From baf56e784f9a060326f34b22e4421d6134addbea Mon Sep 17 00:00:00 2001 From: sligara7 Date: Fri, 23 Oct 2026 16:57:29 -0400 Subject: [PATCH 1/2] Add Perkin Elmer PE1/PE2 as continuous-acquisition detectors pe1c/pe2c are ContAcqDetectors summing in Proc1 and writing TIFF to J:\proposals, as in pdf-profile-collection 80-areadetector2. ContAcqDetector proc_suffix (ophyd-async #1329) and NSLS2PathProvider base_write_dir (nslsii #231) are unreleased, so both come from the git commits hextools uses. #1329 renamed trigger_info_from_num_images to trigger_info_from_driver (XSP driver updated); nslsii main needs BEAMLINE_ACRONYM, now defaulted to PDF. Assisted-by: copilot:claude-opus-5-5 --- pixi.lock | 8923 ++++++------------ pixi.toml | 6 +- pyproject.toml | 4 +- src/pdftools/detectors/xspd.py | 4 +- src/pdftools/profiles/collection.py | 23 +- tests/test_detectors.py/test_perkin_elmer.py | 68 + tests/test_utils.py | 2 +- 7 files changed, 2976 insertions(+), 6054 deletions(-) create mode 100644 tests/test_detectors.py/test_perkin_elmer.py diff --git a/pixi.lock b/pixi.lock index df6ce57..9389896 100644 --- a/pixi.lock +++ b/pixi.lock @@ -15,15 +15,6 @@ environments: packages: linux-64: - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/adbc-driver-manager-1.12.0-py313hbdba758_2.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.16.1-h7cc23a3_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.14.1-pl5321h57e6904_2.conda - - conda: 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requires_python: '>=3.10' +- pypi: https://files.pythonhosted.org/packages/fe/47/deb64c73aec25af7699247e021153a6bfe9a08452f7f7337dcee4aa07a2b/historydict-1.2.6-py3-none-any.whl + name: historydict + version: 1.2.6 + sha256: b4b00a170f05502aa682caba62435da5fe1f73037e884707581fe84f8d7b43f5 +- pypi: https://files.pythonhosted.org/packages/fe/5e/3be305568fe5f34448807976dc82fc151d76c3e0e03958f34770286278c1/flexparser-0.4-py3-none-any.whl + name: flexparser + version: '0.4' + sha256: 3738b456192dcb3e15620f324c447721023c0293f6af9955b481e91d00179846 + requires_dist: + - typing-extensions + - pytest ; extra == 'test' + - pytest-mpl ; extra == 'test' + - pytest-cov ; extra == 'test' + - pytest-subtests ; extra == 'test' + requires_python: '>=3.9' +- pypi: https://files.pythonhosted.org/packages/ff/5d/e4f84c9c448613e12bd62e90b23aa127ea4c46b697f3d760acc32cb94f25/ruamel_yaml_clib-0.2.15-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl + name: ruamel-yaml-clib + version: 0.2.15 + sha256: 4d1032919280ebc04a80e4fb1e93f7a738129857eaec9448310e638c8bccefcf + requires_python: '>=3.9' diff --git a/pixi.toml b/pixi.toml index 5c204fa..8cb8573 100644 --- a/pixi.toml +++ b/pixi.toml @@ -10,13 +10,15 @@ python = ">=3.11,<3.14" ipython = ">=9.16.1,<10" tiled-client = ">=0.2.14,<0.3" bluesky-tiled-plugins = ">=2.0.11,<3" -ophyd-async = ">=0.21.3,<0.22" -nslsii = ">=0.11.9,<0.12" redis-json-dict = ">=0.2.2,<0.3" rich = "*" [pypi-dependencies] pdftools = { path = ".", editable = true } +# ContAcqDetector proc_suffix (ophyd-async #1329) and NSLS2PathProvider base_write_dir +# (nslsii #231) are unreleased; same commits as hextools. +ophyd-async = { git = "https://github.com/bluesky/ophyd-async", rev = "de097ace33ce2fa0ea2eb22572ef81e5af133b16", extras = ["ca", "pva", "sim"] } +nslsii = { git = "https://github.com/NSLS2/nslsii", rev = "b8c69931660f2d74534f44c210499958959a1a0e" } [feature.profile.dependencies] diff --git a/pyproject.toml b/pyproject.toml index f2f2c88..d5dea75 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,8 +28,8 @@ dependencies = [ "bluesky", "tiled[client]", "bluesky-tiled-plugins>=2.0.11", - "ophyd-async[ca, pva, sim]>=0.21.3", - "nslsii", + "ophyd-async[ca, pva, sim] @ git+https://github.com/bluesky/ophyd-async@de097ace33ce2fa0ea2eb22572ef81e5af133b16", + "nslsii @ git+https://github.com/NSLS2/nslsii@b8c69931660f2d74534f44c210499958959a1a0e", "rich", ] diff --git a/src/pdftools/detectors/xspd.py b/src/pdftools/detectors/xspd.py index 686a6e1..6e0a1e6 100644 --- a/src/pdftools/detectors/xspd.py +++ b/src/pdftools/detectors/xspd.py @@ -21,7 +21,7 @@ ADWriterFactory, AreaDetector, NDPluginBaseIO, - trigger_info_from_num_images, + trigger_info_from_driver, ) from ophyd_async.epics.core import ( EpicsDevice, @@ -238,7 +238,7 @@ async def prepare_internal(self, num: int, livetime: float, deadtime: float): await asyncio.gather(*coros) async def default_trigger_info(self): - return await trigger_info_from_num_images(self.driver) + return await trigger_info_from_driver(self.driver.num_images) class XSPDetector(AreaDetector[XSPIO]): diff --git a/src/pdftools/profiles/collection.py b/src/pdftools/profiles/collection.py index 3a39542..e98831f 100644 --- a/src/pdftools/profiles/collection.py +++ b/src/pdftools/profiles/collection.py @@ -2,6 +2,7 @@ import argparse import os +from pathlib import PureWindowsPath import numpy as np from bluesky import plan_stubs as bps @@ -15,7 +16,7 @@ from IPython.core.getipython import get_ipython from IPython.terminal.interactiveshell import TerminalInteractiveShell from nslsii.ophyd_async.providers import NSLS2PathProvider -from ophyd_async.epics.adcore import ADWriterFactory +from ophyd_async.epics.adcore import ADWriterFactory, ContAcqDetector from ophyd_async.epics.adpilatus import PilatusDetector from tiled.client import from_uri, simple @@ -46,6 +47,8 @@ # Beamline Redis for RunEngine metadata, as pdf-profile-collection's 00-base uses it # (port 6380 with SSL is open_redis_client's default when redis_ssl=True). os.environ.setdefault("REDIS_HOST", "xf28id1-pdf-redis1.nsls2.bnl.gov") +# NSLS2PathProvider derives /nsls2/data//proposals from this. +os.environ.setdefault("BEAMLINE_ACRONYM", "PDF") # Have ophyd-async keep detector state constant when not explicitly overridden. os.environ["OPHYD_ASYNC_PRESERVE_DETECTOR_STATE"] = "YES" @@ -115,6 +118,11 @@ # Define our global default path provider for the beamline path_provider = NSLS2PathProvider(RE.md) +# The Perkin Elmer IOCs run on Windows hosts and write to the proposals share as J:. +pe_path_provider = NSLS2PathProvider( + RE.md, base_write_dir=PureWindowsPath("J:\\proposals") +) + # Devices are added here, step by step (detectors, motors, sample environment). with auto_init_devices(timeout=2.0): # Area detectors writing TIFF, as in pdf-profile-collection (81-pilatus, 84-lambda) @@ -129,6 +137,19 @@ ADWriterFactory.tiff(path_provider), name="pilatus-1", ) + # Free-running flat panels; Proc1 sums frames per point, as pe1c/pe2c do today. + pe1c = ContAcqDetector( + "XF:28ID1-ES{Det:PE1}", + ADWriterFactory.tiff(pe_path_provider), + name="pe1", + proc_suffix="Proc1:", + ) + pe2c = ContAcqDetector( + "XF:28ID1-ES{Det:PE2}", + ADWriterFactory.tiff(pe_path_provider), + name="pe2", + proc_suffix="Proc1:", + ) # Add baseline=[, , ...] to SupplementalData as devices arrive. sd = bpp.SupplementalData() diff --git a/tests/test_detectors.py/test_perkin_elmer.py b/tests/test_detectors.py/test_perkin_elmer.py new file mode 100644 index 0000000..304fa5d --- /dev/null +++ b/tests/test_detectors.py/test_perkin_elmer.py @@ -0,0 +1,68 @@ +from pathlib import PurePosixPath, PureWindowsPath + +import bluesky.plans as bp +import pytest +from bluesky.run_engine import RunEngine +from nslsii.ophyd_async.providers import NSLS2PathProvider +from ophyd_async.core import ( + callback_on_mock_put, + get_mock_put, + init_devices, + set_mock_value, +) +from ophyd_async.epics.adcore import ( + ADBaseDataType, + ADImageMode, + ADWriterFactory, + ContAcqDetector, +) + + +def test_perkin_elmer_count_sums_in_proc_and_writes_tiff_to_windows_share( + RE: RunEngine, monkeypatch: pytest.MonkeyPatch +): + # As the profile sets it: a count keeps the frame count summed in the IOC's Proc1. + monkeypatch.setenv("OPHYD_ASYNC_PRESERVE_DETECTOR_STATE", "YES") + RE.md.update({"cycle": "2026-3", "data_session": "pass-123456"}) + path_provider = NSLS2PathProvider( + RE.md, + base_data_dir=PurePosixPath("/nsls2/data/pdf/proposals"), + base_write_dir=PureWindowsPath("J:\\proposals"), + ) + with init_devices(mock=True): + pe = ContAcqDetector( + "TEST:PE2:", + ADWriterFactory.tiff(path_provider), + name="pe2", + proc_suffix="Proc1:", + ) + set_mock_value(pe.driver.image_mode, ADImageMode.CONTINUOUS) + set_mock_value(pe.driver.acquire, True) + set_mock_value(pe.driver.array_size_x, 4) + set_mock_value(pe.driver.array_size_y, 3) + set_mock_value(pe.driver.data_type, ADBaseDataType.UINT16) + set_mock_value(pe.tiff.file_path_exists, True) # pyright: ignore[reportAttributeAccessIssue] + set_mock_value(pe.proc.enable_filter, True) # pyright: ignore[reportAttributeAccessIssue] + set_mock_value(pe.proc.num_filter, 5) # pyright: ignore[reportAttributeAccessIssue] + + def _on_cb_trigger(value, **kwargs): + if value: + set_mock_value(pe.tiff.num_captured, 1) # pyright: ignore[reportAttributeAccessIssue] + return False + + callback_on_mock_put(pe.cb.trigger_, _on_cb_trigger) # pyright: ignore[reportAttributeAccessIssue] + + docs: dict[str, list] = {} + RE(bp.count([pe]), lambda name, doc: docs.setdefault(name, []).append(doc)) + + written_to = get_mock_put(pe.tiff.file_path).call_args.args[0] # pyright: ignore[reportAttributeAccessIssue] + assert written_to.startswith("J:\\proposals\\2026-3\\pass-123456\\") + sres = docs["stream_resource"][0] + assert sres["mimetype"] == "multipart/related;type=image/tiff" + assert sres["uri"].startswith( + "file://localhost/nsls2/data/pdf/proposals/2026-3/pass-123456/" + ) + get_mock_put(pe.proc.num_filter).assert_called_with(5) # pyright: ignore[reportAttributeAccessIssue] + desc = docs["descriptor"][0]["data_keys"]["pe2"] + assert desc["shape"] == [1, 3, 4] + assert desc["dtype_numpy"] == " Date: Fri, 23 Oct 2026 17:23:58 -0400 Subject: [PATCH 2/2] PE path provider: POSIX separator for the read-side date dirs With a PureWindowsPath write root, nslsii defaults the YMD separator to a backslash for both write and read paths, so resource URIs ended in 2026\10\23/. The PE test now checks the complete dated URI. Assisted-by: copilot:claude-opus-5-5 --- src/pdftools/profiles/collection.py | 5 ++++- tests/test_detectors.py/test_perkin_elmer.py | 7 ++++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/src/pdftools/profiles/collection.py b/src/pdftools/profiles/collection.py index e98831f..b81c468 100644 --- a/src/pdftools/profiles/collection.py +++ b/src/pdftools/profiles/collection.py @@ -120,7 +120,10 @@ # The Perkin Elmer IOCs run on Windows hosts and write to the proposals share as J:. pe_path_provider = NSLS2PathProvider( - RE.md, base_write_dir=PureWindowsPath("J:\\proposals") + RE.md, + base_write_dir=PureWindowsPath("J:\\proposals"), + # Else the Windows root sets "\\" for the read-side date dirs too. + separator="/", ) # Devices are added here, step by step (detectors, motors, sample environment). diff --git a/tests/test_detectors.py/test_perkin_elmer.py b/tests/test_detectors.py/test_perkin_elmer.py index 304fa5d..fa3b963 100644 --- a/tests/test_detectors.py/test_perkin_elmer.py +++ b/tests/test_detectors.py/test_perkin_elmer.py @@ -1,3 +1,4 @@ +import datetime from pathlib import PurePosixPath, PureWindowsPath import bluesky.plans as bp @@ -28,6 +29,7 @@ def test_perkin_elmer_count_sums_in_proc_and_writes_tiff_to_windows_share( RE.md, base_data_dir=PurePosixPath("/nsls2/data/pdf/proposals"), base_write_dir=PureWindowsPath("J:\\proposals"), + separator="/", ) with init_devices(mock=True): pe = ContAcqDetector( @@ -59,8 +61,11 @@ def _on_cb_trigger(value, **kwargs): assert written_to.startswith("J:\\proposals\\2026-3\\pass-123456\\") sres = docs["stream_resource"][0] assert sres["mimetype"] == "multipart/related;type=image/tiff" - assert sres["uri"].startswith( + # The read side is POSIX: no Windows separators may leak in from the write root. + today = datetime.date.today() + assert sres["uri"] == ( "file://localhost/nsls2/data/pdf/proposals/2026-3/pass-123456/" + f"assets/pe2/{today:%Y/%m/%d}/" ) get_mock_put(pe.proc.num_filter).assert_called_with(5) # pyright: ignore[reportAttributeAccessIssue] desc = docs["descriptor"][0]["data_keys"]["pe2"]