def test_scale_by_exposure(self):
s1 = LumiSpectrum(np.ones((10, 10, 10)))
s2 = LumiTransient(np.ones((10, 10, 10, 10)))
s3 = LumiSpectrum(np.ones((10, 10)))
s4 = LumiSpectrum(np.ones((10)))
s2.metadata.set_item("Acquisition_instrument.CL.exposure", 2)
s3.metadata.set_item("Acquisition_instrument.CL.dwell_time", 0.5)
s3.metadata.set_item("Signal.quantity", "Intensity (Counts)")
s4.metadata.set_item("Signal.quantity", "Intensity (counts)")
s1a = s1.scale_by_exposure(exposure=4)
s2a = s2.scale_by_exposure()
s3a = s3.scale_by_exposure()
s4a = s4.scale_by_exposure(exposure=0.1)
assert np.all(s1a.data == 0.25)
assert np.all(s2a.data == 0.5)
assert np.all(s3a.data == 2)
assert np.all(s4a.data == 10)
assert s3a.metadata.Signal.quantity == "Intensity (Counts/s)"
assert s4a.metadata.Signal.quantity == "Intensity (counts/s)"
assert s4a.metadata.Signal.scaled == True
s1.scale_by_exposure(exposure=4, inplace=True)
s2.scale_by_exposure(inplace=True)
s3.scale_by_exposure(inplace=True)
s4.scale_by_exposure(exposure=0.1, inplace=True)
assert s1 == s1a
assert s2 == s2a
assert s3 == s3a
assert s4 == s4a
assert s3.metadata.Signal.quantity == "Intensity (Counts/s)"
assert s4.metadata.Signal.quantity == "Intensity (counts/s)"
# Test for errors
s4 = LumiSpectrum(np.ones((10)))
s4.normalize(inplace=True)
with pytest.raises(AttributeError) as excinfo:
s4.scale_by_exposure(inplace=True, exposure=0.5)
assert str(
excinfo.value) == "Data was normalized and cannot be " "scaled."
s5 = LumiSpectrum(np.ones((10)))
with pytest.raises(AttributeError) as excinfo:
s5.scale_by_exposure(inplace=True)
assert (str(excinfo.value) == "Exposure not given and can not be "
"extracted automatically from metadata.")
s5.scale_by_exposure(inplace=True, exposure=0.5)
with pytest.raises(AttributeError) as excinfo:
s5.scale_by_exposure(inplace=True, exposure=0.5)
assert str(excinfo.value) == "Data was already scaled."
def test_normalize(self):
s1 = LumiSpectrum(np.random.random((10, 10, 10))) * 2
s2 = LumiTransient(np.random.random((10, 10, 10, 10))) * 2
s3 = LumiSpectrum(np.random.random((10, 10))) * 2
s4 = LumiSpectrum(np.random.random((10))) * 2
s4.metadata.set_item("Signal.quantity", "Intensity (counts)")
s1a = s1.normalize()
s2a = s2.normalize()
s3a = s3.normalize()
s4a = s4.normalize()
assert s1a.max(axis=[0, 1, 2]).data[0] == 1
assert s2a.max(axis=[0, 1, 2, 3]).data[0] == 1
assert s3a.max(axis=[0, 1]).data[0] == 1
assert s4a.max(axis=[0]).data[0] == 1
assert s4a.metadata.Signal.quantity == "Normalized intensity"
assert s4a.metadata.Signal.normalized == True
s1a = s1.normalize(element_wise=True)
s2a = s2.normalize(element_wise=True)
s3a = s3.normalize(element_wise=True)
s4a = s4.normalize(element_wise=True)
assert np.all(s1a.max(axis=[2]).data[0] == 1)
assert np.all(s2a.max(axis=[3]).data[0] == 1)
assert np.all(s3a.max(axis=[1]).data[0] == 1)
assert s4a.max(axis=[0]).data[0] == 1
s1a = s1.normalize(pos=3)
s2a = s2.normalize(pos=3, element_wise=True)
s3a = s3.normalize(pos=3, element_wise=True)
s4a = s4.normalize(pos=3)
assert s1a.isig[3].max().data[0] == 1
assert np.all(s2a.isig[3] == 1)
assert np.all(s3a.isig[3] == 1)
assert s4a.isig[3].data == 1
s1.normalize(pos=3, inplace=True)
s2.normalize(pos=3, element_wise=True, inplace=True)
s3.normalize(pos=3, element_wise=True, inplace=True)
s4.normalize(pos=3, inplace=True)
assert s1a == s1
assert s2a == s2
assert s3a == s3
assert s4a == s4
assert s4.metadata.Signal.quantity == "Normalized intensity"
with pytest.warns(UserWarning) as warninfo:
s1.normalize(inplace=True)
assert len(warninfo) == 1
assert warninfo[0].message.args[0][:8] == "Data was"