Rewrite of MRS class, tests for MRS and introduction of different nuclei.

fsl_mrs/core/MRSI.py

@@ -192,7 +192,7 @@ class MRSI(object):
                 jj = j - dim2[0]
                 ax = axes[ii,jj]
                 mrs = self.mrs_by_index([i,j,k])
-                ax.plot(mrs.getAxes(ppmlim=ppmlim),np.real(mrs.getSpectrum(ppmlim=ppmlim)))
+                ax.plot(mrs.getAxes(ppmlim=ppmlim),np.real(mrs.get_spec(ppmlim=ppmlim)))
                 ax.invert_xaxis()
                 ax.set_xticks([])
                 ax.set_yticks([])

fsl_mrs/scripts/fsl_mrs

@@ -257,7 +257,6 @@ def main():
         if args.verbose:
             print('--->>  Phase correction\n')
         mrs.FID = misc.phase_correct(mrs, mrs.FID)
-        mrs.Spec = misc.FIDToSpec(mrs.FID)
 
     # Keep/Ignore metabolites
     mrs.keep(args.keep)

fsl_mrs/tests/test_core_mrs.py

+
+
+from pathlib import Path
+from fsl_mrs.core import MRS
+import pytest
+from fsl_mrs.utils import synthetic as syn
+import numpy as np
+from fsl_mrs.utils.misc import FIDToSpec, hz2ppm
+
+# Files
+testsPath = Path(__file__).parent
+svs_metab = testsPath / 'testdata/fsl_mrs/metab.nii'
+svs_water = testsPath / 'testdata/fsl_mrs/water.nii'
+svs_basis = testsPath / 'testdata/fsl_mrs/steam_basis'
+
+
+@pytest.fixture
+def synth_data():
+
+    fid, hdr = syn.syntheticFID()
+    hdr['json'] = {'ResonantNucleus': '1H'}
+
+    basis_1, bhdr_1 = syn.syntheticFID(noisecovariance=[[0.0]],
+                                       chemicalshift=[-2, ],
+                                       amplitude=[0.1, ],
+                                       damping=[5, ])
+
+    basis_2, bhdr_2 = syn.syntheticFID(noisecovariance=[[0.0]],
+                                       chemicalshift=[3, ],
+                                       amplitude=[0.1, ],
+                                       damping=[5, ])
+
+    basis = np.concatenate((basis_1, basis_2))
+    bheader = [bhdr_1, bhdr_2]
+    names = ['ppm_2', 'ppm3']
+
+    timeAxis = np.linspace(hdr['dwelltime'],
+                           hdr['dwelltime'] * 2048,
+                           2048)
+    frequencyAxis = np.linspace(-hdr['bandwidth']/2,
+                                hdr['bandwidth']/2,
+                                2048)
+    ppmAxis = hz2ppm(hdr['centralFrequency']*1E6,
+                     frequencyAxis,
+                     shift=False)
+    ppmAxisShift = hz2ppm(hdr['centralFrequency']*1E6,
+                          frequencyAxis,
+                          shift=True)
+
+    axes = {'time': timeAxis,
+            'freq': frequencyAxis,
+            'ppm': ppmAxis,
+            'ppm_shift': ppmAxisShift}
+
+    return fid[0], hdr, basis, names, bheader, axes
+
+
+def test_load_from_file():
+
+    mrs = MRS()
+    mrs.from_files(str(svs_metab),
+                   str(svs_basis),
+                   H2O_file=str(svs_water))
+
+    assert mrs.FID.shape == (4096,)
+    assert mrs.basis.shape == (4096, 20)
+    assert mrs.H2O.shape == (4096,)
+
+
+def test_load(synth_data):
+
+    fid, hdr, basis, names, bheader, axes = synth_data
+
+    mrs = MRS(FID=fid,
+              header=hdr,
+              basis=basis,
+              names=names,
+              basis_hdr=bheader[0])
+
+    assert mrs.FID.shape == (2048,)
+    assert mrs.basis.shape == (2048, 2)
+    assert mrs.numBasis == 2
+    assert mrs.dwellTime == 1/4000
+    assert mrs.centralFrequency == 123E6
+    assert mrs.nucleus == '1H'
+
+
+def test_access(synth_data):
+
+    fid, hdr, basis, names, bheader, axes = synth_data
+
+    mrs = MRS(FID=fid,
+              header=hdr,
+              basis=basis,
+              names=names,
+              basis_hdr=bheader[0])
+
+    assert np.allclose(mrs.FID, fid)
+    assert np.allclose(mrs.get_spec(), FIDToSpec(fid))
+    assert np.allclose(mrs.basis.T, basis)
+
+    assert np.allclose(mrs.getAxes(axis='ppmshift'), axes['ppm_shift'])
+    assert np.allclose(mrs.getAxes(axis='ppm'), axes['ppm'])
+    assert np.allclose(mrs.getAxes(axis='freq'), axes['freq'])
+    assert np.allclose(mrs.getAxes(axis='time'), axes['time'])
+
+    mrs.rescaleForFitting()
+    assert np.allclose(mrs.get_spec()/mrs.scaling['FID'], FIDToSpec(fid))
+    assert np.allclose(mrs.basis.T/mrs.scaling['basis'], basis)
+
+    mrs.conj_Basis()
+    mrs.conj_FID()
+    assert np.allclose(mrs.get_spec()/mrs.scaling['FID'],
+                       FIDToSpec(fid.conj()))
+    assert np.allclose(mrs.basis.T/mrs.scaling['basis'], basis.conj())
+
+
+def test_basis_manipulations(synth_data):
+
+    fid, hdr, basis, names, bheader, axes = synth_data
+
+    mrs = MRS(FID=fid,
+              header=hdr,
+              basis=basis,
+              names=names,
+              basis_hdr=bheader[0])
+
+    assert mrs.basis.shape == (2048, 2)
+    assert mrs.numBasis == 2
+
+    mrs.keep(['ppm_2'])
+
+    assert mrs.basis.shape == (2048, 1)
+    assert mrs.numBasis == 1
+
+    mrs.add_peak(0, 1, 'test', gamma=10, sigma=10)
+
+    assert mrs.basis.shape == (2048, 2)
+    assert mrs.numBasis == 2
+    assert mrs.names == ['ppm_2', 'test']
+
+    mrs.ignore(['test'])
+
+    assert mrs.basis.shape == (2048, 1)
+    assert mrs.numBasis == 1
+
+    mrs.add_MM_peaks(gamma=10, sigma=10)
+    assert mrs.basis.shape == (2048, 6)
+    assert mrs.numBasis == 6

