mx-bluesky 1.5.4__py3-none-any.whl → 1.5.5__py3-none-any.whl

mx_bluesky/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '1.5.4'
-__version_tuple__ = version_tuple = (1, 5, 4)
+__version__ = version = '1.5.5'
+__version_tuple__ = version_tuple = (1, 5, 5)
 
 __commit_id__ = commit_id = None

mx_bluesky/beamlines/i04/__init__.py

@@ -1,10 +1,15 @@
 from mx_bluesky.beamlines.i04.experiment_plans.i04_grid_detect_then_xray_centre_plan import (
     i04_grid_detect_then_xray_centre,
 )
-from mx_bluesky.beamlines.i04.thawing_plan import thaw, thaw_and_stream_to_redis
+from mx_bluesky.beamlines.i04.thawing_plan import (
+    thaw,
+    thaw_and_murko_centre,
+    thaw_and_stream_to_redis,
+)
 
 __all__ = [
     "thaw",
     "thaw_and_stream_to_redis",
     "i04_grid_detect_then_xray_centre",
+    "thaw_and_murko_centre",
 ]

mx_bluesky/beamlines/i04/redis_to_murko_forwarder.py

@@ -7,6 +7,7 @@ from typing import TypedDict
 import numpy as np
 import zmq
 from dodal.devices.i04.constants import RedisConstants
+from dodal.devices.i04.murko_results import FullMurkoResults, MurkoResult
 from numpy.typing import NDArray
 from PIL import Image
 from redis import StrictRedis
@@ -15,9 +16,6 @@ from mx_bluesky.common.utils.log import LOGGER
 
 MURKO_ADDRESS = "tcp://i04-murko-prod.diamond.ac.uk:8008"
 
-MurkoResult = dict
-FullMurkoResults = dict[str, list[MurkoResult]]
-
 
 class MurkoRequest(TypedDict):
     """See https://github.com/MartinSavko/murko#usage for more information."""
@@ -96,6 +94,7 @@ class BatchMurkoForwarder:
             ],
             "prefix": uuids,
         }
+
         results = send_to_murko_and_get_results(request_arguments)
         results_with_uuids = _correlate_results_to_uuids(request_arguments, results)
         self._send_murko_results_to_redis(sample_id, results_with_uuids)

mx_bluesky/beamlines/i04/thawing_plan.py

@@ -2,10 +2,11 @@ from collections.abc import Callable
 
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
-from bluesky.preprocessors import run_decorator, subs_decorator
+from bluesky.preprocessors import run_decorator, stage_wrapper, subs_decorator
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
 from dodal.devices.i04.constants import RedisConstants
+from dodal.devices.i04.murko_results import MurkoResultsDevice
 from dodal.devices.oav.oav_detector import OAV
 from dodal.devices.oav.oav_to_redis_forwarder import OAVToRedisForwarder, Source
 from dodal.devices.robot import BartRobot
@@ -15,6 +16,26 @@ from dodal.devices.thawer import OnOff, Thawer
 from mx_bluesky.beamlines.i04.callbacks.murko_callback import MurkoCallback
 
 
+def thaw(
+    time_to_thaw: float,
+    rotation: float = 360,
+    thawer: Thawer = inject("thawer"),
+    smargon: Smargon = inject("smargon"),
+) -> MsgGenerator:
+    """Turns on the thawer and rotates the sample by {rotation} degrees to thaw it, then
+    rotates {rotation} degrees back and turns the thawer off. The speed of the goniometer
+    is set such that the process takes whole process will take {time_to_thaw} time.
+
+    Args:
+        time_to_thaw (float): Time to thaw for, in seconds.
+        rotation (float, optional): How much to rotate by whilst thawing, in degrees.
+                                    Defaults to 360.
+        ... devices: These are the specific ophyd-devices used for the plan, the
+                     defaults are always correct.
+    """
+    yield from _thaw(time_to_thaw, rotation, thawer, smargon)
+
+
 def thaw_and_stream_to_redis(
     time_to_thaw: float,
     rotation: float = 360,
@@ -24,19 +45,162 @@ def thaw_and_stream_to_redis(
     oav: OAV = inject("oav"),
     oav_to_redis_forwarder: OAVToRedisForwarder = inject("oav_to_redis_forwarder"),
 ) -> MsgGenerator:
-    zoom_percentage = yield from bps.rd(oav.zoom_controller.percentage)
-    sample_id = yield from bps.rd(robot.sample_id)
+    """Turns on the thawer and rotates the sample by {rotation} degrees to thaw it, then
+    rotates {rotation} degrees back and turns the thawer off. The speed of the goniometer
+    is set such that the process takes whole process will take {time_to_thaw} time.
 
