def test_simple(self):
""" Just one point is not in the convex region. """
data = Table.from_numpy(None, [[1, 2, 1, 1]])
i = RubberbandBaseline()(data)
np.testing.assert_equal(i.X, [[0, 1, 0, 0]])
data = Table.from_numpy(None, [[1, 2, 1, 1]])
i = RubberbandBaseline(peak_dir=RubberbandBaseline.PeakNegative)(data)
np.testing.assert_equal(i.X, [[0, 0, -0.5, 0]])
def test_whole(self):
""" Every point belongs in the convex region. """
data = Table.from_numpy(None, [[2, 1, 2]])
i = RubberbandBaseline()(data)
np.testing.assert_equal(i.X, 0)
data = Table.from_numpy(None, [[1, 2, 1]])
i = RubberbandBaseline(peak_dir=RubberbandBaseline.PeakNegative)(data)
np.testing.assert_equal(i.X, 0)
def createinstance(params):
baseline_type = params.get("baseline_type", 0)
peak_dir = params.get("peak_dir", 0)
sub = params.get("sub", 0)
zero_points = params.get("zero_points", None)
if baseline_type == 0:
return LinearBaseline(peak_dir=peak_dir,
sub=sub,
zero_points=zero_points)
elif baseline_type == 1:
return RubberbandBaseline(peak_dir=peak_dir, sub=sub)
else:
raise Exception("unknown baseline type")
PREPROCESSORS_INDEPENDENT_SAMPLES = [
Interpolate(np.linspace(1000, 1700, 100)),
SavitzkyGolayFiltering(window=9, polyorder=2, deriv=2),
Cut(lowlim=1000, highlim=1800),
GaussianSmoothing(sd=3.),
Absorbance(),
Transmittance(),
Integrate(limits=[[900, 100], [1100, 1200], [1200, 1300]]),
Integrate(methods=Integrate.Simple, limits=[[1100, 1200]]),
Integrate(methods=Integrate.Baseline, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakMax, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakBaseline, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakAt, limits=[[1100]]),
Integrate(methods=Integrate.PeakX, limits=[[1100, 1200]]),
Integrate(methods=Integrate.PeakXBaseline, limits=[[1100, 1200]]),
RubberbandBaseline(),
LinearBaseline(),
Normalize(method=Normalize.Vector),
Normalize(method=Normalize.Area,
int_method=Integrate.PeakMax,
lower=0,
upper=10000),
Normalize(method=Normalize.MinMax),
CurveShift(1),
Despike(threshold=5, cutoff=60, dis=5),
]
xas_norm_collagen = XASnormalization(edge=1630,
preedge_dict={
'from': 1000,
'to': 1300,