datasets: allow passing options to HDF5 backend (e.g. compression)

This breaks the internal dataset representation used by applets
and when saving to disk (``dataset_db.pyon``).

See ``test/test_dataset_db.py`` and ``test/test_datasets.py``
for examples.

Signed-off-by: Etienne Wodey <wodey@iqo.uni-hannover.de>
This commit is contained in:
Etienne Wodey 2020-11-16 21:10:56 +01:00
parent b8ab5f2607
commit d8b1e59538
15 changed files with 248 additions and 50 deletions

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@ -13,6 +13,10 @@ Highlights:
- Improved documentation
- Expose the DAC coarse mixer and sif_sync
- Exposes upconverter calibration and enabling/disabling of upconverter LO & RF outputs.
* HDF5 options can now be passed when creating datasets with ``set_dataset``. This allows
in particular to use transparent compression filters as follows:
``set_dataset(name, value, compression="gzip")``.
Breaking changes:
* Updated Phaser-Upconverter default frequency 2.875 GHz. The new default uses the target PFD
@ -20,6 +24,9 @@ Breaking changes:
* `Phaser.init()` now disables all Kasli-oscillators. This avoids full power RF output being
generated for some configurations.
* Phaser: fixed coarse mixer frequency configuration
* The internal dataset representation was changed to support tracking HDF5 options like e.g.
a compression method. This requires changes to code reading the dataset persistence file
(``dataset_db.pyon``) and to custom applets.
ARTIQ-6
@ -89,6 +96,7 @@ Breaking changes:
* Experiment classes with underscore-prefixed names are now ignored when ``artiq_client``
determines which experiment to submit (consistent with ``artiq_run``).
ARTIQ-5
-------

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@ -13,7 +13,7 @@ class NumberWidget(QtWidgets.QLCDNumber):
def data_changed(self, data, mods):
try:
n = float(data[self.dataset_name][1])
n = float(data[self.dataset_name]["value"])
except (KeyError, ValueError, TypeError):
n = "---"
self.display(n)

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@ -13,7 +13,7 @@ class Image(pyqtgraph.ImageView):
def data_changed(self, data, mods):
try:
img = data[self.args.img][1]
img = data[self.args.img]["value"]
except KeyError:
return
self.setImage(img)

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@ -13,11 +13,11 @@ class HistogramPlot(pyqtgraph.PlotWidget):
def data_changed(self, data, mods, title):
try:
y = data[self.args.y][1]
y = data[self.args.y]["value"]
if self.args.x is None:
x = None
else:
x = data[self.args.x][1]
x = data[self.args.x]["value"]
except KeyError:
return
if x is None:

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@ -5,6 +5,7 @@ import PyQt5 # make sure pyqtgraph imports Qt5
import pyqtgraph
from artiq.applets.simple import TitleApplet
from artiq.master.databases import make_dataset as empty_dataset
class XYPlot(pyqtgraph.PlotWidget):
@ -14,14 +15,14 @@ class XYPlot(pyqtgraph.PlotWidget):
def data_changed(self, data, mods, title):
try:
y = data[self.args.y][1]
y = data[self.args.y]["value"]
except KeyError:
return
x = data.get(self.args.x, (False, None))[1]
x = data.get(self.args.x, empty_dataset())["value"]
if x is None:
x = np.arange(len(y))
error = data.get(self.args.error, (False, None))[1]
fit = data.get(self.args.fit, (False, None))[1]
error = data.get(self.args.error, empty_dataset())["value"]
fit = data.get(self.args.fit, empty_dataset())["value"]
if not len(y) or len(y) != len(x):
return

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@ -112,9 +112,9 @@ class XYHistPlot(QtWidgets.QSplitter):
def data_changed(self, data, mods):
try:
xs = data[self.args.xs][1]
histogram_bins = data[self.args.histogram_bins][1]
histograms_counts = data[self.args.histograms_counts][1]
xs = data[self.args.xs]["value"]
histogram_bins = data[self.args.histogram_bins]["value"]
histograms_counts = data[self.args.histograms_counts]["value"]
except KeyError:
return
if self._can_use_partial(mods):