-    sample_id = int(sample_id)
-    zoom_level_before_thawing = yield from bps.rd(oav.zoom_controller.level)
+    At the same time streams OAV images to redis for later processing (e.g. by murko).
+    On the first rotation the images from the large ROI are streamed, on the second the
+    smaller ROI is used.
 
-    yield from bps.mv(oav.zoom_controller.level, "1.0x")
+    Args:
+        time_to_thaw (float): Time to thaw for, in seconds.
+        rotation (float, optional): How much to rotate by whilst thawing, in degrees.
+                                    Defaults to 360.
+        ... devices: These are the specific ophyd-devices used for the plan, the
+                     defaults are always correct
+    """
 
     def switch_forwarder_to_ROI() -> MsgGenerator:
         yield from bps.complete(oav_to_redis_forwarder, wait=True)
         yield from bps.mv(oav_to_redis_forwarder.selected_source, Source.ROI.value)
         yield from bps.kickoff(oav_to_redis_forwarder, wait=True)
 
+    yield from _thaw_and_stream_to_redis(
+        time_to_thaw,
+        rotation,
+        robot,
+        thawer,
+        smargon,
+        oav,
+        oav_to_redis_forwarder,
+        switch_forwarder_to_ROI,
+    )
+
+
+def thaw_and_murko_centre(
+    time_to_thaw: float,
+    rotation: float = 360,
+    robot: BartRobot = inject("robot"),
+    thawer: Thawer = inject("thawer"),
+    smargon: Smargon = inject("smargon"),
+    oav: OAV = inject("oav"),
+    murko_results: MurkoResultsDevice = inject("murko_results"),
+    oav_to_redis_forwarder: OAVToRedisForwarder = inject("oav_to_redis_forwarder"),
+) -> MsgGenerator:
+    """Thaws the sample and centres it using murko by:
+        1. Turns on the thawer
+        2. Rotates the sample by {rotation} degrees, whilst this is happening images from
+        the large ROI of the OAV are being fed to murko
+        3. After the rotation has completed moves to the average centre returned by murko
+        from these images
+        4. Rotate {rotation} degrees back to the start, whilst this is happening images
+        from the small ROI of the OAV are being fed to murko
+        5. Turns off the thawer
+
+    The speed of the goniometer is set so that all of the above takes about {time_to_thaw}
+    seconds to complete.
+
+    Args:
+        time_to_thaw (float): Time to thaw for, in seconds.
+        rotation (float, optional): How much to rotate by whilst thawing, in degrees.
+                                    Defaults to 360.
+        ... devices: These are the specific ophyd-devices used for the plan, the
+                     defaults are always correct
+    """
+
+    def centre_then_switch_forwarder_to_ROI() -> MsgGenerator:
+        yield from bps.complete(oav_to_redis_forwarder, wait=True)
+
+        yield from bps.trigger(murko_results, group="get_results")
+
+        yield from bps.mv(oav_to_redis_forwarder.selected_source, Source.ROI.value)
+
+        yield from bps.wait("get_results")
+        x_predict = yield from bps.rd(murko_results.x_mm)
+        y_predict = yield from bps.rd(murko_results.y_mm)
+        z_predict = yield from bps.rd(murko_results.z_mm)
+
+        yield from bps.rel_set(smargon.x, x_predict)
+        yield from bps.rel_set(smargon.y, y_predict)
+        yield from bps.rel_set(smargon.z, z_predict)
+
+        yield from bps.kickoff(oav_to_redis_forwarder, wait=True)
+
+    yield from stage_wrapper(
+        _thaw_and_stream_to_redis(
+            time_to_thaw,
+            rotation,
+            robot,
