From 2419c41d3d64b60c67096999f530a88c4b62db1b Mon Sep 17 00:00:00 2001 From: thomashopkins32 Date: Thu, 17 Sep 2026 19:19:38 +0000 Subject: [PATCH 1/6] Port HXNFlyerPanda, ExportSISDataPanda, ExportXpsROI from hxn-profile-collection Move the PandABox fly-scan flyer and its two HDF5 export helpers out of the IPython-profile startup scripts (hxn-profile-collection/startup/93-scanplan-panda.py, 95-xspress3-panda.py) into hxntools so HXNFlyerPanda is importable and testable standalone, independent of the profile's shared IPython namespace. - HXNFlyerPanda gains an explicit constructor: large_file_directory_root/ write_path/read_path are now required keyword-only arguments (previously class attributes resolved from profile-only globals at class-definition time), live_plot_callback replaces the direct panda_live_plot.update_plot(...) call (hxntools has no beamline live-plotting dependency of its own), and n_scaler_mca is a constructor argument (previously the profile global n_scaler_mca). - kickoff()/complete()/describe_collect()/collect()/collect_asset_docs() are otherwise unchanged from the profile version. --- src/hxntools/panda_flyer.py | 566 ++++++++++++++++++++++++++++++++++++ 1 file changed, 566 insertions(+) create mode 100644 src/hxntools/panda_flyer.py diff --git a/src/hxntools/panda_flyer.py b/src/hxntools/panda_flyer.py new file mode 100644 index 0000000..2673b1d --- /dev/null +++ b/src/hxntools/panda_flyer.py @@ -0,0 +1,566 @@ +import itertools +import os +import time +import time as ttime +import uuid +from collections import OrderedDict, deque +from datetime import datetime + +import h5py +import numpy as np +from bluesky.utils import short_uid +from event_model import compose_resource +from ophyd import Device +from ophyd.areadetector.filestore_mixins import resource_factory +from ophyd.sim import NullStatus + +from hxntools.handlers.rasmi2 import SISHDF5Handler + + +class ExportSISDataPanda: + def __init__(self): + self._fp = None + self._filepath = None + + def open(self, filepath, mca_names, ion, panda): + self.close() + self._filepath = filepath + self._fp = h5py.File(filepath, "w", libver="latest") + + print(f'{filepath = }') + + self._fp.swmr_mode = True + + self._ion = ion + self._panda = panda + self._mca_names = mca_names + + def create_ds(ds_name): + ds = self._fp.create_dataset(ds_name, data=np.array([], dtype="f"), maxshape=(None,), dtype="f") + + for ds_name in self._mca_names: + create_ds(ds_name) + + self._fp.flush() + + def close(self): + if self._fp: + self._fp.close() + self._fp = None + + def __del__(self): + self.close() + + def export(self): + + n_mcas = len(self._mca_names) + + mca_data = [] + for n in range(1, n_mcas + 1): + mca = self._ion.mca_by_index[n].spectrum.get(timeout=5.0) + mca_data.append(mca) + + #some problem here ROI data is saved correctly but correct len is 0: AP 04/24/2026 + correct_length = int(self._panda.data.num_captured.get()/self._panda.position_supersample) + # correct_length = int(self._panda.data.num_capture.get()/self._panda.position_supersample) trial on 4/26/2026 + print (f"{'='*30}") + print(f' {correct_length = }') + print (f"{'='*30}") + + for n in range(len(mca_data)): + mca = mca_data[n] + # print(f"Number of mca points: {len(mca)}") + # mca = mca[1::2] + if len(mca) != correct_length: + print(f"Incorrect number of points ({len(mca)}) loaded from MCA{n + 1}: {correct_length} points are expected") + if len(mca > correct_length): + mca = mca[:correct_length] + else: + mca = np.append(mca, [1e10] * (correct_length - len(mca))) + mca_data[n] = mca + + j = 0 + while self._panda.data.capture.get() == 1: + print("Waiting for pandabox data...") + ttime.sleep(0.1) + j += 1 + if j > 10: + print("PANDABOX IS BEHAVING BADLY CARRYING ON") + break + + def add_data(ds_name, data): + ds = self._fp[ds_name] + n_ds = ds.shape[0] + ds.resize((n_ds + len(data),)) + ds[n_ds:] = np.array(data) + + for n, name in enumerate(self._mca_names): + add_data(name, np.asarray(mca_data[n])) + + self._fp.flush() + + +class ExportXpsROI: + def __init__(self): + self._fp = None + self._filepath = None + + def open(self, filepath, xspress3): + self.close() + self._filepath = filepath + self._fp = h5py.File(filepath, "w", libver="latest") + + self._fp.swmr_mode = True + + self._xsp = xspress3 + + def create_ds(det_name): + if not det_name in self._fp: + self._fp.create_dataset(det_name, data=np.array([], dtype="f"), maxshape=(None,), dtype="f") + + for det_name in [roi.name for roi in self._xsp.enabled_rois]: + create_ds(det_name) + + self._fp.flush() + + def close(self): + if self._fp: + self._fp.close() + self._fp = None + + def __del__(self): + self.close() + + def export(self, npoints): + def add_data(det_name, data): + ds = self._fp[det_name] + if ds.size == 0: + ds.resize((npoints,)) + ds[:len(data)] = np.array(data) + ds[len(data):] = ds[len(data)-1] + + for roi in self._xsp.enabled_rois: + if hasattr(roi,'settings'): + add_data(roi.name, roi.settings.array_data.get()) + else: + add_data(roi.name, roi.ts_total.get()) + self._fp.flush() + + +class HXNFlyerPanda(Device): + """ + This is the PandaBox panda1 and panda2 + """ + + @property + def detectors(self): + return tuple(self._dets) + + @detectors.setter + def detectors(self, value): + dets = tuple(value) + # if not all([d.name in self.KNOWN_DETS for d in dets]): + # raise ValueError( + # f"One or more of {[d.name for d in dets]}" + # f"is not known to the panda. " + # f"The known detectors are {self.KNOWN_DETS})" + # ) + self._dets = dets + + @property + def sclr(self): + return self._sis + + def __init__( + self, + panda, + dets, + sclr, + *, + large_file_directory_root, + large_file_directory_write_path, + large_file_directory_read_path, + motor=None, + root_dir=None, + n_scaler_mca=16, + **kwargs, + ): + super().__init__("", parent=None, **kwargs) + self.name = "PandaFlyer" + self.LARGE_FILE_DIRECTORY_ROOT = large_file_directory_root + self.LARGE_FILE_DIRECTORY_WRITE_PATH = large_file_directory_write_path + self.LARGE_FILE_DIRECTORY_READ_PATH = large_file_directory_read_path + if root_dir is None: + root_dir = self.LARGE_FILE_DIRECTORY_ROOT + self._mode = "idle" + self._dets = dets + self._sis = sclr + self._root_dir = root_dir + self._resource_document, self._datum_factory = None, None + self._document_cache = deque() + self._last_bulk = None + + self._point_counter = None + self.frame_per_point = None + # Number of raw PandA gates captured per *scan point*. Real callers + # (flyscan_pd et al.) always set this before kickoff(); default to 1 + # (no oversampling) so the flyer is safe to use standalone. + self.position_supersample = 1 + # Optional hook invoked as `callback(finished: bool)` from complete(); + # hxntools has no beamline live-plotting dependency of its own, so the + # profile wires this to its plot-update function after construction. + self.live_plot_callback = None + self._n_scaler_mca = n_scaler_mca + + self.panda = panda + self.motor = motor + + self._document_cache = [] + self._resource_document = None + self._datum_factory = None + + if self._sis is not None: + self._data_sis_exporter = ExportSISDataPanda() + + self._xsp_roi_exporter = None + + type_map = {"int32": " Date: Thu, 17 Sep 2026 19:20:09 +0000 Subject: [PATCH 2/6] Fix DESCRIPTOR_10X_LENGTH: declare true per-row point count describe_collect() declared the scaler ("sclr1_ch*") and Xspress3-ROI ("Det{n}_") keys' shape using the raw, position_supersample- oversampled PandA gate count (self.frame_per_point) instead of the actual number of scan points. ExportSISDataPanda.export()/ExportXpsROI.export() already collapse that oversampling before writing their HDF5 files (both divide by position_supersample), so the declared shape was always position_supersample times too large -- exactly 10x under every 2D/1D PandA plan's default position_supersample=10. - describe_collect(): num_scan_points = frame_per_point // position_supersample. - kickoff(): matching frame_per_point // position_supersample in both the SIS and ROI resource_factory() resource_kwargs, so Tiled's structure validator reshapes the on-disk array to the same per-row length as the descriptor. - Add tests/test_panda_flyer.py: drives the real HXNFlyerPanda through kickoff/complete/collect against a real, in-process Tiled server and asserts the declared and on-disk array shapes match the true point count, for position_supersample in {1, 10}. - Add the [project.optional-dependencies].test extra (pytest, tiled[server], bluesky-tiled-plugins) needed to run the new test. --- pyproject.toml | 7 + src/hxntools/panda_flyer.py | 28 +++- tests/test_panda_flyer.py | 287 ++++++++++++++++++++++++++++++++++++ 3 files changed, 319 insertions(+), 3 deletions(-) create mode 100644 tests/test_panda_flyer.py diff --git a/pyproject.toml b/pyproject.toml index 1502069..d1a5264 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,6 +47,13 @@ Homepage = "https://github.com/NSLS-II-HXN/hxntools" Discussions = "https://github.com/NSLS-II-HXN/hxntools/discussions" Changelog = "https://github.com/NSLS-II-HXN/hxntools/releases" +[project.optional-dependencies] +test = [ + "pytest>=8.0", + "bluesky-tiled-plugins>=2.0.11", + "tiled[server]>=0.2.18", +] + [tool.setuptools] include-package-data = true diff --git a/src/hxntools/panda_flyer.py b/src/hxntools/panda_flyer.py index 2673b1d..997f92e 100644 --- a/src/hxntools/panda_flyer.py +++ b/src/hxntools/panda_flyer.py @@ -311,7 +311,13 @@ def kickoff(self, *, num): SISHDF5Handler.HANDLER_NAME, root=self.LARGE_FILE_DIRECTORY_ROOT, resource_path=self.__read_filepath_sis, - resource_kwargs={"frame_per_point": self.frame_per_point}, + # `frame_per_point` here is the number of samples represented by a single + # Datum, i.e. the true per-row length (see describe_collect() for the + # matching descriptor shape) -- not the raw, supersampled PandA gate + # count in `self.frame_per_point`. + resource_kwargs={ + "frame_per_point": self.frame_per_point // self.position_supersample + }, path_semantics="posix", ) @@ -342,7 +348,14 @@ def kickoff(self, *, num): 'ROI_HDF5_FLY', root=self.LARGE_FILE_DIRECTORY_ROOT, resource_path=self.__read_filepath_xsp_roi, - resource_kwargs={"frame_per_point": self.frame_per_point}, + # Same true per-row length as the SIS resource above (and + # describe_collect()'s declared shape) -- required so that + # BlueskyRunV3.validate() can reconcile the on-disk, + # single-column-per-ROI dataset shape with the declared + # [1, num_scan_points] structure. + resource_kwargs={ + "frame_per_point": self.frame_per_point // self.position_supersample + }, path_semantics="posix", ) @@ -500,7 +513,16 @@ def describe_collect(self): ext_spec = "FileStore:" - num_scan_points = self.frame_per_point + # `frame_per_point` (== `self._npts` previously) is the raw number of + # PandA gates captured, which is `position_supersample` gates per + # real scan point (see kickoff()/flyscan_pd()). The SIS scaler and + # Xspress3 ROI exporters both collapse that oversampling before + # writing their HDF5 files (ExportSISDataPanda.export() and + # ExportXpsROI.export(), called with frame_per_point / + # position_supersample in complete()), so the declared per-row + # length for those keys must match the reduced, on-disk point count + # -- not the raw supersampled gate count. + num_scan_points = self.frame_per_point // self.position_supersample def _spec(source): return { diff --git a/tests/test_panda_flyer.py b/tests/test_panda_flyer.py new file mode 100644 index 0000000..797273d --- /dev/null +++ b/tests/test_panda_flyer.py @@ -0,0 +1,287 @@ +"""Integration test for HXNFlyerPanda's per-row (declared) array shape. + +Regression test for the DESCRIPTOR_10X_LENGTH bug: the scaler ("sclr1_ch*") +and Xspress3-ROI ("Det{n}_", "xspress3_channel{n}_rois_roi{m}") keys +declared a per-row length equal to the raw, `position_supersample`-oversampled +PandA gate count instead of the real number of scan points. Every 2D/1D PandA +fly-scan plan in hxn-profile-collection (`fly2dpd`, `fly1dpd`, `timescanpd`, +...) defaults `position_supersample=10`. + +Drives the real `hxntools.panda_flyer.HXNFlyerPanda` (no mock of the class +itself) through kickoff/complete/collect using fake `panda`/`sclr`/`xspress3` +stand-ins for the hardware-facing objects, writes real HDF5 files in the same +one-flat-dataset-per-channel layout `ExportSISDataPanda`/`ExportXpsROI` use, +and validates the resulting array shapes via a real, in-process Tiled server +(`bluesky_tiled_plugins.TiledWriter`). + +Run with: `pytest tests/test_panda_flyer.py -v` (from an environment with +`pip install -e ".[test]"`). +""" + +import os +from types import SimpleNamespace + +import bluesky.plan_stubs as bps +import h5py +import numpy as np +import pytest +from bluesky import RunEngine +from bluesky_tiled_plugins import TiledWriter +from bluesky_tiled_plugins.writing.tiled_writer import RunNormalizer + +from hxntools.panda_flyer import HXNFlyerPanda + +# Literal used by HXNFlyerPanda.kickoff() for the ROI resource spec. +ROI_SPEC = "ROI_HDF5_FLY" + + +def _alias_dataset(doc): + """RunNormalizer patch: map the legacy `column`/`det_elem`/`field` datum_kwargs + to `dataset`. + + The real SIS/ROI HDF5 files hold one flat dataset per channel/ROI name at + the file root (see `ExportSISDataPanda.export()` / `ExportXpsROI.export()`), + selected at read time via `column`/`det_elem`; the raw PandA capture file + (spec "PANDA") is likewise one flat dataset per field, selected via `field` + (see `kickoff()`'s `datum_kwargs={"field": value["value"]}`). + `bluesky_tiled_plugins`'s generic HDF5 consolidator expects that selector + under the `dataset` parameter; this mirrors the kind of normalizer patch a + Tiled deployment supplies for these HXN-specific legacy handler specs. + """ + dk = dict(doc.get("datum_kwargs", {})) + for legacy_key in ("column", "det_elem", "field"): + if legacy_key in dk: + dk["dataset"] = dk.pop(legacy_key) + doc["datum_kwargs"] = dk + return doc + + +def _fix_external_dtype(doc): + """RunNormalizer patch: declare the true on-disk dtype for the legacy + SIS/ROI external array data keys. + + `ExportSISDataPanda`/`ExportXpsROI` both write their flat HDF5 datasets + with a hardcoded 32-bit float dtype (`dtype="f"`), but `describe_collect()`'s + `_spec()` predates the `dtype_numpy`/`dtype_str` descriptor convention and + leaves those keys' dtype unset. Left unset, `bluesky_tiled_plugins` falls + back to the JSON-schema default (`float64`) and then rejects the + mismatched on-disk dtype at read time. This mirrors the kind of + normalizer patch a Tiled deployment supplies for these HXN-specific + legacy handler specs. + """ + for key in SCLR_CHANNELS + ROI_NAMES: + if key in doc.get("data_keys", {}): + doc["data_keys"][key]["dtype_str"] = " Date: Mon, 21 Sep 2026 19:50:40 +0000 Subject: [PATCH 3/6] CI: actually run the test suite CI previously only ran pre-commit (ruff) and a package-import smoke check (regular/editable install + first few discovered submodules); no job ever invoked pytest, so tests/test_panda_flyer.py was never exercised in CI. - Add a tests job (matrix: Python 3.11/3.12) that runs 'uv sync --locked --group dev' + 'pytest tests -v'. - Add doct/pims to [project.dependencies]: hxntools.handlers unconditionally imports timepix.py, which needs databroker.assets.handlers, which needs doct (databroker.utils) and pims (databroker.assets.readers.spe) -- both only declared as optional extras of databroker, not pulled in by our bare 'databroker' dependency. Without this, pytest can't even collect tests/test_panda_flyer.py (ModuleNotFoundError: No module named 'doct'), since it imports hxntools.panda_flyer -> hxntools.handlers.rasmi2 -> hxntools.handlers (package __init__, which eagerly imports every handler submodule including timepix). - Regenerate uv.lock (it was already stale relative to pyproject.toml before this change, from the prior merge of upstream main's packaging migration; 'uv lock --check' failed until this commit). --- .github/workflows/ci.yml | 24 + pyproject.toml | 2 + uv.lock | 2137 +++++++++++++++++++++++++++++++++++++- 3 files changed, 2162 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d92962b..e6fa78b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -80,3 +80,27 @@ jobs: except ImportError as e: print(f'⚠ {module} import failed: {e}') " + + tests: + name: Tests (Python ${{ matrix.python-version }}) + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.11", "3.12"] + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - uses: astral-sh/setup-uv@v7 + + - name: Run test suite + run: | + uv sync --locked --group dev --python "${{ matrix.python-version }}" + uv run --no-sync pytest tests -v diff --git a/pyproject.toml b/pyproject.toml index 0eb95d6..ae13c17 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,12 +28,14 @@ dependencies = [ "boltons", "cycler", "databroker", + "doct", "h5py", "matplotlib", "nslsii", "numpy", "ophyd", "pandas", + "pims", "pyepics", "scipy", ] diff --git a/uv.lock b/uv.lock index 4f8d5da..7279bfd 100644 --- a/uv.lock +++ b/uv.lock @@ -13,6 +13,108 @@ resolution-markers = [ "python_full_version < '3.12' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] +[[package]] +name = "adbc-driver-manager" +version = "1.12.0" +source = { registry = 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upload-time = "2025-09-14T22:18:19.088Z" }, +] From 5b5ef39cfe77e59c2122f9dde4cdfe3bf780bc59 Mon Sep 17 00:00:00 2001 From: Thomas Hopkins Date: Mon, 21 Sep 2026 15:59:03 -0400 Subject: [PATCH 4/6] Potential fix for pull request finding 'CodeQL / Workflow does not contain permissions' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com> --- .github/workflows/ci.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e6fa78b..8a3315c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,6 +7,9 @@ on: branches: - main +permissions: + contents: read + concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true From 1532941c660fd7da0ddcd439654a7f11f7c396ce Mon Sep 17 00:00:00 2001 From: thomashopkins32 Date: Mon, 21 Sep 2026 16:00:21 -0400 Subject: [PATCH 5/6] pre-commit --- tests/test_panda_flyer.