def test_feat_min_height():
qm = AFMQMap(data_dir / "map2x2_extracted.jpk-force-map")
qd = qm.get_qmap("data: lowest height", 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_get_coords_bad():
qm = AFMQMap(data_dir / "map2x2_extracted.jpk-force-map")
try:
qm.get_coords(which="mm")
except ValueError:
pass
else:
assert False, "Units [mm] should not be supported."
def test_feat_scan_order():
qm = AFMQMap(data_dir / "map2x2_extracted.jpk-force-map")
order = qm.get_qmap("meta: 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 = AFMQMap(data_dir / "map2x2_extracted.jpk-force-map")
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_missing():
fake_qmap_dict = {
"test-key": ["A description for the test key", "m", float],
}
group = AFMGroup(data_dir / "map2x2_extracted.jpk-force-map")
with mock.patch("afmformats.afm_qmap.META_FIELDS",
{"qmap": fake_qmap_dict}):
with pytest.raises(ValueError,
match="QMap metadata missing .* test-key"):
AFMQMap(group)
def test_shape():
qm = AFMQMap(data_dir / "map2x2_extracted.jpk-force-map")
assert np.allclose(
qm.extent,
[1.97265625, 601.97265625, -783.53515625, -183.53515625000006])
assert qm.shape == (10, 10)
def test_init_with_group_meta_override_meaningless():
group = AFMGroup(data_dir / "map2x2_extracted.jpk-force-map")
with pytest.raises(ValueError, match="meaningless"):
AFMQMap(group, meta_override={"spring constant": 1, "sensitivity": 2})
def test_init_with_group():
group = AFMGroup(data_dir / "map2x2_extracted.jpk-force-map")
qm = AFMQMap(group)
assert qm.shape == (10, 10)
def test_get_qmap():
qm = AFMQMap(data_dir / "map2x2_extracted.jpk-force-map")
x, y, _ = qm.get_qmap(feature="data: lowest height", qmap_only=False)
assert x.size == 10
assert y.size == 10