+            thawer,
+            smargon,
+            oav,
+            oav_to_redis_forwarder,
+            centre_then_switch_forwarder_to_ROI,
+        ),
+        [murko_results],
+    )
+
+
+def _thaw(
+    time_to_thaw: float,
+    rotation: float,
+    thawer: Thawer,
+    smargon: Smargon,
+    plan_between_rotations: Callable[[], MsgGenerator] | None = None,
+) -> MsgGenerator:
+    """Turns on the thawer and rotates the sample by {rotation} degrees to thaw it, then
+    rotates {rotation} degrees back and turns the thawer off. The speed of the goniometer
+    is set such that the process takes whole process will take {time_to_thaw} time.
+
+    Args:
+        time_to_thaw (float): Time to thaw for, in seconds.
+        rotation (float): How much to rotate by whilst thawing, in degrees.
+        thawer (Thawer): The thawing device.
+        smargon (Smargon): The smargon used to rotate.
+        plan_between_rotations (MsgGenerator, optional): A plan to run between rotations
+                                    of the smargon. Defaults to no plan.
+    """
+    inital_velocity = yield from bps.rd(smargon.omega.velocity)
+    new_velocity = abs(rotation / time_to_thaw) * 2.0
+
+    def do_thaw():
+        yield from bps.abs_set(smargon.omega.velocity, new_velocity, wait=True)
+        yield from bps.abs_set(thawer.control, OnOff.ON, wait=True)
+        yield from bps.rel_set(smargon.omega, rotation, wait=True)
+        if plan_between_rotations:
+            yield from plan_between_rotations()
+        yield from bps.rel_set(smargon.omega, -rotation, wait=True)
+
+    def cleanup():
+        yield from bps.abs_set(smargon.omega.velocity, inital_velocity, wait=True)
+        yield from bps.abs_set(thawer.control, OnOff.OFF, wait=True)
+
+    # Always cleanup even if there is a failure
+    yield from bpp.contingency_wrapper(
+        do_thaw(),
+        final_plan=cleanup,
+    )
+
+
+def _thaw_and_stream_to_redis(
+    time_to_thaw: float,
+    rotation: float,
+    robot: BartRobot,
+    thawer: Thawer,
+    smargon: Smargon,
+    oav: OAV,
+    oav_to_redis_forwarder: OAVToRedisForwarder,
+    plan_between_rotations: Callable[[], MsgGenerator],
+) -> MsgGenerator:
+    zoom_percentage = yield from bps.rd(oav.zoom_controller.percentage)
+    sample_id = yield from bps.rd(robot.sample_id)
+
+    sample_id = int(sample_id)
+    zoom_level_before_thawing = yield from bps.rd(oav.zoom_controller.level)
+
+    yield from bps.mv(oav.zoom_controller.level, "1.0x")
+
     microns_per_pixel_x = yield from bps.rd(oav.microns_per_pixel_x)
     microns_per_pixel_y = yield from bps.rd(oav.microns_per_pixel_y)
     beam_centre_i = yield from bps.rd(oav.beam_centre_i)
@@ -59,7 +223,7 @@ def thaw_and_stream_to_redis(
             "sample_id": sample_id,
         }
     )
-    def _thaw_and_stream_to_redis():
+    def _main_plan():
         yield from bps.mv(
             oav_to_redis_forwarder.sample_id,
             sample_id,
@@ -71,7 +235,7 @@ def thaw_and_stream_to_redis(
         yield from bps.monitor(smargon.omega.user_readback, name="smargon")
         yield from bps.monitor(oav_to_redis_forwarder.uuid, name="oav")
         yield from _thaw(
-            time_to_thaw, rotation, thawer, smargon, switch_forwarder_to_ROI
+            time_to_thaw, rotation, thawer, smargon, plan_between_rotations
         )
         yield from bps.complete(oav_to_redis_forwarder)
 
@@ -79,56 +243,6 @@ def thaw_and_stream_to_redis(
         yield from bps.mv(oav.zoom_controller.level, zoom_level_before_thawing)
 
