def _prepare_environ(self):
self.environ = dict()
self.environ["startts"] = ts = time.time()
self.environ["starttime"] = datetime.datetime.fromtimestamp(ts)
self.environ["serialno"] = 0
data_desc = list()
data_desc.append(
ColumnDesc(name="point_nb", label="#Pt No", dtype="int64"))
for i in range(self.nb_of_scalars):
data_desc.append(
ColumnDesc(name="spectrum%d" % i,
label="spectrum%d" % i,
dtype="float64"))
for i in range(self.nb_of_spectrums):
data_desc.append(
ColumnDesc(name="spectrum%d" % i,
label="spectrum%d" % i,
dtype="(float64, )"))
for i in range(self.nb_of_images):
data_desc.append(
ColumnDesc(name="image%d" % i,
label="image%d" % i,
dtype="((float64, ), )"))
data_desc.append(
ColumnDesc(name="timestamp", label="dt", dtype="float64"))
self.environ["datadesc"] = data_desc
self.environ["title"] = DESCRIPTION
self.environ["user"] = "******"
def test_dtype_float64(recorder):
"""Test creation of dataset with float64 data type"""
nb_records = 1
# create description of channel data
data_desc = [
ColumnDesc(name=COL1_NAME, label=COL1_NAME, dtype="float64",
shape=tuple())
]
environ = ENV.copy()
environ["datadesc"] = data_desc
# simulate sardana scan
environ["starttime"] = datetime.now()
record_list = RecordList(environ)
recorder._startRecordList(record_list)
for i in range(nb_records):
record = Record({COL1_NAME: 0.1}, i)
recorder._writeRecord(record)
environ["endtime"] = datetime.now()
recorder._endRecordList(record_list)
# assert if reading datasets from the sardana file access to the
# dataset of the partial files
file_ = h5py.File(recorder.filename)
for i in range(nb_records):
expected_data = 0.1
data = file_["entry0"]["measurement"][COL1_NAME][i]
msg = "data does not match"
assert data == expected_data, msg
def test_value_ref(recorder):
"""Test creation of dataset with str data type"""
nb_records = 1
# create description of channel data
data_desc = [
ColumnDesc(name=COL1_NAME, label=COL1_NAME, dtype="float64",
shape=(1024, 1024), value_ref_enabled=True)
]
environ = ENV.copy()
environ["datadesc"] = data_desc
# simulate sardana scan
environ["starttime"] = datetime.now()
record_list = RecordList(environ)
recorder._startRecordList(record_list)
for i in range(nb_records):
record = Record({COL1_NAME: "file:///tmp/test.edf"}, i)
recorder._writeRecord(record)
environ["endtime"] = datetime.now()
recorder._endRecordList(record_list)
# assert if reading datasets from the sardana file access to the
# dataset of the partial files
file_ = h5py.File(recorder.filename)
for i in range(nb_records):
expected_data = "file:///tmp/test.edf"
try:
dataset = file_["entry0"]["measurement"][COL1_NAME].asstr()
except AttributeError:
# h5py < 3
dataset = file_["entry0"]["measurement"][COL1_NAME]
data = dataset[i]
msg = "data does not match"
assert data == expected_data, msg
def test_dtype_float64(self):
"""Test creation of dataset with float64 data type"""
nb_records = 1
# create description of channel data
data_desc = [
ColumnDesc(name=COL1_NAME,
label=COL1_NAME,
dtype="float64",
shape=tuple())
]
self.env["datadesc"] = data_desc
# simulate sardana scan
recorder = NXscanH5_FileRecorder(filename=self.path)
self.env["starttime"] = datetime.now()
recorder._startRecordList(self.record_list)
for i in range(nb_records):
record = Record({COL1_NAME: 0.1}, i)
recorder._writeRecord(record)
self.env["endtime"] = datetime.now()
recorder._endRecordList(self.record_list)
# assert if reading datasets from the sardana file access to the
# dataset of the partial files
file_ = h5py.File(self.path)
for i in range(nb_records):
expected_data = 0.1
data = file_["entry0"]["measurement"][COL1_NAME][i]
msg = "data does not match"
self.assertEqual(data, expected_data, msg)
def test_VDS(self):
"""Test creation of VDS when channel reports URIs (str) of h5file
scheme in a simulated sardana scan (3 points).
"""
try:
h5py.VirtualLayout
except AttributeError:
self.skipTest("VDS not available in this version of h5py")
nb_records = 3
# create partial files
part_file_name_pattern = "test_vds_part{0}.h5"
part_file_paths = []
for i in range(nb_records):
path = os.path.join(self.dir_name,
part_file_name_pattern.format(i))
part_file_paths.append(path)
part_file = h5py.File(path, "w")
img = numpy.array([[i, i], [i, i]])
dataset = "dataset"
part_file.create_dataset(dataset, data=img)
part_file.flush()
part_file.close()
try:
# create description of channel data
data_desc = [
ColumnDesc(name=COL1_NAME,
label=COL1_NAME,
dtype="float64",
shape=(2, 2),
value_ref_enabled=True)
]
self.env["datadesc"] = data_desc
# simulate sardana scan
recorder = NXscanH5_FileRecorder(filename=self.path)
self.env["starttime"] = datetime.now()
recorder._startRecordList(self.record_list)
for i in range(nb_records):
ref = "h5file://" + part_file_paths[i] + "::" + dataset
record = Record({COL1_NAME: ref}, i)
recorder._writeRecord(record)
self.env["endtime"] = datetime.now()
recorder._endRecordList(self.record_list)
# assert if reading datasets from the sardana file access to the
# dataset of the partial files
file_ = h5py.File(self.path)
for i in range(nb_records):
expected_img = numpy.array([[i, i], [i, i]])
img = file_["entry0"]["measurement"][COL1_NAME][i]
msg = "VDS extracted image does not match"
# TODO: check if this assert works well
numpy.testing.assert_array_equal(img, expected_img, msg)
finally:
# remove partial files
for path in part_file_paths:
os.remove(path)
def _scan(path, serialno=0):
env = ENV.copy()
env["serialno"] = serialno
record_list = RecordList(env)
nb_records = 2
# create description of channel data
data_desc = [
ColumnDesc(name=COL1_NAME,
label=COL1_NAME,
dtype="float64",
shape=())
]
env["datadesc"] = data_desc
# simulate sardana scan
recorder = NXscanH5_FileRecorder(filename=path)
env["starttime"] = datetime.now()
recorder._startRecordList(record_list)
for i in range(nb_records):
record = Record({COL1_NAME: 0.1}, i)
recorder._writeRecord(record)
env["endtime"] = datetime.now()
recorder._endRecordList(record_list)