Ispyb integration vmxm grid scan

docs/developer/hyperion/reference/gridscan.puml

@@ -1,38 +1,70 @@
 @startuml
 title Gridscan Parameter Relationships
 
-class DiffractionExperiment
-class DiffractionExperimentWithSample
-class GridCommon {
-    grid_width_um
-    exposure_time_s
+package dodal {
+    class AbstractExperimentParameterBase
+    class AbstractExperimentWithBeamParams {
+        transmission_fraction
+    }
+    class GridScanParamsCommon {
+        x_steps
+        y_steps
+        x_step_size_mm
+        y_step_size_mm
+        x_start_mm
+        y1_start_mm
+        z1_start_mm
+        set_stub_offsets
+    }
+    class GridScanParamsThreeD
+    class PandAGridScanParams
+    class ZebraGridScanParamsThreeD
+    class ZebraGridScanParamsTwoD
 }
-class GridScanWithEdgeDetect {
-    box_size_um
-}
-class HyperionGridCommon {
-    enable_dev_shm
+
+rectangle "Internal Experiment Parameter Model" {
+    class MxBlueSkyParameters
+    class DiffractionExperiment
+    class DiffractionExperimentWithSample
+    class GenericGrid {
+        grid_width_um
+        exposure_time_s
+    }
+    class GenericGridWithHyperionDetectorParams
+    class GridScanWithEdgeDetect {
+        box_size_um
+    }
+    class PinTipCentreThenXrayCentre
+    class RobotLoadThenCentre
 }
-class HyperionThreeDGridScan {
-    x_step_size_um
-    y_step_size_um
-    z_step_size_um
-    y2_start_um
-    z2_start_um
-    --
-    grid_1_spec
-    grid_2_spec
-    scan_indices
-    scan_spec
-    scan_points
-    scan_points_first_grid
-    scan_points_second_grid
-    num_images
-    FGS_Params
-    panda_FGS_Params
+
+
+
+rectangle "Specified Grids" {
+    class SpecifiedGrids<GenericParamType> {
+        omega_starts_deg: float[]
+        x_step_size_um
+        y_step_sizes_um
+        x_steps
+        y_steps: int[]
+        --
+        fast_grid_scan_params: GenericParamType
+        grid_specs
+        scan_indices
+        scan_points
+        scan_spec
+        num_images
+    }
+    class "SpecifiedGrids<ZebraGridScanParamsThreeD>" as SpecifiedGridsZebraGridScanParamsThreeD
+    class "SpecifiedGrids<ZebraGridScanParamsTwoD>" as SpecifiedGridsZebraGridScanParamsTwoD
+    class SpecifiedTwoDGridScan
+    class SpecifiedThreeDGridScan
+    class HyperionSpecifiedThreeDGridScan {
+        --
+        panda_fast_gridscan_params: PandAGridScanParams
+    }
 }
-class MxBlueSkyParameters
-class SpecifiedGrid
+
 class XyzStarts {
     x_start_um
     y_start_um
@@ -43,67 +75,51 @@ class OptionalXYZStarts {
     y_start_um
     z_start_um
 }
-class RotationScanPerSweep
 
 MxBlueSkyParameters <|-- DiffractionExperiment
 DiffractionExperiment <|-- DiffractionExperimentWithSample
-DiffractionExperimentWithSample <|-- GridCommon
-GridCommon <|-- GridScanWithEdgeDetect
-GridCommon <|-- HyperionGridCommon
-HyperionGridCommon <|-- HyperionThreeDGridScan
-SpecifiedGrid <|-- HyperionThreeDGridScan
-XyzStarts <|-- SpecifiedGrid
+DiffractionExperimentWithSample <|-- GenericGrid
+GenericGrid <|-- GenericGridWithHyperionDetectorParams
+GenericGridWithHyperionDetectorParams <|-- GridScanWithEdgeDetect
+GenericGridWithHyperionDetectorParams <|-- PinTipCentreThenXrayCentre
+GenericGridWithHyperionDetectorParams <|-- RobotLoadThenCentre
+GenericGrid <|-- SpecifiedGrids
+SpecifiedGridsZebraGridScanParamsTwoD <|-- SpecifiedTwoDGridScan
+SpecifiedGridsZebraGridScanParamsThreeD <|-- SpecifiedThreeDGridScan
+SpecifiedThreeDGridScan <|-- HyperionSpecifiedThreeDGridScan
+XyzStarts <|-- SpecifiedGrids
 OptionalXYZStarts <|-- RotationScanPerSweep
 class GridParamUpdate {
-    x_start_um
-    y_start_um
-    y2_start_um
-    z_start_um
-    z2_start_um
-    x_steps
-    y_steps
-    z_steps
-    x_step_size_um
-    y_step_size_um
-    z_step_size_um
+    x_start_um: float
+    y_starts_um: float[]
+    z_starts_um: float[]
+    x_steps: float
+    y_steps: float[]
+    x_step_size_um: float
+    y_step_sizes_um: float[]
 }
 
