def test_load_jpk():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
md = jpkr.get_metadata(0, 1)
assert md["imaging mode"] == "force-distance"
assert len(jpkr) == 1, "Only one measurement"
assert len(jpkr.get_index_segment_numbers(0)) == 2, "approach and retract"
def test_open_jpk_simple():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
p_seg = jpkr.get_index_segment_path(0, 0)
loc_list = [ff for ff in jpkr.files if ff.count(p_seg)]
name, slot, dat = jpk_data.find_column_dat(loc_list, "height (piezo)")
properties = jpkr._get_index_segment_properties(0, 0)
with jpkr.arc.open(dat, "r") as fd:
height = jpk_data.load_dat_raw(fd, name=name, properties=properties)
assert height[0] == 50.425720226584403
def test_get_single_custom_slot():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
p_seg = jpkr.get_index_segment_path(0, 0)
loc_list = [ff for ff in jpkr.files if ff.count(p_seg)]
name, slot, dat = jpk_data.find_column_dat(loc_list, "height (piezo)")
properties = jpkr._get_index_segment_properties(0, 0)
with jpkr.arc.open(dat, "r") as fd:
data, unit, _ = jpk_data.load_dat_unit(fd, name=name,
properties=properties,
slot="nominal")
assert data[0] == 4.9574279773415606e-05
def test_get_time():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
time1 = jpkr.get_data(column="time", index=0, segment=0)
time2 = jpkr.get_data(column="time", index=0, segment=1)
m1 = jpkr.get_metadata(0, 0)
m2 = jpkr.get_metadata(0, 1)
assert np.allclose(m1["duration"], time2[0])
assert len(time1) == m1["point count"]
assert len(time2) == m2["point count"]
assert np.all(time1 < m1["duration"])
assert np.all(time2 < (m1["duration"] + m2["duration"]))
md = jpkr.get_metadata(0)
assert md["duration"] == m1["duration"] + m2["duration"]
assert md["point count"] == m1["point count"] + m2["point count"]
def test_get_both_metadata():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
md1 = jpkr.get_metadata(index=0, segment=0)
md2 = jpkr.get_metadata(index=0, segment=1)
md = jpkr.get_metadata(index=0, segment=None)
for key1 in md1:
if key1 in ["duration", "point count"]:
assert md1[key1] != md[key1], key1
else:
assert md1[key1] == md[key1], key1
for key2 in md2:
if key2 in ["duration", "point count", "time"]:
# time from approach curve should be used
assert md2[key2] != md[key2], key2
else:
assert md2[key2] == md[key2], key2
def test_open_jpk_conversion():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
p_seg = jpkr.get_index_segment_path(0, 0)
loc_list = [ff for ff in jpkr.files if ff.count(p_seg)]
properties = jpkr._get_index_segment_properties(0, 0)
chan_data = {}
for column in ["force", "height (piezo)", "height (measured)"]:
name, slot, dat = jpk_data.find_column_dat(loc_list, column)
with jpkr.arc.open(dat, "r") as fd:
chan_data[name] = jpk_data.load_dat_unit(fd, name, properties,
slot)
assert chan_data["vDeflection"][2] == "vDeflection (Force)"
assert chan_data["vDeflection"][1] == "N"
assert chan_data["vDeflection"][0][0] == -5.145579192349918e-10
assert chan_data["height"][0][0] == 2.8783223430683289e-05
assert chan_data["strainGaugeHeight"][0][0] == 2.2815672438768612e-05
def test_get_single_curves():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
jpkr.get_data(column="force", index=0, segment=0)
jpkr.get_data(column="height (piezo)", index=0, segment=0)
jpkr.get_data(column="height (measured)", index=0, segment=0)
def test_meta():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
md = jpkr.get_metadata(0, 1)
assert md["spring constant"] == 0.043493666407368466
def test_meta_single():
jpkfile = datadir / "spot3-0192.jpk-force"
jpkr = JPKReader(jpkfile)
md = jpkr.get_metadata(index=0, segment=0)
assert md["imaging modality"] == "force-distance"
assert md["duration"] == 0.9999999999999998
def test_meta_simple():
jpkfilemap = datadir / "map0d_extracted.jpk-force-map"
jpkr = JPKReader(jpkfilemap)
jpkr.get_metadata(index=0, segment=0)