def test_feat_min_height():
qm = qmap.QMap(jpkfile)
qd = qm.get_qmap("data: height base point", qmap_only=True)
assert np.allclose(qd[0, 0], 40.55030392499141)
assert np.allclose(qd[0, -1], 47.354988549298945)
assert np.allclose(qd[-1, -1], 96.1627883099352)
assert np.allclose(qd[-1, 0], 89.95170867840217)
def test_feat_emod_withfit():
qm = qmap.QMap(jpkfile2)
# fit data
for idnt in qm.group:
idnt.apply_preprocessing([
"compute_tip_position",
"correct_force_offset",
"correct_tip_offset",
])
inparams = model.model_sneddon_spherical_approximation \
.get_parameter_defaults()
inparams["E"].value = 50
inparams["R"].value = 37.28e-6 / 2
inparams["baseline"].vary = False
# Fit with absolute full range
idnt.fit_model(model_key="sneddon_spher_approx",
params_initial=inparams,
range_x=(0, 0),
range_type="absolute",
x_axis="tip position",
y_axis="force",
segment="approach",
weight_cp=2e-6)
qd = qm.get_qmap("fit: Young's modulus", qmap_only=True)
vals = qd.flat[~np.isnan(qd.flat)]
assert np.allclose(vals[0], 57.62946472325552), "gray matter"
assert np.allclose(vals[2], 46.61406865570242), "white matter"
assert np.allclose(vals[1], 17605.034077063443), "background"
def test_feat_cp():
qm = qmap.QMap(jpkfile2)
# fit data
for idnt in qm.group:
idnt.apply_preprocessing([
"compute_tip_position",
"correct_force_offset",
"correct_tip_offset",
])
inparams = model.model_sneddon_spherical_approximation \
.get_parameter_defaults()
inparams["E"].value = 50
inparams["R"].value = 37.28e-6 / 2
inparams["baseline"].vary = False
# Fit with absolute full range
idnt.fit_model(model_key="sneddon_spher_approx",
params_initial=inparams,
range_x=(0, 0),
range_type="absolute",
x_axis="tip position",
y_axis="force",
segment="approach",
weight_cp=2e-6)
qd = qm.get_qmap("fit: contact point", qmap_only=True)
vals = qd.flat[~np.isnan(qd.flat)]
# These are subject to change when contact point preprocessing
# changes.
assert np.allclose(vals[0], -1820.431327293334), "gray matter"
assert np.allclose(vals[2], -3581.010097829371), "white matter"
assert np.allclose(vals[1], -2106.9835957851064), "background"
def test_feat_rating():
"""Reproduces rating in figures 5K-M"""
qm = qmap.QMap(jpkfile2)
# fit data
for idnt in qm.group:
idnt.apply_preprocessing([
"compute_tip_position", "correct_force_offset",
"correct_tip_offset"
])
inparams = model.model_sneddon_spherical_approximation \
.get_parameter_defaults()
inparams["E"].value = 50
inparams["R"].value = 37.28e-6 / 2
inparams["baseline"].vary = False
# Fit with absolute full range
idnt.fit_model(model_key="sneddon_spher_approx",
params_initial=inparams,
range_x=(0, 0),
range_type="absolute",
x_axis="tip position",
y_axis="force",
segment="approach",
weight_cp=2e-6)
idnt.rate_quality(training_set="zef18", regressor="Extra Trees")
qd = qm.get_qmap("fit: rating", qmap_only=True)
vals = qd.flat[~np.isnan(qd.flat)]
assert np.allclose(vals[0], 9.370435813605962), "gray matter"
assert np.allclose(vals[2], 4.942804081687071), "white matter"
assert np.allclose(vals[1], 2.432396277782555), "background"
def test_feat_emod_nofit():
qm = qmap.QMap(jpkfile)
with warnings.catch_warnings(record=True) as w:
# No data available, because there is no fit
qd = qm.get_qmap("fit: Young's modulus", qmap_only=True)
assert len(w) == 4
assert w[0].category is qmap.DataMissingWarning
assert np.alltrue(np.isnan(qd))
def test_get_coords_bad():
qm = qmap.QMap(jpkfile)
try:
qm.get_coords(which="mm")
except ValueError:
pass
else:
assert False, "Units [mm] should not be supported."
def test_feat_scan_order():
qm = qmap.QMap(jpkfile)
order = qm.get_qmap("data: scan order", qmap_only=True)
assert order[0, 0] == 0
assert order[0, -1] == 1
assert order[-1, -1] == 2
assert order[-1, 0] == 3
assert np.isnan(order[0, 1])
def test_get_coords():
qm = qmap.QMap(jpkfile)
px = qm.get_coords(which="px")
refpx = np.array([[0, 0], [9, 0], [9, 9], [0, 9]])
assert np.all(px == refpx)
um = qm.get_coords(which="um")
refum = np.array([[31.972656250000004, -753.5351562500001],
[571.8359375000001, -753.90625],
[571.8359375000001, -213.73046875000003],
[31.855468750000004, -213.73046875000003]])
assert np.all(um == refum)
def test_metadata():
qm = qmap.QMap(jpkfile)
assert np.allclose(
qm.extent,
[1.97265625, 601.97265625, -783.53515625, -183.53515625000006])
assert qm.shape == (10, 10)
def test_init_with_dataset():
ds = IndentationGroup(jpkfile)
qm = qmap.QMap(ds)
assert qm.shape == (10, 10)
def test_get_qmap():
qm = qmap.QMap(jpkfile)
x, y, _ = qm.get_qmap(feature="data: height base point", qmap_only=False)
assert x.size == 10
assert y.size == 10