fsl_mrs/tests/test_utils_preproc.py

@@ -207,7 +207,7 @@ def test_shiftToRef():
 
     mrs = MRS(FID=shiftFID,header=testHdrs)
 
-    maxindex = np.argmax(mrs.getSpectrum(shift=False))
+    maxindex = np.argmax(mrs.get_spec(shift=False))
     position = mrs.getAxes(axis='ppm')[maxindex]
     
     assert np.isclose(position,-2.0,atol=1E-1)

fsl_mrs/tests/test_utils_qc.py

@@ -16,13 +16,13 @@ def test_calcQC():
     synMRS_basis = MRS(FID =synFID[0],header=synHdr,basis =basisFID[0] ,basis_hdr=basisHdr,names=['Peak1'])
 
     truenoiseSD = np.sqrt(synHdrNoise['cov'][0,0])
-    pureNoiseMeasured = np.std(synMRSNoise.getSpectrum())
-    realnoise = np.std(np.real(synMRSNoise.getSpectrum()))
-    imagNoise = np.std(np.imag(synMRSNoise.getSpectrum()))
+    pureNoiseMeasured = np.std(synMRSNoise.get_spec())
+    realnoise = np.std(np.real(synMRSNoise.get_spec()))
+    imagNoise = np.std(np.imag(synMRSNoise.get_spec()))
     print(f'True cmplx noise = {truenoiseSD:0.3f}, pure noise measured = {pureNoiseMeasured:0.3f} (real/imag = {realnoise:0.3f}/{imagNoise:0.3f})')
 
