def test_checksum(self):
with tempfile.TemporaryDirectory() as tdir:
for dclass in self.classes:
dname = os.path.join(tdir, "dummy")
dummy = getattr(swd, dclass)(self.data[dclass],
samplerate=1000)
dummy.trialdefintion = self.trl[dclass]
save(dummy, dname)
# perform checksum-matching - this must work
dummy2 = load(dname, checksum=True)
# manipulate data file
hname = dummy._filename
del dummy, dummy2
time.sleep(0.1) # wait to kick-off garbage collection
h5f = h5py.File(hname, "r+")
dset = h5f["data"]
# provoke checksum error by adding 1 to all datasets
dset[()] += 1
h5f.close()
with pytest.raises(SPYValueError):
load(dname, checksum=True)
shutil.rmtree(dname + ".spy")
def test_logging(self):
with tempfile.TemporaryDirectory() as tdir:
fname = os.path.join(tdir, "dummy")
dummy = generate_artificial_data(inmemory=True)
ldum = len(dummy._log)
save(dummy, filename=fname)
# ensure saving is logged correctly
assert len(dummy._log) > ldum
assert dummy.filename in dummy._log
assert dummy.filename + FILE_EXT["info"] in dummy._log
assert dummy.cfg["method"] == "save"
assert dummy.filename in dummy.cfg["files"]
assert dummy.filename + FILE_EXT["info"] in dummy.cfg["files"]
# ensure loading is logged correctly
dummy2 = load(filename=fname + ".analog")
assert len(dummy2._log) > len(dummy._log)
assert dummy2.filename in dummy2._log
assert dummy2.filename + FILE_EXT["info"] in dummy._log
assert dummy2.cfg.cfg["method"] == "load"
assert dummy2.filename in dummy2.cfg.cfg["files"]
assert dummy2.filename + FILE_EXT["info"] in dummy2.cfg.cfg[
"files"]
# Delete all open references to file objects b4 closing tmp dir
del dummy, dummy2
def test_saveload(self):
with tempfile.TemporaryDirectory() as tdir:
fname = os.path.join(tdir, "dummy")
# basic but most important: ensure object integrity is preserved
checkAttr = [
"data", "dimord", "sampleinfo", "samplerate", "trialinfo"
]
dummy = EventData(self.data, samplerate=10)
dummy.save(fname)
filename = construct_spy_filename(fname, dummy)
dummy2 = load(filename)
for attr in checkAttr:
assert np.array_equal(getattr(dummy, attr),
getattr(dummy2, attr))
dummy3 = load(fname)
for attr in checkAttr:
assert np.array_equal(getattr(dummy3, attr),
getattr(dummy, attr))
save(dummy3, container=os.path.join(tdir, "ymmud"))
dummy4 = load(os.path.join(tdir, "ymmud"))
for attr in checkAttr:
assert np.array_equal(getattr(dummy4, attr),
getattr(dummy, attr))
del dummy2, dummy3, dummy4 # avoid PermissionError in Windows
# overwrite existing file w/new data
dummy.samplerate = 20
dummy.save()
dummy2 = load(filename=filename)
assert dummy2.samplerate == 20
del dummy, dummy2
time.sleep(0.1) # wait to kick-off garbage collection
# ensure trialdefinition is saved and loaded correctly
dummy = EventData(self.data,
trialdefinition=self.trl,
samplerate=10)
dummy.save(fname, overwrite=True)
dummy2 = load(filename)
assert np.array_equal(dummy.sampleinfo, dummy2.sampleinfo)
assert np.array_equal(dummy._t0, dummy2._t0)
assert np.array_equal(dummy.trialinfo, dummy2.trialinfo)
del dummy, dummy2
# swap dimensions and ensure `dimord` is preserved
dummy = EventData(self.data,
dimord=["eventid", "sample"],
samplerate=10)
dummy.save(fname + "_dimswap")
filename = construct_spy_filename(fname + "_dimswap", dummy)
dummy2 = load(filename)
assert dummy2.dimord == dummy.dimord
assert dummy2.eventid.size == self.num_smp # swapped
assert dummy2.data.shape == dummy.data.shape
# Delete all open references to file objects b4 closing tmp dir
del dummy, dummy2
time.sleep(0.1)
def test_saveload(self):
with tempfile.TemporaryDirectory() as tdir:
fname = os.path.join(tdir, "dummy")
# basic but most important: ensure object integrity is preserved
checkAttr = [
