dls-dodal 1.29.3__py3-none-any.whl → 1.30.0__py3-none-any.whl

dodal/devices/zocalo/zocalo_interaction.py

@@ -1,5 +1,6 @@
 import dataclasses
 import getpass
+import os
 import socket
 from dataclasses import dataclass
 
@@ -37,6 +38,12 @@ class ZocaloStartInfo:
     message_index: int
 
 
+def _get_zocalo_headers() -> tuple[str, str]:
+    user = os.environ.get("ZOCALO_GO_USER", getpass.getuser())
+    hostname = os.environ.get("ZOCALO_GO_HOSTNAME", socket.gethostname())
+    return user, hostname
+
+
 class ZocaloTrigger:
     """This class just sends 'run_start' and 'run_end' messages to zocalo, it is
     intended to be used in bluesky callback classes. To get results from zocalo back
@@ -55,9 +62,10 @@ class ZocaloTrigger:
                 "recipes": ["mimas"],
                 "parameters": parameters,
             }
+            user, hostname = _get_zocalo_headers()
             header = {
-                "zocalo.go.user": getpass.getuser(),
-                "zocalo.go.host": socket.gethostname(),
+                "zocalo.go.user": user,
+                "zocalo.go.host": hostname,
             }
             transport.send("processing_recipe", message, headers=header)
         finally:

dodal/devices/zocalo/zocalo_results.py

@@ -1,8 +1,9 @@
 import asyncio
 from collections import OrderedDict
+from collections.abc import Generator, Sequence
 from enum import Enum
 from queue import Empty, Queue
-from typing import Any, Generator, Sequence, Tuple, TypedDict
+from typing import Any, TypedDict
 
 import bluesky.plan_stubs as bps
 import numpy as np
@@ -10,7 +11,7 @@ import workflows.recipe
 import workflows.transport
 from bluesky.protocols import Descriptor, Triggerable
 from numpy.typing import NDArray
-from ophyd_async.core import StandardReadable, soft_signal_r_and_setter
+from ophyd_async.core import HintedSignal, StandardReadable, soft_signal_r_and_setter
 from ophyd_async.core.async_status import AsyncStatus
 from workflows.transport.common_transport import CommonTransport
 
@@ -79,34 +80,41 @@ class ZocaloResults(StandardReadable, Triggerable):
         self._raw_results_received: Queue = Queue()
         self.transport: CommonTransport | None = None
 
-        self.results, _ = soft_signal_r_and_setter(list[XrcResult], name="results")
-        self.centres_of_mass, _ = soft_signal_r_and_setter(
+        self.results, self._results_setter = soft_signal_r_and_setter(
+            list[XrcResult], name="results"
+        )
+        self.centres_of_mass, self._com_setter = soft_signal_r_and_setter(
             NDArray[np.uint64], name="centres_of_mass"
         )
-        self.bbox_sizes, _ = soft_signal_r_and_setter(
+        self.bbox_sizes, self._bbox_setter = soft_signal_r_and_setter(
             NDArray[np.uint64], "bbox_sizes", self.name
         )
-        self.ispyb_dcid, _ = soft_signal_r_and_setter(int, name="ispyb_dcid")
-        self.ispyb_dcgid, _ = soft_signal_r_and_setter(int, name="ispyb_dcgid")
-        self.set_readable_signals(
-            read=[
+        self.ispyb_dcid, self._ispyb_dcid_setter = soft_signal_r_and_setter(
+            int, name="ispyb_dcid"
+        )
+        self.ispyb_dcgid, self._ispyb_dcgid_setter = soft_signal_r_and_setter(
+            int, name="ispyb_dcgid"
+        )
+        self.add_readables(
+            [
                 self.results,
                 self.centres_of_mass,
                 self.bbox_sizes,
                 self.ispyb_dcid,
                 self.ispyb_dcgid,
-            ]
+            ],
+            wrapper=HintedSignal,
         )
         super().__init__(name)
 
