Merge pull request #842 from DiamondLightSource/835_transmission_bug

Fix issue with transmission being set incorrectly

src/artemis/experiment_plans/full_grid_scan.py

@@ -92,7 +92,7 @@ def start_arming_then_do_grid(
     yield from bps.abs_set(eiger.do_arm, 1, group="ready_for_data_collection")
     yield from bps.abs_set(
         attenuator,
-        parameters.artemis_params.ispyb_params.transmission,
+        parameters.artemis_params.ispyb_params.transmission_fraction,
         group="ready_for_data_collection",
     )
 

src/artemis/experiment_plans/tests/test_fast_grid_scan_plan.py

@@ -116,7 +116,10 @@ def standalone_read_hardware_for_ispyb(und, syn, slits, attn, fl):
     assert params.artemis_params.ispyb_params.synchrotron_mode == synchrotron_test_value
     assert params.artemis_params.ispyb_params.slit_gap_size_x == xgap_test_value
     assert params.artemis_params.ispyb_params.slit_gap_size_y == ygap_test_value
-    assert params.artemis_params.ispyb_params.transmission == transmission_test_value
+    assert (
+        params.artemis_params.ispyb_params.transmission_fraction
+        == transmission_test_value
+    )
     assert params.artemis_params.ispyb_params.flux == flux_test_value
 
 

src/artemis/experiment_plans/tests/test_full_grid_scan_plan.py

@@ -284,5 +284,5 @@ def test_when_start_arming_then_transmission_set(
 
     # Check transmission set
     attenuator.set.assert_called_once_with(
-        test_full_grid_scan_params.artemis_params.ispyb_params.transmission
+        test_full_grid_scan_params.artemis_params.ispyb_params.transmission_fraction
     )

src/artemis/external_interaction/callbacks/ispyb_callback_base.py

@@ -63,7 +63,7 @@ def event(self, doc: dict):
             self.params.artemis_params.ispyb_params.slit_gap_size_y = doc["data"][
                 "s4_slit_gaps_ygap"
             ]
-            self.params.artemis_params.ispyb_params.transmission = doc["data"][
+            self.params.artemis_params.ispyb_params.transmission_fraction = doc["data"][
                 "attenuator_actual_transmission"
             ]
 

src/artemis/external_interaction/ispyb/ispyb_dataclass.py

@@ -15,7 +15,7 @@
     "position": [0, 0, 0],
     "xtal_snapshots_omega_start": ["test_1_y", "test_2_y", "test_3_y"],
     "xtal_snapshots_omega_end": ["test_1_z", "test_2_z", "test_3_z"],
-    "transmission": 1.0,
+    "transmission_fraction": 1.0,
     "flux": 10.0,
     "wavelength": 0.01,
     "beam_size_x": 0.1,
@@ -55,7 +55,7 @@ def _parse_position(
             return position
         return np.array(position)
 
-    transmission: float
+    transmission_fraction: float
     wavelength: float
     beam_size_x: float
     beam_size_y: float
@@ -76,6 +76,14 @@ def _parse_position(
     xtal_snapshots_omega_start: Optional[List[str]] = None
     xtal_snapshots_omega_end: Optional[List[str]] = None
 
+    @validator("transmission_fraction")
+    def transmission_not_percentage(cls, transmission_fraction: float):
+        if transmission_fraction > 1:
+            raise ValueError(
+                "Transmission_fraction of >1 given. Did you give a percentage instead of a fraction?"
+            )
+        return transmission_fraction
+
 
 class RotationIspybParams(IspybParams):
     ...

