def test_peakfinder_double_peaks():
"""Test that the new peakfinder logic correctly gives only one peak, even
when min_sep is not specified, while old logic gives two peaks.
"""
# Toy data: gaussian lineshape
x = np.arange(31)
y = 1.5 * np.exp(-0.5 * (x[:-1] - 15) ** 2 / (2 * 3**2))
spec = bq.Spectrum(bin_edges_raw=x, counts=y)
kernel = bq.GaussianPeakFilter(15, 7.5, fwhm_at_0=7.5)
finder = bq.PeakFinder(spec, kernel)
# OLD code from PeakFinder.find_peaks
d1 = (finder.snr[2:] - finder.snr[:-2]) / 2
d1 = np.append(0, d1)
d1 = np.append(d1, 0)
d2 = finder.snr[2:] - 2 * finder.snr[1:-1] + finder.snr[:-2]
d2 = np.append(0, d2)
d2 = np.append(d2, 0)
peak_old = (d1[2:] < 0) & (d1[:-2] > 0) & (d2[1:-1] < 0)
peak_old = np.append(False, peak_old)
peak_old = np.append(peak_old, False)
assert peak_old.sum() == 2
# NEW peakfind
finder.find_peaks(min_snr=1.0)
assert len(finder.centroids) == 1
assert finder.centroids[0] in finder.spectrum.bin_centers_raw[peak_old]
peak_new = np.isclose(finder.spectrum.bin_centers_raw, finder.centroids[0])
assert peak_new.sum() == 1
def test_autocal_spec3():
"""Test AutoCalibrator on spectrum 3."""
kernel = bq.GaussianPeakFilter(700, 50, 10)
finder = bq.PeakFinder(spec3, kernel)
cal = bq.AutoCalibrator(finder)
cal.peakfinder.find_peaks(min_snr=3, xmin=100)
assert len(cal.peakfinder.centroids) == 8
# this fit succeeds but misidentifies the lines
cal.fit(
[609.32, 1460.82],
optional=[],
gain_range=[0.1, 5.0],
de_max=50.0,
)
assert len(cal.fit_channels) == 2
assert np.isclose(cal.gain, 2.59, rtol=1e-2)
# this fit correctly identifies the lines
cal.fit(
[609.32, 1460.82],
optional=OPTIONAL,
gain_range=[0.1, 5.0],
de_max=50.0,
)
assert len(cal.fit_channels) == 7
assert np.isclose(cal.gain, 2.02, rtol=1e-2)
def test_peakfinder_plot():
"""Test PeakFinder.plot."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
finder = bq.PeakFinder(spec1, kernel)
# finder.find_peaks(min_snr=2, xmin=50)
finder.find_peaks(min_snr=0.5, xmin=50, xmax=1000, max_num=10)
plt.figure()
finder.plot(linecolor="k")
plt.show()
def test_peakfinder_exceptions():
"""Test PeakFinder exceptions."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
# init
with pytest.raises(bq.PeakFinderError):
finder = bq.PeakFinder(spec1, kernel, min_sep=-10)
with pytest.raises(bq.PeakFinderError):
finder = bq.PeakFinder(None, kernel)
with pytest.raises(bq.PeakFinderError):
finder = bq.PeakFinder(spec1, None)
finder = bq.PeakFinder(spec1, kernel)
# sort_by
with pytest.raises(bq.PeakFinderError):
finder.sort_by([1, 2, 3])
# add_peak
with pytest.raises(bq.PeakFinderError):
finder.add_peak(-10)
with pytest.raises(bq.PeakFinderError):
finder.add_peak(5) # below threshold so no peak here
# find_peak
with pytest.raises(bq.PeakFinderError):
finder.find_peak(-1)
with pytest.raises(bq.PeakFinderError):
finder.find_peak(3000)
with pytest.raises(bq.PeakFinderError):
finder.find_peak(700, frac_range=(-0.1, 1.1))
with pytest.raises(bq.PeakFinderError):
finder.find_peak(700, frac_range=(1.1, 1.2))
with pytest.raises(bq.PeakFinderError):
finder.find_peak(700, frac_range=(0.8, 0.9))
with pytest.raises(bq.PeakFinderError):
finder.find_peak(700, frac_range=(1.2, 0.8))
with pytest.raises(bq.PeakFinderError):
finder.find_peak(700, min_snr=-3)
with pytest.raises(bq.PeakFinderError):
finder.find_peak(700, min_snr=10)
with pytest.raises(bq.PeakFinderError):
finder.find_peak(700, min_snr=100)
# find_peaks
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(xmin=-1)
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(xmin=3000)
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(xmax=-1)
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(xmax=3000)
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(xmin=700, xmax=600)
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(min_snr=-3)
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(min_snr=50)
with pytest.raises(bq.PeakFinderError):
finder.find_peaks(max_num=0)
def test_peakfinder():
"""Test basic functionality of PeakFinder."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
finder = bq.PeakFinder(spec1, kernel)
finder.find_peak(500, min_snr=3.0)
assert np.isclose(finder.centroids[0], 485.5)
finder.reset()
finder.find_peaks()
assert len(finder.centroids) == 9
finder.reset()
finder.find_peaks(min_snr=0.5, xmin=50, xmax=1000, max_num=10)
assert len(finder.centroids) == 10
def test_autocal_no_fit():
"""Test AutoCalibrator with no valid fit found."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
finder = bq.PeakFinder(spec1, kernel)
cal = bq.AutoCalibrator(finder)
finder.find_peaks(min_snr=2, xmin=50)
assert len(cal.peakfinder.centroids) == 8
with pytest.raises(bq.AutoCalibratorError):
cal.fit(
REQUIRED,
optional=OPTIONAL,
gain_range=[1, 2.0],
de_max=20.0,
)
def test_autocal_one_line():
"""Test AutoCalibrator with one line."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
finder = bq.PeakFinder(spec1, kernel)
cal = bq.AutoCalibrator(finder)
finder.find_peaks(min_snr=8, xmin=50)
assert len(cal.peakfinder.centroids) == 1
cal.fit(
[1460.82],
gain_range=[2.5, 4.0],
de_max=20.0,
)
assert len(cal.fit_channels) == 1
assert np.isclose(cal.gain, 3.01, rtol=1e-2)
def test_autocal_spec4():
"""Test AutoCalibrator on spectrum 4."""