     yield from bpp.contingency_wrapper(
-        _thaw_and_stream_to_redis(),
-        final_plan=cleanup,
-    )
-
-
-def thaw(
-    time_to_thaw: float,
-    rotation: float = 360,
-    thawer: Thawer = inject("thawer"),
-    smargon: Smargon = inject("smargon"),
-) -> MsgGenerator:
-    yield from _thaw(time_to_thaw, rotation, thawer, smargon)
-
-
-def _thaw(
-    time_to_thaw: float,
-    rotation: float = 360,
-    thawer: Thawer = inject("thawer"),
-    smargon: Smargon = inject("smargon"),
-    plan_between_rotations: Callable[[], MsgGenerator] | None = None,
-) -> MsgGenerator:
-    """Rotates the sample and thaws it at the same time.
-
-    Args:
-        time_to_thaw (float): Time to thaw for, in seconds.
-        rotation (float, optional): How much to rotate by whilst thawing, in degrees.
-                                    Defaults to 360.
-        thawer (Thawer, optional): The thawing device. Defaults to inject("thawer").
-        smargon (Smargon, optional): The smargon used to rotate.
-                                     Defaults to inject("smargon")
-        plan_between_rotations (MsgGenerator, optional): A plan to run between rotations
-                                    of the smargon. Defaults to no plan.
-    """
-    inital_velocity = yield from bps.rd(smargon.omega.velocity)
-    new_velocity = abs(rotation / time_to_thaw) * 2.0
-
-    def do_thaw():
-        yield from bps.abs_set(smargon.omega.velocity, new_velocity, wait=True)
-        yield from bps.abs_set(thawer.control, OnOff.ON, wait=True)
-        yield from bps.rel_set(smargon.omega, rotation, wait=True)
-        if plan_between_rotations:
-            yield from plan_between_rotations()
-        yield from bps.rel_set(smargon.omega, -rotation, wait=True)
-
-    def cleanup():
-        yield from bps.abs_set(smargon.omega.velocity, inital_velocity, wait=True)
-        yield from bps.abs_set(thawer.control, OnOff.OFF, wait=True)
-
-    # Always cleanup even if there is a failure
-    yield from bpp.contingency_wrapper(
-        do_thaw(),
+        _main_plan(),
         final_plan=cleanup,
     )

mx_bluesky/beamlines/i24/serial/blueapi_config.yaml

@@ -14,4 +14,4 @@ api:
       - "*"
 stomp:
   enabled: true
-  url: http://i24-control.diamond.ac.uk:61613
+  url: tcp://i24-control.diamond.ac.uk:61613

mx_bluesky/beamlines/i24/serial/dcid.py

@@ -11,7 +11,6 @@ from bluesky.utils import MsgGenerator
 from dodal.devices.i24.beam_center import DetectorBeamCenter
 from dodal.devices.i24.dcm import DCM
 from dodal.devices.i24.focus_mirrors import FocusMirrorsMode
-from dodal.devices.i24.pilatus_metadata import PilatusMetadata
 
 from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import PumpProbeSetting
 from mx_bluesky.beamlines.i24.serial.log import SSX_LOGGER
@@ -21,7 +20,7 @@ from mx_bluesky.beamlines.i24.serial.parameters import (
     ExtruderParameters,
     FixedTargetParameters,
 )
-from mx_bluesky.beamlines.i24.serial.setup_beamline import Detector, Eiger, Pilatus
+from mx_bluesky.beamlines.i24.serial.setup_beamline import Detector, Eiger
 
 # Collection start/end script to kick off analysis
 COLLECTION_START_SCRIPT = "/dls_sw/i24/scripts/RunAtStartOfCollect-i24-ssx.sh"
@@ -67,9 +66,7 @@ def read_beam_info_from_hardware(
     wavelength = yield from bps.rd(dcm.wavelength_in_a)
     beamsize_x = yield from bps.rd(mirrors.beam_size_x)
     beamsize_y = yield from bps.rd(mirrors.beam_size_y)
-    pixel_size = (
-        Eiger().pixel_size_mm if detector_name == "eiger" else Pilatus().pixel_size_mm
-    )
+    pixel_size = Eiger().pixel_size_mm
     beam_center_x = yield from bps.rd(beam_center.beam_x)
     beam_center_y = yield from bps.rd(beam_center.beam_y)
     return BeamSettings(
@@ -115,8 +112,6 @@ class DCID:
         match expt_params.detector_name:
             case "eiger":
                 self.detector = Eiger()
-            case "pilatus":
-                self.detector = Pilatus()
 
         self.server = server or DEFAULT_ISPYB_SERVER
         self.emit_errors = emit_errors
@@ -161,9 +156,7 @@ class DCID:
             transmission = self.parameters.transmission * 100
             xbeam, ybeam = beam_settings.beam_center_in_mm
 
-            if isinstance(self.detector, Pilatus):
-                startImageNumber = 0
-            elif isinstance(self.detector, Eiger):
+            if isinstance(self.detector, Eiger):
                 startImageNumber = 1
             else:
                 raise ValueError("Unknown detector:", self.detector)
@@ -361,20 +354,6 @@ class DCID:
             SSX_LOGGER.warning("Error completing DCID: %s (%s)", e, resp_str)
 
 
-def get_pilatus_filename_template_from_device(
-    pilatus_metadata: PilatusMetadata,
-) -> MsgGenerator[str]:
-    """
-    Get the template file path by querying the detector PVs, mirror the construction \
-    that the PPU does.
-
-    Returns:
-        A template string, with the image numbers replaced with '#'
-    """
-    filename_template = yield from bps.rd(pilatus_metadata.filename_template)
-    return filename_template
-
-
 def get_resolution(detector: Detector, distance: float, wavelength: float) -> float:
     """ Calculate the inscribed resolution for detector.
 