     async def _put_results(self, results: Sequence[XrcResult], ispyb_ids):
-        await self.results._backend.put(list(results))
+        self._results_setter(list(results))
         centres_of_mass = np.array([r["centre_of_mass"] for r in results])
         bbox_sizes = np.array([bbox_size(r) for r in results])
-        await self.centres_of_mass._backend.put(centres_of_mass)
-        await self.bbox_sizes._backend.put(bbox_sizes)
-        await self.ispyb_dcid._backend.put(ispyb_ids["dcid"])
-        await self.ispyb_dcgid._backend.put(ispyb_ids["dcgid"])
+        self._com_setter(centres_of_mass)
+        self._bbox_setter(bbox_sizes)
+        self._ispyb_dcid_setter(ispyb_ids["dcid"])
+        self._ispyb_dcgid_setter(ispyb_ids["dcgid"])
 
     def _clear_old_results(self):
         LOGGER.info("Clearing queue")
@@ -120,7 +128,12 @@ class ZocaloResults(StandardReadable, Triggerable):
         before triggering processing for the experiment"""
 
         LOGGER.info("Subscribing to results queue")
-        self._subscribe_to_results()
+        try:
+            self._subscribe_to_results()
+        except Exception as e:
+            print(f"GOT {e}")
+            raise
+
         await asyncio.sleep(CLEAR_QUEUE_WAIT_S)
         self._clear_old_results()
 
@@ -152,7 +165,7 @@ class ZocaloResults(StandardReadable, Triggerable):
             )
 
             raw_results = self._raw_results_received.get(timeout=self.timeout_s)
-            LOGGER.info(f"Zocalo: found {len(raw_results)} crystals.")
+            LOGGER.info(f"Zocalo: found {len(raw_results['results'])} crystals.")
             # Sort from strongest to weakest in case of multiple crystals
             await self._put_results(
                 sorted(
@@ -242,7 +255,7 @@ class ZocaloResults(StandardReadable, Triggerable):
 
 def get_processing_result(
     zocalo: ZocaloResults,
-) -> Generator[Any, Any, Tuple[np.ndarray, np.ndarray] | Tuple[None, None]]:
+) -> Generator[Any, Any, tuple[np.ndarray, np.ndarray] | tuple[None, None]]:
     """A minimal plan which will extract the top ranked xray centre and crystal bounding
     box size from the zocalo results. Returns (None, None) if no crystals were found."""
 

dodal/log.py

@@ -6,7 +6,7 @@ from logging import Logger, StreamHandler
 from logging.handlers import TimedRotatingFileHandler
 from os import environ
 from pathlib import Path
-from typing import Deque, Tuple, TypedDict
+from typing import TypedDict
 
 from bluesky.log import logger as bluesky_logger
 from graypy import GELFTCPHandler
@@ -37,11 +37,14 @@ class CircularMemoryHandler(logging.Handler):
     that always contains the last {capacity} number of messages, this is only flushed
     when a log of specific {flushLevel} comes in. On flush this buffer is then passed to
     the {target} handler.
+
+    The CircularMemoryHandler becomes the owner of the target handler which will be closed
+    on close of this handler.
     """
 
     def __init__(self, capacity, flushLevel=logging.ERROR, target=None):
         logging.Handler.__init__(self)
-        self.buffer: Deque[logging.LogRecord] = deque(maxlen=capacity)
+        self.buffer: deque[logging.LogRecord] = deque(maxlen=capacity)
         self.flushLevel = flushLevel
         self.target = target
 
@@ -66,6 +69,12 @@ class CircularMemoryHandler(logging.Handler):
         self.acquire()
         try:
             self.buffer.clear()
+            if self.target:
+                self.target.acquire()
+                try:
+                    self.target.close()
+                finally:
+                    self.target.release()
             self.target = None
             logging.Handler.close(self)
         finally:
@@ -121,7 +130,7 @@ 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 {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
@@ -137,8 +146,8 @@ def set_up_DEBUG_memory_handler(
     """Set up a Memory handler which holds 200k lines, and writes them to an hourly
     log file when it sees a message of severity ERROR. Creates the directory if
     necessary"""
-    print(f"Logging to {path/filename}")
     debug_path = path / "debug"
+    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
@@ -240,7 +249,7 @@ def get_logging_file_path() -> Path:
 
 def get_graylog_configuration(
     dev_mode: bool, graylog_port: int | None = None
-) -> Tuple[str, int]:
+) -> tuple[str, int]:
     """Get the host and port for the graylog handler.
 
