Merge tidy-ups

deploy/deploy_hyperion.py

@@ -67,13 +67,10 @@ def get_hyperion_release_dir_from_args(repo: repo) -> str:
     if args.beamline == "dev":
         print("Running as dev")
         return "/tmp/hyperion_release_test/bluesky"
-<<<<<<< HEAD
     elif args.beamline == "i03":
         return f"/dls_sw/{args.beamline}/software/bluesky"
     elif args.beamline == "i02-1":
         return f"/dls_sw/{args.beamline}/software/bluesky"
-=======
->>>>>>> origin/main
     else:
         return f"/dls_sw/{args.beamline}/software/bluesky"
 

setup.cfg

@@ -36,7 +36,7 @@ install_requires =
     xarray
     doct
     databroker
-    dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@9adc9ee996ff70a1e3f340def3f85e10a318af82
+    dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@93923f92ead4cfae30d8f2257b8c8f55815ff207
     pydantic<2.0 # See https://github.com/DiamondLightSource/hyperion/issues/774
     scipy
 

src/hyperion/experiment_plans/vmxm_flyscan_xray_centre_plan.py

@@ -30,7 +30,7 @@
     VmxmFastGridScanCallbackCollection,
 )
 from hyperion.parameters import external_parameters
-from hyperion.parameters.constants import ISPYB_PLAN_NAME, SIM_BEAMLINE
+from hyperion.parameters.constants import ISPYB_HARDWARE_READ_PLAN, SIM_BEAMLINE
 from hyperion.tracing import TRACER
 from hyperion.utils.context import device_composite_from_context, setup_context
 
@@ -90,7 +90,7 @@ def run_gridscan(
 ):
     fgs_motors = fgs_composite.fast_grid_scan
 
-    yield from bps.create(name=ISPYB_PLAN_NAME)
+    yield from bps.create(name=ISPYB_HARDWARE_READ_PLAN)
     yield from bps.read(fgs_composite.synchrotron.machine_status.synchrotron_mode)
     yield from bps.save()
 

src/hyperion/external_interaction/callbacks/ispyb_callback_base.py

@@ -78,9 +78,9 @@ def event(self, doc: dict):
                 "flux_flux_reading", 0.0
             )
 
-        LOGGER.info("Creating ispyb entry.")
-        self.ispyb_ids = self.ispyb.begin_deposition()
-        LOGGER.info(f"Recieved ISPYB IDs: {self.ispyb_ids}")
+            LOGGER.info("Creating ispyb entry.")
+            self.ispyb_ids = self.ispyb.begin_deposition()
+            LOGGER.info(f"Recieved ISPYB IDs: {self.ispyb_ids}")
 
     def stop(self, doc: dict):
         """Subclasses must check that they are recieving a stop document for the correct

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

@@ -15,6 +15,7 @@
 from hyperion.external_interaction.callbacks.rotation.zocalo_callback import (
     RotationZocaloCallback,
 )
+from hyperion.external_interaction.nexus.nexus_utils import create_i03_goniometer_axes
 
 if TYPE_CHECKING:
     from hyperion.parameters.plan_specific.rotation_scan_internal_params import (
@@ -25,15 +26,19 @@
 @dataclass(frozen=True, order=True)
 class RotationCallbackCollection(AbstractPlanCallbackCollection):
     """Groups the callbacks for external interactions for a rotation scan.
-    Cast to a list to pass it to Bluesky.preprocessors.subs_decorator()."""
+    Cast to a list to pass it to Bluesky.preprocessors.subs_decorator().
+
+    Note: specific to i03."""
 
     nexus_handler: RotationNexusFileCallback
     ispyb_handler: RotationISPyBCallback
     zocalo_handler: RotationZocaloCallback
 
     @classmethod
     def from_params(cls, parameters: RotationInternalParameters):
-        nexus_handler = RotationNexusFileCallback()
+        nexus_handler = RotationNexusFileCallback(
+            create_goniometer_axes=create_i03_goniometer_axes
+        )
         ispyb_handler = RotationISPyBCallback(parameters)
         zocalo_handler = RotationZocaloCallback(
             parameters.hyperion_params.zocalo_environment, ispyb_handler