 class GridDetectionCallback {
     get_grid_parameters() -> GridParamUpdate
 }
 
 GridDetectionCallback --> GridParamUpdate : generates from event. Adds 0.5 to get box-centres
-GridParamUpdate --> HyperionThreeDGridScan : combines with GridScanWithEdgeDetect
+GridParamUpdate --> HyperionSpecifiedThreeDGridScan : combines with GridScanWithEdgeDetect
 
 class experiment_plans {
     grid_detect_then_xray_centre()
     common_flyscan_xray_centre()
-    create_parameters_for_flyscan_xray_centre(GridScanWithEdgeDetect, GridParamUpdate) -> HyperionThreeDGridScan
-}
-
-class AbstractExperimentBase
-class AbstractExperimentWithBeamParams
-class GridScanParamsCommon {
-    x_steps
-    y_steps
-    z_steps
-    x_step_size_mm
-    y_step_size_mm
-    z_step_size_mm
-    x_start_mm
-    y1_start_mm
-    y2_start_mm
-    z1_start_mm
-    z2_start_mm
+    create_parameters_for_flyscan_xray_centre(GridScanWithEdgeDetect, GridParamUpdate) -> HyperionSpecifiedThreeDGridScan
 }
-class PandAGridScanParams
-class ZebraGridScanParamsThreeD
 
-AbstractExperimentBase <|-- AbstractExperimentWithBeamParams
+AbstractExperimentParameterBase <|-- AbstractExperimentWithBeamParams
 AbstractExperimentWithBeamParams <|-- GridScanParamsCommon
-GridScanParamsCommon <|-- PandAGridScanParams
-GridScanParamsCommon <|-- ZebraGridScanParamsThreeD
+GridScanParamsCommon <|-- ZebraGridScanParamsTwoD
+GridScanParamsCommon <|-- GridScanParamsThreeD
+GridScanParamsThreeD <|-- PandAGridScanParams
+GridScanParamsThreeD <|-- ZebraGridScanParamsThreeD
 
-HyperionThreeDGridScan --> ZebraGridScanParamsThreeD : generates
-HyperionThreeDGridScan --> PandAGridScanParams : generates
+HyperionSpecifiedThreeDGridScan --> ZebraGridScanParamsThreeD : generates
+HyperionSpecifiedThreeDGridScan --> PandAGridScanParams : generates
+SpecifiedTwoDGridScan --> ZebraGridScanParamsTwoD : generates
 @enduml

pyproject.toml

@@ -94,7 +94,7 @@ dev = [
     "tox-uv",
     "types-mock",
     "types-requests",
-    "sphinxcontrib.mermaid", # To build dodal docs
+    "sphinxcontrib.mermaid",     # To build dodal docs
 ]
 
 [project.scripts]

src/mx_bluesky/beamlines/i02_1/__init__.py

@@ -0,0 +1,3 @@
+from mx_bluesky.beamlines.i02_1.i02_1_gridscan_plan import i02_1_gridscan_plan
+
+__all__ = ["i02_1_gridscan_plan"]

src/mx_bluesky/beamlines/i02_1/composites.py

@@ -0,0 +1,16 @@
+from pathlib import Path
+
+from mx_bluesky.beamlines.i02_1.parameters.gridscan import SpecifiedTwoDGridScan
+
+
+class I02_1FgsParams(SpecifiedTwoDGridScan):  # noqa: N801
+    """For VMXm gridscans, GDA currently takes the snapshots and provides bluesky with a path, and
+    sends over the grid parameters"""
+
+    path_to_xtal_snapshot: Path
+    beam_size_x: float
+    beam_size_y: float
+    microns_per_pixel_x: float
+    microns_per_pixel_y: float
+    upper_left_x: int  # position of X,Y for the top left of the grid, in pixels
+    upper_left_y: int

src/mx_bluesky/beamlines/i02_1/device_setup_plans/setup_zebra.py

@@ -0,0 +1,45 @@
+import bluesky.plan_stubs as bps
+from dodal.devices.zebra.zebra import Zebra
+
+from mx_bluesky.common.parameters.constants import PlanGroupCheckpointConstants
+
+ZEBRA_STATUS_TIMEOUT = 30
+
+
+# Control Eiger from motion controller. Fast shutter is configured in GDA
+def setup_zebra_for_gridscan(
+    zebra: Zebra,
+    ttl_detector: int | None = None,
+    group=PlanGroupCheckpointConstants.SETUP_ZEBRA_FOR_GRIDSCAN,
+    wait=True,
+):
+    """
+    Assumes that the motion controller, as part of its gridscan PLC, will send triggers as required to the zebra's
+    IN1_TTL to control the detector. The fast shutter is configured in GDA, don't need to touch it in Bluesky for now.
+    """
+    ttl_detector = ttl_detector or zebra.mapping.outputs.TTL_EIGER
+    yield from bps.abs_set(
+        zebra.output.out_pvs[ttl_detector],
+        zebra.mapping.sources.IN1_TTL,
+    )
+    if wait:
+        yield from bps.wait(group, timeout=ZEBRA_STATUS_TIMEOUT)
+
+
+def tidy_up_zebra_after_gridscan(
+    zebra: Zebra,
+    ttl_detector: int | None = None,
+    group=PlanGroupCheckpointConstants.TIDY_ZEBRA_AFTER_GRIDSCAN,
+    wait=False,
+):
+    """Revert zebra to state expected by GDA"""
+    ttl_detector = ttl_detector or zebra.mapping.outputs.TTL_EIGER
+
+    yield from bps.abs_set(
+        zebra.output.out_pvs[ttl_detector],
+        zebra.mapping.sources.OR1,
+        group=group,
+    )
+
+    if wait:
+        yield from bps.wait(group)

