Merge branch 'main' into 1033_clarify_desired_transmission

DiamondLightSource · Apr 3, 2024 · 5458fd5 · 5458fd5
2 parents 9602e39 + cfc7796
commit 5458fd5
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Showing 29 changed files with 88 additions and 200 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -12,7 +12,6 @@ markers = [
 addopts = "--cov=src/hyperion --cov-report term --cov-report xml:cov.xml"
 testpaths = "tests"
 
-
 [tool.ruff]
 src = ["src", "tests"]
 line-length = 88

diff --git a/src/hyperion/device_setup_plans/setup_oav.py b/src/hyperion/device_setup_plans/setup_oav.py
@@ -4,61 +4,24 @@
 import bluesky.plan_stubs as bps
 import numpy as np
 from bluesky.utils import Msg
-from dodal.devices.areadetector.plugins.MXSC import MXSC, PinTipDetect
 from dodal.devices.oav.oav_calculations import camera_coordinates_to_xyz
 from dodal.devices.oav.oav_detector import OAV, OAVConfigParams
 from dodal.devices.oav.oav_errors import OAVError_ZoomLevelNotFound
 from dodal.devices.oav.oav_parameters import OAVParameters
 from dodal.devices.oav.pin_image_recognition import PinTipDetection
-from dodal.devices.oav.utils import ColorMode, EdgeOutputArrayImageType
+from dodal.devices.oav.utils import ColorMode
 from dodal.devices.smargon import Smargon
 
 from hyperion.exceptions import WarningException
-from hyperion.log import LOGGER
 
 Pixel = Tuple[int, int]
 oav_group = "oav_setup"
 # Helper function to make sure we set the waiting groups correctly
 set_using_group = partial(bps.abs_set, group=oav_group)
 
 
-def start_mxsc(oav: OAV, min_callback_time, filename):
-    """
-    Sets PVs relevant to edge detection plugin.
-
-    Args:
-        min_callback_time: the value to set the minimum callback time to
-        filename: filename of the python script to detect edge waveforms from camera stream.
-    Returns: None
-    """
-    # Turns the area detector plugin on
-    yield from set_using_group(oav.mxsc.enable_callbacks, 1)
-
-    # Set the minimum time between updates of the plugin
-    yield from set_using_group(oav.mxsc.min_callback_time, min_callback_time)
-
-    # Stop the plugin from blocking the IOC and hogging all the CPU
-    yield from set_using_group(oav.mxsc.blocking_callbacks, 0)
-
-    # Set the python file to use for calculating the edge waveforms
-    current_filename = yield from bps.rd(oav.mxsc.filename)
-    if current_filename != filename:
-        LOGGER.info(
-            f"Current OAV MXSC plugin python file is {current_filename}, setting to {filename}"
-        )
-        yield from set_using_group(oav.mxsc.filename, filename)
-        yield from set_using_group(oav.mxsc.read_file, 1)
-
-    # Image annotations
-    yield from set_using_group(oav.mxsc.draw_tip, True)
-    yield from set_using_group(oav.mxsc.draw_edges, True)
-
-    # Use the original image type for the edge output array
-    yield from set_using_group(oav.mxsc.output_array, EdgeOutputArrayImageType.ORIGINAL)
-
-
 def setup_pin_tip_detection_params(
-    pin_tip_detect_device: MXSC | PinTipDetection, parameters: OAVParameters
+    pin_tip_detect_device: PinTipDetection, parameters: OAVParameters
 ):
     # select which blur to apply to image
     yield from set_using_group(
@@ -102,7 +65,7 @@ def setup_pin_tip_detection_params(
 def pre_centring_setup_oav(
     oav: OAV,
     parameters: OAVParameters,
-    pin_tip_detection_device: PinTipDetection | MXSC,
+    pin_tip_detection_device: PinTipDetection,
 ):
     """
     Setup OAV PVs with required values.
@@ -114,12 +77,6 @@ def pre_centring_setup_oav(
 
     yield from setup_pin_tip_detection_params(pin_tip_detection_device, parameters)
 
-    yield from start_mxsc(
-        oav,
-        parameters.min_callback_time,
-        parameters.detection_script_filename,
-    )
-
     zoom_level_str = f"{float(parameters.zoom)}x"
     if zoom_level_str not in oav.zoom_controller.allowed_zoom_levels:
         raise OAVError_ZoomLevelNotFound(
@@ -132,10 +89,6 @@ def pre_centring_setup_oav(
         wait=True,
     )
 
-    # Connect MXSC output to MJPG input for debugging
-    if isinstance(pin_tip_detection_device, MXSC):
-        yield from set_using_group(oav.snapshot.input_plugin, "OAV.MXSC")
-
     yield from bps.wait(oav_group)
 
