diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d92962b..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 @@ -80,3 +83,27 @@ 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 33c3294..ae13c17 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,35 +9,35 @@ description = "NSLS-II Hard X-ray Nanoprobe data acquisition tools" readme = "README.md" requires-python = ">=3.11" license = "BSD-3-Clause" -authors = [ - {name = "Brookhaven National Laboratory", email = "DAMA@bnl.gov"} -] +authors = [{ name = "Brookhaven National Laboratory", email = "DAMA@bnl.gov" }] classifiers = [ - "Development Status :: 5 - Production/Stable", - "Intended Audience :: Science/Research", - "Intended Audience :: Developers", - "Natural Language :: English", - "Operating System :: OS Independent", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Topic :: Scientific/Engineering", + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "Intended Audience :: Developers", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Topic :: Scientific/Engineering", ] dependencies = [ - "bluesky", - "boltons", - "cycler", - "databroker", - "h5py", - "matplotlib", - "nslsii", - "numpy", - "ophyd", - "pandas", - "pyepics", - "scipy", + "bluesky", + "boltons", + "cycler", + "databroker", + "doct", + "h5py", + "matplotlib", + "nslsii", + "numpy", + "ophyd", + "pandas", + "pims", + "pyepics", + "scipy", ] [project.urls] @@ -48,7 +48,10 @@ Changelog = "https://github.com/NSLS-II-HXN/hxntools/releases" [dependency-groups] dev = [ - "pre-commit>=4.3", + "pre-commit>=4.3", + "pytest>=8.0", + "bluesky-tiled-plugins>=2.0.11", + "tiled[server]>=0.2.18", ] [tool.hatch.version] diff --git a/src/hxntools/panda_flyer.py b/src/hxntools/panda_flyer.py new file mode 100644 index 0000000..961cb2e --- /dev/null +++ b/src/hxntools/panda_flyer.py @@ -0,0 +1,592 @@ +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*. 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