params
         return values
 
+    @model_validator(mode="after")
+    def _ensure_features_are_internally_consistent(self) -> Self:
+        self.robot_load_then_centre.features = self.features
+        self.multi_rotation_scan.features = self.features
+        return self
+
     @model_validator(mode="after")
     def _check_rotation_start_xyz_is_not_specified(self) -> Self:
         for scan in self.multi_rotation_scan.single_rotation_scans:

mx_bluesky/hyperion/parameters/rotation.py

@@ -18,12 +18,14 @@ from scanspec.core import Path as ScanPath
 from scanspec.specs import Line
 
 from mx_bluesky.common.parameters.components import (
+    DiffractionExperiment,
     DiffractionExperimentWithSample,
     IspybExperimentType,
     OptionalGonioAngleStarts,
     OptionalXyzStarts,
     RotationAxis,
     SplitScan,
+    WithSample,
     WithScan,
 )
 from mx_bluesky.hyperion.parameters.components import WithHyperionUDCFeatures
@@ -33,7 +35,7 @@ from mx_bluesky.hyperion.parameters.constants import (
 )
 
 
-class RotationScanPerSweep(OptionalGonioAngleStarts, OptionalXyzStarts):
+class RotationScanPerSweep(OptionalGonioAngleStarts, OptionalXyzStarts, WithSample):
     """
     Describes a rotation scan about the specified axis.
 
@@ -54,7 +56,7 @@ class RotationScanPerSweep(OptionalGonioAngleStarts, OptionalXyzStarts):
     nexus_vds_start_img: int = Field(default=0, ge=0)
 
 
-class RotationExperiment(DiffractionExperimentWithSample, WithHyperionUDCFeatures):
+class RotationExperiment(DiffractionExperiment, 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(
@@ -105,7 +107,9 @@ class RotationExperiment(DiffractionExperimentWithSample, WithHyperionUDCFeature
             return aperture_position
 
 
-class SingleRotationScan(WithScan, RotationScanPerSweep, RotationExperiment):
+class SingleRotationScan(
+    WithScan, RotationScanPerSweep, RotationExperiment, DiffractionExperimentWithSample
+):
     @property
     def detector_params(self):
         return self._detector_params(self.omega_start_deg)

mx_bluesky/hyperion/utils/context.py

@@ -1,5 +1,6 @@
 from blueapi.core import BlueskyContext
-from dodal.utils import get_beamline_based_on_environment_variable
+from dodal.common.beamlines.beamline_utils import clear_devices
+from dodal.utils import collect_factories, get_beamline_based_on_environment_variable
 
 import mx_bluesky.hyperion.experiment_plans as hyperion_plans
 from mx_bluesky.common.utils.log import LOGGER
@@ -9,11 +10,24 @@ def setup_context(dev_mode: bool = False) -> BlueskyContext:
     context = BlueskyContext()
     context.with_plan_module(hyperion_plans)
 
-    context.with_dodal_module(
-        get_beamline_based_on_environment_variable(),
-        mock=dev_mode,
-    )
+    setup_devices(context, dev_mode)
 
     LOGGER.info(f"Plans found in context: {context.plan_functions.keys()}")
 
     return context
+
+
+def clear_all_device_caches(context: BlueskyContext):
+    context.unregister_all_devices()
+    clear_devices()
+
+    for f in collect_factories(get_beamline_based_on_environment_variable()).values():
+        if hasattr(f, "cache_clear"):
+            f.cache_clear()  # type: ignore
+
+
+def setup_devices(context: BlueskyContext, dev_mode: bool):
+    context.with_dodal_module(
+        get_beamline_based_on_environment_variable(),
+        mock=dev_mode,
+    )

mx_bluesky/phase1_zebra/__init__.py

@@ -0,0 +1 @@
+"""The zebra on i03 and i04 (phase1 beamlines) are configured in a specific way which are compatible to the plans in this module"""

