dls-dodal 1.36.2__py3-none-any.whl → 1.37.0__py3-none-any.whl

dodal/devices/zebra.py

@@ -59,28 +59,33 @@ class TrigSource(StrictEnum):
 
 
 class EncEnum(StrictEnum):
-    Enc1 = "Enc1"
-    Enc2 = "Enc2"
-    Enc3 = "Enc3"
-    Enc4 = "Enc4"
-    Enc1_4Av = "Enc1-4Av"
+    ENC1 = "Enc1"
+    ENC2 = "Enc2"
+    ENC3 = "Enc3"
+    ENC4 = "Enc4"
+    ENC1_4AV = "Enc1-4Av"
 
 
 class I03Axes:
-    SMARGON_X1 = EncEnum.Enc1
-    SMARGON_Y = EncEnum.Enc2
-    SMARGON_Z = EncEnum.Enc3
-    OMEGA = EncEnum.Enc4
+    SMARGON_X1 = EncEnum.ENC1
+    SMARGON_Y = EncEnum.ENC2
+    SMARGON_Z = EncEnum.ENC3
+    OMEGA = EncEnum.ENC4
 
 
 class I24Axes:
-    VGON_Z = EncEnum.Enc1
-    OMEGA = EncEnum.Enc2
-    VGON_X = EncEnum.Enc3
-    VGON_YH = EncEnum.Enc4
+    VGON_Z = EncEnum.ENC1
+    OMEGA = EncEnum.ENC2
+    VGON_X = EncEnum.ENC3
+    VGON_YH = EncEnum.ENC4
 
 
 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)