def test_missing_file():
pytest.importorskip("nptdms")
h5path = retrieve_data("fmt-tdms_2fl-no-image_2017.zip")
h5path.with_name("M1_para.ini").unlink()
try:
check_dataset(h5path)
except fmt_tdms.IncompleteTDMSFileFormatError:
pass
else:
assert False
def test_exact():
pytest.importorskip("nptdms")
h5path = retrieve_data("fmt-tdms_2fl-no-image_2017.zip")
viol, aler, info = check_dataset(h5path)
known_viol = [
"Metadata: Missing key [fluorescence] 'channel count'",
"Metadata: Missing key [fluorescence] 'channels installed'",
"Metadata: Missing key [fluorescence] 'laser count'",
"Metadata: Missing key [fluorescence] 'lasers installed'",
"Metadata: Missing key [fluorescence] 'samples per event'",
]
known_aler = [
"Metadata: Missing key [fluorescence] 'channel 1 name'",
"Metadata: Missing key [fluorescence] 'channel 2 name'",
"Metadata: Missing key [online_contour] 'no absdiff'",
"Metadata: Missing key [setup] 'identifier'",
"Metadata: Missing key [setup] 'module composition'",
"Negative value for feature(s): fl2_max",
]
known_info = [
'Compression: None',
'Data file format: tdms',
'Fluorescence: True',
]
assert set(viol) == set(known_viol)
assert set(aler) == set(known_aler)
assert set(info) == set(known_info)
def test_basic():
h5path = retrieve_data("fmt-hdf5_fl_2017.zip")
viol, aler, info = check_dataset(h5path)