src/artemis/external_interaction/ispyb/store_in_ispyb.py

@@ -204,7 +204,8 @@ def _store_data_collection_table(
         params["slitgap_horizontal"] = self.ispyb_params.slit_gap_size_x
         params["beamsize_at_samplex"] = self.ispyb_params.beam_size_x
         params["beamsize_at_sampley"] = self.ispyb_params.beam_size_y
-        params["transmission"] = self.ispyb_params.transmission
+        # Ispyb wants the transmission in a percentage, we use fractions
+        params["transmission"] = self.ispyb_params.transmission_fraction * 100
         params["comments"] = self._construct_comment()
         params["data_collection_number"] = self.run_number
         params["detector_distance"] = self.detector_params.detector_distance

src/artemis/external_interaction/nexus/nexus_utils.py

@@ -114,5 +114,5 @@ def create_beam_and_attenuator_parameters(
     """
     return (
         Beam(ispyb_params.wavelength, ispyb_params.flux),
-        Attenuator(ispyb_params.transmission),
+        Attenuator(ispyb_params.transmission_fraction),
     )

src/artemis/external_interaction/system_tests/test_write_rotation_nexus.py

@@ -38,7 +38,7 @@ def test_params():
     params.experiment_params.z = 0
     params.artemis_params.detector_params.exposure_time = 0.004
     params.artemis_params.detector_params.current_energy_ev = 12700
-    params.artemis_params.ispyb_params.transmission = 0.49118047952
+    params.artemis_params.ispyb_params.transmission_fraction = 0.49118047952
     params.artemis_params.ispyb_params.wavelength = 0.9762535433
     return params
 

src/artemis/external_interaction/unit_tests/conftest.py

@@ -26,7 +26,7 @@ def test_rotation_params():
     params.experiment_params.z = 0
     params.artemis_params.detector_params.exposure_time = 0.004
     params.artemis_params.detector_params.current_energy_ev = 12700
-    params.artemis_params.ispyb_params.transmission = 0.49118047952
+    params.artemis_params.ispyb_params.transmission_fraction = 0.49118047952
     params.artemis_params.ispyb_params.wavelength = 0.9762535433
     return params
 
@@ -36,7 +36,7 @@ def test_fgs_params(request):
     params = FGSInternalParameters(**default_raw_params())
     params.artemis_params.ispyb_params.wavelength = 1.0
     params.artemis_params.ispyb_params.flux = 9.0
-    params.artemis_params.ispyb_params.transmission = 0.5
+    params.artemis_params.ispyb_params.transmission_fraction = 0.5
     params.artemis_params.detector_params.use_roi_mode = True
     params.artemis_params.detector_params.num_triggers = request.param
     params.artemis_params.detector_params.directory = (

src/artemis/external_interaction/unit_tests/test_ispyb_dataclass.py

@@ -0,0 +1,37 @@
+from copy import deepcopy
+
+import numpy as np
+import pytest
+
+from artemis.external_interaction.ispyb.ispyb_dataclass import (
+    GRIDSCAN_ISPYB_PARAM_DEFAULTS,
+    IspybParams,
+)
+
+
+def test_given_position_as_list_when_ispyb_params_created_then_converted_to_numpy_array():
+    params = deepcopy(GRIDSCAN_ISPYB_PARAM_DEFAULTS)
+    params["position"] = [1, 2, 3]
+
+    ispyb_params = IspybParams(**params)
+
+    assert isinstance(ispyb_params.position, np.ndarray)
+    assert np.array_equal(ispyb_params.position, [1, 2, 3])
+
+
+def test_given_ispyb_params_when_converted_to_dict_then_position_is_a_list():
+    params = deepcopy(GRIDSCAN_ISPYB_PARAM_DEFAULTS)
+    params["position"] = [1, 2, 3]
+
+    ispyb_params_dict = IspybParams(**params).dict()
+
+    assert isinstance(ispyb_params_dict["position"], list)
+    assert ispyb_params_dict["position"] == [1, 2, 3]
+
+
+def test_given_transmission_greater_than_1_when_ispyb_params_created_then_throws_exception():
+    params = deepcopy(GRIDSCAN_ISPYB_PARAM_DEFAULTS)
+    params["transmission_fraction"] = 20.5
+
+    with pytest.raises(ValueError):
+        IspybParams(**params)

