forked from M-Labs/artiq
Merge pull request #1544 from airwoodix/dataset-compression
datasets: support compression in HDF5 archives
This commit is contained in:
GitHub
commit
311a818a49
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@ -34,6 +34,9 @@ Highlights:
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* Previously detected RTIO async errors are reported to the host after each kernel terminates and a
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warning is logged. The warning is additional to the one already printed in the core device log upon
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detection of the error.
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* HDF5 options can now be passed when creating datasets with ``set_dataset``. This allows
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in particular to use transparent compression filters as follows:
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``set_dataset(name, value, hdf5_options={"compression": "gzip"})``.
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Breaking changes:
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@ -46,6 +49,10 @@ Breaking changes:
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calling `ADF5356.init()`.
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* DRTIO: Changed message alignment from 32-bits to 64-bits.
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* The deprecated ``set_dataset(..., save=...)`` is no longer supported.
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* The internal dataset representation was changed to support tracking HDF5 options like e.g.
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a compression method. This requires changes to code reading the dataset persistence file
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(``dataset_db.pyon``) and to custom applets.
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ARTIQ-6
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-------
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@ -117,6 +124,7 @@ Breaking changes:
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* Experiment classes with underscore-prefixed names are now ignored when ``artiq_client``
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determines which experiment to submit (consistent with ``artiq_run``).
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ARTIQ-5
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-------
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@ -13,7 +13,7 @@ class NumberWidget(QtWidgets.QLCDNumber):
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def data_changed(self, data, mods):
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try:
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n = float(data[self.dataset_name][1])
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n = float(data[self.dataset_name]["value"])
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except (KeyError, ValueError, TypeError):
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n = "---"
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self.display(n)
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@ -13,7 +13,7 @@ class Image(pyqtgraph.ImageView):
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def data_changed(self, data, mods):
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try:
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img = data[self.args.img][1]
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img = data[self.args.img]["value"]
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except KeyError:
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return
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self.setImage(img)
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@ -17,11 +17,11 @@ class HistogramPlot(pyqtgraph.PlotWidget):
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def data_changed(self, data, mods, title):
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try:
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y = data[self.args.y][1]
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y = data[self.args.y]["value"]
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if self.args.x is None:
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x = None
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else:
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x = data[self.args.x][1]
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x = data[self.args.x]["value"]
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except KeyError:
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return
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if x is None:
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@ -6,6 +6,7 @@ from PyQt5.QtCore import QTimer
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import pyqtgraph
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from artiq.applets.simple import TitleApplet
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from artiq.master.databases import make_dataset as empty_dataset
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class XYPlot(pyqtgraph.PlotWidget):
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@ -21,14 +22,14 @@ class XYPlot(pyqtgraph.PlotWidget):
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def data_changed(self, data, mods, title):
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try:
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y = data[self.args.y][1]
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y = data[self.args.y]["value"]
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except KeyError:
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return
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x = data.get(self.args.x, (False, None))[1]
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x = data.get(self.args.x, empty_dataset())["value"]
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if x is None:
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x = np.arange(len(y))
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error = data.get(self.args.error, (False, None))[1]
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fit = data.get(self.args.fit, (False, None))[1]
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error = data.get(self.args.error, empty_dataset())["value"]
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fit = data.get(self.args.fit, empty_dataset())["value"]
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if not len(y) or len(y) != len(x):
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self.mismatch['X values'] = True
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@ -126,9 +126,9 @@ class XYHistPlot(QtWidgets.QSplitter):
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def data_changed(self, data, mods):
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try:
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xs = data[self.args.xs][1]
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histogram_bins = data[self.args.histogram_bins][1]
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histograms_counts = data[self.args.histograms_counts][1]
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xs = data[self.args.xs]["value"]
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histogram_bins = data[self.args.histogram_bins]["value"]
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histograms_counts = data[self.args.histograms_counts]["value"]