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@ -10,6 +10,7 @@ from sipyco.sync_struct import Subscriber, process_mod
from sipyco import pyon
from sipyco.pipe_ipc import AsyncioChildComm
from artiq.master.databases import make_dataset as empty_dataset
logger = logging.getLogger(__name__)
@ -251,7 +252,7 @@ class TitleApplet(SimpleApplet):
def emit_data_changed(self, data, mod_buffer):
if self.args.title is not None:
title_values = {k.replace(".", "/"): data.get(k, (False, None))[1]
title_values = {k.replace(".", "/"): data.get(k, empty_dataset())["value"]
for k in self.dataset_title}
try:
title = self.args.title.format(**title_values)

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@ -104,8 +104,8 @@ class DatasetsDock(QtWidgets.QDockWidget):
idx = self.table_model_filter.mapToSource(idx[0])
key = self.table_model.index_to_key(idx)
if key is not None:
persist, value = self.table_model.backing_store[key]
asyncio.ensure_future(self._upload_dataset(key, value))
dataset = self.table_model.backing_store[key]
asyncio.ensure_future(self._upload_dataset(key, dataset["value"]))
def save_state(self):
return bytes(self.table.header().saveState())

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@ -83,16 +83,16 @@ class StringEditor(Editor):
class Model(DictSyncTreeSepModel):
def __init__(self, init):
DictSyncTreeSepModel.__init__(self, ".",
["Dataset", "Persistent", "Value"],
init)
def __init__(self, init):
DictSyncTreeSepModel.__init__(
self, ".", ["Dataset", "Persistent", "Value"], init
)
def convert(self, k, v, column):
if column == 1:
return "Y" if v[0] else "N"
return "Y" if v["persist"] else "N"
elif column == 2:
return short_format(v[1])
return short_format(v["value"])
else:
raise ValueError
@ -152,8 +152,8 @@ class DatasetsDock(QtWidgets.QDockWidget):
idx = self.table_model_filter.mapToSource(idx[0])
key = self.table_model.index_to_key(idx)
if key is not None:
persist, value = self.table_model.backing_store[key]
t = type(value)
dataset = self.table_model.backing_store[key]
t = type(dataset["value"])
if np.issubdtype(t, np.number):
dialog_cls = NumberEditor
elif np.issubdtype(t, np.bool_):
@ -164,7 +164,7 @@ class DatasetsDock(QtWidgets.QDockWidget):
logger.error("Cannot edit dataset %s: "
"type %s is not supported", key, t)
return
dialog_cls(self, self.dataset_ctl, key, value).open()
dialog_cls(self, self.dataset_ctl, key, dataset["value"]).open()
def delete_clicked(self):
idx = self.table.selectedIndexes()

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@ -331,7 +331,8 @@ class HasEnvironment:
@rpc(flags={"async"})
def set_dataset(self, key, value,
broadcast=False, persist=False, archive=True, save=None):
broadcast=False, persist=False, archive=True, save=None,
**hdf5_options):
"""Sets the contents and handling modes of a dataset.
Datasets must be scalars (``bool``, ``int``, ``float`` or NumPy scalar)
@ -344,12 +345,20 @@ class HasEnvironment:
:param archive: the data is saved into the local storage of the current
run (archived as a HDF5 file).
:param save: deprecated.
:param hdf5_options: additional keyword arguments are passed to
:meth:`h5py.Group.create_dataset`. For example, pass ``compression="gzip"``
to enable transparent zlib compression of this dataset in the HDF5 archive.
See the `h5py documentation <https://docs.h5py.org/en/stable/high/group.html#h5py.Group.create_dataset>`_
for a list of valid options.
"""
if save is not None:
warnings.warn("set_dataset save parameter is deprecated, "
"use archive instead", FutureWarning)
archive = save
self.__dataset_mgr.set(key, value, broadcast, persist, archive)
self.__dataset_mgr.set(
key, value, broadcast, persist, archive, hdf5_options
)
@rpc(flags={"async"})
def mutate_dataset(self, key, index, value):

