def test_with_rtdc_warning():
keys = ["area_um", "deform"]
ddict = example_data_dict(size=8472, keys=keys)
# legacy
ds = dclab.new_dataset(ddict)
ds.config["setup"]["flow rate"] = 0.16
ds.config["setup"]["channel width"] = 30
ds.config["setup"]["medium"] = "CellCarrier"
ds.config["imaging"]["pixel size"] = .34
i1 = iso.get_default()
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning (temperature missing).
i1.get_with_rtdcbase(col1="area_um",
col2="deform",
lut_identifier="LE-2D-FEM-19",
dataset=ds,
viscosity=None,
add_px_err=False)
# Verify some things
assert len(w) == 1
assert issubclass(w[-1].category,
iso.IsoelasticsEmodulusMeaninglessWarning)
assert "plotting" in str(w[-1].message)
def get_isoelastics(mm):
isotype = mm.config["plotting"]["isoelastics"]
xax = mm.config["plotting"]["axis x"].lower()
yax = mm.config["plotting"]["axis y"].lower()
if isotype == "not shown":
# nothing to do
isoel = None
else:
if "legacy" in isotype:
method = "analytical"
isosource = legacy_isoelastics
add_px_err = False
px_um = None
else:
method = isotype
isosource = isoelastics.get_default()
add_px_err = True
px_um = mm.config["imaging"]["pixel size"]
kwargs = dict(method=method,
channel_width=mm.config["setup"]["channel width"],
flow_rate=None,
viscosity=None,
col1=xax,
col2=yax,
add_px_err=add_px_err,
px_um=px_um,
)
try:
isoel = isosource.get(**kwargs)
except KeyError:
warnings.warn("Could not find matching isoelastics for"+
" Setting: x={}, y={}, method: {}".
format(xax, yax, kwargs["method"]))
isoel = None
return isoel
def test_with_rtdc():
keys = ["area_um", "deform"]
ddict = example_data_dict(size=8472, keys=keys)
# legacy
ds = dclab.new_dataset(ddict)
ds.config["setup"]["flow rate"] = 0.16
ds.config["setup"]["channel width"] = 30
ds.config["setup"]["temperature"] = 23.0
ds.config["setup"]["medium"] = "CellCarrier"
ds.config["imaging"]["pixel size"] = .34
i1 = iso.get_default()
data1 = i1.get_with_rtdcbase(col1="area_um",
col2="deform",
lut_identifier="LE-2D-FEM-19",
dataset=ds,
viscosity=None,
add_px_err=False)
viscosity = emodulus.viscosity.get_viscosity(
medium="CellCarrier",
channel_width=ds.config["setup"]["channel width"],
flow_rate=ds.config["setup"]["flow rate"],
temperature=ds.config["setup"]["temperature"])
data2 = i1.get(col1="area_um",
col2="deform",
lut_identifier="LE-2D-FEM-19",
channel_width=ds.config["setup"]["channel width"],
flow_rate=ds.config["setup"]["flow rate"],
viscosity=viscosity,
add_px_err=False,
px_um=ds.config["imaging"]["pixel size"])
for d1, d2 in zip(data1, data2):
assert np.allclose(d1, d2, atol=0, rtol=1e-14)
def test_volume_switch():
"""Switch the columns"""
i1 = iso.get_default()
data = i1.get(col1="deform",
col2="volume",
channel_width=20,
flow_rate=0.04,
viscosity=15,
lut_identifier="LE-2D-FEM-19",
add_px_err=False,
px_um=None)
assert np.allclose(data[0][0], [4.18005e-02, 1.61819e+02, 1.08000e+00])
assert np.allclose(data[-1][-1], [1.26408e-02, 3.16212e+03, 1.08400e+01])
def test_volume_scale_2():
"""The default values are used if set to None"""
i1 = iso.get_default()
data = i1.get(col1="volume",
col2="deform",
channel_width=25,
flow_rate=None,
viscosity=None,
lut_identifier="LE-2D-FEM-19",
add_px_err=False,
px_um=None)
assert np.allclose(
data[0][0],
[1.61819e+02 * (25 / 20)**3, 4.18005e-02, 1.08000e+00 * (20 / 25)**3])
def test_volume_pxcorr():
"""Deformation is pixelation-corrected using volume"""
i1 = iso.get_default()
data = i1.get(col1="volume",
col2="deform",
channel_width=20,
flow_rate=None,
viscosity=None,
lut_identifier="LE-2D-FEM-19",
add_px_err=True,
px_um=0.34)
ddelt = pxcorr.corr_deform_with_volume(1.61819e+02, px_um=0.34)
assert np.allclose(data[0][0],
[1.61819e+02, 4.18005e-02 + ddelt, 1.08000e+00])
def test_volume_basic():
"""Reproduce exact data from simulation result"""
i1 = iso.get_default()
data = i1.get(col1="volume",
col2="deform",
channel_width=20,
flow_rate=0.04,
viscosity=15,
lut_identifier="LE-2D-FEM-19",
add_px_err=False,
px_um=None)
assert np.allclose(data[0][0], [1.61819e+02, 4.18005e-02, 1.08000e+00])
assert np.allclose(data[0][-1], [5.90127e+02, 1.47449e-01, 1.08000e+00])
assert np.allclose(data[1][0], [1.61819e+02, 2.52114e-02, 1.36000e+00])
assert np.allclose(data[-1][-1], [3.16212e+03, 1.26408e-02, 1.08400e+01])
def get_isoelastics(mm):
isotype = mm.config["plotting"]["isoelastics"]
xax = mm.config["plotting"]["axis x"].lower()
yax = mm.config["plotting"]["axis y"].lower()
if isotype == "not shown":
# nothing to do
isoel = None
else:
if "legacy" in isotype:
method = "analytical"
isosource = legacy_isoelastics
add_px_err = False
px_um = None
else:
method = isotype
isosource = isoelastics.get_default()
add_px_err = True
px_um = mm.config["imaging"]["pixel size"]
kwargs = dict(
method=method,
channel_width=mm.config["setup"]["channel width"],
flow_rate=None,
viscosity=None,
col1=xax,
col2=yax,
add_px_err=add_px_err,
px_um=px_um,
)
try:
isoel = isosource.get(**kwargs)
except KeyError:
warnings.warn("Could not find matching isoelastics for" +
" Setting: x={}, y={}, method: {}".format(
xax, yax, kwargs["method"]))
isoel = None
return isoel