     # Calc SNR without apodisation from the no noise and pure noise spectra
-    truePeakHeight = np.max(np.real(synMRSNoNoise.getSpectrum()))
+    truePeakHeight = np.max(np.real(synMRSNoNoise.get_spec()))
     SNR_noApod = truePeakHeight/pureNoiseMeasured
     print(f'SNR no apod: {SNR_noApod:0.1f} ({truePeakHeight:0.2e}/{pureNoiseMeasured:0.2e})')
 

fsl_mrs/utils/constants.py

@@ -8,8 +8,22 @@
 # Copyright (C) 2019 University of Oxford
 # SHBASECOPYRIGHT
 
+# From https://en.wikipedia.org/wiki/Gyromagnetic_ratio
+# except for 1H https://physics.nist.gov/cgi-bin/cuu/Value?gammappbar
+# MHz/tesla
+H1_gamma = 42.576
+GYRO_MAG_RATIO = {'1H': H1_gamma,
+                  '13C': 10.7084,
+                  '31P': 17.235}
+
 H2O_PPM_TO_TMS = 4.65  # Shift of water to Tetramethylsilane
-H1_gamma = 42.576      # MHz/tesla
+PPM_SHIFT = {'1H': H2O_PPM_TO_TMS,
+             '13C': 0.0,
+             '31P': 0.0}
+
+PPM_RANGE = {'1H': (0.2, 4.2),
+             '13C': (10, 100),
+             '31P': (-20, 10)}
 
 # Concentration scaling parameters
 TISSUE_WATER_DENSITY = {'GM': 0.78, 'WM': 0.65, 'CSF': 0.97}

fsl_mrs/utils/fitting.py

@@ -38,7 +38,7 @@ def print_params(x,mrs,metab_groups,ref_metab='Cr',scale_factor=1):
 # New strategy for init
 def init_params(mrs,baseline,ppmlim):
     first,last = mrs.ppmlim_to_range(ppmlim)
-    y = mrs.getSpectrum(ppmlim=ppmlim)
+    y = mrs.get_spec(ppmlim=ppmlim)
     y = np.concatenate((np.real(y),np.imag(y)),axis=0).flatten()
     B = baseline[first:last,:].copy()
     B = np.concatenate((np.real(B),np.imag(B)),axis=0)
@@ -94,7 +94,7 @@ def init_FSLModel(mrs,metab_groups,baseline,ppmlim):
 
 def init_params_voigt(mrs,baseline,ppmlim):
     first,last = mrs.ppmlim_to_range(ppmlim)
-    y = mrs.getSpectrum(ppmlim=ppmlim)
+    y = mrs.get_spec(ppmlim=ppmlim)
     y = np.concatenate((np.real(y),np.imag(y)),axis=0).flatten()
     B = baseline[first:last,:].copy()
     B = np.concatenate((np.real(B),np.imag(B)),axis=0)
@@ -286,7 +286,7 @@ def fit_FSLModel(mrs,
     elif model.lower() == 'voigt':        
         init_func  = init_FSLModel_Voigt    # initialisation of params
 
-    data       = mrs.Spec.copy()              # data copied to keep it safe
+    data       = mrs.get_spec().copy()              # data copied to keep it safe
     first,last = mrs.ppmlim_to_range(ppmlim)  # data range
 
     if metab_groups is None:

fsl_mrs/utils/misc.py

@@ -5,7 +5,7 @@
 # Author: Saad Jbabdi <saad@fmrib.ox.ac.uk>
 #         William Clarke <william.clarke@ndcn.ox.ac.uk>
 #
-# Copyright (C) 2019 University of Oxford 
+# Copyright (C) 2019 University of Oxford
 # SHBASECOPYRIGHT
 
 import numpy as np
@@ -13,32 +13,27 @@ import scipy.fft
 from scipy.signal import butter, lfilter
 from scipy.interpolate import interp1d
 import itertools as it
-from copy import deepcopy
 
