Merge pull request #1271 from DiamondLightSource/1033_clarify_desired…

…_transmission

Clarify which transmission is which

setup.cfg

@@ -35,7 +35,7 @@ install_requires =
     xarray
     doct
     databroker
-    dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git
+    dls-dodal @ git+https://github.com/DiamondLightSource/dodal.git@7068bf2f0e75f8fffa83693136cb555b03ce8545
     pydantic<2.0 # See https://github.com/DiamondLightSource/hyperion/issues/774
     scipy
     pyzmq<25 # See https://github.com/DiamondLightSource/hyperion/issues/1103

src/hyperion/experiment_plans/experiment_registry.py

@@ -4,7 +4,7 @@
 
 from dodal.devices.fast_grid_scan import GridScanParams
 from dodal.devices.panda_fast_grid_scan import PandAGridScanParams
-from dodal.parameters.experiment_parameter_base import AbstractExperimentParameterBase
+from dodal.parameters.experiment_parameter_base import AbstractExperimentWithBeamParams
 
 import hyperion.experiment_plans.flyscan_xray_centre_plan as flyscan_xray_centre_plan
 import hyperion.experiment_plans.panda_flyscan_xray_centre_plan as panda_flyscan_xray_centre_plan
@@ -61,7 +61,7 @@ class ExperimentRegistryEntry(TypedDict):
         | RobotLoadThenCentreInternalParameters
         | PandAGridscanInternalParameters
     ]
-    experiment_param_type: type[AbstractExperimentParameterBase]
+    experiment_param_type: type[AbstractExperimentWithBeamParams]
     callbacks_factory: CallbacksFactory
 
 

src/hyperion/experiment_plans/flyscan_xray_centre_plan.py

@@ -356,7 +356,7 @@ def flyscan_xray_centre(
     @transmission_and_xbpm_feedback_for_collection_decorator(
         composite.xbpm_feedback,
         composite.attenuator,
-        parameters.hyperion_params.ispyb_params.transmission_fraction,
+        parameters.experiment_params.transmission_fraction,
     )
     def run_gridscan_and_move_and_tidy(fgs_composite, params):
         yield from run_gridscan_and_move(fgs_composite, params)

src/hyperion/experiment_plans/panda_flyscan_xray_centre_plan.py

@@ -289,7 +289,7 @@ def panda_flyscan_xray_centre(
     @transmission_and_xbpm_feedback_for_collection_decorator(
         composite.xbpm_feedback,
         composite.attenuator,
-        parameters.hyperion_params.ispyb_params.transmission_fraction,
+        parameters.experiment_params.transmission_fraction,
     )
     def run_gridscan_and_move_and_tidy(fgs_composite, params):
         yield from run_gridscan_and_move(fgs_composite, params)

src/hyperion/experiment_plans/rotation_scan_plan.py

@@ -293,7 +293,7 @@ def rotation_with_cleanup_and_stage(params: RotationInternalParameters):
                 composite.detector_motion,
                 composite.backlight,
                 composite.attenuator,
-                params.hyperion_params.ispyb_params.transmission_fraction,
+                params.experiment_params.transmission_fraction,
                 params.hyperion_params.detector_params.detector_distance,
             )
             LOGGER.info("moving to position (if specified)")

src/hyperion/experiment_plans/set_energy_plan.py

@@ -8,8 +8,8 @@
 import dataclasses
 from typing import Any, Generator
 
-from bluesky import Msg
 from bluesky import plan_stubs as bps
+from bluesky.utils import Msg
 from dodal.devices.attenuator import Attenuator
 from dodal.devices.DCM import DCM
 from dodal.devices.focusing_mirror import FocusingMirror, VFMMirrorVoltages

src/hyperion/external_interaction/callbacks/grid_detection_callback.py

@@ -63,6 +63,7 @@ def event(self, doc: Event):
 