mx_bluesky/phase1_zebra/device_setup_plans/setup_zebra.py

@@ -0,0 +1,112 @@
+from typing import Protocol, runtime_checkable
+
+import bluesky.plan_stubs as bps
+from bluesky.utils import MsgGenerator
+from dodal.devices.zebra.zebra import (
+    Zebra,
+)
+from dodal.devices.zebra.zebra_controlled_shutter import (
+    ZebraShutter,
+    ZebraShutterControl,
+)
+
+from mx_bluesky.common.parameters.constants import ZEBRA_STATUS_TIMEOUT
+from mx_bluesky.common.utils.log import LOGGER
+
+
+@runtime_checkable
+class GridscanSetupDevices(Protocol):
+    zebra: Zebra
+    sample_shutter: ZebraShutter
+
+
+def setup_zebra_for_gridscan(
+    composite: GridscanSetupDevices,  # XRC gridscan's generic trigger setup expects a composite rather than individual devices
+    group="setup_zebra_for_gridscan",
+    wait=True,
+) -> MsgGenerator:
+    zebra = composite.zebra
+    # Set shutter to automatic and to trigger via motion controller GPIO signal (IN4_TTL)
+    yield from configure_zebra_and_shutter_for_auto_shutter(
+        zebra, composite.sample_shutter, zebra.mapping.sources.IN4_TTL, group=group
+    )
+
+    yield from bps.abs_set(
+        zebra.output.out_pvs[zebra.mapping.outputs.TTL_DETECTOR],
+        zebra.mapping.sources.IN3_TTL,
+        group=group,
+    )
+    yield from bps.abs_set(
+        zebra.output.out_pvs[zebra.mapping.outputs.TTL_XSPRESS3],
+        zebra.mapping.sources.DISCONNECT,
+        group=group,
+    )
+    yield from bps.abs_set(
+        zebra.output.pulse_1.input, zebra.mapping.sources.DISCONNECT, group=group
+    )
+
+    if wait:
+        yield from bps.wait(group, timeout=ZEBRA_STATUS_TIMEOUT)
+
+
+def set_shutter_auto_input(zebra: Zebra, input: int, group="set_shutter_trigger"):
+    """Set the signal that controls the shutter. We use the second input to the
+    Zebra's AND2 gate for this input. ZebraShutter control mode must be in auto for this input to take control
+
+    For more details see the ZebraShutter device."""
+    auto_gate = zebra.mapping.AND_GATE_FOR_AUTO_SHUTTER
+    auto_shutter_control = zebra.logic_gates.and_gates[auto_gate]
+    yield from bps.abs_set(auto_shutter_control.sources[2], input, group)
+
+
+def configure_zebra_and_shutter_for_auto_shutter(
+    zebra: Zebra, zebra_shutter: ZebraShutter, input: int, group="use_automatic_shutter"
+):
+    """Set the shutter to auto mode, and configure the zebra to trigger the shutter on
+    an input source. For the input, use one of the source constants in zebra.py
+
+    When the shutter is in auto/manual, logic in EPICS sets the Zebra's
+    SOFT_IN1 to low/high respectively. The Zebra's AND2 gate should be used to control the shutter while in auto mode.
+    To do this, we need (AND2 = SOFT_IN1 AND input), where input is the zebra signal we want to control the shutter when in auto mode.
+    """
+    # See https://github.com/DiamondLightSource/dodal/issues/813 for better typing here.
+
+    # Set shutter to auto mode
+    yield from bps.abs_set(
+        zebra_shutter.control_mode, ZebraShutterControl.AUTO, group=group
+    )
+
+    auto_gate = zebra.mapping.AND_GATE_FOR_AUTO_SHUTTER
+
+    # Set first input of AND2 gate to SOFT_IN1, which is high when shutter is in auto mode
+    # Note the Zebra should ALWAYS be setup this way. See https://github.com/DiamondLightSource/mx-bluesky/issues/551
+    yield from bps.abs_set(
+        zebra.logic_gates.and_gates[auto_gate].sources[1],
+        zebra.mapping.sources.SOFT_IN1,
+        group=group,
+    )
+
+    # Set the second input of AND2 gate to the requested zebra input source
+    yield from set_shutter_auto_input(zebra, input, group=group)
+
+
+def tidy_up_zebra_after_gridscan(
+    zebra: Zebra,
+    zebra_shutter: ZebraShutter,
+    group="tidy_up_zebra_after_gridscan",
+    wait=True,
+) -> MsgGenerator:
+    LOGGER.info("Tidying up Zebra")
+
+    yield from bps.abs_set(
+        zebra.output.out_pvs[zebra.mapping.outputs.TTL_DETECTOR],
+        zebra.mapping.sources.PC_PULSE,
+        group=group,
+    )
+    yield from bps.abs_set(
+        zebra_shutter.control_mode, ZebraShutterControl.MANUAL, group=group
+    )
+    yield from set_shutter_auto_input(zebra, zebra.mapping.sources.PC_GATE, group=group)
+
+    if wait:
+        yield from bps.wait(group, timeout=ZEBRA_STATUS_TIMEOUT)

{mx_bluesky-1.5.0.dist-info → mx_bluesky-1.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mx-bluesky
-Version: 1.5.0
+Version: 1.5.2
 Summary: Bluesky tools for MX Beamlines at DLS
 Author-email: Dominic Oram <dominic.oram@diamond.ac.uk>
 License:                                  Apache License
@@ -221,7 +221,7 @@ Requires-Dist: ispyb
 Requires-Dist: jupyterlab
 Requires-Dist: matplotlib
 Requires-Dist: nexgen>=0.11.0
-Requires-Dist: numpy
+Requires-Dist: numpy==2.2.6
 Requires-Dist: opencv-python
 Requires-Dist: opentelemetry-distro
 Requires-Dist: opentelemetry-exporter-otlp
@@ -233,13 +233,14 @@ Requires-Dist: requests
 Requires-Dist: scanspec
 Requires-Dist: scipy
 Requires-Dist: semver
+Requires-Dist: deepdiff
 Requires-Dist: matplotlib
-Requires-Dist: blueapi>=0.11.1
+Requires-Dist: blueapi>=0.15.0
 Requires-Dist: daq-config-server==0.1.1
 Requires-Dist: ophyd>=1.10.5
 Requires-Dist: ophyd-async>=0.10.0a2
 Requires-Dist: bluesky>=1.13.1
-Requires-Dist: dls-dodal==1.49.0
+Requires-Dist: dls-dodal==1.52.0
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: build; extra == "dev"