     If running in dev mode, this switches to localhost. Otherwise it publishes to the

dodal/plans/data_session_metadata.py

@@ -37,6 +37,7 @@ def attach_data_session_metadata_wrapper(
     directory_info: DirectoryInfo = provider()
     # https://github.com/DiamondLightSource/dodal/issues/452
     # As part of 452, write each dataCollection into their own folder, then can use resource_dir directly
+    assert directory_info.prefix is not None
     data_session = directory_info.prefix.removesuffix("-")
     yield from bpp.inject_md_wrapper(plan, md={DATA_SESSION: data_session})
 

dodal/plans/motor_util_plans.py

@@ -0,0 +1,117 @@
+import uuid
+from collections.abc import Generator
+from typing import Any, TypeVar
+
+from bluesky import plan_stubs as bps
+from bluesky.preprocessors import finalize_wrapper, pchain
+from bluesky.utils import Msg, make_decorator
+from ophyd_async.core import Device
+from ophyd_async.epics.motion import Motor
+
+from dodal.common import MsgGenerator
+
+AnyDevice = TypeVar("AnyDevice", bound=Device)
+
+
+class MoveTooLarge(Exception):
+    def __init__(
+        self, axis: Device, maximum_move: float, position: float, *args: object
+    ) -> None:
+        self.axis = axis
+        self.maximum_move = maximum_move
+        self.position = position
+        super().__init__(*args)
+
+
+def _check_and_cache_values(
+    devices_and_positions: dict[AnyDevice, float],
+    smallest_move: float,
+    maximum_move: float,
+) -> Generator[Msg, Any, dict[AnyDevice, float]]:
+    """Caches the positions of all Motors on specified device if they are within
+    smallest_move of home_position. Throws MoveTooLarge if they are outside maximum_move
+    of the home_position
+    """
+    positions = {}
+    for axis, new_position in devices_and_positions.items():
+        position = yield from bps.rd(axis)
+        if abs(position - new_position) > maximum_move:
+            raise MoveTooLarge(axis, maximum_move, position)
+        if abs(position - new_position) > smallest_move:
+            positions[axis] = position
+    return positions
+
+
+def home_and_reset_wrapper(
+    plan: MsgGenerator,
+    device: Device,
+    smallest_move: float,
+    maximum_move: float,
+    group: str | None = None,
+    wait_for_all: bool = True,
+) -> MsgGenerator:
+    home_positions = {
+        axis: 0.0 for _, axis in device.children() if isinstance(axis, Motor)
+    }
+    return move_and_reset_wrapper(
+        plan, home_positions, smallest_move, maximum_move, group, wait_for_all
+    )
+
+
+def move_and_reset_wrapper(
+    plan: MsgGenerator,
+    device_and_positions: dict[AnyDevice, float],
+    smallest_move: float,
+    maximum_move: float,
+    group: str | None = None,
+    wait_for_all: bool = True,
+) -> MsgGenerator:
+    """Wrapper that does the following:
+       1. Caches the positions of all Motors on device
+       2. Throws a MoveTooLarge exception if any positions are maximum_move away from home_position
+       2. Moves any motor that is more than smallest_move away from the home_position to home_position
+       3. Runs the specified plan
+       4. Moves all motors back to their cached positions
+
+    Args:
+        plan (Callable[[], MsgGenerator]): The plan to move between homing and returning to the cache
+        device (Device): The device to move. All Motors in the device will be cached and moved
+        smallest_move (float): The smallest move that we care about doing the home and cache for.
+                               Useful for not wearing out motors if you have large tolerances
+        maximum_move (float): If any Motor starts this far from the home an exception is raised
+                              and no moves occur
+        home_position (float): The position to move every motor to after caching
+        group (str, optional): If set the home move will be done using the home-{group}
+                               group and the reset to cache done using reset-{group}
+        wait_for_all (bool, optional): If true the home and reset to cache will be waited
+                                       on. If false it is left up to the caller to wait on
+                                       them. Defaults to True.
+    """
+    initial_positions = yield from _check_and_cache_values(
+        device_and_positions, smallest_move, maximum_move
+    )
+
+    def move_to_home():
+        home_group = f"home-{group if group else str(uuid.uuid4())[:6]}"
+        for axis, position in device_and_positions.items():
+            if axis in initial_positions.keys():
+                yield from bps.abs_set(axis, position, group=home_group)
+        if wait_for_all:
+            yield from bps.wait(home_group)
+
+    def return_to_initial_position():
+        reset_group = f"reset-{group if group else str(uuid.uuid4())[:6]}"
+        for axis, position in initial_positions.items():
+            yield from bps.abs_set(axis, position, group=reset_group)
+        if wait_for_all:
+            yield from bps.wait(reset_group)
+
+    return (
+        yield from finalize_wrapper(
+            pchain(move_to_home(), plan),
+            return_to_initial_position(),
+        )
+    )
+
+
+home_and_reset_decorator = make_decorator(home_and_reset_wrapper)