# Features: Unknown key 'ncells'
# Metadata: Mismatch [imaging] 'roi size x' and feature image (50 vs 90)
# Metadata: Mismatch [imaging] 'roi size y' and feature image (90 vs 50)
# Metadata: Missing key [fluorescence] 'channels installed'
# Metadata: Missing key [fluorescence] 'laser count'
# Metadata: Missing key [fluorescence] 'lasers installed'
# Metadata: Missing key [fluorescence] 'samples per event'
# Metadata: fluorescence channel count inconsistent
assert len(viol) == 8
# "HDF5: '/image': attribute 'CLASS' should be fixed-length ASCII string",
# "HDF5: '/image': attribute 'IMAGE_SUBCLASS' should be fixed-length ...
# "HDF5: '/image': attribute 'IMAGE_VERSION' should be fixed-length ...
# "Metadata: Flow rates don't add up (sh 0.6 + sam 0.1 != channel 0.16)",
# "Metadata: Flow rates don't add up (sh 0.6 + sam 0.1 != channel 0.16)",
# "Metadata: Flow rates don't add up (sh 0.6 + sam 0.1 != channel 0.16)",
# "Metadata: Missing key [fluorescence] 'channel 1 name'",
# "Metadata: Missing key [fluorescence] 'channel 2 name'",
# "Metadata: Missing key [fluorescence] 'channel 3 name'",
# "Metadata: Missing key [setup] 'identifier'",
# "Metadata: Missing section 'online_contour'"
# "UnknownConfigurationKeyWarning: Unknown key 'exposure time' ...",
# "UnknownConfigurationKeyWarning: Unknown key 'flash current' ...",
# "UserWarning: Type of confguration key [fluorescence]: sample rate ...",
# "UserWarning: Type of confguration key [imaging]: roi position x ...",
# "UserWarning: Type of confguration key [imaging]: roi position y ..."]
assert len(aler) == 16
assert "Data file format: hdf5" in info
assert "Fluorescence: True" in info
assert "Compression: Partial (1 of 25)" in info
def test_wrong_samples_per_event():
pytest.importorskip("nptdms")
h5path = retrieve_data("fmt-tdms_2fl-no-image_2017.zip")
with h5path.with_name("M1_para.ini").open("a") as fd:
fd.write("Samples Per Event = 10\n")
msg = "Metadata: wrong number of samples per event: fl1_median " \
+ "(expected 10, got 566)"
viol, _, _ = check_dataset(h5path)
assert msg in viol
def test_temperature():
# there are probably a million things wrong with this dataset, but
# we are only looking for the temperature thing
ddict = example_data_dict(size=8472, keys=["area_um", "deform", "temp"])
ds = new_dataset(ddict)
sstr = "Metadata: Missing key [setup] 'temperature', " \
+ "because the 'temp' feature is given"
_, aler, _ = check_dataset(ds)
assert sstr in aler
def test_complete():
h5path = retrieve_data("fmt-hdf5_fl_2018.zip")
viol, aler, info = check_dataset(h5path)
assert len(viol) == 0
# [fluorescence]: sample rate should be <class 'numbers.Integral'>
# [imaging]: roi position x should be <class 'numbers.Integral'>
# [imaging]: roi position y should be <class 'numbers.Integral'>
assert len(aler) == 3
assert "Data file format: hdf5" in info
assert "Fluorescence: True" in info
def test_no_fluorescence():
pytest.importorskip("nptdms")
h5path = retrieve_data("fmt-tdms_minimal_2016.zip")
_, _, info = check_dataset(h5path)
known_info = [
'Compression: None',
'Data file format: tdms',
'Fluorescence: False',
]
assert set(info) == set(known_info)
def test_invalid_medium():
pytest.importorskip("nptdms")
h5path = retrieve_data("fmt-tdms_minimal_2016.zip")
para = h5path.with_name("M1_para.ini")
cfg = para.read_text().split("\n")
cfg.insert(3, "Buffer Medium = unknown_bad!")
para.write_text("\n".join(cfg))
viol, _, _ = check_dataset(h5path)
# changed in 0.29.1: medium can now be an arbitrary string
# except for an empty string.
assert "Metadata: Invalid value [setup] medium: 'unknown_bad!'" not in viol
def test_complete_user_metadata():
"""Setting any user metadata is allowed"""
h5path = retrieve_data("fmt-hdf5_fl_2018.zip")
metadata = {
"channel area": 100.5,
"inlet": True,
"n_constrictions": 3,
"channel information": "other information"
}
with new_dataset(h5path) as ds:
ds.config.update({"user": metadata})
expath = h5path.with_name("exported.rtdc")
ds.export.hdf5(expath, features=ds.features_innate)
viol, aler, info = check_dataset(ds)
assert len(viol) == 0
assert len(aler) == 0
assert "Data file format: hdf5" in info
assert "Fluorescence: True" in info
def test_load_with():
pytest.importorskip("nptdms")
h5path = retrieve_data("fmt-tdms_minimal_2016.zip")
known_aler = [
"Metadata: Missing key [setup] 'flow rate sample'",
"Metadata: Missing key [setup] 'flow rate sheath'",
"Metadata: Missing key [setup] 'identifier'",
"Metadata: Missing key [setup] 'module composition'",
"Metadata: Missing key [setup] 'software version'",
]
known_viol = [
"Features: wrong event count: 'contour' (14 of 156)",
"Features: wrong event count: 'mask' (14 of 156)",
"Metadata: Missing key [setup] 'medium'",
]
with new_dataset(h5path) as ds:
viol, aler, _ = check_dataset(ds)
assert set(viol) == set(known_viol)
assert set(aler) == set(known_aler)
def test_basic():
h5path = retrieve_data("rtdc_data_hdf5_contour_image_trace.zip")
viol, aler, info = check_dataset(h5path)
# Features: Unknown key 'ncells'
# Metadata: Missing key [fluorescence] 'channels installed'
# Metadata: Missing key [fluorescence] 'laser count'
# Metadata: Missing key [fluorescence] 'lasers installed'
# Metadata: Missing key [fluorescence] 'samples per event'
# Metadata: Unknown key [imaging] 'exposure time'
# Metadata: Unknown key [imaging] 'flash current'
# Metadata: Unknown key [setup] 'temperature'
# Metadata: fluorescence channel count inconsistent
assert len(viol) == 9
# Metadata: Missing key [setup] identifier'
# Metadata: Missing section 'online_contour'
# "HDF5: '/image': attribute 'CLASS' should be fixed-length ASCII string",
# "HDF5: '/image': attribute 'IMAGE_SUBCLASS' should be fixed-length ...",
# "HDF5: '/image': attribute 'IMAGE_VERSION' should be fixed-length ...",
assert len(aler) == 5
assert "Data file format: hdf5" in info
assert "Fluorescence: True" in info
cleanup()