src/mx_bluesky/beamlines/i02_1/external_interaction/callbacks/gridscan/ispyb_callback.py

@@ -0,0 +1,88 @@
+from collections.abc import Sequence
+
+from mx_bluesky.beamlines.i02_1.composites import I02_1FgsParams
+from mx_bluesky.common.external_interaction.callbacks.grid.grid_detect_and_scan.ispyb_mapping import (
+    construct_comment_for_gridscan,
+)
+from mx_bluesky.common.external_interaction.callbacks.grid.gridscan.ispyb_callback import (
+    GridscanISPyBCallback as CommonGridscanISPyBCallback,
+)
+from mx_bluesky.common.external_interaction.ispyb.data_model import (
+    DataCollectionGridInfo,
+    DataCollectionInfo,
+    Orientation,
+    ScanDataInfo,
+)
+from mx_bluesky.common.utils.log import ISPYB_ZOCALO_CALLBACK_LOGGER
+
+
+def _make_comment(x_steps: int, y_steps: int) -> str:
+    return f"Diffraction grid scan of {x_steps} by {y_steps}."
+
+
+class GridscanISPyBCallback(CommonGridscanISPyBCallback):
+    def _get_scan_infos(self, doc) -> Sequence[ScanDataInfo]:
+        """
+        For VMXm, grid information is available immediately after the plan is triggered.
+        """
+        assert isinstance(self.params, I02_1FgsParams)
+        assert self.ispyb_ids.data_collection_ids, "No current data collection"
+        assert self.data_collection_group_info, "No data collection group"
+        data = doc["data"]
+        scan_data_infos = []
+
+        for grid_num in range(self.params.num_grids):
+            omega = data.get("gonio-omega", self.params.omega_starts_deg[grid_num])
+
+            ISPYB_ZOCALO_CALLBACK_LOGGER.info(
+                f"Generating dc info for gridplane XY, omega {omega}"
+            )
+            data_collection_number = self.params.detector_params.run_number
+            file_template = f"{self.params.detector_params.prefix}_{data_collection_number}_master.h5"
+            # Snapshots have already been taken in GDA
+
+            data_collection_info = DataCollectionInfo(
+                xtal_snapshot1=str(self.params.path_to_xtal_snapshot),
+                xtal_snapshot2=str(self.params.path_to_xtal_snapshot),
+                xtal_snapshot3=str(self.params.path_to_xtal_snapshot),
+                n_images=self.params.num_images,
+                data_collection_number=data_collection_number,
+                file_template=file_template,
+            )
+            data_collection_grid_info = DataCollectionGridInfo(
+                dx_in_mm=self.params.x_step_size_um / 1000,
+                dy_in_mm=self.params.y_step_sizes_um[grid_num] / 1000,
+                steps_x=self.params.x_steps,
+                steps_y=self.params.y_steps[grid_num],
+                microns_per_pixel_x=self.params.microns_per_pixel_x,
+                microns_per_pixel_y=self.params.microns_per_pixel_y,
+                snapshot_offset_x_pixel=self.params.upper_left_x,
+                snapshot_offset_y_pixel=self.params.upper_left_y,
+                orientation=Orientation.HORIZONTAL,
+                snaked=True,
+            )
+            data_collection_info.comments = construct_comment_for_gridscan(
+                data_collection_grid_info
+            )
+
+            data_collection_id = self.ispyb_ids.data_collection_ids[0]
+
+            self.data_collection_group_info.comments = _make_comment(
+                self.params.x_steps, self.params.y_steps[0]
+            )
+
+            self._populate_axis_info(data_collection_info, doc["data"])
+
+            scan_data_info = ScanDataInfo(
+                data_collection_info=data_collection_info,
+                data_collection_id=data_collection_id,
+                data_collection_grid_info=data_collection_grid_info,
+            )
+
+            scan_data_infos.append(scan_data_info)
+
+        ISPYB_ZOCALO_CALLBACK_LOGGER.info(
+            "Updating ispyb data collection after loading grid params"
+        )
+
+        return scan_data_infos