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except KeyError:
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return
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if len(xs) != histograms_counts.shape[0]:
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@ -10,6 +10,7 @@ from sipyco.sync_struct import Subscriber, process_mod
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from sipyco import pyon
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from sipyco.pipe_ipc import AsyncioChildComm
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from artiq.master.databases import make_dataset as empty_dataset
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logger = logging.getLogger(__name__)
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@ -251,7 +252,7 @@ class TitleApplet(SimpleApplet):
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def emit_data_changed(self, data, mod_buffer):
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if self.args.title is not None:
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title_values = {k.replace(".", "/"): data.get(k, (False, None))[1]
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title_values = {k.replace(".", "/"): data.get(k, empty_dataset())["value"]
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for k in self.dataset_title}
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try:
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title = self.args.title.format(**title_values)
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@ -104,8 +104,8 @@ class DatasetsDock(QtWidgets.QDockWidget):
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idx = self.table_model_filter.mapToSource(idx[0])
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key = self.table_model.index_to_key(idx)
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if key is not None:
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persist, value = self.table_model.backing_store[key]
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asyncio.ensure_future(self._upload_dataset(key, value))
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dataset = self.table_model.backing_store[key]
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asyncio.ensure_future(self._upload_dataset(key, dataset["value"]))
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def save_state(self):
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return bytes(self.table.header().saveState())
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@ -146,16 +146,16 @@ class Creator(QtWidgets.QDialog):
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class Model(DictSyncTreeSepModel):
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def __init__(self, init):
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DictSyncTreeSepModel.__init__(self, ".",
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["Dataset", "Persistent", "Value"],
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init)
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def __init__(self, init):
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DictSyncTreeSepModel.__init__(
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self, ".", ["Dataset", "Persistent", "Value"], init
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)
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def convert(self, k, v, column):
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if column == 1:
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return "Y" if v[0] else "N"
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return "Y" if v["persist"] else "N"
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elif column == 2:
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return short_format(v[1])
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return short_format(v["value"])
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else:
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raise ValueError
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@ -223,8 +223,8 @@ class DatasetsDock(QtWidgets.QDockWidget):
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idx = self.table_model_filter.mapToSource(idx[0])
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key = self.table_model.index_to_key(idx)
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if key is not None:
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persist, value = self.table_model.backing_store[key]
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t = type(value)
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dataset = self.table_model.backing_store[key]
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t = type(dataset["value"])
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if np.issubdtype(t, np.number):
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dialog_cls = NumberEditor
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elif np.issubdtype(t, np.bool_):
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@ -235,7 +235,7 @@ class DatasetsDock(QtWidgets.QDockWidget):
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logger.error("Cannot edit dataset %s: "
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"type %s is not supported", key, t)
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return
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dialog_cls(self, self.dataset_ctl, key, value).open()
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dialog_cls(self, self.dataset_ctl, key, dataset["value"]).open()
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def delete_clicked(self):
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idx = self.table.selectedIndexes()
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@ -330,7 +330,8 @@ class HasEnvironment:
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@rpc(flags={"async"})
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def set_dataset(self, key, value,
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broadcast=False, persist=False, archive=True):
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broadcast=False, persist=False, archive=True,
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hdf5_options=None):
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"""Sets the contents and handling modes of a dataset.
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Datasets must be scalars (``bool``, ``int``, ``float`` or NumPy scalar)
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@ -342,8 +343,16 @@ class HasEnvironment:
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broadcast.
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:param archive: the data is saved into the local storage of the current
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run (archived as a HDF5 file).
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:param hdf5_options: dict of keyword arguments to pass to
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:meth:`h5py.Group.create_dataset`. For example, pass ``{"compression": "gzip"}``
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to enable transparent zlib compression of this dataset in the HDF5 archive.
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See the `h5py documentation <https://docs.h5py.org/en/stable/high/group.html#h5py.Group.create_dataset>`_
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for a list of valid options.