"channel", "data", "dimord", "freq", "sampleinfo",
"samplerate", "taper", "trialinfo"
]
dummy = SpectralData(self.data, samplerate=1000)
dummy.save(fname)
filename = construct_spy_filename(fname, dummy)
# dummy2 = SpectralData(filename)
# for attr in checkAttr:
# assert np.array_equal(getattr(dummy, attr), getattr(dummy2, attr))
dummy3 = load(fname)
for attr in checkAttr:
assert np.array_equal(getattr(dummy3, attr),
getattr(dummy, attr))
save(dummy3, container=os.path.join(tdir, "ymmud"))
dummy4 = load(os.path.join(tdir, "ymmud"))
for attr in checkAttr:
assert np.array_equal(getattr(dummy4, attr),
getattr(dummy, attr))
del dummy, dummy3, dummy4 # avoid PermissionError in Windows
# ensure trialdefinition is saved and loaded correctly
dummy = SpectralData(self.data,
trialdefinition=self.trl,
samplerate=1000)
dummy.save(fname, overwrite=True)
dummy2 = load(filename)
assert np.array_equal(dummy.trialdefinition,
dummy2.trialdefinition)
# test getters
assert np.array_equal(dummy.sampleinfo, dummy2.sampleinfo)
assert np.array_equal(dummy._t0, dummy2._t0)
assert np.array_equal(dummy.trialinfo, dummy2.trialinfo)
# swap dimensions and ensure `dimord` is preserved
dummy = SpectralData(self.data,
dimord=["time", "channel", "taper", "freq"],
samplerate=1000)
dummy.save(fname + "_dimswap")
filename = construct_spy_filename(fname + "_dimswap", dummy)
dummy2 = load(filename)
assert dummy2.dimord == dummy.dimord
assert dummy2.channel.size == self.nt # swapped
assert dummy2.taper.size == self.nf # swapped
assert dummy2.data.shape == dummy.data.shape
# Delete all open references to file objects b4 closing tmp dir
del dummy, dummy2
def test_save_mmap(self):
with tempfile.TemporaryDirectory() as tdir:
fname = os.path.join(tdir, "vdat.npy")
dname = os.path.join(tdir, "dummy")
vdata = np.ones((1000, 5000)) # ca. 38.2 MB
np.save(fname, vdata)
del vdata
dmap = open_memmap(fname)
adata = AnalogData(dmap, samplerate=10)
# Ensure memory consumption stays within provided bounds
mem = memory_usage()[0]
save(adata, filename=dname, memuse=60)
assert (mem - memory_usage()[0]) < 70
# Delete all open references to file objects b4 closing tmp dir
del dmap, adata
def test_save_fname(self):
for dclass in self.classes:
with tempfile.TemporaryDirectory() as tdir:
dummy = getattr(swd, dclass)(self.data[dclass],
samplerate=1000)
dummy.trialdefintion = self.trl[dclass]
# object w/o container association
with pytest.raises(SPYError):
dummy.save()
# filename without extension
filename = "some_filename"
save(dummy, filename=os.path.join(tdir, filename))
assert len(glob(os.path.join(tdir, filename + "*"))) == 2
# filename with extension
filename = "some_filename_w_ext" + dummy._classname_to_extension(
)
save(dummy, filename=os.path.join(tdir, filename))
assert len(glob(os.path.join(tdir, filename + "*"))) == 2
# filename with invalid extension
filename = "some_filename_w_ext.invalid"
with pytest.raises(SPYError):
save(dummy, filename=os.path.join(tdir, filename))
# filename with multiple extensions
filename = "some_filename.w.ext" + dummy._classname_to_extension(
)
with pytest.raises(SPYError):
save(dummy, filename=os.path.join(tdir, filename))
# container with extension
container = "test_container.spy"
save(dummy, container=os.path.join(tdir, container))
assert len(glob(os.path.join(tdir, container, "*"))) == 2
# container with invalid extension
container = "test_container.invalid"
with pytest.raises(SPYError):
save(dummy, container=os.path.join(tdir, container))
# container with multiple extensions
container = "test_container.invalid.too"
with pytest.raises(SPYValueError):
save(dummy, container=os.path.join(tdir, container))
# container w/o extension
container = "test_container2"
save(dummy, container=os.path.join(tdir, container))