kernel = bq.GaussianPeakFilter(2400, 120, 30)
finder = bq.PeakFinder(spec4, kernel)
cal = bq.AutoCalibrator(finder)
cal.peakfinder.find_peaks(min_snr=3, xmin=100)
assert len(cal.peakfinder.centroids) == 7
cal.fit(
[356.0129, 661.657, 1460.82],
optional=[911.20, 1120.294, 1620.50, 1764.49, 2118.514, 2614.3],
gain_range=[0.3, 0.7],
de_max=100.0,
)
assert len(cal.fit_channels) == 4
assert np.isclose(cal.gain, 0.6133, rtol=1e-2)
def test_autocal_spec2():
"""Test AutoCalibrator on spectrum 2."""
kernel = bq.GaussianPeakFilter(3700, 10, 5)
finder = bq.PeakFinder(spec2, kernel)
cal = bq.AutoCalibrator(finder)
cal.peakfinder.find_peaks(min_snr=20, xmin=1000)
assert len(cal.peakfinder.centroids) == 9
cal.fit(
REQUIRED,
optional=OPTIONAL,
gain_range=[0.1, 0.6],
de_max=5.0,
)
assert len(cal.fit_channels) == 3
assert np.isclose(cal.gain, 0.3785, rtol=1e-2)
def test_autocal_plot():
"""Test AutoCalibrator.plot."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
finder = bq.PeakFinder(spec1, kernel)
cal = bq.AutoCalibrator(finder)
finder.find_peaks(min_snr=1, xmin=50)
assert len(cal.peakfinder.centroids) == 10
cal.fit(
REQUIRED,
optional=OPTIONAL,
gain_range=[2.5, 4.0],
de_max=20.0,
)
plt.figure()
cal.plot()
plt.show()
def test_autocal_spec1():
"""Test basic functionality of AutoCalibrator."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
finder = bq.PeakFinder(spec1, kernel)
cal = bq.AutoCalibrator(finder)
finder.find_peaks(min_snr=1, xmin=50)
assert len(cal.peakfinder.centroids) == 10
cal.fit(
REQUIRED,
optional=OPTIONAL,
gain_range=[2.5, 4.0],
de_max=25.0,
verbose=True,
)
assert len(cal.fit_channels) == 7
assert np.isclose(cal.gain, 3.01, rtol=1e-2)
def test_autocal_exceptions():
"""Test AutoCalibrator exceptions."""
kernel = bq.GaussianPeakFilter(500, 50, fwhm_at_0=10)
finder = bq.PeakFinder(spec1, kernel)
# init error
with pytest.raises(bq.AutoCalibratorError):
cal = bq.AutoCalibrator(None)
cal = bq.AutoCalibrator(finder)
# only one peak found, but multiple energies required
finder.find_peaks(min_snr=10, xmin=50)
assert len(cal.peakfinder.centroids) == 1
with pytest.raises(bq.AutoCalibratorError):
cal.fit(
REQUIRED,
gain_range=[2.5, 4.0],
de_max=20.0,
)
# multiple peaks found, but only one energy given
finder.reset()
finder.find_peaks(min_snr=1, xmin=50)
assert len(cal.peakfinder.centroids) == 10
with pytest.raises(bq.AutoCalibratorError):
cal.fit(
[1460.82],
gain_range=[2.5, 4.0],
de_max=20.0,
)
# more energies required than peaks found
finder.reset()
finder.find_peaks(min_snr=4, xmin=50)
assert len(cal.peakfinder.centroids) == 4
with pytest.raises(bq.AutoCalibratorError):
cal.fit(
[238.63, 351.93, 609.32, 1460.82, 2614.3],
gain_range=[2.5, 4.0],
de_max=20.0,
)
