Merge branch 'main' into 779_fix_fluo_optimise

run_artemis.sh

@@ -112,7 +112,7 @@ if [[ $START == 1 ]]; then
             ARTEMIS_LOG_DIR=/dls_sw/$BEAMLINE/logs/bluesky
         fi
     fi
-    echo "Logging to $ARTEMIS_LOG_DIR"
+    echo "$(date) Logging to $ARTEMIS_LOG_DIR"
     export ARTEMIS_LOG_DIR
     mkdir -p $ARTEMIS_LOG_DIR
     start_log_path=$ARTEMIS_LOG_DIR/start_log.txt
@@ -129,15 +129,16 @@ if [[ $START == 1 ]]; then
     for i in "${!args[@]}"
     do
         if [ "${args[$i]}" != false ]; then commands+="${arg_strings[$i]} "; fi;
-    done 
+    done
 
     python -m artemis `echo $commands;`>$start_log_path 2>&1 &
 
-    echo "Waiting for Artemis to boot"
+    echo "$(date) Waiting for Artemis to boot"
 
-    for i in {1..10}
+    for i in {1..30}
     do
         curl --head -X GET http://localhost:5005/status >/dev/null
+        echo "$(date)"
         ret_value=$?
         if [ $ret_value -ne 0 ]; then
             sleep 1
@@ -147,10 +148,10 @@ if [[ $START == 1 ]]; then
     done
 
     if [ $ret_value -ne 0 ]; then
-        echo "Artemis Failed to start!!!!"
+        echo "$(date) Artemis Failed to start!!!!"
         exit 1
     else
-        echo "Artemis started"
+        echo "$(date) Artemis started"
     fi
 fi
 

setup.cfg

@@ -36,7 +36,7 @@ install_requires =
     xarray
     doct
     databroker
-    dodal @ git+https://github.com/DiamondLightSource/python-dodal.git@c2cf54029018fa82b568fa067e2ef479d10cf634
+    dodal @ git+https://github.com/DiamondLightSource/python-dodal.git@2dbcb05d2ce6223880c24fca3c6b8a9b88b2ba03
     pydantic<2.0 # See https://github.com/DiamondLightSource/python-artemis/issues/774
 
 

src/artemis/device_setup_plans/setup_oav.py

@@ -76,13 +76,15 @@ def pre_centring_setup_oav(oav: OAV, parameters: OAVParameters):
         parameters.minimum_height,
     )
 
-    # Connect MXSC output to MJPG input
     yield from start_mxsc(
         oav,
         parameters.min_callback_time,
         parameters.detection_script_filename,
     )
 
+    # Connect MXSC output to MJPG input for debugging
+    yield from bps.abs_set(oav.snapshot.input_plugin, "OAV.MXSC")
+
     zoom_level_str = f"{float(parameters.zoom)}x"
     if zoom_level_str not in oav.zoom_controller.allowed_zoom_levels:
         raise OAVError_ZoomLevelNotFound(

src/artemis/experiment_plans/fast_grid_scan_plan.py

@@ -14,6 +14,7 @@
     Backlight,
     EigerDetector,
     FastGridScan,
+    Flux,
     S4SlitGaps,
     Smargon,
     Synchrotron,
@@ -54,6 +55,7 @@ class FGSComposite:
     backlight: Backlight
     eiger: EigerDetector
     fast_grid_scan: FastGridScan
+    flux: Flux
     s4_slit_gaps: S4SlitGaps
     sample_motors: Smargon
     synchrotron: Synchrotron
@@ -74,6 +76,7 @@ def __init__(
             wait_for_connection=False, fake_with_ophyd_sim=fake, params=detector_params
         )
         self.fast_grid_scan = i03.fast_grid_scan(fake_with_ophyd_sim=fake)
+        self.flux = i03.flux(fake_with_ophyd_sim=fake)
         self.s4_slit_gaps = i03.s4_slit_gaps(fake_with_ophyd_sim=fake)
         self.sample_motors = i03.smargon(fake_with_ophyd_sim=fake)
         self.undulator = i03.undulator(fake_with_ophyd_sim=fake)
@@ -128,6 +131,7 @@ def read_hardware_for_ispyb(
     undulator: Undulator,
     synchrotron: Synchrotron,
     s4_slit_gaps: S4SlitGaps,
+    flux: Flux,
 ):
     artemis.log.LOGGER.info(
         "Reading status of beamline parameters for ispyb deposition."
@@ -139,6 +143,7 @@ def read_hardware_for_ispyb(
     yield from bps.read(synchrotron.machine_status.synchrotron_mode)
     yield from bps.read(s4_slit_gaps.xgap)
     yield from bps.read(s4_slit_gaps.ygap)
+    yield from bps.read(flux.flux_reading)
     yield from bps.save()
 
 
@@ -208,6 +213,7 @@ def run_gridscan(
             fgs_composite.undulator,
             fgs_composite.synchrotron,
             fgs_composite.s4_slit_gaps,
+            fgs_composite.flux,
         )
 
     fgs_motors = fgs_composite.fast_grid_scan
@@ -218,24 +224,21 @@ def run_gridscan(
 