@@ -382,7 +361,7 @@ def get_resolution(detector: Detector, distance: float, wavelength: float) -> fl
     position parameters yet.
 
     Args:
-        detector (Detector): Detector instance, Eiger() or Pilatus().
+        detector (Detector): Detector instance, Eiger().
         distance (float): Distance to detector, in mm.
         wavelength (float): Beam wavelength, in Å.
 

mx_bluesky/beamlines/i24/serial/extruder/EX-gui-edm/DetStage.edl

@@ -3,8 +3,8 @@ beginScreenProperties
 major 4
 minor 0
 release 1
-x 1316
-y 610
+x 2937
+y 184
 w 450
 h 180
 font "arial-medium-r-18.0"
@@ -78,20 +78,17 @@ fgColour index 14
 bgColour index 4
 topShadowColour index 1
 botShadowColour index 8
-controlPv "BL24I-EA-IOC-12:GP15"
+controlPv "BL24I-MO-IOC-13:GP15"
 font "arial-medium-r-18.0"
 numItems 2
 symbolTag {
   0 "Eiger"
-  1 "Pilatus"
 }
 symbol0 {
   0 "E9M"
-  1 "P6M"
 }
 PV0 {
   0 "eiger"
-  1 "pilatus"
 }
 endObjectProperties
 
@@ -113,7 +110,7 @@ font "arial-medium-r-18.0"
 buttonLabel "Move Stage"
 numCmds 1
 command {
-  0 "blueapi -c CONFIG_LOCATION controller run setup_detector_stage '\{\"expt_type\":\"Serial Jet\"\}'"
+  0 "blueapi -c CONFIG_LOCATION controller run -i $INSTRUMENT_SESSION setup_detector_stage '\{\"expt_type\":\"Serial Jet\"\}'"
 }
 endObjectProperties
 

mx_bluesky/beamlines/i24/serial/extruder/EX-gui-edm/DiamondExtruder-I24-py3v1.edl

@@ -370,7 +370,7 @@ font "arial-medium-r-24.0"
 buttonLabel "Start"
 numCmds 1
 command {
-  0 "blueapi -c CONFIG_LOCATION controller run run_extruder_plan"
+  0 "blueapi -c CONFIG_LOCATION controller run -i $INSTRUMENT_SESSION run_extruder_plan"
 }
 endObjectProperties
 
@@ -832,7 +832,7 @@ botShadowColor index 11
 font "arial-medium-r-18.0"
 numCmds 1
 command {
-  0 "blueapi -c CONFIG_LOCATION controller run initialise_extruder"
+  0 "blueapi -c CONFIG_LOCATION controller run -i $INSTRUMENT_SESSION initialise_extruder"
 }
 endObjectProperties
 
@@ -2179,7 +2179,7 @@ font "arial-medium-r-20.0"
 buttonLabel "Laser On"
 numCmds 1
 command {
-  0 "blueapi -c CONFIG_LOCATION controller run laser_check '\{\"mode\":\"laseron\"\}'"
+  0 "blueapi -c CONFIG_LOCATION controller run -i $INSTRUMENT_SESSION laser_check '\{\"mode\":\"laseron\"\}'"
 }
 endObjectProperties
 
@@ -2201,7 +2201,7 @@ font "arial-medium-r-20.0"
 buttonLabel "Laser Off"
 numCmds 1
 command {
-  0 "blueapi -c CONFIG_LOCATION controller run laser_check '\{\"mode\":\"laseroff\"\}'"
+  0 "blueapi -c CONFIG_LOCATION controller run -i $INSTRUMENT_SESSION laser_check '\{\"mode\":\"laseroff\"\}'"
 }
 endObjectProperties
 
@@ -2223,7 +2223,7 @@ font "arial-medium-r-18.0"
 buttonLabel "Enter hutch"
 numCmds 1
 command {
-  0 "blueapi -c CONFIG_LOCATION controller run enter_hutch"
+  0 "blueapi -c CONFIG_LOCATION controller run -i $INSTRUMENT_SESSION enter_hutch"
 }
 endObjectProperties