     """
@@ -178,7 +131,7 @@ def get_move_required_so_that_beam_is_at_pixel(
 
 
 def wait_for_tip_to_be_found(
-    ophyd_pin_tip_detection: PinTipDetection | PinTipDetect,
+    ophyd_pin_tip_detection: PinTipDetection,
 ) -> Generator[Msg, None, Pixel]:
     yield from bps.trigger(ophyd_pin_tip_detection, wait=True)
     found_tip = yield from bps.rd(ophyd_pin_tip_detection.triggered_tip)

diff --git a/src/hyperion/experiment_plans/pin_centre_then_xray_centre_plan.py b/src/hyperion/experiment_plans/pin_centre_then_xray_centre_plan.py
@@ -66,7 +66,6 @@ def pin_centre_then_xray_centre_plan(
         pin_tip_centring_composite,
         parameters.experiment_params.tip_offset_microns,
         oav_config_file,
-        parameters.experiment_params.use_ophyd_pin_tip_detect,
     )
 
     grid_detect_params = create_parameters_for_grid_detection(parameters)

diff --git a/src/hyperion/experiment_plans/pin_tip_centring_plan.py b/src/hyperion/experiment_plans/pin_tip_centring_plan.py
@@ -5,7 +5,6 @@
 import numpy as np
 from blueapi.core import BlueskyContext
 from bluesky.utils import Msg
-from dodal.devices.areadetector.plugins.MXSC import PinTipDetect
 from dodal.devices.backlight import Backlight
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.oav_parameters import OAV_CONFIG_JSON, OAVParameters
@@ -41,7 +40,7 @@ def create_devices(context: BlueskyContext) -> PinTipCentringComposite:
 
 
 def trigger_and_return_pin_tip(
-    pin_tip: PinTipDetect | PinTipDetection,
+    pin_tip: PinTipDetection,
 ) -> Generator[Msg, None, Pixel]:
     yield from bps.trigger(pin_tip, wait=True)
     tip_x_y_px = yield from bps.rd(pin_tip.triggered_tip)
@@ -50,7 +49,7 @@ def trigger_and_return_pin_tip(
 
 
 def move_pin_into_view(
-    pin_tip_device: PinTipDetect | PinTipDetection,
+    pin_tip_device: PinTipDetection,
     smargon: Smargon,
     step_size_mm: float = DEFAULT_STEP_SIZE,
     max_steps: int = 2,
@@ -60,7 +59,7 @@ def move_pin_into_view(
     would take it past its limit, it moves to the limit instead.
 
     Args:
-        pin_tip_device (PinTipDetect | PinTipDetection): The device being used to detect the pin
+        pin_tip_device (PinTipDetection): The device being used to detect the pin
         smargon (Smargon): The gonio to move the tip
         step_size (float, optional): Distance to move the gonio (in mm) for each
                                     step of the search. Defaults to 0.5.
@@ -134,7 +133,6 @@ def pin_tip_centre_plan(
     composite: PinTipCentringComposite,
     tip_offset_microns: float,
     oav_config_file: str = OAV_CONFIG_JSON,
-    use_ophyd_pin_tip_detect: bool = False,
 ):
     """Finds the tip of the pin and moves to roughly the centre based on this tip. Does
     this at both the current omega angle and +90 deg from this angle so as to get a
@@ -143,19 +141,13 @@ def pin_tip_centre_plan(
     Args:
         tip_offset_microns (float): The x offset from the tip where the centre is assumed
                                     to be.
-        use_ophyd_pin_tip_detect (bool): If true use the ophyd device to find the tip,
-                                    rather than the AD plugin.
     """
     oav: OAV = composite.oav
     smargon: Smargon = composite.smargon
     oav_params = OAVParameters("pinTipCentring", oav_config_file)
 
-    if use_ophyd_pin_tip_detect:
-        pin_tip_setup = composite.pin_tip_detection
-        pin_tip_detect = composite.pin_tip_detection
-    else:
-        pin_tip_setup = oav.mxsc
-        pin_tip_detect = oav.mxsc.pin_tip
+    pin_tip_setup = composite.pin_tip_detection
+    pin_tip_detect = composite.pin_tip_detection
 
     assert oav.parameters.micronsPerXPixel is not None
     tip_offset_px = int(tip_offset_microns / oav.parameters.micronsPerXPixel)
@@ -174,8 +166,6 @@ def offset_and_move(tip: Pixel):
     # See #673 for improvements
     yield from bps.sleep(0.3)
 
-    # Set up the old pin tip centring as we will need it for grid detection. Remove once #1068 is done
-    yield from pre_centring_setup_oav(oav, oav_params, oav.mxsc)
     yield from pre_centring_setup_oav(oav, oav_params, pin_tip_setup)
 
     tip = yield from move_pin_into_view(pin_tip_detect, smargon)

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
@@ -40,10 +40,6 @@ class PinCentreThenXrayCentreParams(AbstractExperimentWithBeamParams):
     # Whether to set the stub offsets after centering
     set_stub_offsets: bool = False
 