     @bpp.set_run_key_decorator("do_fgs")
     @bpp.run_decorator(md={"subplan_name": "do_fgs"})
+    @bpp.contingency_decorator(
+        except_plan=lambda e: (yield from bps.stop(fgs_composite.eiger)),
+        else_plan=lambda: (yield from bps.unstage(fgs_composite.eiger)),
+    )
     def do_fgs():
-        try:
-            yield from bps.wait()  # Wait for all moves to complete
-            yield from bps.kickoff(fgs_motors)
-            yield from bps.complete(fgs_motors, wait=True)
-        finally:
-            yield from bps.unstage(fgs_composite.eiger)
-
-    # Wait for arming to finish
-    artemis.log.LOGGER.info("Waiting for arming...")
-    yield from bps.wait("arming")
-    artemis.log.LOGGER.info("Arming finished")
+        yield from bps.wait()  # Wait for all moves to complete
+        yield from bps.kickoff(fgs_motors)
+        yield from bps.complete(fgs_motors, wait=True)
+
+    yield from bps.stage(fgs_composite.eiger)
 
     with TRACER.start_span("do_fgs"):
         yield from do_fgs()
 
-    with TRACER.start_span("move_to_z_0"):
-        yield from bps.abs_set(fgs_motors.z_steps, 0, wait=False)
+    yield from bps.abs_set(fgs_motors.z_steps, 0, wait=False)
 
 
 @bpp.set_run_key_decorator("run_gridscan_and_move")

src/artemis/experiment_plans/full_grid_scan.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
 
+import json
 from typing import TYPE_CHECKING, Callable
 
+import numpy as np
 from bluesky import plan_stubs as bps
 from bluesky import preprocessors as bpp
 from dodal.beamlines import i03
@@ -19,15 +21,15 @@
     create_devices as oav_create_devices,
 )
 from artemis.experiment_plans.oav_grid_detection_plan import grid_detection_plan
-from artemis.external_interaction.callbacks.fgs.fgs_callback_collection import (
-    FGSCallbackCollection,
-)
 from artemis.external_interaction.callbacks.oav_snapshot_callback import (
     OavSnapshotCallback,
 )
 from artemis.log import LOGGER
 from artemis.parameters.beamline_parameters import get_beamline_parameters
-from artemis.parameters.plan_specific.fgs_internal_params import GridScanParams
+from artemis.parameters.plan_specific.fgs_internal_params import (
+    FGSInternalParameters,
+    GridScanParams,
+)
 
 if TYPE_CHECKING:
     from artemis.parameters.plan_specific.grid_scan_with_edge_detect_params import (
@@ -65,6 +67,17 @@ def wait_for_det_to_finish_moving(detector: DetectorMotion, timeout=120):
     raise TimeoutError("Detector not finished moving")
 
 
+def create_parameters_for_fast_grid_scan(
+    grid_scan_with_edge_params: GridScanWithEdgeDetectInternalParameters,
+    grid_parameters: GridScanParams,
+) -> FGSInternalParameters:
+    params_json = json.loads(grid_scan_with_edge_params.json())
+    params_json["experiment_params"] = json.loads(grid_parameters.json())
+    fast_grid_scan_parameters = FGSInternalParameters(**params_json)
+    LOGGER.info(f"Parameters for FGS: {fast_grid_scan_parameters}")
+    return fast_grid_scan_parameters
+
+
 def start_arming_then_do_grid(
     parameters: GridScanWithEdgeDetectInternalParameters,
     backlight: Backlight,
@@ -76,15 +89,15 @@ def start_arming_then_do_grid(
     # Start stage with asynchronous arming here
     yield from bps.abs_set(eiger.do_arm, 1, group="arming")
 
-    yield from bpp.finalize_wrapper(
+    yield from bpp.contingency_wrapper(
         detect_grid_and_do_gridscan(
             parameters,
             backlight,
             aperture_scatterguard,
             detector_motion,
             oav_params,
         ),
-        bps.unstage(eiger),
+        except_plan=lambda e: (yield from bps.stop(eiger)),
     )
 
 
@@ -96,7 +109,7 @@ def detect_grid_and_do_gridscan(
     oav_params: OAVParameters,
 ):
     experiment_params: GridScanWithEdgeDetectParams = parameters.experiment_params
-    fgs_params = GridScanParams(dwell_time=experiment_params.exposure_time * 1000)
+    grid_params = GridScanParams(dwell_time=experiment_params.exposure_time * 1000)
 
     detector_params = parameters.artemis_params.detector_params
     snapshot_template = (
@@ -121,15 +134,15 @@ def run_grid_detection_plan(
 
     yield from run_grid_detection_plan(
         oav_params,
-        fgs_params,
+        grid_params,
         snapshot_template,
         experiment_params.snapshot_dir,
     )
 
     # Hack because GDA only passes 3 values to ispyb
-    out_upper_left = oav_callback.out_upper_left[0] + [
-        oav_callback.out_upper_left[1][1]
-    ]
+    out_upper_left = np.array(
+        oav_callback.out_upper_left[0] + [oav_callback.out_upper_left[1][1]]
+    )
 