     def get_grid_parameters(self) -> GridScanParams:
         return GridScanParams(
+            transmission_fraction=0.01,
             dwell_time_ms=self.exposure_time * 1000,
             x_start=self.start_positions[0][0],
             y1_start=self.start_positions[0][1],
@@ -80,6 +81,7 @@ def get_grid_parameters(self) -> GridScanParams:
 
     def get_panda_grid_parameters(self) -> PandAGridScanParams:
         return PandAGridScanParams(
+            transmission_fraction=0.01,
             run_up_distance_mm=self.run_up_distance_mm,
             x_start=self.start_positions[0][0],
             y1_start=self.start_positions[0][1],

src/hyperion/parameters/internal_parameters.py

@@ -2,7 +2,7 @@
 from typing import Any
 
 from dodal.devices.eiger import DetectorParams
-from dodal.parameters.experiment_parameter_base import AbstractExperimentParameterBase
+from dodal.parameters.experiment_parameter_base import AbstractExperimentWithBeamParams
 from pydantic import BaseModel, root_validator
 from semver import Version
 
@@ -73,10 +73,7 @@ def extract_experiment_params_from_flat_dict(
     experiment_param_class, flat_params: dict[str, Any]
 ):
     # Use __fields__ to get inherited attributes from BaseModels
-    if issubclass(experiment_param_class, BaseModel):
-        experiment_field_keys = list(experiment_param_class.__fields__.keys())
-    else:
-        experiment_field_keys = list(experiment_param_class.__annotations__.keys())
+    experiment_field_keys = list(experiment_param_class.__fields__.keys())
 
     experiment_params_args = fetch_subdict_from_bucket(
         experiment_field_keys, flat_params
@@ -159,7 +156,7 @@ def _hyperion_param_key_definitions():
     def _preprocess_experiment_params(
         cls,
         experiment_params: dict[str, Any],
-    ) -> AbstractExperimentParameterBase: ...
+    ) -> AbstractExperimentWithBeamParams: ...
 
     @abstractmethod
     def _preprocess_hyperion_params(

src/hyperion/parameters/plan_specific/grid_scan_with_edge_detect_params.py

@@ -4,9 +4,8 @@
 
 import numpy as np
 from dodal.devices.detector import TriggerMode
-from dodal.parameters.experiment_parameter_base import AbstractExperimentParameterBase
+from dodal.parameters.experiment_parameter_base import AbstractExperimentWithBeamParams
 from pydantic import validator
-from pydantic.dataclasses import dataclass
 
 from hyperion.external_interaction.ispyb.ispyb_dataclass import GridscanIspybParams
 from hyperion.parameters.internal_parameters import (
@@ -20,8 +19,7 @@
 )
 
 
-@dataclass
-class GridScanWithEdgeDetectParams(AbstractExperimentParameterBase):
+class GridScanWithEdgeDetectParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a grid scan that uses edge detection to detect the grid.
     """

src/hyperion/parameters/plan_specific/pin_centre_then_xray_centre_params.py

@@ -4,9 +4,8 @@
 
 import numpy as np
 from dodal.devices.detector import TriggerMode
-from dodal.parameters.experiment_parameter_base import AbstractExperimentParameterBase
+from dodal.parameters.experiment_parameter_base import AbstractExperimentWithBeamParams
 from pydantic import validator
-from pydantic.dataclasses import dataclass
 
 from hyperion.external_interaction.ispyb.ispyb_dataclass import GridscanIspybParams
 from hyperion.parameters.internal_parameters import (
@@ -20,8 +19,7 @@
 )
 