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"""
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self.__dataset_mgr.set(key, value, broadcast, persist, archive)
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self.__dataset_mgr.set(
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key, value, broadcast, persist, archive, hdf5_options
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)
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@rpc(flags={"async"})
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def mutate_dataset(self, key, index, value):
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@ -35,6 +35,15 @@ class DeviceDB:
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return desc
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def make_dataset(*, persist=False, value=None, hdf5_options=None):
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"PYON-serializable representation of a dataset in the DatasetDB"
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return {
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"persist": persist,
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"value": value,
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"hdf5_options": hdf5_options or {},
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}
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class DatasetDB(TaskObject):
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def __init__(self, persist_file, autosave_period=30):
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self.persist_file = persist_file
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@ -44,10 +53,23 @@ class DatasetDB(TaskObject):
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file_data = pyon.load_file(self.persist_file)
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except FileNotFoundError:
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file_data = dict()
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self.data = Notifier({k: (True, v) for k, v in file_data.items()})
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self.data = Notifier(
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{
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k: make_dataset(
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persist=True,
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value=v["value"],
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hdf5_options=v["hdf5_options"]
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)
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for k, v in file_data.items()
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}
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)
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def save(self):
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data = {k: v[1] for k, v in self.data.raw_view.items() if v[0]}
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data = {
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k: d
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for k, d in self.data.raw_view.items()
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if d["persist"]
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}
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pyon.store_file(self.persist_file, data)
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async def _do(self):
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@ -59,20 +81,23 @@ class DatasetDB(TaskObject):
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self.save()
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def get(self, key):
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return self.data.raw_view[key][1]
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return self.data.raw_view[key]
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def update(self, mod):
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process_mod(self.data, mod)
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# convenience functions (update() can be used instead)
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def set(self, key, value, persist=None):
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def set(self, key, value, persist=None, hdf5_options=None):
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if persist is None:
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if key in self.data.raw_view:
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persist = self.data.raw_view[key][0]
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persist = self.data.raw_view[key]["persist"]
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else:
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persist = False
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self.data[key] = (persist, value)
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self.data[key] = make_dataset(
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persist=persist,
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value=value,
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hdf5_options=hdf5_options,
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)
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def delete(self, key):
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del self.data[key]
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#
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@ -8,9 +8,12 @@ from operator import setitem
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import importlib
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import logging
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import numpy as np
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from sipyco.sync_struct import Notifier
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from sipyco.pc_rpc import AutoTarget, Client, BestEffortClient
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from artiq.master.databases import make_dataset
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logger = logging.getLogger(__name__)
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@ -115,7 +118,8 @@ class DatasetManager:
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self.ddb = ddb
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self._broadcaster.publish = ddb.update
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def set(self, key, value, broadcast=False, persist=False, archive=True):
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def set(self, key, value, broadcast=False, persist=False, archive=True,
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hdf5_options=None):
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if key in self.archive:
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logger.warning("Modifying dataset '%s' which is in archive, "
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"archive will remain untouched",
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@ -125,12 +129,20 @@ class DatasetManager:
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broadcast = True
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if broadcast:
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self._broadcaster[key] = persist, value
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self._broadcaster[key] = make_dataset(
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persist=persist,
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value=value,
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hdf5_options=hdf5_options,
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)
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elif key in self._broadcaster.raw_view:
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del self._broadcaster[key]
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if archive:
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self.local[key] = value
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self.local[key] = make_dataset(
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persist=persist,
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value=value,
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hdf5_options=hdf5_options,
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)
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elif key in self.local:
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del self.local[key]
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@ -138,11 +150,11 @@ class DatasetManager:
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target = self.local.get(key, None)
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if key in self._broadcaster.raw_view:
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if target is not None:
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assert target is self._broadcaster.raw_view[key][1]
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return self._broadcaster[key][1]
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assert target["value"] is self._broadcaster.raw_view[key]["value"]
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return self._broadcaster[key]["value"]
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if target is None:
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raise KeyError("Cannot mutate nonexistent dataset '{}'".format(key))
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return target
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return target["value"]
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def mutate(self, key, index, value):
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target = self._get_mutation_target(key)
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@ -158,15 +170,15 @@ class DatasetManager:
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def get(self, key, archive=False):
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if key in self.local:
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return self.local[key]
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data = self.ddb.get(key)
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return self.local[key]["value"]
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dataset = self.ddb.get(key)
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if archive:
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if key in self.archive:
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logger.warning("Dataset '%s' is already in archive, "
|
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"overwriting", key, stack_info=True)
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self.archive[key] = data
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return data
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self.archive[key] = dataset
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return dataset["value"]
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def write_hdf5(self, f):
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datasets_group = f.create_group("datasets")
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|
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@ -182,7 +194,7 @@ def _write(group, k, v):
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# Add context to exception message when the user writes a dataset that is
|
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# not representable in HDF5.