-from .constants import H2O_PPM_TO_TMS 
+from .constants import H2O_PPM_TO_TMS
 
 
-# Convention:
-#  freq in Hz
-#  ppm = freq/1e6
-#  ppm_shift = ppm - 4.65
-#  why is there a minus sign here? 
-
-def ppm2hz(cf,ppm,shift=True):
+def ppm2hz(cf, ppm, shift=True, shift_amount=H2O_PPM_TO_TMS):
     if shift:
-        return (ppm-H2O_PPM_TO_TMS)*cf*1E-6
+        return (ppm-shift_amount)*cf*1E-6
     else:
         return (ppm)*cf*1E-6
 
-def hz2ppm(cf,hz,shift=True):
+
+def hz2ppm(cf, hz, shift=True, shift_amount=H2O_PPM_TO_TMS):
     if shift:
-        return 1E6 *hz/cf + H2O_PPM_TO_TMS
+        return 1E6 * hz/cf + shift_amount
     else:
-        return 1E6 *hz/cf
+        return 1E6 * hz/cf
+
 
-def FIDToSpec(FID,axis=0):
+def FIDToSpec(FID, axis=0):
     """ Convert FID to spectrum
-    
+
         Performs fft along indicated axis
         Args:
             FID (np.array)      : array of FIDs
@@ -49,16 +44,20 @@ def FIDToSpec(FID,axis=0):
     """
     # By convention the first point of the fid is special cased
     ss = [slice(None) for i in range(FID.ndim)]
-    ss[axis] = slice(0,1)
-    ss = tuple(ss)   
-    FID[ss] *=0.5
-    out = scipy.fft.fftshift(scipy.fft.fft(FID,axis=axis,norm='ortho'),axes=axis)
-    FID[ss] *=2
+    ss[axis] = slice(0, 1)
+    ss = tuple(ss)
+    FID[ss] *= 0.5
+    out = scipy.fft.fftshift(scipy.fft.fft(FID,
+                                           axis=axis,
+                                           norm='ortho'),
+                             axes=axis)
+    FID[ss] *= 2
     return out
 
-def SpecToFID(spec,axis=0):
+
+def SpecToFID(spec, axis=0):
     """ Convert spectrum to FID
-    
+
         Performs fft along indicated axis
         Args:
             spec (np.array)     : array of spectra
@@ -66,30 +65,40 @@ def SpecToFID(spec,axis=0):
 
         Returns:
             x (np.array)        : array of FIDs
-    """    
-    fid = scipy.fft.ifft(scipy.fft.ifftshift(spec,axes=axis),axis=axis,norm='ortho')
+    """
+    fid = scipy.fft.ifft(scipy.fft.ifftshift(spec,
+                                             axes=axis),
+                         axis=axis, norm='ortho')
     ss = [slice(None) for i in range(fid.ndim)]
-    ss[axis] = slice(0,1)
-    ss = tuple(ss)   
+    ss[axis] = slice(0, 1)
+    ss = tuple(ss)
     fid[ss] *= 2
     return fid
 