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

@@ -2,7 +2,11 @@
 
 from bluesky.callbacks import CallbackBase
 
-from hyperion.external_interaction.nexus.write_nexus import NexusWriter
+from hyperion.external_interaction.nexus.nexus_utils import create_i03_goniometer_axes
+from hyperion.external_interaction.nexus.write_nexus import (
+    CreateGoniometerProtocol,
+    NexusWriter,
+)
 from hyperion.log import LOGGER
 from hyperion.parameters.plan_specific.rotation_scan_internal_params import (
     RotationInternalParameters,
@@ -24,10 +28,11 @@ class RotationNexusFileCallback(CallbackBase):
     Usually used as part of a RotationCallbackCollection.
     """
 
-    def __init__(self):
+    def __init__(self, create_goniometer_axes: CreateGoniometerProtocol):
         self.run_uid: str | None = None
         self.parameters: RotationInternalParameters | None = None
         self.writer: NexusWriter | None = None
+        self.create_goniometer_axes = create_goniometer_axes
 
     def start(self, doc: dict):
         if doc.get("subplan_name") == "rotation_scan_with_cleanup":
@@ -42,5 +47,6 @@ def start(self, doc: dict):
                 self.parameters,
                 self.parameters.get_scan_points(),
                 self.parameters.get_data_shape(),
+                create_goniometer_func=self.create_goniometer_axes,
             )
             self.writer.create_nexus_file()

src/hyperion/external_interaction/callbacks/xray_centre/callback_collection.py

@@ -16,6 +16,10 @@
 from hyperion.external_interaction.callbacks.xray_centre.zocalo_callback import (
     XrayCentreZocaloCallback,
 )
+from hyperion.external_interaction.nexus.nexus_utils import (
+    create_i03_goniometer_axes,
+    create_vmxm_goniometer_axes,
+)
 
 if TYPE_CHECKING:
     from hyperion.parameters.internal_parameters import InternalParameters
@@ -25,15 +29,17 @@
 class XrayCentreCallbackCollection(AbstractPlanCallbackCollection):
     """Groups the callbacks for external interactions in the fast grid scan, and
     connects the Zocalo and ISPyB handlers. Cast to a list to pass it to
-    Bluesky.preprocessors.subs_decorator()."""
+    Bluesky.preprocessors.subs_decorator().
+
+    Note: currently specific to i03 as it creates i03's goniometer axes."""
 
     nexus_handler: GridscanNexusFileCallback
     ispyb_handler: GridscanISPyBCallback
     zocalo_handler: XrayCentreZocaloCallback
 
     @classmethod
     def from_params(cls, parameters: InternalParameters):
-        nexus_handler = GridscanNexusFileCallback()
+        nexus_handler = GridscanNexusFileCallback(create_i03_goniometer_axes)
         ispyb_handler = GridscanISPyBCallback(parameters)
         zocalo_handler = XrayCentreZocaloCallback(parameters, ispyb_handler)
         callback_collection = cls(
@@ -46,14 +52,16 @@ def from_params(cls, parameters: InternalParameters):
 
 @dataclass(frozen=True, order=True)
 class VmxmFastGridScanCallbackCollection(AbstractPlanCallbackCollection):
-    """Like XRayCentreCallbackCollection, but without zocalo."""
+    """Like XRayCentreCallbackCollection, but without zocalo.
+
+    Note: currently specific to VMXm as it creates VMXm's goniometer axes."""
 
     nexus_handler: Gridscan2DNexusFileCallback
     ispyb_handler: GridscanISPyBCallback
 
     @classmethod
     def from_params(cls, parameters: InternalParameters):
-        nexus_handler = Gridscan2DNexusFileCallback()
+        nexus_handler = Gridscan2DNexusFileCallback(create_vmxm_goniometer_axes)
         ispyb_handler = GridscanISPyBCallback(parameters)
         callback_collection = cls(
             nexus_handler=nexus_handler,

src/hyperion/external_interaction/callbacks/xray_centre/nexus_callback.py

@@ -2,7 +2,10 @@
 
 from bluesky.callbacks import CallbackBase
 
-from hyperion.external_interaction.nexus.write_nexus import NexusWriter
+from hyperion.external_interaction.nexus.write_nexus import (
+    CreateGoniometerProtocol,
+    NexusWriter,
+)
 from hyperion.log import LOGGER
 from hyperion.parameters.constants import ISPYB_HARDWARE_READ_PLAN
 from hyperion.parameters.plan_specific.gridscan_internal_params import (
@@ -29,11 +32,12 @@ class GridscanNexusFileCallback(CallbackBase):
     Usually used as part of an FGSCallbackCollection.
     """
 