assert len(glob(os.path.join(tdir, container + ".spy",
"*"))) == 2
# container with extension and tag
container = "test_container.spy"
tag = "sometag"
save(dummy, container=os.path.join(tdir, container), tag=tag)
assert len(
glob(
os.path.join(tdir, container,
"test_container_sometag*"))) == 2
# explicit overwrite
save(dummy,
container=os.path.join(tdir, container),
tag=tag,
overwrite=True)
assert len(
glob(
os.path.join(tdir, container,
"test_container_sometag*"))) == 2
# implicit overwrite
dummy.save()
assert len(
glob(
os.path.join(tdir, container,
"test_container_sometag*"))) == 2
# attempted overwrite w/o keyword
with pytest.raises(SPYIOError):
save(dummy,
container=os.path.join(tdir, container),
tag=tag)
# shortcut with new tag
dummy.save(tag="newtag")
assert len(
glob(
os.path.join(tdir, container,
"test_container_newtag*"))) == 2
# overwrite new tag
dummy.save(tag="newtag", overwrite=True)
assert len(
glob(
os.path.join(tdir, container,
"test_container_newtag*"))) == 2
# attempted overwrite w/o keyword
with pytest.raises(SPYIOError):
dummy.save(tag="newtag")
# both container and filename
with pytest.raises(SPYError):
save(dummy, container="container", filename="someFile")
# neither container nor filename
with pytest.raises(SPYError):
save(dummy)
del dummy
def test_saveload(self):
with tempfile.TemporaryDirectory() as tdir:
fname = os.path.join(tdir, "dummy")
# basic but most important: ensure object integrity is preserved
checkAttr = [
"channel", "data", "dimord", "sampleinfo", "samplerate",
"trialinfo"
]
dummy = AnalogData(data=self.data, samplerate=1000)
dummy.save(fname)
filename = construct_spy_filename(fname, dummy)
# NOTE: We removed support for loading data via the constructor
# dummy2 = AnalogData(filename)
# for attr in checkAttr:
# assert np.array_equal(getattr(dummy, attr), getattr(dummy2, attr))
dummy3 = load(fname)
for attr in checkAttr:
assert np.array_equal(getattr(dummy3, attr),
getattr(dummy, attr))
save(dummy3, container=os.path.join(tdir, "ymmud"))
dummy4 = load(os.path.join(tdir, "ymmud"))
for attr in checkAttr:
assert np.array_equal(getattr(dummy4, attr),
getattr(dummy, attr))
del dummy, dummy3, dummy4 # avoid PermissionError in Windows
# # FIXME: either remove or repair this
# # save object hosting VirtualData
# np.save(fname + ".npy", self.data)
# dmap = open_memmap(fname + ".npy", mode="r")
# vdata = VirtualData([dmap, dmap])
# dummy = AnalogData(vdata, samplerate=1000)
# dummy.save(fname, overwrite=True)
# dummy2 = AnalogData(filename)
# assert dummy2.mode == "r+"
# assert np.array_equal(dummy2.data, vdata[:, :])
# del dummy, dummy2 # avoid PermissionError in Windows
# ensure trialdefinition is saved and loaded correctly
dummy = AnalogData(data=self.data,
trialdefinition=self.trl,
samplerate=1000)
dummy.save(fname + "_trl")
filename = construct_spy_filename(fname + "_trl", dummy)
dummy2 = load(filename)
assert np.array_equal(dummy.trialdefinition,
dummy2.trialdefinition)
# test getters
assert np.array_equal(dummy.sampleinfo, dummy2.sampleinfo)
assert np.array_equal(dummy._t0, dummy2._t0)
assert np.array_equal(dummy.trialinfo, dummy2.trialinfo)
del dummy, dummy2 # avoid PermissionError in Windows
# swap dimensions and ensure `dimord` is preserved
dummy = AnalogData(data=self.data,
dimord=["channel", "time"],
samplerate=1000)
dummy.save(fname + "_dimswap")
filename = construct_spy_filename(fname + "_dimswap", dummy)
dummy2 = load(filename)
assert dummy2.dimord == dummy.dimord
assert dummy2.channel.size == self.ns # swapped
assert dummy2.data.shape == dummy.data.shape
# Delete all open references to file objects and wait 0.1s for changes
# to take effect (thanks, Windows!)
del dummy, dummy2
time.sleep(0.1)
