Merge pull request #68 from DiamondLightSource/66-update-system-testp99

66 update system test and bug fixes for test.

Author: Relm-Arrowny

demo/p99/MVP_demo.ipynb

@@ -10,7 +10,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "2121d7fe-965b-4fed-94aa-897c7133d689",
    "metadata": {},
    "outputs": [],
@@ -19,7 +19,8 @@
     "from blueapi.client.event_bus import AnyEvent\n",
     "from blueapi.config import ApplicationConfig, RestConfig, StompConfig\n",
     "from blueapi.worker.task import Task\n",
-    "from bluesky_stomp.models import BasicAuthentication"
+    "from bluesky_stomp.models import BasicAuthentication\n",
+    "from pydantic import HttpUrl"
    ]
   },
   {
@@ -36,18 +37,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "424f8c5c-98df-4e5e-a0ab-356f3e3b6111",
    "metadata": {},
    "outputs": [],
    "source": [
-    "p99Config = ApplicationConfig(\n",
-    "            stomp=StompConfig(\n",
-    "                host=\"172.23.177.208\",\n",
-    "                auth=BasicAuthentication(username=\"p99\", password=\"\"),  # type: ignore\n",
-    "            ),\n",
-    "            api=RestConfig(host=\"p99-blueapi.diamond.ac.uk\", port=443, protocol=\"https\"),\n",
-    "        )"
+    "p99Config =ApplicationConfig(\n",
+    "        stomp=StompConfig(\n",
+    "            url=HttpUrl(\"http://172.23.177.208\"),\n",
+    "            auth=BasicAuthentication(username=\"p99\", password=password),  # type: ignore\n",
+    "        ),\n",
+    "        api=RestConfig(url=HttpUrl(\"https://p99-blueapi.diamond.ac.uk:443\")),\n",
+    "    )"
    ]
   },
   {

demo/p99/stxm_demo_fast_step.ipynb

@@ -0,0 +1,40 @@
+Troubleshooting
+===============
+
+This section provides solutions to common problems you may encounter.
+
+.. contents::
+   :local:
+   :depth: 2
+
+Data Writing Issues
+~~~~~~~~~~~~~~~~~~~
+
+**Problem:**  
+The Nexus writer is not creating a .nxs file.
+
+**Solution:**  
+
+- Ensure that the output directory exists and that the nexus-file-converter service has write permissions.
+- Verify that the RabbitMQ configuration is correct and able to handle messages from BlueAPI.
+- Add detectors as metadata so that the nexus-file-converter can identify them, rather than relying on discovery from the data stream.
+
+.. code-block:: python
+
+    md["detectors"] = [det.name for det in dets]
+    md["motors"] = [scan_motor.name, step_motor.name]
+    
+Common Issues
+~~~~~~~~~~~~~
+
+.. _installation-issues:
+
+Installation Issues
+~~~~~~~~~~~~~~~~~~~
+
+.. _dependency-errors:
+
+Dependency Errors
+~~~~~~~~~~~~~~~~~
+
+.. _runtime-errors:

docs/how-to/42_trobleshooting.rst

@@ -4,6 +4,7 @@
 P99_DEFAULT_METADATA = {
     "energy": {"value": 1.8, "unit": "eV"},
     "detector_dist": {"value": 88, "unit": "mm"},
+    "pixel_size": {"value": 16, "unit": "µm"},
 }
 
 stxm_step = add_default_metadata(grid_step_scan, P99_DEFAULT_METADATA)

src/sm_bluesky/beamlines/p99/plans/__init__.py

@@ -1,3 +1,3 @@
-from .add_meta import add_default_metadata
+from .add_meta import add_default_metadata, add_extra_names_to_meta
 
-__all__ = ["add_default_metadata"]
+__all__ = ["add_default_metadata", "add_extra_names_to_meta"]

src/sm_bluesky/common/helper/__init__.py

@@ -1,24 +1,46 @@
 from collections.abc import Callable
 from functools import wraps
-from typing import TypeVar, cast
+from typing import Any, TypeVar, cast
 
 from blueapi.core import MsgGenerator
 
 TCallable = TypeVar("TCallable", bound=Callable[..., MsgGenerator])
 
 
 def add_default_metadata(
-    funcs: TCallable, extra_metadata: dict | None = None
+    func: TCallable, extra_metadata: dict[str, Any] | None = None
 ) -> TCallable:
-    @wraps(funcs)
+    """
+    Decorator to add or update default metadata in the 'md' keyword argument.
+
+    If 'md' is not provided, it will be set to extra_metadata.
+    If 'md' is provided and not None, it will be updated with extra_metadata.
+    If 'md' is provided and is None, it will be set to extra_metadata.
+    """
+
+    @wraps(func)
     def inner(
         *args,
         **kwargs,
     ) -> MsgGenerator:
-        if "md" in kwargs:
-            kwargs["md"].update(extra_metadata)
-        else:
-            kwargs["md"] = extra_metadata
-        yield from (funcs(*args, **kwargs))
+        md = kwargs.get("md")
+        if extra_metadata:
+            if md is None:
+                kwargs["md"] = extra_metadata
+            elif isinstance(md, dict):
+                kwargs["md"] = {**md, **extra_metadata}
+            else:
+                raise ValueError("md is reserved for meta data.")
+        elif md is None:
+            kwargs["md"] = {}
+        return func(*args, **kwargs)
 