-    def __init__(self) -> None:
+    def __init__(self, create_goniometer_func: CreateGoniometerProtocol) -> None:
         self.parameters: GridscanInternalParameters | None = None
         self.run_start_uid: str | None = None
         self.nexus_writer_1: NexusWriter | None = None
         self.nexus_writer_2: NexusWriter | None = None
+        self.create_goniometer_func = create_goniometer_func
 
     def start(self, doc: dict):
         if doc.get("subplan_name") == "run_gridscan_move_and_tidy":
@@ -57,9 +61,14 @@ def descriptor(self, doc):
             nexus_data_1 = self.parameters.get_nexus_info(1)
             LOGGER.info(f"Nexus data 1: {nexus_data_1}")
             nexus_data_2 = self.parameters.get_nexus_info(2)
-            self.nexus_writer_1 = NexusWriter(self.parameters, **nexus_data_1)
+            self.nexus_writer_1 = NexusWriter(
+                self.parameters,
+                create_goniometer_func=self.create_goniometer_func,
+                **nexus_data_1,
+            )
             self.nexus_writer_2 = NexusWriter(
                 self.parameters,
+                create_goniometer_func=self.create_goniometer_func,
                 **nexus_data_2,
                 vds_start_index=nexus_data_1["data_shape"][0],
             )
@@ -70,10 +79,11 @@ def descriptor(self, doc):
 class Gridscan2DNexusFileCallback(CallbackBase):
     """Similar to above, but for a 2D gridscan"""
 
-    def __init__(self) -> None:
+    def __init__(self, create_goniometer_func: CreateGoniometerProtocol) -> None:
         self.parameters: GridscanInternalParameters | None = None
         self.run_start_uid: str | None = None
         self.nexus_writer: NexusWriter | None = None
+        self.create_goniometer_func = create_goniometer_func
 
     def start(self, doc: dict):
         if doc.get("subplan_name") == "run_gridscan_move_and_tidy":
@@ -85,7 +95,7 @@ def start(self, doc: dict):
             self.run_start_uid = doc.get("uid")
 
     def descriptor(self, doc):
-        if doc.get("name") == ISPYB_PLAN_NAME:
+        if doc.get("name") == ISPYB_HARDWARE_READ_PLAN:
             assert (
                 self.parameters is not None
             ), "Nexus callback did not receive parameters before being asked to write!"
@@ -96,5 +106,9 @@ def descriptor(self, doc):
             LOGGER.info("Initialising nexus writer")
             nexus_data = self.parameters.get_nexus_info(1)
             LOGGER.info(f"Nexus data: {nexus_data}")
-            self.nexus_writer = NexusWriter(self.parameters, **nexus_data)
+            self.nexus_writer = NexusWriter(
+                self.parameters,
+                create_goniometer_func=self.create_goniometer_func,
+                **nexus_data,
+            )
             self.nexus_writer.create_nexus_file()

src/hyperion/external_interaction/callbacks/xray_centre/tests/test_nexus_handler.py

@@ -5,6 +5,7 @@
 from hyperion.external_interaction.callbacks.xray_centre.nexus_callback import (
     GridscanNexusFileCallback,
 )
+from hyperion.external_interaction.nexus.nexus_utils import create_i03_goniometer_axes
 from hyperion.parameters.constants import ISPYB_HARDWARE_READ_PLAN
 from hyperion.parameters.external_parameters import from_file as default_raw_params
 from hyperion.parameters.plan_specific.gridscan_internal_params import (
@@ -36,7 +37,7 @@ def test_writers_not_setup_on_plan_start_doc(
     nexus_writer: MagicMock,
     dummy_params: GridscanInternalParameters,
 ):
-    nexus_handler = GridscanNexusFileCallback()
+    nexus_handler = GridscanNexusFileCallback(create_i03_goniometer_axes)
     nexus_writer.assert_not_called()
     nexus_handler.start(
         {
@@ -51,7 +52,7 @@ def test_writers_dont_create_on_init_but_do_on_ispyb_event(
     nexus_writer: MagicMock,
     dummy_params: GridscanInternalParameters,
 ):
-    nexus_handler = GridscanNexusFileCallback()
+    nexus_handler = GridscanNexusFileCallback(create_i03_goniometer_axes)
 
     assert nexus_handler.nexus_writer_1 is None
     assert nexus_handler.nexus_writer_2 is None
@@ -85,7 +86,7 @@ def test_writers_do_create_one_file_each_on_start_doc_for_run_gridscan(
 ):
     nexus_writer.side_effect = [MagicMock(), MagicMock()]
 
