dls-dodal 1.36.3__py3-none-any.whl → 1.37.0__py3-none-any.whl

dodal/devices/i10/rasor/rasor_motors.py

@@ -0,0 +1,62 @@
+from ophyd_async.core import StandardReadable
+from ophyd_async.epics.motor import Motor
+
+
+class PinHole(StandardReadable):
+    "Two motors stage for rasor pinhole"
+
+    def __init__(
+        self,
+        prefix: str,
+        name: str = "",
+    ):
+        with self.add_children_as_readables():
+            self.x = Motor(prefix + "X")
+            self.y = Motor(prefix + "Y")
+        super().__init__(name=name)
+
+
+class Diffractometer(StandardReadable):
+    def __init__(
+        self,
+        prefix: str,
+        name: str = "",
+    ):
+        with self.add_children_as_readables():
+            self.tth = Motor(prefix + "TWOTHETA")
+            self.th = Motor(prefix + "THETA")
+            self.chi = Motor(prefix + "CHI")
+            self.chamber_x = Motor(prefix + "X")
+            self.alpha = Motor(prefix + "ALPHA")
+        super().__init__(name=name)
+
+
+class DetSlits(StandardReadable):
+    "Detector slits"
+
+    def __init__(
+        self,
+        prefix: str,
+        name: str = "",
+    ):
+        with self.add_children_as_readables():
+            self.upstream = Motor(prefix + "1:TRANS")
+            self.downstream = Motor(prefix + "2:TRANS")
+        super().__init__(name=name)
+
+
+class PaStage(StandardReadable):
+    "Rasor detector stage"
+
+    def __init__(
+        self,
+        prefix: str,
+        name: str = "",
+    ):
+        with self.add_children_as_readables():
+            self.ttp = Motor(prefix + "TWOTHETA")
+            self.thp = Motor(prefix + "THETA")
+            self.py = Motor(prefix + "Y")
+            self.pz = Motor(prefix + "Z")
+            self.eta = Motor(prefix + "ETA")
+        super().__init__(name=name)

dodal/devices/i10/rasor/rasor_scaler_cards.py

@@ -0,0 +1,12 @@
+from ophyd_async.core import Device
+
+from dodal.devices.current_amplifiers import StruckScaler
+
+
+class RasorScalerCard1(Device):
+    def __init__(self, prefix, name: str = "") -> None:
+        self.mon = StruckScaler(prefix=prefix, suffix=".16")
+        self.det = StruckScaler(prefix=prefix, suffix=".17")
+        self.fluo = StruckScaler(prefix=prefix, suffix=".18")
+        self.drain = StruckScaler(prefix=prefix, suffix=".19")
+        super().__init__(name)

dodal/devices/p99/sample_stage.py

@@ -1,5 +1,5 @@
-from ophyd_async.core import StandardReadable, SubsetEnum
-from ophyd_async.epics.core import epics_signal_rw, epics_signal_rw_rbv
+from ophyd_async.core import StandardReadable
+from ophyd_async.epics.core import epics_signal_rw_rbv
 
 
 class SampleAngleStage(StandardReadable):
@@ -9,29 +9,3 @@ class SampleAngleStage(StandardReadable):
             self.roll = epics_signal_rw_rbv(float, prefix + "WRITEROLL", ":RBV")
             self.pitch = epics_signal_rw_rbv(float, prefix + "WRITEPITCH", ":RBV")
         super().__init__(name=name)
-
-
-class p99StageSelections(SubsetEnum):
-    EMPTY = "Empty"
-    MN5UM = "Mn 5um"
-    FE = "Fe (empty)"
-    CO5UM = "Co 5um"
-    NI5UM = "Ni 5um"
-    CU5UM = "Cu 5um"
-    ZN5UM = "Zn 5um"
-    ZR = "Zr (empty)"
-    MO = "Mo (empty)"
-    RH = "Rh (empty)"
-    PD = "Pd (empty)"
-    AG = "Ag (empty)"
-    CD25UM = "Cd 25um"
-    W = "W (empty)"
-    PT = "Pt (empty)"
-    USER = "User"
-
-
-class FilterMotor(StandardReadable):
-    def __init__(self, prefix: str, name: str = ""):
-        with self.add_children_as_readables():
-            self.user_setpoint = epics_signal_rw(p99StageSelections, prefix)
-        super().__init__(name=name)