dodal/utils.py

@@ -4,6 +4,7 @@ import os
 import re
 import socket
 import string
+from collections.abc import Callable, Iterable, Mapping
 from dataclasses import dataclass
 from functools import wraps
 from importlib import import_module
@@ -12,13 +13,6 @@ from os import environ
 from types import ModuleType
 from typing import (
     Any,
-    Callable,
-    Dict,
-    Iterable,
-    List,
-    Mapping,
-    Tuple,
-    Type,
     TypeVar,
 )
 
@@ -46,7 +40,7 @@ import dodal.log
 try:
     from typing import TypeAlias
 except ImportError:
-    from typing_extensions import TypeAlias
+    from typing import TypeAlias
 
 
 #: Protocols defining interface to hardware
@@ -108,9 +102,35 @@ def skip_device(precondition=lambda: True):
     return decorator
 
 
+def make_device(
+    module: str | ModuleType,
+    device_name: str,
+    **kwargs,
+) -> dict[str, AnyDevice]:
+    """Make a single named device and its dependencies from the given beamline module.
+
+    Args:
+        module (str | ModuleType): The module to make devices from.
+        device_name: Name of the device to construct
+        **kwargs: Arguments passed on to every device factory
+
+    Returns:
+        dict[str, AnyDevice]: A dict mapping device names to the constructed devices
+    """
+    if isinstance(module, str):
+        module = import_module(module)
+
+    device_collector = {}
+    factories = collect_factories(module)
+    device_collector[device_name] = _make_one_device(
+        module, device_name, device_collector, factories, **kwargs
+    )
+    return device_collector
+
+
 def make_all_devices(
     module: str | ModuleType | None = None, include_skipped: bool = False, **kwargs
-) -> Tuple[Dict[str, AnyDevice], Dict[str, Exception]]:
+) -> tuple[dict[str, AnyDevice], dict[str, Exception]]:
     """Makes all devices in the given beamline module.
 
     In cases of device interdependencies it ensures a device is created before any which
@@ -129,7 +149,7 @@ def make_all_devices(
     if isinstance(module, str) or module is None:
         module = import_module(module or __name__)
     factories = collect_factories(module, include_skipped)
-    devices: Tuple[Dict[str, AnyDevice], Dict[str, Exception]] = invoke_factories(
+    devices: tuple[dict[str, AnyDevice], dict[str, Exception]] = invoke_factories(
         factories, **kwargs
     )
 
@@ -139,7 +159,7 @@ def make_all_devices(
 def invoke_factories(
     factories: Mapping[str, AnyDeviceFactory],
     **kwargs,
-) -> Tuple[Dict[str, AnyDevice], Dict[str, Exception]]:
+) -> tuple[dict[str, AnyDevice], dict[str, Exception]]:
     """Call device factory functions in the correct order to resolve dependencies.
     Inspect function signatures to work out dependencies and execute functions in
     correct order.
@@ -259,15 +279,13 @@ def is_any_device_factory(func: Callable) -> bool:
     return is_v1_device_factory(func) or is_v2_device_factory(func)
 