|
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try:
|
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group[k] = v
|
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group.create_dataset(k, data=v["value"], **v["hdf5_options"])
|
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except TypeError as e:
|
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raise TypeError("Error writing dataset '{}' of type '{}': {}".format(
|
||||
k, type(v), e))
|
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k, type(v["value"]), e))
|
||||
|
|
|
|||
|
|
@ -0,0 +1,111 @@
|
|||
"""Test internal dataset representation (persistence, applets)"""
|
||||
import unittest
|
||||
import tempfile
|
||||
|
||||
from artiq.master.databases import DatasetDB
|
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from sipyco import pyon
|
||||
|
||||
KEY1 = "key1"
|
||||
KEY2 = "key2"
|
||||
KEY3 = "key3"
|
||||
DATA = list(range(10))
|
||||
COMP = "gzip"
|
||||
|
||||
|
||||
class TestDatasetDB(unittest.TestCase):
|
||||
def setUp(self):
|
||||
# empty dataset persistance file
|
||||
self.persist_file = tempfile.NamedTemporaryFile(mode="w+")
|
||||
print("{}", file=self.persist_file, flush=True)
|
||||
|
||||
self.ddb = DatasetDB(self.persist_file.name)
|
||||
|
||||
self.ddb.set(KEY1, DATA, persist=True)
|
||||
self.ddb.set(KEY2, DATA, persist=True, hdf5_options=dict(compression=COMP))
|
||||
self.ddb.set(KEY3, DATA, hdf5_options=dict(shuffle=True))
|
||||
|
||||
self.save_ddb_to_disk()
|
||||
|
||||
def save_ddb_to_disk(self):
|
||||
self.ddb.save()
|
||||
self.persist_file.flush()
|
||||
|
||||
def load_ddb_from_disk(self):
|
||||
return pyon.load_file(self.persist_file.name)
|
||||
|
||||
def test_persist_format(self):
|
||||
data = pyon.load_file(self.persist_file.name)
|
||||
|
||||
for key in [KEY1, KEY2]:
|
||||
self.assertTrue(data[key]["persist"])
|
||||
self.assertEqual(data[key]["value"], DATA)
|
||||
|
||||
self.assertEqual(data[KEY2]["hdf5_options"]["compression"], COMP)
|
||||
self.assertEqual(data[KEY1]["hdf5_options"], dict())
|
||||
|
||||
def test_only_persist_marked_datasets(self):
|
||||
data = self.load_ddb_from_disk()
|
||||
|
||||
with self.assertRaises(KeyError):
|
||||
data[KEY3]
|
||||
|
||||
def test_memory_format(self):
|
||||
ds = self.ddb.get(KEY2)
|
||||
self.assertTrue(ds["persist"])
|
||||
self.assertEqual(ds["value"], DATA)
|
||||
self.assertEqual(ds["hdf5_options"]["compression"], COMP)
|
||||
|
||||
ds = self.ddb.get(KEY3)
|
||||
self.assertFalse(ds["persist"])
|
||||
self.assertEqual(ds["value"], DATA)
|
||||
self.assertTrue(ds["hdf5_options"]["shuffle"])
|
||||
|
||||
def test_delete(self):
|
||||
self.ddb.delete(KEY1)
|
||||
self.save_ddb_to_disk()
|
||||
|
||||
data = self.load_ddb_from_disk()
|
||||
|
||||
with self.assertRaises(KeyError):
|
||||
data[KEY1]
|
||||
|
||||
self.assertTrue(data[KEY2]["persist"])
|
||||
|
||||
def test_update(self):
|
||||
self.assertFalse(self.ddb.get(KEY3)["persist"])
|
||||
|
||||
mod = {
|
||||
"action": "setitem",
|
||||
"path": [KEY3],
|
||||
"key": "persist",
|
||||
"value": True,
|
||||
}
|
||||
|
||||
self.ddb.update(mod)
|
||||
self.assertTrue(self.ddb.get(KEY3)["persist"])
|
||||
|
||||
def test_update_hdf5_options(self):
|
||||
with self.assertRaises(KeyError):
|
||||
self.ddb.get(KEY1)["hdf5_options"]["shuffle"]
|
||||
|
||||
mod = {
|
||||
"action": "setitem",
|
||||
"path": [KEY1, "hdf5_options"],
|
||||
"key": "shuffle",
|
||||
"value": False,
|
||||
}
|
||||
|
||||
self.ddb.update(mod)
|
||||
self.assertFalse(self.ddb.get(KEY1)["hdf5_options"]["shuffle"])
|
||||
|
||||
def test_reset_copies_persist(self):
|
||||
self.assertTrue(self.ddb.get(KEY1)["persist"])
|
||||
self.ddb.set(KEY1, DATA)
|
||||