     # Hack because the callback returns the list in inverted order
     parameters.artemis_params.ispyb_params.xtal_snapshots_omega_start = (
@@ -140,12 +153,9 @@ def run_grid_detection_plan(
     )
     parameters.artemis_params.ispyb_params.upper_left = out_upper_left
 
-    parameters.experiment_params = fgs_params
-
-    parameters.artemis_params.detector_params.num_triggers = fgs_params.get_num_images()
-
-    LOGGER.info(f"Parameters for FGS: {parameters}")
-    subscriptions = FGSCallbackCollection.from_params(parameters)
+    fast_grid_scan_parameters = create_parameters_for_fast_grid_scan(
+        parameters, grid_params
+    )
 
     yield from bps.abs_set(backlight.pos, Backlight.OUT)
     LOGGER.info(
@@ -156,7 +166,7 @@ def run_grid_detection_plan(
     )
     yield from wait_for_det_to_finish_moving(detector_motion)
 
-    yield from fgs_get_plan(parameters, subscriptions)
+    yield from fgs_get_plan(fast_grid_scan_parameters)
 
 
 def get_plan(

src/artemis/experiment_plans/oav_grid_detection_plan.py

@@ -8,10 +8,9 @@
 import numpy as np
 from bluesky.preprocessors import finalize_wrapper
 from dodal.beamlines import i03
-from dodal.devices.areadetector.plugins.MXSC import PinTipDetect
 from dodal.devices.fast_grid_scan import GridScanParams
 from dodal.devices.oav.oav_calculations import camera_coordinates_to_xyz
-from dodal.devices.oav.oav_detector import OAV
+from dodal.devices.oav.oav_detector import MXSC, OAV
 from dodal.devices.smargon import Smargon
 
 from artemis.device_setup_plans.setup_oav import pre_centring_setup_oav
@@ -49,10 +48,16 @@ def grid_detection_plan(
     )
 
 
-def wait_for_tip_to_be_found(pin_tip: PinTipDetect):
+def wait_for_tip_to_be_found(mxsc: MXSC):
+    pin_tip = mxsc.pin_tip
     yield from bps.trigger(pin_tip, wait=True)
     found_tip = yield from bps.rd(pin_tip)
     if found_tip == pin_tip.INVALID_POSITION:
+        top_edge = yield from bps.rd(mxsc.top)
+        bottom_edge = yield from bps.rd(mxsc.bottom)
+        LOGGER.info(
+            f"No tip found with top/bottom of {list(top_edge), list(bottom_edge)}"
+        )
         raise WarningException(
             f"No pin found after {pin_tip.validity_timeout.get()} seconds"
         )
@@ -104,7 +109,7 @@ def grid_detection_main_plan(
         # See #673 for improvements
         yield from bps.sleep(0.3)
 
-        tip_x_px, tip_y_px = yield from wait_for_tip_to_be_found(oav.mxsc.pin_tip)
+        tip_x_px, tip_y_px = yield from wait_for_tip_to_be_found(oav.mxsc)
 
         LOGGER.info(f"Tip is at x,y: {tip_x_px},{tip_y_px}")
 
@@ -208,5 +213,7 @@ def grid_detection_main_plan(
 
 
 def reset_oav():
+    """Changes the MJPG stream to look at the camera without the edge detection and turns off the edge detcetion plugin."""
     oav = i03.oav()
+    yield from bps.abs_set(oav.snapshot.input_plugin, "OAV.CAM")
     yield from bps.abs_set(oav.mxsc.enable_callbacks, 0)

src/artemis/experiment_plans/tests/conftest.py

@@ -4,6 +4,7 @@
 from bluesky.run_engine import RunEngine
 from dodal.beamlines import i03
 from dodal.devices.aperturescatterguard import AperturePositions
+from dodal.devices.smargon import Smargon
 
 from artemis.experiment_plans.fast_grid_scan_plan import FGSComposite
 from artemis.external_interaction.callbacks.fgs.fgs_callback_collection import (
@@ -44,7 +45,7 @@ def eiger():
 
 
 @pytest.fixture
-def smargon():
+def smargon() -> Smargon:
     smargon = i03.smargon(fake_with_ophyd_sim=True)
     smargon.x.user_setpoint._use_limits = False
     smargon.y.user_setpoint._use_limits = False
@@ -104,7 +105,7 @@ def test_full_grid_scan_params():
 
 
 @pytest.fixture
-def fake_fgs_composite(test_fgs_params: InternalParameters):
+def fake_fgs_composite(smargon: Smargon, test_fgs_params: InternalParameters):
     fake_composite = FGSComposite(
         aperture_positions=AperturePositions(
             LARGE=(1, 2, 3, 4, 5),
@@ -128,6 +129,8 @@ def fake_fgs_composite(test_fgs_params: InternalParameters):
     fake_composite.fast_grid_scan.scan_invalid.sim_put(False)
     fake_composite.fast_grid_scan.position_counter.sim_put(0)
 
+    fake_composite.sample_motors = smargon
+
     return fake_composite