     return cast(TCallable, inner)
+
+
+def add_extra_names_to_meta(md: dict, key: str, names: list[str]):
+    if key in md:
+        md[key] = md[key] + names
+        return md
+    md[key] = names
+    return md

src/sm_bluesky/common/helper/add_meta.py

@@ -168,7 +168,7 @@ def get_velocity_and_step_size(
     max_velocity = yield from bps.rd(scan_motor.max_velocity)  # type: ignore
     # if motor does not move fast enough increase step_motor step size
     if ideal_velocity > max_velocity:
-        ideal_step_size = ideal_step_size / (ideal_velocity / max_velocity)
+        ideal_step_size = ideal_step_size * (ideal_velocity / max_velocity)
         ideal_velocity = round(max_velocity, 3)
 
     return ideal_velocity, ideal_step_size

src/sm_bluesky/common/plan_stubs/motions.py

@@ -5,7 +5,7 @@
 
 """
 
-from .ad_plans import tigger_img
+from .ad_plans import trigger_img
 from .alignments import (
     StatPosition,
     align_slit_with_look_up,
@@ -24,5 +24,5 @@
     "fast_scan_grid",
     "grid_fast_scan",
     "grid_step_scan",
-    "tigger_img",
+    "trigger_img",
 ]

src/sm_bluesky/common/plans/__init__.py

@@ -1,12 +1,18 @@
+from typing import Any
+
 from blueapi.core import MsgGenerator
 from bluesky import plan_stubs as bps
 from bluesky import preprocessors as bpp
 from bluesky.utils import Msg, plan
+from dodal.plan_stubs.data_session import attach_data_session_metadata_decorator
 from ophyd_async.epics.adandor import Andor2Detector
 
 
 @plan
-def tigger_img(dets: Andor2Detector, value: int) -> MsgGenerator:
+@attach_data_session_metadata_decorator()
+def trigger_img(
+    dets: Andor2Detector, acquire_time: int, md: dict[str, Any] | None = None
+) -> MsgGenerator:
     """
     Set the acquire time and trigger the detector to read data.
 
@@ -22,11 +28,13 @@ def tigger_img(dets: Andor2Detector, value: int) -> MsgGenerator:
     MsgGenerator
         A Bluesky generator for triggering the detector.
     """
-    yield Msg("set", dets.driver.acquire_time, value)
+    if md is None:
+        md = {}
+    yield Msg("set", dets.driver.acquire_time, acquire_time)
 
     @bpp.stage_decorator([dets])
-    @bpp.run_decorator()
-    def innertigger_img():
+    @bpp.run_decorator(md=md)
+    def inner_trigger_img():
         return (yield from bps.trigger_and_read([dets]))
 
-    yield from innertigger_img()
+    yield from inner_trigger_img()

src/sm_bluesky/common/plans/ad_plans.py

@@ -1,7 +1,7 @@
 from collections.abc import Callable
 from enum import Enum
 from functools import wraps
-from typing import TypeVar, cast
+from typing import ParamSpec, TypeVar
 
 from bluesky import preprocessors as bpp
 from bluesky.callbacks.fitting import PeakStats
@@ -38,10 +38,14 @@ class StatPosition(tuple, Enum):
     D_MAX = ("derivative_stats", "max")
 
 
-TCallable = TypeVar("TCallable", bound=Callable)
+P = ParamSpec("P")
+T = TypeVar("T")
+TCallable = Callable[
+    P, T
+]  # Type for callable functions with parameters P and return type T
 
 
-def scan_and_move_to_fit_pos(funcs: TCallable) -> TCallable:
+def scan_and_move_to_fit_pos(func: TCallable) -> TCallable:
     """
     Wrapper to add a PeakStats callback before performing a scan
     and move to the fitted position after the scan.
@@ -57,30 +61,30 @@ def scan_and_move_to_fit_pos(funcs: TCallable) -> TCallable:
         The wrapped scan function.
     """
 
-    @wraps(funcs)
+    @wraps(func)
     def inner(
         det: StandardReadable,
         motor: Motor,
         fitted_loc: StatPosition,
         detname_suffix: str,
         *args,
         **kwargs,
-    ):
+    ) -> MsgGenerator:
         ps = PeakStats(
             f"{motor.name}",
             f"{det.name}-{detname_suffix}",
             calc_derivative_and_stats=True,
         )
         yield from bpp.subs_wrapper(
-            funcs(det, motor, fitted_loc, detname_suffix, *args, **kwargs),
+            func(det, motor, fitted_loc, detname_suffix, *args, **kwargs),
             ps,
         )
         peak_position = get_stat_loc(ps, fitted_loc)
 
         LOGGER.info(f"Fit info {ps}")
         yield from abs_set(motor, peak_position, wait=True)
 
-    return cast(TCallable, inner)
+    return inner
 
 
 @plan