class TestBleach(unittest.TestCase):
pixel = np.arange(1, 100)
pp_delays = np.linspace(-1, 10, 20)
wavenumber = pixel[::-1]
xx, yy = np.meshgrid(pixel, pp_delays, sparse=True)
intensity = 100000 * gaussian(50, 30).pdf(xx) * gaussian(4, 4).pdf(yy) + 1
baseline = np.ones_like(intensity)
intensityE = (intensity - 0.9) * 0.1
norm = 100000 * gaussian(55, 40).pdf(pixel)
pp = pysfg.PumpProbe(intensity, baseline, norm, wavenumber, pp_delays,
2500, 80, 0.2, intensityE, pixel)
intensity2 = 100000 * gaussian(52, 30).pdf(xx) * gaussian(4, 4).pdf(yy) + 1
pp2 = pysfg.PumpProbe(intensity2, baseline, norm, wavenumber, pp_delays,
2500, 80, 0.2, intensityE, pixel)
bleach = pp - pp2
def test_shape(self):
self.assertTrue(self.bleach.normalized.shape == (20, 99))
def test_trace_shape(self):
tr = self.bleach.get_trace(slice(20, 30))
self.assertTrue(tr.bleach.shape == (20, ))
def test_trace_result(self):
tr = self.bleach.get_trace(slice(20, 30))
self.assertEqual(tr.bleach.mean(), 0.005120605673482265)
def test_to_and_from_json(self):
os.chdir(dir_path)
self.bleach.to_json(Path("bleach.json"))
bleach = pysfg.spectrum.json_to_bleach(Path("results/bleach.json"))
self.assertTrue(
np.all(bleach.intensity - self.bleach.intensity < 0.0001))
def test_PumpProbe_baselines(self):
for baseline in (1, np.ones_like(self.pixel),
np.ones_like(self.intensity)):
pp = pysfg.PumpProbe(self.intensity, baseline, self.norm,
self.wavenumber, self.pp_delays, 2500, 80,
0.2, self.intensityE, self.pixel)
self.assertEqual(pp.basesubed.mean(), 66.76760137069422)
def test_PumpProbe_norms_3(self):
norm = 100000 * gaussian(55, 40).pdf(self.xx) * gaussian(2, 2).pdf(
self.yy) + 1
pp = pysfg.PumpProbe(self.intensity, self.baseline, norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 7.731632631662137)
def test_PumpProbe_norms_2(self):
norm = 2
pp = pysfg.PumpProbe(self.intensity, self.baseline, norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 33.38380068534711)
def test_PumpProbe_norms_1(self):
pp = pysfg.PumpProbe(self.intensity, self.baseline, self.norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 0.0823400053566616)
def test_PumpProbe_norms_0(self):
norm = None
pp = pysfg.PumpProbe(self.intensity, self.baseline, norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 66.76760137069422)
def test_PumpProbe_baseline_0(self):
baseline = None
pp = pysfg.PumpProbe(self.intensity, baseline, self.norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.basesubed.mean(), 67.76760137069422)
class TestPumpProbe(unittest.TestCase):
pixel = np.arange(1, 100)
pp_delays = np.linspace(-1, 10, 20)
wavenumber = pixel[::-1]
xx, yy = np.meshgrid(pixel, pp_delays, sparse=True)
intensity = 100000 * gaussian(50, 30).pdf(xx) * gaussian(4, 4).pdf(yy) + 1
baseline = np.ones_like(intensity)
intensityE = (intensity - 0.9) * 0.1
norm = 100000 * gaussian(55, 40).pdf(pixel)
pp = pysfg.PumpProbe(intensity, baseline, norm, wavenumber, pp_delays,
2500, 80, 0.2, intensityE, pixel)
intensity2 = 100000 * gaussian(52, 30).pdf(xx) * gaussian(4, 4).pdf(yy) + 1
pp2 = pysfg.PumpProbe(intensity2, baseline, norm, wavenumber, pp_delays,
2500, 80, 0.2, intensityE, pixel)
def test_basesubed(self):
self.assertTrue(np.all(self.pp.basesubed == self.intensity - 1))
def test_normalized(self):
self.assertTrue(
np.all(self.pp.normalized == (self.intensity - 1) / self.norm))
def test_to_and_from_json(self):
os.chdir(dir_path)
self.pp.to_json(Path("pumpprobe.json"))
ppp = pysfg.json_to_pumpprobe(Path("results/pumpprobe.json"))
self.assertTrue(np.all(self.pp.normalized - ppp.normalized < 0.0001))
def test_PumpProbe_baseline_0(self):
baseline = None
pp = pysfg.PumpProbe(self.intensity, baseline, self.norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.basesubed.mean(), 67.76760137069422)
def test_PumpProbe_baselines(self):
for baseline in (1, np.ones_like(self.pixel),
np.ones_like(self.intensity)):
pp = pysfg.PumpProbe(self.intensity, baseline, self.norm,
self.wavenumber, self.pp_delays, 2500, 80,
0.2, self.intensityE, self.pixel)
self.assertEqual(pp.basesubed.mean(), 66.76760137069422)
def test_PumpProbe_norms_0(self):
norm = None
pp = pysfg.PumpProbe(self.intensity, self.baseline, norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 66.76760137069422)
def test_PumpProbe_norms_1(self):
pp = pysfg.PumpProbe(self.intensity, self.baseline, self.norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 0.0823400053566616)
def test_PumpProbe_norms_2(self):
norm = 2
pp = pysfg.PumpProbe(self.intensity, self.baseline, norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 33.38380068534711)
def test_PumpProbe_norms_3(self):
norm = 100000 * gaussian(55, 40).pdf(self.xx) * gaussian(2, 2).pdf(
self.yy) + 1
pp = pysfg.PumpProbe(self.intensity, self.baseline, norm,
self.wavenumber, self.pp_delays, 2500, 80, 0.2,
self.intensityE, self.pixel)
self.assertEqual(pp.normalized.mean(), 7.731632631662137)
def test_substration(self):
bleach = self.pp - self.pp2
self.assertEqual(bleach.normalized.mean(), 0.0004376967887611049)
def test_deviation(self):
bleach = self.pp / self.pp2
self.assertEqual(bleach.normalized.mean(), 1.0042468628341095)