 
-def is_v2_device_type(obj: Type[Any]) -> bool:
-    return inspect.isclass(obj) and issubclass(obj, OphydV2Device)
+def is_v2_device_type(obj: type[Any]) -> bool:
+    return inspect.isclass(obj) and isinstance(obj, OphydV2Device)
 
 
-def is_v1_device_type(obj: Type[Any]) -> bool:
+def is_v1_device_type(obj: type[Any]) -> bool:
     is_class = inspect.isclass(obj)
-    follows_protocols = any(
-        (isinstance(obj, protocol) for protocol in BLUESKY_PROTOCOLS)
-    )
+    follows_protocols = any(isinstance(obj, protocol) for protocol in BLUESKY_PROTOCOLS)
     return is_class and follows_protocols and not is_v2_device_type(obj)
 
 
@@ -292,13 +310,11 @@ def get_beamline_based_on_environment_variable() -> ModuleType:
         or any(c not in valid_characters for c in beamline)
     ):
         raise ValueError(
-            "Invalid BEAMLINE variable - module name is not a permissible python module name, got '{}'".format(
-                beamline
-            )
+            f"Invalid BEAMLINE variable - module name is not a permissible python module name, got '{beamline}'"
         )
 
     try:
-        return importlib.import_module("dodal.beamlines.{}".format(beamline))
+        return importlib.import_module(f"dodal.beamlines.{beamline}")
     except ImportError as e:
         raise ValueError(
             f"Failed to import beamline-specific dodal module 'dodal.beamlines.{beamline}'."
@@ -306,7 +322,7 @@ def get_beamline_based_on_environment_variable() -> ModuleType:
         ) from e
 
 
-def _find_next_run_number_from_files(file_names: List[str]) -> int:
+def _find_next_run_number_from_files(file_names: list[str]) -> int:
     valid_numbers = []
 
     for file_name in file_names:
@@ -322,12 +338,44 @@ def _find_next_run_number_from_files(file_names: List[str]) -> int:
     return max(valid_numbers) + 1 if valid_numbers else 1
 
 
-def get_run_number(directory: str) -> int:
-    """Looks at the numbers coming from all nexus files with the format "xxx_(any number}.nxs", and returns the highest number + 1,
-    or 1 if there are no numbers found"""
-    nexus_file_names = [file for file in os.listdir(directory) if file.endswith(".nxs")]
+def get_run_number(directory: str, prefix: str = "") -> int:
+    """Looks at the numbers coming from all nexus files with the format
+    "{prefix}_(any number}.nxs", and returns the highest number + 1, or 1 if there are
+    no matching numbers found. If no prefix is given, considers all files in the dir."""
+    nexus_file_names = [
+        file
+        for file in os.listdir(directory)
+        if file.endswith(".nxs") and file.startswith(prefix)
+    ]
 
     if len(nexus_file_names) == 0:
         return 1
     else:
         return _find_next_run_number_from_files(nexus_file_names)
+
+
+def _make_one_device(
+    module: ModuleType,
+    device_name: str,
+    devices: dict[str, AnyDevice],
+    factories: dict[str, AnyDeviceFactory],
+    **kwargs,
+) -> AnyDevice:
+    factory = factories.get(device_name)
+    if not factory:
+        raise ValueError(f"Unable to find factory for {device_name}")
+
+    dependencies = list(extract_dependencies(factories, device_name))
+    for dependency_name in dependencies:
+        if dependency_name not in devices:
+            try:
+                devices[dependency_name] = _make_one_device(
+                    module, dependency_name, devices, factories, **kwargs
+                )
+            except Exception as e:
+                raise RuntimeError(
+                    f"Unable to construct device {dependency_name}"
+                ) from e
+
+    params = {name: devices[name] for name in dependencies}
+    return factory(**params, **kwargs)

