DiamondLightSource/hyperion#1033 fix param classes and test files

olliesilvester · Mar 18, 2024 · 5dce042 · 5dce042
1 parent ea74313
commit 5dce042
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Showing 35 changed files with 84 additions and 66 deletions.
diff --git a/src/hyperion/external_interaction/callbacks/grid_detection_callback.py b/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],

diff --git a/src/hyperion/parameters/internal_parameters.py b/src/hyperion/parameters/internal_parameters.py
@@ -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

diff --git a/src/hyperion/parameters/plan_specific/grid_scan_with_edge_detect_params.py b/src/hyperion/parameters/plan_specific/grid_scan_with_edge_detect_params.py
@@ -6,7 +6,6 @@
 from dodal.devices.detector import TriggerMode
 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 (
@@ -20,7 +19,6 @@
 )
 
 
-@dataclass
 class GridScanWithEdgeDetectParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a grid scan that uses edge detection to detect the grid.

diff --git a/src/hyperion/parameters/plan_specific/pin_centre_then_xray_centre_params.py b/src/hyperion/parameters/plan_specific/pin_centre_then_xray_centre_params.py
@@ -6,7 +6,6 @@
 from dodal.devices.detector import TriggerMode
 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 (
@@ -20,7 +19,6 @@
 )
 
 
-@dataclass
 class PinCentreThenXrayCentreParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a plan that does a pin centre then xray centre

diff --git a/src/hyperion/parameters/plan_specific/rotation_scan_internal_params.py b/src/hyperion/parameters/plan_specific/rotation_scan_internal_params.py
@@ -7,7 +7,7 @@
 from dodal.devices.motors import XYZLimitBundle
 from dodal.devices.zebra import RotationDirection
 from dodal.parameters.experiment_parameter_base import AbstractExperimentWithBeamParams
-from pydantic import BaseModel, validator
+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, AbstractExperimentWithBeamParams):
+class RotationScanParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a rotation data collection.
     """

diff --git a/src/hyperion/parameters/plan_specific/wait_for_robot_load_then_center_params.py b/src/hyperion/parameters/plan_specific/wait_for_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 WaitForRobotLoadThenCentreParams(AbstractExperimentParameterBase):
+class WaitForRobotLoadThenCentreParams(AbstractExperimentWithBeamParams):
     """
     Holder class for the parameters of a plan that waits for robot load then does a
     centre.
@@ -56,6 +54,9 @@ class WaitForRobotLoadThenCentreParams(AbstractExperimentParameterBase):
     # plugin
     use_ophyd_pin_tip_detect: bool = False
 
+    def get_num_images(self):
+        return 0
+
 
 class WaitForRobotLoadThenCentreInternalParameters(InternalParameters):
     experiment_params: WaitForRobotLoadThenCentreParams

diff --git a/src/hyperion/parameters/schemas/experiment_schemas/grid_scan_params_schema.json b/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"
         }

diff --git a/...erion/parameters/schemas/experiment_schemas/grid_scan_with_edge_detect_params_schema.json b/...erion/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",

diff --git a/src/hyperion/parameters/schemas/experiment_schemas/panda_grid_scan_params_schema.json b/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

diff --git a/src/hyperion/parameters/schemas/experiment_schemas/rotation_scan_params_schema.json b/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": [

diff --git a/...yperion/parameters/schemas/experiment_schemas/wait_for_robot_load_then_centre_schema.json b/...yperion/parameters/schemas/experiment_schemas/wait_for_robot_load_then_centre_schema.json
@@ -18,12 +18,17 @@
             "type": "boolean"
         },
         "requested_energy_kev": {
-            "type": ["number", "null"]
+            "type": [
+                "number",
+                "null"
+            ]
         },
         "use_panda": {
             "type": "boolean"
+        },
+        "transmission_fraction": {
+            "type": "number"
         }
-
     },
     "required": [
         "exposure_time",

diff --git a/src/hyperion/parameters/schemas/full_external_parameters_schema.json b/src/hyperion/parameters/schemas/full_external_parameters_schema.json
@@ -3,7 +3,7 @@
     "type": "object",
     "properties": {
         "params_version": {
-            "const": "4.0.4"
+            "const": "5.0.0"
         },
         "hyperion_params": {
             "type": "object",

diff --git a/src/hyperion/parameters/schemas/ispyb_parameters_schema.json b/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",

diff --git a/tests/test_data/parameter_json_files/good_test_grid_with_edge_detect_parameters.json b/tests/test_data/parameter_json_files/good_test_grid_with_edge_detect_parameters.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "4.0.4",
+    "params_version": "5.0.0",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -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
     }
 }
diff --git a/tests/test_data/parameter_json_files/good_test_parameters.json b/tests/test_data/parameter_json_files/good_test_parameters.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "4.0.4",
+    "params_version": "5.0.0",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -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
     }
 }
diff --git a/tests/test_data/parameter_json_files/good_test_pin_centre_then_xray_centre_parameters.json b/tests/test_data/parameter_json_files/good_test_pin_centre_then_xray_centre_parameters.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "4.0.4",
+    "params_version": "5.0.0",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -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,
@@ -44,6 +43,7 @@
         "tip_offset_microns": 108.9,
         "grid_width_microns": 290.6,
         "oav_centring_file": "tests/test_data/test_OAVCentring.json",
-        "use_ophyd_pin_tip_detect": true
+        "use_ophyd_pin_tip_detect": true,
+        "transmission_fraction": 1.0
     }
 }
diff --git a/tests/test_data/parameter_json_files/good_test_rotation_scan_parameters.json b/tests/test_data/parameter_json_files/good_test_rotation_scan_parameters.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "4.0.4",
+    "params_version": "5.0.0",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -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,

diff --git a/tests/test_data/parameter_json_files/good_test_rotation_scan_parameters_nomove.json b/tests/test_data/parameter_json_files/good_test_rotation_scan_parameters_nomove.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "4.0.4",
+    "params_version": "5.0.0",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -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,
@@ -56,6 +55,7 @@
         }
     },
     "experiment_params": {
+        "transmission_fraction": 1.0,
         "rotation_axis": "omega",
         "rotation_angle": 180.0,
         "omega_start": 0.0,

diff --git a/tests/test_data/parameter_json_files/good_test_stepped_grid_scan_parameters.json b/tests/test_data/parameter_json_files/good_test_stepped_grid_scan_parameters.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "4.0.4",
+    "params_version": "5.0.0",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -44,7 +44,6 @@
                 "test_2",
                 "test_3"
             ],
-            "transmission_fraction": 1.0,
             "flux": 10.0,
             "beam_size_x": 1.0,
             "beam_size_y": 1.0,
@@ -60,6 +59,7 @@
         "x_steps": 5,
         "y_steps": 10,
         "z_steps": 2,
+        "transmission_fraction": 1.0,
         "x_step_size": 0.1,
         "y_step_size": 0.1,
         "z_step_size": 0.1,

diff --git a/tests/test_data/parameter_json_files/good_test_wait_for_robot_load_params.json b/tests/test_data/parameter_json_files/good_test_wait_for_robot_load_params.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "4.0.4",
+    "params_version": "5.0.0",
     "hyperion_params": {
         "zocalo_environment": "artemis",
         "beamline": "BL03I",
@@ -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",