-def calculateAxes(bandwidth,centralFrequency,points):
+
+def calculateAxes(bandwidth, centralFrequency, points, shift):
     dwellTime = 1/bandwidth
-    timeAxis         = np.linspace(dwellTime,
-                                    dwellTime*points,
-                                    points)  
-    frequencyAxis    = np.linspace(-bandwidth/2,
-                                    bandwidth/2,
-                                    points)        
-    ppmAxis          = hz2ppm(centralFrequency,
-                                    frequencyAxis,shift=False)
-    ppmAxisShift     = hz2ppm(centralFrequency,
-                                    frequencyAxis,shift=True)
-
-    return {'time':timeAxis,'freq':frequencyAxis,'ppm':ppmAxis,'ppmshift':ppmAxisShift}
-
-def checkCFUnits(cf,units='Hz'):
+    timeAxis = np.linspace(dwellTime,
+                           dwellTime * points,
+                           points)
+    frequencyAxis = np.linspace(-bandwidth/2,
+                                bandwidth/2,
+                                points)
+    ppmAxis = hz2ppm(centralFrequency,
+                     frequencyAxis,
+                     shift=False)
+    ppmAxisShift = hz2ppm(centralFrequency,
+                          frequencyAxis,
+                          shift=True,
+                          shift_amount=shift)
+
+    return {'time': timeAxis,
+            'freq': frequencyAxis,
+            'ppm': ppmAxis,
+            'ppmshift': ppmAxisShift}
+
+
+def checkCFUnits(cf, units='Hz'):
     """ Check the units of central frequency and adjust if required."""
     # Assume cf in Hz > 1E5, if it isn't assume that user has passed in MHz
     if cf<1E5:

fsl_mrs/utils/plotting.py

@@ -144,8 +144,8 @@ def plot_fit_new(mrs,ppmlim=(0.40,4.2)):
         mrs : MRS object
         ppmlim : tuple
     """
-    axis   = np.flipud(mrs.ppmAxisFlip)
-    spec   = np.flipud(np.fft.fftshift(mrs.Spec))
+    axis   = mrs.ppmAxisShift
+    spec   = np.flipud(np.fft.fftshift(mrs.get_spec()))
     pred   = FIDToSpec(mrs.pred)
     pred   = np.flipud(np.fft.fftshift(pred))
 
@@ -243,7 +243,7 @@ def plot_spectrum(mrs,ppmlim=(0.0,4.5),FID=None,proj='real',c='k'):
         f,l = mrs.ppmlim_to_range(ppmlim)
         data = FIDToSpec(FID)[f:l]
     else:
-        data = mrs.getSpectrum(ppmlim=ppmlim)
+        data = mrs.get_spec(ppmlim=ppmlim)
 
 
     #m = min(np.real(data))
@@ -265,6 +265,49 @@ def plot_spectrum(mrs,ppmlim=(0.0,4.5),FID=None,proj='real',c='k'):
     return plt.gcf()
     
 
+def plot_fid(mrs, tlim=None, FID=None, proj='real', c='k'):
+    ''' Plot time domain FID'''
+
+    time_axis = mrs.getAxes(axis='time')
+
+    if FID is not None:        
+        data = FID
+    else:
+        data = mrs.FID
+
+    data = getattr(np, proj)(data)
+
+    plt.plot(time_axis, data, color=c, linewidth=2)
+
+    if tlim is not None:
+        plt.xlim(tlim)
+    plt.xlabel('Time (s)')
+    plt.minorticks_on()
+    plt.grid(b=True, axis='x', which='major',color='k', linestyle='--', linewidth=.3)
+    plt.grid(b=True, axis='x', which='minor', color='k', linestyle=':',linewidth=.3)
+
+    plt.tight_layout()
+    return plt.gcf()
+
+def plot_basis(mrs,plot_spec=False,ppmlim=(0.0, 4.5)):
+    first, last = mrs.ppmlim_to_range(ppmlim=ppmlim)
+        
+    for idx, n in enumerate(mrs.names):
+        plt.plot(mrs.getAxes(ppmlim=ppmlim),
+                 np.real(FID2Spec(mrs.basis[:, idx]))[first:last],
+                 label=n)
+
+    if plot_spec:
+        plt.plot(mrs.getAxes(ppmlim=ppmlim),
+                    np.real(mrs.get_spec(ppmlim=ppmlim)),
+                    'k',label='Data')
+
+    plt.gca().invert_xaxis()
+    plt.xlabel('Chemical shift (ppm)')
+    plt.legend()
+
+    return plt.gcf()
+
 def plot_spectra(MRSList,ppmlim=(0,4.5),single_FID=None,plot_avg=True):
 
     plt.figure(figsize=(10,10))
@@ -278,12 +321,12 @@ def plot_spectra(MRSList,ppmlim=(0,4.5),single_FID=None,plot_avg=True):
     