 
-@dataclass
-class PinCentreThenXrayCentreParams(AbstractExperimentParameterBase):
+class PinCentreThenXrayCentreParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a plan that does a pin centre then xray centre
     """

src/hyperion/parameters/plan_specific/robot_load_then_center_params.py

@@ -4,9 +4,8 @@
 
 import numpy as np
 from dodal.devices.detector import DetectorParams, TriggerMode
-from dodal.parameters.experiment_parameter_base import AbstractExperimentParameterBase
+from dodal.parameters.experiment_parameter_base import AbstractExperimentWithBeamParams
 from pydantic import validator
-from pydantic.dataclasses import dataclass
 
 from hyperion.external_interaction.ispyb.ispyb_dataclass import (
     GRIDSCAN_ISPYB_PARAM_DEFAULTS,
@@ -33,8 +32,7 @@ class Config:
         }
 
 
-@dataclass
-class RobotLoadThenCentreParams(AbstractExperimentParameterBase):
+class RobotLoadThenCentreParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a plan that waits for robot load then does a
     centre.

src/hyperion/parameters/plan_specific/rotation_scan_internal_params.py

@@ -6,8 +6,8 @@
 from dodal.devices.detector import DetectorParams
 from dodal.devices.motors import XYZLimitBundle
 from dodal.devices.zebra import RotationDirection
-from dodal.parameters.experiment_parameter_base import AbstractExperimentParameterBase
-from pydantic import BaseModel, validator
+from dodal.parameters.experiment_parameter_base import AbstractExperimentWithBeamParams
+from pydantic import validator
 from scanspec.core import Path as ScanPath
 from scanspec.specs import Line
 
@@ -36,7 +36,7 @@ class Config:
         }
 
 
-class RotationScanParams(BaseModel, AbstractExperimentParameterBase):
+class RotationScanParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a rotation data collection.
     """

src/hyperion/parameters/schemas/experiment_schemas/grid_scan_params_schema.json

@@ -47,6 +47,9 @@
         "omega_start": {
             "type": "number"
         },
+        "transmission_fraction": {
+            "type": "number"
+        },
         "set_stub_offsets": {
             "type": "boolean"
         }

src/hyperion/parameters/schemas/experiment_schemas/grid_scan_with_edge_detect_params_schema.json

@@ -22,8 +22,10 @@
         },
         "use_panda": {
             "type": "boolean"
+        },
+        "transmission_fraction": {
+            "type": "number"
         }
-
     },
     "required": [
         "exposure_time",

src/hyperion/parameters/schemas/experiment_schemas/panda_grid_scan_params_schema.json

@@ -47,10 +47,12 @@
         "set_stub_offsets": {
             "type": "boolean"
         },
+        "transmission_fraction": {
+            "type": "number"
+        },
         "run_up_distance_mm": {
             "type": "number"
         }
-
     },
     "minProperties": 12,
     "additionalProperties": false

src/hyperion/parameters/schemas/experiment_schemas/rotation_scan_params_schema.json

@@ -61,6 +61,9 @@
         },
         "shutter_opening_time_s": {
             "type": "number"
+        },
+        "transmission_fraction": {
+            "type": "number"
         }
     },
     "required": [

src/hyperion/parameters/schemas/experiment_schemas/wait_for_robot_load_then_centre_schema.json

@@ -22,6 +22,9 @@
         },
         "use_panda": {
             "type": "boolean"
+        },
+        "transmission_fraction": {
+            "type": "number"
         }
     },
     "required": [

src/hyperion/parameters/schemas/ispyb_parameters_schema.json

@@ -45,9 +45,6 @@
                 "type": "string"
             }
         },
-        "transmission_fraction": {
-            "type": "number"
-        },
         "flux": {
             "type": "number"
         },
@@ -76,15 +73,17 @@
             "type": "number"
         },
         "ispyb_experiment_type": {
-            "type": ["string", "null"]
+            "type": [
+                "string",
+                "null"
+            ]
         }
     },
     "required": [
         "visit_path",
         "microns_per_pixel_x",
         "microns_per_pixel_y",
         "position",
-        "transmission_fraction",
         "flux",
         "beam_size_x",
         "beam_size_y",

tests/system_tests/experiment_plans/test_fgs_plan.py

@@ -191,7 +191,7 @@ def test_xbpm_feedback_decorator(
     @transmission_and_xbpm_feedback_for_collection_decorator(
         fxc_composite.xbpm_feedback,
         fxc_composite.attenuator,
-        params.hyperion_params.ispyb_params.transmission_fraction,
+        params.experiment_params.transmission_fraction,
     )
     def decorated_plan():
         yield from bps.sleep(0.1)

tests/test_data/parameter_json_files/good_test_grid_with_edge_detect_parameters.json