src/artemis/external_interaction/unit_tests/test_store_in_ispyb.py

@@ -60,7 +60,7 @@
     "comments": None,
     "slitgapvertical": None,
     "slitgaphorizontal": None,
-    "transmission": None,
+    "transmission_fraction": None,
     "synchrotronmode": None,
     "xtalsnapshot1": None,
     "xtalsnapshot2": None,

src/artemis/parameters/schemas/full_external_parameters_schema.json

@@ -3,7 +3,7 @@
     "type": "object",
     "properties": {
         "params_version": {
-            "const": "2.0.0"
+            "const": "2.1.0"
         },
         "artemis_params": {
             "type": "object",

src/artemis/parameters/schemas/ispyb_parameters_schema.json

@@ -45,7 +45,7 @@
                 "type": "string"
             }
         },
-        "transmission": {
+        "transmission_fraction": {
             "type": "number"
         },
         "flux": {
@@ -84,7 +84,7 @@
         "microns_per_pixel_x",
         "microns_per_pixel_y",
         "position",
-        "transmission",
+        "transmission_fraction",
         "flux",
         "wavelength",
         "beam_size_x",

src/artemis/parameters/tests/test_data/artemis_parameters.json

@@ -36,7 +36,7 @@
             20.0,
             30.0
         ],
-        "transmission": 1.0,
+        "transmission_fraction": 1.0,
         "flux": 10.0,
         "wavelength": 0.01,
         "beam_size_x": 1.0,

src/artemis/parameters/tests/test_data/bad_test_parameters_wrong_version.json

@@ -47,7 +47,7 @@
                 "test_2",
                 "test_3"
             ],
-            "transmission": 1.0,
+            "transmission_fraction": 1.0,
             "flux": 10.0,
             "wavelength": 0.01,
             "beam_size_x": 1.0,

src/artemis/parameters/tests/test_data/good_test_grid_with_edge_detect_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.0.0",
+    "params_version": "2.1.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -23,7 +23,7 @@
                 20.0,
                 30.0
             ],
-            "transmission": 1.0,
+            "transmission_fraction": 1.0,
             "flux": 10.0,
             "wavelength": 0.01,
             "beam_size_x": 1.0,

src/artemis/parameters/tests/test_data/good_test_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.0.0",
+    "params_version": "2.1.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -43,7 +43,7 @@
                 "test_2",
                 "test_3"
             ],
-            "transmission": 1.0,
+            "transmission_fraction": 1.0,
             "flux": 10.0,
             "wavelength": 0.01,
             "beam_size_x": 1.0,

src/artemis/parameters/tests/test_data/good_test_rotation_scan_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.0.0",
+    "params_version": "2.1.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -43,7 +43,7 @@
                 "test_2",
                 "test_3"
             ],
-            "transmission": 1.0,
+            "transmission_fraction": 1.0,
             "flux": 10.0,
             "wavelength": 0.01,
             "beam_size_x": 1.0,

test_parameter_defaults.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.0.0",
+    "params_version": "2.1.0",
     "artemis_params": {
         "zocalo_environment": "dev_artemis",
         "beamline": "BL03S",
@@ -37,7 +37,7 @@
                 "test_2_z",
                 "test_3_z"
             ],
-            "transmission": 1.0,
+            "transmission_fraction": 1.0,
             "flux": 10.0,
             "wavelength": 0.01,
             "beam_size_x": 0.1,

test_parameters.json

@@ -1,5 +1,5 @@
 {
-    "params_version": "2.0.0",
+    "params_version": "2.1.0",
     "artemis_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -43,7 +43,7 @@
                 "test_2",
                 "test_3"
             ],
-            "transmission": 1.0,
+            "transmission_fraction": 1.0,
             "flux": 10.0,
             "wavelength": 0.01,
             "beam_size_x": 1.0,