dodal/devices/robot.py

@@ -70,8 +70,8 @@ class BartRobot(StandardReadable, Movable):
         self.program_running = epics_signal_r(bool, prefix + "PROGRAM_RUNNING")
         self.program_name = epics_signal_r(str, prefix + "PROGRAM_NAME")
         self.error_str = epics_signal_r(str, prefix + "PRG_ERR_MSG")
-        # Change error_code to int type when https://github.com/bluesky/ophyd-async/issues/280 released
-        self.error_code = epics_signal_r(float, prefix + "PRG_ERR_CODE")
+        self.error_code = epics_signal_r(int, prefix + "PRG_ERR_CODE")
+        self.reset = epics_signal_x(prefix + "RESET.PROC")
         super().__init__(name=name)
 
     async def pin_mounted_or_no_pin_found(self):

dodal/devices/undulator_dcm.py

@@ -1,7 +1,7 @@
 import asyncio
 
 from bluesky.protocols import Movable
-from ophyd_async.core import AsyncStatus, StandardReadable
+from ophyd_async.core import AsyncStatus, Reference, StandardReadable
 
 from dodal.common.beamlines.beamline_parameters import get_beamline_parameters
 
@@ -33,12 +33,8 @@ class UndulatorDCM(StandardReadable, Movable):
         prefix: str = "",
         name: str = "",
     ):
-        super().__init__(name)
-
-        # Attributes are set after super call so they are not renamed to
-        # <name>-undulator, etc.
-        self.undulator = undulator
-        self.dcm = dcm
+        self.undulator_ref = Reference(undulator)
+        self.dcm_ref = Reference(dcm)
 
         # These attributes are just used by hyperion for lookup purposes
         self.pitch_energy_table_path = (
@@ -53,13 +49,15 @@ class UndulatorDCM(StandardReadable, Movable):
             daq_configuration_path + "/domain/beamlineParameters"
         )["DCM_Perp_Offset_FIXED"]
 
+        super().__init__(name)
+
     @AsyncStatus.wrap
     async def set(self, value: float):
-        await self.undulator.raise_if_not_enabled()
+        await self.undulator_ref().raise_if_not_enabled()
         await asyncio.gather(
-            self.dcm.energy_in_kev.set(value, timeout=ENERGY_TIMEOUT_S),
-            self.undulator.set(value),
+            self.dcm_ref().energy_in_kev.set(value, timeout=ENERGY_TIMEOUT_S),
+            self.undulator_ref().set(value),
         )
         # DCM Perp pitch
         LOGGER.info(f"Adjusting DCM offset to {self.dcm_fixed_offset_mm} mm")
-        await self.dcm.offset_in_mm.set(self.dcm_fixed_offset_mm)
+        await self.dcm_ref().offset_in_mm.set(self.dcm_fixed_offset_mm)

dodal/devices/zebra.py

@@ -81,6 +81,11 @@ class I24Axes:
 
 
 class RotationDirection(StrictEnum):
+    """
+    Defines for a swept angle whether the scan width (sweep) is to be added or subtracted from
+    the initial angle to obtain the final angle.
+    """
+
     POSITIVE = "Positive"
     NEGATIVE = "Negative"
 
@@ -281,7 +286,7 @@ class LogicGateConfiguration:
         for input, (source, invert) in enumerate(
             zip(self.sources, self.invert, strict=False)
         ):
-            input_strings.append(f"INP{input+1}={'!' if invert else ''}{source}")
+            input_strings.append(f"INP{input + 1}={'!' if invert else ''}{source}")
 
         return ", ".join(input_strings)
 

dodal/devices/zocalo/zocalo_interaction.py

@@ -55,7 +55,8 @@ class ZocaloTrigger:
     intended to be used in bluesky callback classes. To get results from zocalo back
     into a plan, use the ZocaloResults ophyd device.
 
