Minor bug fixes

fsl_mrs/core.py

@@ -246,7 +246,7 @@ class MRS(object):
 
         
     # Helper functions
-    def check_FID(self,ppmlim=(.2,4.2),repare=False):
+    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
@@ -254,7 +254,7 @@ class MRS(object):
         Parameters
         ----------
         ppmlim : list
-        repare : if True applies conjugation to FID
+        repair : if True applies conjugation to FID
 
         Returns
         -------
@@ -266,7 +266,7 @@ class MRS(object):
         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 repare is False:
+            if repair is False:
                 warnings.warn('YOU MAY NEED TO CONJUGATE YOUR FID!!!')
                 return -1
             else:
@@ -282,7 +282,7 @@ class MRS(object):
         self.FID  = np.conj(self.FID)
         self.Spec = misc.FIDToSpec(self.FID)
 
-    def check_Basis(self,ppmlim=(.2,4.2),repare=False):
+    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
@@ -290,7 +290,7 @@ class MRS(object):
         Parameters
         ----------
         ppmlim : list
-        repare : if True applies conjugation to basis
+        repair : if True applies conjugation to basis
 
         Returns
         -------
@@ -309,7 +309,7 @@ class MRS(object):
                 conjOrNot.append(0.0)
 
         if (sum(conjOrNot)/len(conjOrNot))>0.5:
-            if repare is False:
+            if repair is False:
                 warnings.warn('YOU MAY NEED TO CONJUGATE YOUR BASIS!!!')
                 return -1
             else:

fsl_mrs/scripts/fsl_mrs

@@ -197,7 +197,7 @@ def main():
         if args.conjfid:
             mrs.conj_FID()
     else:
-        conjugated = mrs.check_FID(repare=True)
+        conjugated = mrs.check_FID(repair=True)
         if args.verbose:
             if conjugated == 1:
                 warnings.warn('FID has been checked and conjugated. Please check!',UserWarning)
@@ -206,7 +206,7 @@ def main():
         if args.conjbasis:
             mrs.conj_Basis()
     else:
-        conjugated = mrs.check_Basis(repare=True)
+        conjugated = mrs.check_Basis(repair=True)
         if args.verbose:
             if conjugated == 1:
                 warnings.warn('Basis has been checked and conjugated. Please check!',UserWarning)

fsl_mrs/utils/plotting.py

@@ -285,13 +285,7 @@ def plot_spectrum(mrs,ppmlim=(0.0,4.5),FID=None,proj='real',c='k'):
     return plt.gcf()
     
 
-def plot_spectra(FIDlist,bandwidth,centralFrequency,ppmlim=(0,4.5),single_FID=None,plot_avg=True):
-    numPoints        = FIDlist[0].size
-    frequencyAxis    = np.linspace(-bandwidth/2,
-                                   bandwidth/2,
-                                   numPoints)    
-    ppmAxisShift     = hz2ppm(centralFrequency,
-                              frequencyAxis,shift=True)
+def plot_spectra(MRSList,ppmlim=(0,4.5),single_FID=None,plot_avg=True):
 
     plt.figure(figsize=(10,10))
     plt.xlim(ppmlim)
@@ -303,15 +297,16 @@ def plot_spectra(FIDlist,bandwidth,centralFrequency,ppmlim=(0,4.5),single_FID=No
     plt.autoscale(enable=True, axis='y', tight=True)
     
     avg=0
-    for FID in FIDlist:
-        data = np.real(FID2Spec(FID))
+    for mrs in MRSList:
+        data = np.real(mrs.getSpectrum(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(FID2Spec(single_FID))
+        data = np.real(single_FID.getSpectrum(ppmlim=ppmlim))
         plt.plot(ppmAxisShift,data,color='r',linewidth=2,linestyle='-')
     if plot_avg:
-        avg /= len(FIDlist)
+        avg /= len(MRSList)
         plt.plot(ppmAxisShift,avg,color='g',linewidth=2,linestyle='-')
     
     autoscale_y(plt.gca(),margin=0.05)

fsl_mrs/utils/qc.py

@@ -216,7 +216,7 @@ def getNoiseSDDist(specIn,noiseregionmask):
     noiseOnlySpec = specIn[noiseregionmask]
 
     npoints = noiseOnlySpec.size
-    regionPoints = 100
+    regionPoints = min(100,int(npoints/10))
     
     def running_std_strides(seq, window=100):
         stride = seq.strides[0]

fsl_mrs/utils/results.py

@@ -247,20 +247,17 @@ class FitRes(object):
     # Functions to return physically meaningful units from the fitting results
     def getConc(self,scaling='raw',metab=None,function='mean'):
         if function is None:
-            dfFunc = lambda m : self.fitResults[m].values
+            dfFunc = lambda m : self.fitResults[m]
         else:
-            dfFunc = lambda m : self.fitResults[m].apply(function)
+            dfFunc = lambda m : self.fitResults[m].apply(function).to_numpy()
 
         # Extract concentrations from parameters.
         if metab is not None:
             if metab not in self.metabs:
                 raise ValueError(f'{metab} is not a recognised metabolite.')
-            rawConc = np.asarray(dfFunc(metab))
-        else:
-            rawConc = []
-            for m in self.metabs:
-                rawConc.append(dfFunc(m))
-            rawConc = np.asarray(rawConc)
+            rawConc = dfFunc(metab)
+        else:            
+            rawConc = dfFunc(self.metabs)
 
         if scaling == 'raw':            
             return rawConc