dls_dodal-1.29.3.dist-info/RECORD

@@ -1,124 +0,0 @@
-dodal/__init__.py,sha256=y-VRpfiX-Lm5nchB9N0VfMy_6dwFqVxpSn5SiAQql9I,114
-dodal/__main__.py,sha256=kP2S2RPitnOWpNGokjZ1Yq-1umOtp5sNOZk2B3tBPLM,111
-dodal/_version.py,sha256=MFlkKJKBPRaG5o-APjK5uWe00dvrrzhYEjQcU5M7B2I,413
-dodal/adsim.py,sha256=OW2dcS7ciD4Yq9WFw4PN_c5Bwccrmu7R-zr-u6ZCbQM,497
-dodal/cli.py,sha256=z0UBESrNrq6Kq4rttp4uHcwS1fnOnRkKBRDHSriPpGY,2058
-dodal/log.py,sha256=dfo1rfYrGG8oIm2HkNxaa_ldVs4vJKtgWSoKe1Z_Xno,8533
-dodal/utils.py,sha256=aH-W94t6NFOoGHZ7awbUKY8_k7qIYDourCFs3MKIjjA,10024
-dodal/beamline_specific_utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dodal/beamline_specific_utils/i03.py,sha256=Ixe1anFQl-kwRJubmQx28TIW4Zw8qDxpElNNNapWQHI,396
-dodal/beamlines/README.md,sha256=K9MkL_GomxlsoTB7Mz-_dJA5NNSbmCfMiutchGg3C8o,404
-dodal/beamlines/__init__.py,sha256=U0dQYFEUloCdQOs24zyfpPTncJXOO4cDcfHSevVOAw4,2890
-dodal/beamlines/i03.py,sha256=J-4GawTxAhrYDQZh87n11L9ehTgObEQ1Lz2PueXCWbc,16892
-dodal/beamlines/i04.py,sha256=JOyNcUnC3wva4no2MHKp6b8gOKAcQXL_c4cBo7oneVs,13034
-dodal/beamlines/i04_1.py,sha256=KDxSUQNhIs_NFiRaLY-Jiory0DeN7Y0ErvGuoTrwCDU,4731
-dodal/beamlines/i20_1.py,sha256=MaPgONHqpoZuBtkiKEzYtViJnKBM2_ekeP4OdbmuXHE,1158
-dodal/beamlines/i22.py,sha256=3VFdA4Wc7O40-64lwUtUBIN23fH4JVNbLKJ1JLjy9as,9870
-dodal/beamlines/i23.py,sha256=2j5qLoqE_hg9ETHqNkOVu7LLkVB8qalgXeORnVYKN_I,1075
-dodal/beamlines/i24.py,sha256=dCMQGcBZ6ADZ6_rEDFcV2BPHGKBC9iVFvfxewxVts4k,6111
-dodal/beamlines/p38.py,sha256=TC78u4GwEnj6X0r5cnHhqNdBbbDRnh8lY8pEucBZjEU,8006
-dodal/beamlines/p45.py,sha256=TNIkC-SBfj0ayZtlLLXW9xCSi5CzJkO8XpAMIo8fjao,2957
-dodal/common/__init__.py,sha256=ZC4ICKUDB0BDxRaVy8nmqclVmDBne-dPtk6UJsoFq6I,258
-dodal/common/coordination.py,sha256=OxIjDiO1-9A9KESRPFtzwkvvQlavbgA5RHemlbubBPg,1168
-dodal/common/maths.py,sha256=JRSBhbMzwlicKp1_Bsfu9gA79JJA_Dgq9EpbExFH65M,1829
-dodal/common/types.py,sha256=M0gZs9F7--gREF8VYJn-Y1Mt9mIEgp1aLY3oUpUkSno,546
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dls_dodal-1.29.3.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-dodal = dodal.__main__:main

dodal/devices/qbpm1.py

@@ -1,8 +0,0 @@
-from ophyd import Component as Cpt
-from ophyd import Device, EpicsSignalRO, Kind
-
-
-class QBPM1(Device):
-    """Quadrant Beam Position Monitor"""
-
-    intensity = Cpt(EpicsSignalRO, "-DI-QBPM-01:INTEN", kind=Kind.normal)