     avg=0
     for mrs in MRSList:
-        data = np.real(mrs.getSpectrum(ppmlim=ppmlim))
+        data = np.real(mrs.get_spec(ppmlim=ppmlim))
         ppmAxisShift = mrs.getAxes(ppmlim=ppmlim)
         avg += data
         plt.plot(ppmAxisShift,data,color='k',linewidth=.5,linestyle='-')
     if single_FID is not None:
-        data = np.real(single_FID.getSpectrum(ppmlim=ppmlim))
+        data = np.real(single_FID.get_spec(ppmlim=ppmlim))
         plt.plot(ppmAxisShift,data,color='r',linewidth=2,linestyle='-')
     if plot_avg:
         avg /= len(MRSList)
@@ -407,7 +450,7 @@ def plotly_fit(mrs,res,ppmlim=(.2,4.2),proj='real',metabs = None,phs=(0,0)):
 
     # Prepare the data
     base   = FID2Spec(res.baseline)
-    axis   = np.flipud(mrs.ppmAxisFlip)
+    axis   = mrs.ppmAxisShift
     data   = FID2Spec(mrs.FID)
 
     if ppmlim is None:
@@ -667,7 +710,7 @@ def plot_real_imag(mrs,res,ppmlim=(.2,4.2)):
             return np.abs(x)
     
     # Prepare the data
-    axis        = np.flipud(mrs.ppmAxisFlip)
+    axis        = mrs.ppmAxisShift
     data_real   = project(FID2Spec(mrs.FID),'real')
     pred_real   = project(FID2Spec(res.pred),'real')
     data_imag   = project(FID2Spec(mrs.FID),'imag')
@@ -777,7 +820,7 @@ def plot_indiv_stacked(mrs,res,ppmlim=(.2,4.2)):
     line_size = dict(data=.5, 
                      indiv=2)
     fig = go.Figure()
-    axis        = np.flipud(mrs.ppmAxisFlip)
+    axis        = mrs.ppmAxisShift
     y_data  = np.real(FID2Spec(mrs.FID))
     trace1 = go.Scatter(x=axis, y=y_data,
                         mode='lines',
@@ -821,7 +864,7 @@ def plot_indiv(mrs,res,ppmlim=(.2,4.2)):
 
     fig = make_subplots(rows=nrows, cols=ncols,subplot_titles=mrs.names)
     traces = []
-    axis        = np.flipud(mrs.ppmAxisFlip)
+    axis        = mrs.ppmAxisShift
     for i,metab in enumerate(mrs.names):
         c,r = i%ncols,i//ncols
         #r = i//ncols

fsl_mrs/utils/preproc/align.py

@@ -273,7 +273,7 @@ def phase_freq_align_report(inFIDs,outFIDs,hdr,phi,eps,ppmlim=None,shift=True,ht
 
     def addline(fig,mrs,lim,name,linestyle):
         trace = go.Scatter(x=mrs.getAxes(ppmlim=lim, axis=axis),
-                        y=np.real(mrs.getSpectrum(ppmlim=lim, shift=shift)),
+                        y=np.real(mrs.get_spec(ppmlim=lim, shift=shift)),
                         mode='lines',
                         name=name,
                         line=linestyle)
@@ -399,7 +399,7 @@ def phase_freq_align_diff_report(inFIDs0,inFIDs1,outFIDs0,outFIDs1,hdr,eps,phi,p
     
     def addline(fig,mrs,lim,name,linestyle):
         trace = go.Scatter(x=mrs.getAxes(ppmlim=lim, axis=axis),
-                        y=np.real(mrs.getSpectrum(ppmlim=lim, shift=shift)),
+                        y=np.real(mrs.get_spec(ppmlim=lim, shift=shift)),
                         mode='lines',
                         name=name,
                         line=linestyle)

fsl_mrs/utils/preproc/combine.py

@@ -205,7 +205,7 @@ def combine_FIDs_report(inFIDs,outFID,hdr,ncha=2,ppmlim = (0.0,6.0),method='not
 