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/tests/test_panda_flyer.py b/tests/test_panda_flyer.py index 797273d..f996287 100644 --- a/tests/test_panda_flyer.py +++ b/tests/test_panda_flyer.py @@ -163,7 +163,10 @@ def _fake_panda(): def _fake_scaler(channel_names, real_points): channels = SimpleNamespace( - **{f"chan{i}": SimpleNamespace(name=name) for i, name in enumerate(channel_names, start=1)} + **{ + f"chan{i}": SimpleNamespace(name=name) + for i, name in enumerate(channel_names, start=1) + } ) mca_by_index = { i: SimpleNamespace( @@ -173,7 +176,9 @@ def _fake_scaler(channel_names, real_points): ) for i in range(1, len(channel_names) + 1) } - return SimpleNamespace(channels=channels, stop_all=_FakeSignal(), mca_by_index=mca_by_index) + return SimpleNamespace( + channels=channels, stop_all=_FakeSignal(), mca_by_index=mca_by_index + ) def _fake_xspress3(roi_names, real_points): @@ -284,4 +289,6 @@ def plan(): assert node.structure().shape == (1, REAL_POINTS) assert node.read().shape == (1, REAL_POINTS) - assert tiled_client[uid].validate(fix_errors=False, raise_on_error=True, write_notes=False) + assert tiled_client[uid].validate( + fix_errors=False, raise_on_error=True, write_notes=False + ) From 2b1c8f05ce81ecc26374e557456fa7d1411cd6ac Mon Sep 17 00:00:00 2001 From: thomashopkins32 Date: Mon, 21 Sep 2026 20:32:43 +0000 Subject: [PATCH 6/6] describe_collect(): declare true on-disk dtype for SIS/ROI keys _spec() left dtype unset for the scaler ('sclr1_ch*') and Xspress3-ROI ('Det{n}_') external keys, even though it's known and fixed: ExportSISDataPanda/ExportXpsROI both hardcode a 32-bit float HDF5 dataset (dtype="f") for every channel/ROI. Left unset, bluesky_tiled_plugins fell back to the JSON-schema default (float64) and rejected the mismatched on-disk dtype at read time -- worked around in the test via a 'descriptor' normalizer patch (_fix_external_dtype). Unlike the datum_kwargs naming (column/det_elem/field, still required by the registered legacy SISHDF5Handler/ROIHDF5Handler/PandAHandlerHDF5 __call__ signatures in hxntools/handlers/), nothing depends on this dtype being *unset* -- it's purely additive metadata, safe to declare directly. Add dtype_str="", "xspress3_channel{n}_rois_roi{m}") keys -declared a per-row length equal to the raw, `position_supersample`-oversampled -PandA gate count instead of the real number of scan points. Every 2D/1D PandA -fly-scan plan in hxn-profile-collection (`fly2dpd`, `fly1dpd`, `timescanpd`, -...) defaults `position_supersample=10`. - -Drives the real `hxntools.panda_flyer.HXNFlyerPanda` (no mock of the class -itself) through kickoff/complete/collect using fake `panda`/`sclr`/`xspress3` -stand-ins for the hardware-facing objects, writes real HDF5 files in the same -one-flat-dataset-per-channel layout `ExportSISDataPanda`/`ExportXpsROI` use, -and validates the resulting array shapes via a real, in-process Tiled server -(`bluesky_tiled_plugins.TiledWriter`). - -Run with: `pytest tests/test_panda_flyer.py -v` (from an environment with -`pip install -e ".[test]"`). -""" +"""Integration tests for HXNFlyerPanda.""" import os from types import SimpleNamespace @@ -56,25 +38,6 @@ def _alias_dataset(doc): return doc -def _fix_external_dtype(doc): - """RunNormalizer patch: declare the true on-disk dtype for the legacy - SIS/ROI external array data keys. - - `ExportSISDataPanda`/`ExportXpsROI` both write their flat HDF5 datasets - with a hardcoded 32-bit float dtype (`dtype="f"`), but `describe_collect()`'s - `_spec()` predates the `dtype_numpy`/`dtype_str` descriptor convention and - leaves those keys' dtype unset. Left unset, `bluesky_tiled_plugins` falls - back to the JSON-schema default (`float64`) and then rejects the - mismatched on-disk dtype at read time. This mirrors the kind of - normalizer patch a Tiled deployment supplies for these HXN-specific - legacy handler specs. - """ - for key in SCLR_CHANNELS + ROI_NAMES: - if key in doc.get("data_keys", {}): - doc["data_keys"][key]["dtype_str"] = "