-    # Whether to use the ophyd device for tip centring rather than the area detector
-    # plugin
-    use_ophyd_pin_tip_detect: bool = False
-
     # Distance for the smargon to accelerate into the grid and decelerate out of the grid when using the panda
     run_up_distance_mm: float = 0.15
 

diff --git a/src/hyperion/parameters/plan_specific/robot_load_then_center_params.py b/src/hyperion/parameters/plan_specific/robot_load_then_center_params.py
@@ -54,10 +54,6 @@ class RobotLoadThenCentreParams(AbstractExperimentWithBeamParams):
     # Use constant motion panda scans instead of fast grid scans
     use_panda: bool = False
 
-    # Whether to use the ophyd device for tip centring rather than the area detector
-    # plugin
-    use_ophyd_pin_tip_detect: bool = False
-
     def get_num_images(self):
         return 0
 

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
@@ -14,9 +14,6 @@
         "omega_start": {
             "type": "number"
         },
-        "use_ophyd_pin_tip_detect": {
-            "type": "boolean"
-        },
         "requested_energy_kev": {
             "type": [
                 "number",

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": "5.0.0"
+            "const": "4.0.5"
         },
         "hyperion_params": {
             "type": "object",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -290,6 +290,11 @@ def flux():
     return i03.flux(fake_with_ophyd_sim=True)
 
 
+@pytest.fixture
+def pin_tip():
+    return i03.pin_tip_detection(fake_with_ophyd_sim=True)
+
+
 @pytest.fixture
 def ophyd_pin_tip_detection():
     RunEngine()  # A RE is needed to start the bluesky loop

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": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

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": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

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": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",
@@ -43,7 +43,6 @@
         "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,
         "transmission_fraction": 1.0
     }
 }
diff --git a/tests/test_data/parameter_json_files/good_test_robot_load_params.json b/tests/test_data/parameter_json_files/good_test_robot_load_params.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "zocalo_environment": "artemis",
         "beamline": "BL03I",
@@ -37,7 +37,6 @@
         "exposure_time": 0.004,
         "detector_distance": 255,
         "snapshot_dir": "/tmp",
-        "use_ophyd_pin_tip_detect": true,
         "requested_energy_kev": 11.1,
         "sample_puck": 40,
         "sample_pin": 3

diff --git a/tests/test_data/parameter_json_files/good_test_robot_load_params_no_energy.json b/tests/test_data/parameter_json_files/good_test_robot_load_params_no_energy.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "zocalo_environment": "artemis",
         "beamline": "BL03I",

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": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

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": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

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": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

diff --git a/tests/test_data/parameter_json_files/live_test_rotation_params.json b/tests/test_data/parameter_json_files/live_test_rotation_params.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03I",
         "insertion_prefix": "SR03I",

diff --git a/tests/test_data/parameter_json_files/live_test_rotation_params_move_xyz.json b/tests/test_data/parameter_json_files/live_test_rotation_params_move_xyz.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03I",
         "insertion_prefix": "SR03I",

diff --git a/tests/test_data/parameter_json_files/panda_test_parameters.json b/tests/test_data/parameter_json_files/panda_test_parameters.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03I",
         "insertion_prefix": "SR03I",

diff --git a/tests/test_data/parameter_json_files/system_test_parameter_defaults.json b/tests/test_data/parameter_json_files/system_test_parameter_defaults.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "zocalo_environment": "dev_artemis",
         "beamline": "BL03S",

diff --git a/tests/test_data/parameter_json_files/test_internal_parameter_defaults.json b/tests/test_data/parameter_json_files/test_internal_parameter_defaults.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "zocalo_environment": "dev_artemis",
         "beamline": "BL03S",

diff --git a/tests/test_data/parameter_json_files/test_parameter_defaults.json b/tests/test_data/parameter_json_files/test_parameter_defaults.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "zocalo_environment": "dev_artemis",
         "beamline": "BL03S",

diff --git a/tests/test_data/parameter_json_files/test_parameter_defaults_2d.json b/tests/test_data/parameter_json_files/test_parameter_defaults_2d.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "zocalo_environment": "dev_artemis",
         "beamline": "BL03S",

diff --git a/tests/test_data/parameter_json_files/test_parameters.json b/tests/test_data/parameter_json_files/test_parameters.json
@@ -1,5 +1,5 @@
 {
-    "params_version": "5.0.0",
+    "params_version": "4.0.5",
     "hyperion_params": {
         "beamline": "BL03S",
         "insertion_prefix": "SR03S",

diff --git a/tests/unit_tests/device_setup_plans/test_setup_oav.py b/tests/unit_tests/device_setup_plans/test_setup_oav.py
@@ -92,7 +92,6 @@ def test_when_set_up_oav_with_different_zoom_levels_then_flat_field_applied_corr
 
     RE = RunEngine()
     RE(pre_centring_setup_oav(oav, mock_parameters, ophyd_pin_tip_detection))
-    assert oav.mxsc.input_plugin.get() == expected_plugin
     assert oav.snapshot.input_plugin.get() == expected_plugin