def spectrum_baseline(y, x=[], display=0, algorithm='derpsalsa', wl_level=9):
"""
----------
x, y : spectral data
display : 0, 1 or 2, optional
The default is 2.
0: no display, 1: final, 2: verbose with plots
algorithm : derpsalsa, psalsa, als, morph_pspline, Koch, wavelet
The default is 'derpsalsa'.
Returns
baseline
"""
if len(x) == 0:
x = np.linspace(0, 1000, num=len(y))
if display > 0:
print('algorithm = ', algorithm, ' , starting')
if algorithm == 'psalsa':
baseline = psalsa_baseline(x, y, display)
if algorithm == 'derpsalsa':
baseline = derpsalsa_baseline(x, y, display)
elif algorithm == 'als':
baseline = baseline_als(x, y, display)
elif algorithm == 'Koch':
baseline = kolifier_morph_baseline(x, y, display)
elif algorithm == 'morph_pspline':
baseline = morph_pspline_baseline(x, y, display)
elif algorithm == 'wavelet':
from skued import baseline_dt, spectrum_colors
max_iteration_number = 512
baseline = baseline_dt(y,
level=wl_level,
max_iter=max_iteration_number,
wavelet='qshift3')
if display >= 1:
levels = list(range(wl_level - 2, wl_level + 3))
colors = spectrum_colors(levels)
for l, c in zip(levels, colors):
if l == wl_level:
continue
bltmp = baseline_dt(y,
level=l,
max_iter=max_iteration_number,
wavelet='qshift3')
plt.plot(x, bltmp, color=c)
plt.plot(x, y, 'r', x, baseline, 'k--', linewidth=2)
plot_annotation = 'wavelet bl; black-- at level ' + str(wl_level)
plt.text(0.5,
0.92,
plot_annotation,
horizontalalignment='center',
verticalalignment='center',
transform=plt.gca().transAxes)
plt.show()
return baseline
def test_on_ints(self):
""" Test spectrum_colors on an int """
colors = spectrum_colors(10)
self.assertEqual(len(list(colors)), 10)
def test_on_length_1_iterable(self):
""" Test that spectrum_colors is working on single-length iterables """
self.assertSequenceEqual(list(spectrum_colors(1)),
list(spectrum_colors([0])))
def test_on_unsized_iterable(self):
""" Test spectrum_colors on unsized_iterable (e.g. generator) """
colors = spectrum_colors(range(0, 10))
self.assertEqual(len(list(colors)), 10)
def test_on_sized_iterable(self):
""" Test on iterable that has a __len__ attribute: list, tuple, etc. """
colors = spectrum_colors([1, 2, 3, 4, 5])
self.assertEqual(len(list(colors)), 5)
def pens_and_brushes(num):
qcolors = tuple(map(lambda c: QtGui.QColor.fromRgbF(*c), spectrum_colors(num)))
pens = list(map(mkPen, qcolors))
brushes = list(map(mkBrush, qcolors))
return pens, brushes
def test_spectrum_colors_on_ints():
""" Test spectrum_colors on an int """
colors = spectrum_colors(10)
assert len(list(colors)) == 10
def test_spectrum_colorson_length_1_iterable():
""" Test that spectrum_colors is working on single-length iterables """
assert list(spectrum_colors(1)) == list(spectrum_colors([0]))
def test_spectrum_colorson_unsized_iterable():
""" Test spectrum_colors on unsized_iterable (e.g. generator) """
colors = spectrum_colors(range(0, 10))
assert len(list(colors)) == 10
def test_spectrum_colorson_sized_iterable():
""" Test on iterable that has a __len__ attribute: list, tuple, etc. """
colors = spectrum_colors([1, 2, 3, 4, 5])
assert len(list(colors)) == 5