     def addline(fig,mrs,lim,name,linestyle):
         trace = go.Scatter(x=mrs.getAxes(ppmlim=lim),
-                        y=np.real(mrs.getSpectrum(ppmlim=lim)),
+                        y=np.real(mrs.get_spec(ppmlim=lim)),
                         mode='lines',
                         name=name,
                         line=linestyle)
@@ -293,8 +293,8 @@ def combine_FIDs_report(inFIDs,outFID,hdr,ncha=2,ppmlim = (0.0,6.0),method='not
 #     style = ['--']*len(colors)
 #     ax.set_prop_cycle(color =colors,linestyle=style)
 #     for fid in toPlotIn:
-#         ax.plot(fid.getAxes(ppmlim=ppmlim),np.real(fid.getSpectrum(ppmlim=ppmlim)))
+#         ax.plot(fid.getAxes(ppmlim=ppmlim),np.real(fid.get_spec(ppmlim=ppmlim)))
 #     for fid in toPlotOut:
-#         ax.plot(fid.getAxes(ppmlim=ppmlim),np.real(fid.getSpectrum(ppmlim=ppmlim)),'k-')    
+#         ax.plot(fid.getAxes(ppmlim=ppmlim),np.real(fid.get_spec(ppmlim=ppmlim)),'k-')    
 #     styleSpectrumAxes(ax)
 #     plt.show()

fsl_mrs/utils/preproc/eddycorrect.py

@@ -49,7 +49,7 @@ def eddy_correct_report(inFID,outFID,phsRef,hdr,ppmlim = (0.2,4.2),html=None):
 
     # Add lines to figure
     def addline(fig,mrs,lim,name,linestyle):        
-        y = np.real(mrs.getSpectrum(ppmlim=lim))
+        y = np.real(mrs.get_spec(ppmlim=lim))
         trace = go.Scatter(x=mrs.getAxes(ppmlim=lim),
                         y=y,
                         mode='lines',

fsl_mrs/utils/preproc/filtering.py

@@ -56,7 +56,7 @@ def apodize_report(inFID,outFID,hdr,plotlim = (0.2,6),html=None):
     # Add lines to figure
     def addline(fig,mrs,lim,name,linestyle):
         trace = go.Scatter(x=mrs.getAxes(ppmlim=lim),
-                        y=np.real(mrs.getSpectrum(ppmlim=lim)),
+                        y=np.real(mrs.get_spec(ppmlim=lim)),
                         mode='lines',
                         name=name,
                         line=linestyle)

fsl_mrs/utils/preproc/general.py

@@ -71,7 +71,7 @@ def add_subtract_report(inFID,inFID2,outFID,hdr,ppmlim=(0.2,4.2),function='Not s
     # Add lines to figure
     def addline(fig,mrs,lim,name,linestyle):
         trace = go.Scatter(x=mrs.getAxes(ppmlim=lim),
-                        y=np.real(mrs.getSpectrum(ppmlim=lim)),
+                        y=np.real(mrs.get_spec(ppmlim=lim)),
                         mode='lines',
                         name=name,
                         line=linestyle)
@@ -137,12 +137,12 @@ def generic_report(inFID,outFID,inHdr,outHdr,ppmlim = (0.2,4.2),html=None,functi
 
     # Add lines to figure
     trace1 = go.Scatter(x=plotIn.getAxes(ppmlim=ppmlim),
-                        y=np.real(plotIn.getSpectrum(ppmlim=ppmlim)),
+                        y=np.real(plotIn.get_spec(ppmlim=ppmlim)),
                         mode='lines',
                         name='Original',
                         line=lines['in'])
     trace2 = go.Scatter(x=plotOut.getAxes(ppmlim=ppmlim),
-                        y=np.real(plotOut.getSpectrum(ppmlim=ppmlim)),
+                        y=np.real(plotOut.get_spec(ppmlim=ppmlim)),
                         mode='lines',
                         name='Shifted',
                         line=lines['out'])