def check_FID(self, ppmlim=(.2, 4.2), repair=False):
"""
Check if FID needs to be conjugated
by looking at total power within ppmlim range
Parameters
----------
ppmlim : list
repair : if True applies conjugation to FID
Returns
-------
0 if check successful and -1 if not (also issues warning)
"""
first, last = self.ppmlim_to_range(ppmlim)
Spec1 = np.real(misc.FIDToSpec(self.FID))[first:last]
Spec2 = np.real(misc.FIDToSpec(np.conj(self.FID)))[first:last]
if np.linalg.norm(misc.detrend(Spec1, deg=4)) < np.linalg.norm(
misc.detrend(Spec2, deg=4)):
if repair is False:
warnings.warn('YOU MAY NEED TO CONJUGATE YOUR FID!!!')
return -1
else:
self.conj_FID()
return 1
return 0
def test_FIDToSpec_SpecToFID():
testFID, hdr = synth.syntheticFID(amplitude=[10],
chemicalshift=[0],
phase=[0],
damping=[20])
# SVS case
spec = misc.FIDToSpec(testFID[0])
reformedFID = misc.SpecToFID(spec)
assert np.allclose(reformedFID, testFID)
testMRSI = np.tile(testFID, (4, 4, 4, 1)).T
testspec = misc.FIDToSpec(testMRSI)
assert np.argmax(np.abs(testspec[:, 2, 2, 2])) == 1024
testspec = misc.FIDToSpec(testMRSI.T, axis=3)
assert np.argmax(np.abs(testspec[2, 2, 2, :])) == 1024
reformedFID = misc.SpecToFID(testspec, axis=3)
assert np.allclose(reformedFID, testMRSI.T)
reformedFID = misc.SpecToFID(testspec.T)
assert np.allclose(reformedFID, testMRSI)
# Odd number of points - guard against fftshift/ifftshift errors
testFID, hdr = synth.syntheticFID(amplitude=[1],
chemicalshift=[0],
phase=[0],
damping=[20],
points=1025)
assert np.allclose(misc.SpecToFID(misc.FIDToSpec(testFID[0])), testFID)
def set_FID(self, FID):
"""
Sets the FID and calculates spectrum
"""
if FID.ndim > 1:
raise ValueError(
f'MRS objects only handle one FID at a time. FID shape is {FID.shape}.'
)
self.FID = FID.copy()
self.numPoints = self.FID.size
self.Spec = misc.FIDToSpec(self.FID)
def check_Basis(self, ppmlim=(.2, 4.2), repair=False):
"""
Check if Basis needs to be conjugated
by looking at total power within ppmlim range
Parameters
----------
ppmlim : list
repair : if True applies conjugation to basis
Returns
-------
0 if check successful and -1 if not (also issues warning)
"""
first, last = self.ppmlim_to_range(ppmlim)
conjOrNot = []
for b in self.basis.T:
Spec1 = np.real(misc.FIDToSpec(b))[first:last]
Spec2 = np.real(misc.FIDToSpec(np.conj(b)))[first:last]
if np.linalg.norm(misc.detrend(Spec1, deg=4)) < np.linalg.norm(
misc.detrend(Spec2, deg=4)):
conjOrNot.append(1.0)
else:
conjOrNot.append(0.0)
if (sum(conjOrNot) / len(conjOrNot)) > 0.5:
if repair is False:
warnings.warn('YOU MAY NEED TO CONJUGATE YOUR BASIS!!!')
return -1
else:
self.conj_Basis()
return 1
return 0
def modify_basis(mrs, gamma, eps):
bs = mrs.basis * np.exp(-(gamma + 1j * eps) * mrs.timeAxis)
bs = misc.FIDToSpec(bs, axis=0)
bs = bs[first:last, :]
return np.concatenate((np.real(bs), np.imag(bs)), axis=0)
def conj_FID(self):
"""
Conjugate FID and recalculate spectrum
"""
self.FID = np.conj(self.FID)
self.Spec = misc.FIDToSpec(self.FID)
def getSpectrum(self, ppmlim=None, shift=True):
spectrum = misc.FIDToSpec(self.FID)
f, l = self.ppmlim_to_range(ppmlim, shift=shift)
return spectrum[f:l]