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@ -35,6 +35,15 @@ class DeviceDB:
return desc
def make_dataset(*, persist=False, value=None, hdf5_options=None):
"PYON-serializable representation of a dataset in the DatasetDB"
return {
"persist": persist,
"value": value,
"hdf5_options": hdf5_options or {},
}
class DatasetDB(TaskObject):
def __init__(self, persist_file, autosave_period=30):
self.persist_file = persist_file
@ -44,10 +53,23 @@ class DatasetDB(TaskObject):
file_data = pyon.load_file(self.persist_file)
except FileNotFoundError:
file_data = dict()
self.data = Notifier({k: (True, v) for k, v in file_data.items()})
self.data = Notifier(
{
k: make_dataset(
persist=True,
value=v["value"],
hdf5_options=v["hdf5_options"]
)
for k, v in file_data.items()
}
)
def save(self):
data = {k: v[1] for k, v in self.data.raw_view.items() if v[0]}
data = {
k: d
for k, d in self.data.raw_view.items()
if d["persist"]
}
pyon.store_file(self.persist_file, data)
async def _do(self):
@ -59,20 +81,23 @@ class DatasetDB(TaskObject):
self.save()
def get(self, key):
return self.data.raw_view[key][1]
return self.data.raw_view[key]
def update(self, mod):
process_mod(self.data, mod)
# convenience functions (update() can be used instead)
def set(self, key, value, persist=None):
def set(self, key, value, persist=None, **hdf5_options):
if persist is None:
if key in self.data.raw_view:
persist = self.data.raw_view[key][0]
persist = self.data.raw_view[key].persist
else:
persist = False
self.data[key] = (persist, value)
self.data[key] = make_dataset(
persist=persist,
value=value,
hdf5_options=hdf5_options,
)
def delete(self, key):
del self.data[key]
#

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@ -8,9 +8,12 @@ from operator import setitem
import importlib
import logging
import numpy as np
from sipyco.sync_struct import Notifier
from sipyco.pc_rpc import AutoTarget, Client, BestEffortClient
from artiq.master.databases import make_dataset
logger = logging.getLogger(__name__)
@ -115,7 +118,8 @@ class DatasetManager:
self.ddb = ddb
self._broadcaster.publish = ddb.update
def set(self, key, value, broadcast=False, persist=False, archive=True):
def set(self, key, value, broadcast=False, persist=False, archive=True,
hdf5_options=None):
if key in self.archive:
logger.warning("Modifying dataset '%s' which is in archive, "
"archive will remain untouched",
@ -125,12 +129,20 @@ class DatasetManager:
broadcast = True
if broadcast:
self._broadcaster[key] = persist, value
self._broadcaster[key] = make_dataset(
persist=persist,
value=value,
hdf5_options=hdf5_options,
)
elif key in self._broadcaster.raw_view:
del self._broadcaster[key]
if archive:
self.local[key] = value
self.local[key] = make_dataset(
persist=persist,
value=value,
hdf5_options=hdf5_options,
)
elif key in self.local:
del self.local[key]
@ -138,11 +150,11 @@ class DatasetManager:
target = self.local.get(key, None)
if key in self._broadcaster.raw_view:
if target is not None:
assert target is self._broadcaster.raw_view[key][1]
return self._broadcaster[key][1]
assert target["value"] is self._broadcaster.raw_view[key]["value"]
return self._broadcaster[key]["value"]
if target is None:
raise KeyError("Cannot mutate nonexistent dataset '{}'".format(key))
return target
return target["value"]
def mutate(self, key, index, value):
target = self._get_mutation_target(key)
@ -158,15 +170,15 @@ class DatasetManager:
def get(self, key, archive=False):
if key in self.local:
return self.local[key]
data = self.ddb.get(key)
return self.local[key]["value"]
dataset = self.ddb.get(key)
if archive:
if key in self.archive:
logger.warning("Dataset '%s' is already in archive, "
"overwriting", key, stack_info=True)
self.archive[key] = data
return data
self.archive[key] = dataset
return dataset["value"]
def write_hdf5(self, f):
datasets_group = f.create_group("datasets")
@ -182,7 +194,7 @@ def _write(group, k, v):
# Add context to exception message when the user writes a dataset that is
# not representable in HDF5.
try:
group[k] = v
group.create_dataset(k, data=v["value"], **v["hdf5_options"])
except TypeError as e:
raise TypeError("Error writing dataset '{}' of type '{}': {}".format(
k, type(v), e))
k, type(v["value"]), e))

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@ -0,0 +1,99 @@
"""Test internal dataset representation (persistence, applets)"""
import unittest
import tempfile
from artiq.master.databases import DatasetDB
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, compression=COMP)
self.ddb.set(KEY3, DATA, 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"])

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@ -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 +106,37 @@ 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,
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)

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@ -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