self.assertTrue(self.ddb.get(KEY1)["persist"])
|
||||
|
||||
self.assertFalse(self.ddb.get(KEY3)["persist"])
|
||||
self.ddb.set(KEY3, DATA)
|
||||
self.assertFalse(self.ddb.get(KEY3)["persist"])
|
||||
|
||||
self.ddb.set(KEY3, DATA, persist=True)
|
||||
self.assertTrue(self.ddb.get(KEY3)["persist"])
|
||||
|
|
@ -3,6 +3,9 @@
|
|||
import copy
|
||||
import unittest
|
||||
|
||||
import h5py
|
||||
import numpy as np
|
||||
|
||||
from sipyco.sync_struct import process_mod
|
||||
|
||||
from artiq.experiment import EnvExperiment
|
||||
|
|
@ -14,7 +17,7 @@ class MockDatasetDB:
|
|||
self.data = dict()
|
||||
|
||||
def get(self, key):
|
||||
return self.data[key][1]
|
||||
return self.data[key]["value"]
|
||||
|
||||
def update(self, mod):
|
||||
# Copy mod before applying to avoid sharing references to objects
|
||||
|
|
@ -82,9 +85,9 @@ class ExperimentDatasetCase(unittest.TestCase):
|
|||
def test_append_broadcast(self):
|
||||
self.exp.set(KEY, [], broadcast=True)
|
||||
self.exp.append(KEY, 0)
|
||||
self.assertEqual(self.dataset_db.data[KEY][1], [0])
|
||||
self.assertEqual(self.dataset_db.data[KEY]["value"], [0])
|
||||
self.exp.append(KEY, 1)
|
||||
self.assertEqual(self.dataset_db.data[KEY][1], [0, 1])
|
||||
self.assertEqual(self.dataset_db.data[KEY]["value"], [0, 1])
|
||||
|
||||
def test_append_array(self):
|
||||
for broadcast in (True, False):
|
||||
|
|
@ -103,3 +106,44 @@ class ExperimentDatasetCase(unittest.TestCase):
|
|||
with self.assertRaises(KeyError):
|
||||
self.exp.append(KEY, 0)
|
||||
|
||||
def test_write_hdf5_options(self):
|
||||
data = np.random.randint(0, 1024, 1024)
|
||||
self.exp.set(
|
||||
KEY,
|
||||
data,
|
||||
hdf5_options=dict(
|
||||
compression="gzip",
|
||||
compression_opts=6,
|
||||
shuffle=True,
|
||||
fletcher32=True
|
||||
),
|
||||
)
|
||||
|
||||
with h5py.File("test.h5", "a", "core", backing_store=False) as f:
|
||||
self.dataset_mgr.write_hdf5(f)
|
||||
|
||||
self.assertTrue(np.array_equal(f["datasets"][KEY][()], data))
|
||||
self.assertEqual(f["datasets"][KEY].compression, "gzip")
|
||||
self.assertEqual(f["datasets"][KEY].compression_opts, 6)
|
||||
self.assertTrue(f["datasets"][KEY].shuffle)
|
||||
self.assertTrue(f["datasets"][KEY].fletcher32)
|
||||
|
||||
def test_write_hdf5_no_options(self):
|
||||
data = np.random.randint(0, 1024, 1024)
|
||||
self.exp.set(KEY, data)
|
||||
|
||||
with h5py.File("test.h5", "a", "core", backing_store=False) as f:
|
||||
self.dataset_mgr.write_hdf5(f)
|
||||
self.assertTrue(np.array_equal(f["datasets"][KEY][()], data))
|
||||
self.assertIsNone(f["datasets"][KEY].compression)
|
||||
|
||||
def test_write_hdf5_invalid_type(self):
|
||||
class CustomType:
|
||||
def __init__(self, x):
|
||||
self.x = x
|
||||
|
||||
self.exp.set(KEY, CustomType(42))
|
||||
|
||||
with h5py.File("test.h5", "w", "core", backing_store=False) as f:
|
||||
with self.assertRaisesRegex(TypeError, "CustomType"):
|
||||
self.dataset_mgr.write_hdf5(f)
|
||||
|
|
|
|||
|
|
@ -7,6 +7,7 @@ from time import time, sleep
|
|||
|
||||
from artiq.experiment import *
|
||||
from artiq.master.scheduler import Scheduler
|
||||
from artiq.master.databases import make_dataset
|
||||
|
||||
|
||||
class EmptyExperiment(EnvExperiment):
|
||||
|
|
@ -291,8 +292,13 @@ class SchedulerCase(unittest.TestCase):
|
|||
nonlocal termination_ok
|
||||
self.assertEqual(
|
||||
mod,
|
||||
{"action": "setitem", "key": "termination_ok",
|
||||
"value": (False, True), "path": []})
|
||||
{
|
||||
"action": "setitem",
|
||||
"key": "termination_ok",
|
||||
"value": make_dataset(value=True),
|
||||
"path": []
|
||||
}
|
||||
)
|
||||
termination_ok = True
|
||||
handlers = {
|
||||
"update_dataset": check_termination
|
||||
|
|
|
|||
Loading…
Reference in New Issue