@@ -23,7 +23,6 @@
                 20.0,
                 30.0
             ],
-            "transmission_fraction": 1.0,
             "flux": 10.0,
             "beam_size_x": 1.0,
             "beam_size_y": 1.0,
@@ -41,6 +40,7 @@
         "exposure_time": 0.1,
         "detector_distance": 100.0,
         "omega_start": 0.0,
-        "grid_width_microns": 151
+        "grid_width_microns": 151,
+        "transmission_fraction": 1.0
     }
 }

tests/test_data/parameter_json_files/good_test_parameters.json

@@ -43,7 +43,6 @@
                 "test_2",
                 "test_3"
             ],
-            "transmission_fraction": 1.0,
             "flux": 10.0,
             "beam_size_x": 1.0,
             "beam_size_y": 1.0,
@@ -70,6 +69,7 @@
         "z2_start": 0.0,
         "exposure_time": 0.1,
         "detector_distance": 100.0,
-        "omega_start": 0.0
+        "omega_start": 0.0,
+        "transmission_fraction": 1.0
     }
 }

tests/test_data/parameter_json_files/good_test_pin_centre_then_xray_centre_parameters.json

@@ -23,7 +23,6 @@
                 20.0,
                 30.0
             ],
-            "transmission_fraction": 1.0,
             "flux": 10.0,
             "beam_size_x": 1.0,
             "beam_size_y": 1.0,
@@ -43,6 +42,7 @@
         "omega_start": 0.0,
         "tip_offset_microns": 108.9,
         "grid_width_microns": 290.6,
-        "oav_centring_file": "tests/test_data/test_OAVCentring.json"
+        "oav_centring_file": "tests/test_data/test_OAVCentring.json",
+        "transmission_fraction": 1.0
     }
 }

tests/test_data/parameter_json_files/good_test_robot_load_params.json

@@ -21,7 +21,6 @@
                 0,
                 0
             ],
-            "transmission_fraction": 1.0,
             "flux": 10.0,
             "beam_size_x": 0.1,
             "beam_size_y": 0.1,
@@ -34,6 +33,7 @@
     },
     "experiment_params": {
         "omega_start": 0,
+        "transmission_fraction": 1.0,
         "exposure_time": 0.004,
         "detector_distance": 255,
         "snapshot_dir": "/tmp",

tests/test_data/parameter_json_files/good_test_robot_load_params_no_energy.json

@@ -21,7 +21,6 @@
                 0,
                 0
             ],
-            "transmission_fraction": 1.0,
             "flux": 10.0,
             "beam_size_x": 0.1,
             "beam_size_y": 0.1,
@@ -35,6 +34,7 @@
     },
     "experiment_params": {
         "omega_start": 0,
+        "transmission_fraction": 1.0,
         "exposure_time": 0.004,
         "detector_distance": 255,
         "snapshot_dir": "/tmp",

tests/test_data/parameter_json_files/good_test_rotation_scan_parameters.json

@@ -43,7 +43,6 @@
                 "test_2",
                 "test_3"
             ],
-            "transmission_fraction": 1.0,
             "flux": 10.0,
             "beam_size_x": 1.0,
             "beam_size_y": 1.0,
@@ -62,6 +61,7 @@
         "phi_start": 0.0,
         "chi_start": 0,
         "x": 1.0,
+        "transmission_fraction": 1.0,
         "y": 2.0,
         "z": 3.0,
         "exposure_time": 0.1,