-    nexus_handler = GridscanNexusFileCallback()
+    nexus_handler = GridscanNexusFileCallback(create_i03_goniometer_axes)
     nexus_handler.start(
         {
             "subplan_name": "run_gridscan_move_and_tidy",
@@ -113,7 +114,7 @@ def test_writers_do_create_one_file_each_on_start_doc_for_run_gridscan(
 def test_sensible_error_if_writing_triggered_before_params_received(
     nexus_writer: MagicMock, dummy_params
 ):
-    nexus_handler = GridscanNexusFileCallback()
+    nexus_handler = GridscanNexusFileCallback(create_i03_goniometer_axes)
     with pytest.raises(AssertionError) as excinfo:
         nexus_handler.descriptor(
             {

src/hyperion/external_interaction/nexus/nexus_utils.py

@@ -10,8 +10,6 @@
 
 from hyperion.external_interaction.ispyb.ispyb_dataclass import IspybParams
 
-BL = get_beamline_name(None)
-
 
 def create_i03_goniometer_axes(
     omega_start: float,
@@ -72,7 +70,7 @@ def create_vmxm_goniometer_axes(
     omega_start: float,
     scan_points: dict | None,
     x_y_z_increments: tuple[float, float, float] = (0.0, 0.0, 0.0),
-):
+) -> Goniometer:
     """Returns a Nexgen 'Goniometer' object with the dependency chain of I03's Smargon
     goniometer. If scan points is provided these values will be used in preference to
     those from the params object.
@@ -117,16 +115,6 @@ def create_vmxm_goniometer_axes(
     return Goniometer(gonio_axes, scan_points)
 
 
-if BL == "i03":
-    create_goniometer_axes = create_i03_goniometer_axes
-elif BL == "i02-1":
-    create_goniometer_axes = create_vmxm_goniometer_axes
-else:
-
-    def create_goniometer_axes(*a, **k):
-        raise ValueError("Cannot create goniometer axes on unknown beamline")
-
-
 def get_start_and_predicted_end_time(time_expected: float) -> tuple[str, str]:
     time_format = r"%Y-%m-%dT%H:%M:%SZ"
     start = datetime.utcfromtimestamp(time.time())

src/hyperion/external_interaction/nexus/write_nexus.py

@@ -6,25 +6,38 @@
 
 import math
 from pathlib import Path
+from typing import Protocol
 
 from nexgen.nxs_utils import Detector, Goniometer, Source
 from nexgen.nxs_write.NXmxWriter import NXmxFileWriter
 
 from hyperion.external_interaction.nexus.nexus_utils import (
     create_beam_and_attenuator_parameters,
     create_detector_parameters,
-    create_goniometer_axes,
     get_start_and_predicted_end_time,
 )
 from hyperion.parameters.internal_parameters import InternalParameters
 
 
+class CreateGoniometerProtocol(Protocol):
+    @staticmethod
+    def __call__(
+        omega_start: float,
+        scan_points: dict | None,
+        x_y_z_increments: tuple[float, float, float] = (0.0, 0.0, 0.0),
+        chi: float = 0.0,
+        phi: float = 0.0,
+    ) -> Goniometer:
+        ...
+
+
 class NexusWriter:
     def __init__(
         self,
         parameters: InternalParameters,
         scan_points: dict,
         data_shape: tuple[int, int, int],
+        create_goniometer_func: CreateGoniometerProtocol,
         omega_start: float | None = None,
         run_number: int | None = None,
         vds_start_index: int = 0,
@@ -66,12 +79,11 @@ def __init__(
         self.master_file: Path = (
             self.directory / f"{self.filename}_{self.run_number}_master.h5"
         )
-
         try:
             chi = parameters.experiment_params.chi_start
         except Exception:
             chi = 0.0
-        self.goniometer: Goniometer = create_goniometer_axes(
+        self.goniometer: Goniometer = create_goniometer_func(
             self.omega_start, self.scan_points, chi=chi
         )