-    see https://github.com/DiamondLightSource/dodal/wiki/How-to-Interact-with-Zocalo"""
+    see https://diamondlightsource.github.io/dodal/main/how-to/zocalo.html for
+    more information about zocalo."""
 
     def __init__(self, environment: str = ZOCALO_ENV):
         self.zocalo_environment: str = environment

dodal/devices/zocalo/zocalo_results.py

@@ -11,7 +11,7 @@ import workflows.recipe
 import workflows.transport
 from bluesky.protocols import Triggerable
 from bluesky.utils import Msg
-from deepdiff import DeepDiff
+from deepdiff.diff import DeepDiff
 from ophyd_async.core import (
     Array1D,
     AsyncStatus,
@@ -53,6 +53,26 @@ ZOCALO_STAGE_GROUP = "clear zocalo queue"
 
 
 class XrcResult(TypedDict):
+    """
+    Information about a diffracting centre.
+
+    NOTE: the coordinate systems of centre_of_mass and max_voxel/bounding_box are not
+        the same; centre_of_mass coordinates are continuous whereas max_voxel and bounding_box
+        coordinates are discrete.
+    Attributes:
+         centre_of_mass: The position of the centre of mass of the crystal, adjusted so that
+         grid box centres lie on integer grid coordinates, such that a 1x1x1 crystal detected in
+         a single grid box at 0, 0, 0, has c.o.m. of 0, 0, 0, not 0.5, 0.5, 0.5
+         max_voxel: Position of the voxel with the maximum count, in integer coordinates
+         max_count: max count achieved in a single voxel for the crystal
+         n_voxels: Number of voxels (aka grid boxes) in the diffracting centre
+         total_count: Total of above-threshold spot counts in the labelled voxels
+         bounding_box: The rectangular prism that bounds the crystal, expressed
+            as the volume of whole boxes as a half-open range i.e such that
+            p1 = (x1, y1, z1) <= p < p2 = (x2, y2, z2) and
+            p2 - p1 gives the dimensions in whole voxels.
+    """
+
     centre_of_mass: list[float]
     max_voxel: list[int]
     max_count: int
@@ -133,7 +153,7 @@ class ZocaloResults(StandardReadable, Triggerable):
         self.use_cpu_and_gpu = use_cpu_and_gpu
 
         self.centre_of_mass, self._com_setter = soft_signal_r_and_setter(
-            Array1D[np.uint64], name="centre_of_mass"
+            Array1D[np.float64], name="centre_of_mass"
         )
         self.bounding_box, self._bounding_box_setter = soft_signal_r_and_setter(
             Array1D[np.uint64], name="bounding_box"

dodal/log.py

@@ -152,7 +152,7 @@ def set_up_graylog_handler(logger: Logger, host: str, port: int):
 def set_up_INFO_file_handler(logger, path: Path, filename: str):
     """Set up a file handler for the logger, at INFO level, which will keep 30 days
     of logs, rotating once per day. Creates the directory if necessary."""
-    print(f"Logging to INFO file handler {path/filename}")
+    print(f"Logging to INFO file handler {path / filename}")
     path.mkdir(parents=True, exist_ok=True)
     file_handler = TimedRotatingFileHandler(
         filename=path / filename, when="MIDNIGHT", backupCount=INFO_LOG_DAYS
@@ -169,7 +169,7 @@ def set_up_DEBUG_memory_handler(
     log file when it sees a message of severity ERROR. Creates the directory if
     necessary"""
     debug_path = path / "debug"
-    print(f"Logging to DEBUG handler {debug_path/filename}")
+    print(f"Logging to DEBUG handler {debug_path / filename}")
     debug_path.mkdir(parents=True, exist_ok=True)
     file_handler = TimedRotatingFileHandler(
         filename=debug_path / filename, when="H", backupCount=DEBUG_LOG_FILES_TO_KEEP

dodal/plans/wrapped.py

@@ -49,9 +49,9 @@ def count(
     Wraps bluesky.plans.count(det, num, delay, md=metadata) exposing only serializable
     parameters and metadata."""
     if isinstance(delay, Sequence):
-        assert (
-            len(delay) == num - 1
-        ), f"Number of delays given must be {num - 1}: was given {len(delay)}"
+        assert len(delay) == num - 1, (
+            f"Number of delays given must be {num - 1}: was given {len(delay)}"
+        )
     metadata = metadata or {}
     metadata["shape"] = (num,)
     yield from bp.count(tuple(detectors), num, delay=delay, md=metadata)