Git add additional scaling option to results and fsl_mrs to allow for fixed...

Git add additional scaling option to results and fsl_mrs to allow for fixed water cencentration scaling.

fsl_mrs/scripts/fsl_mrs

@@ -99,6 +99,8 @@ def main():
                           nargs='+',
                           help='Metabolite(s) used as an internal reference.'
                                ' Defaults to tCr (Cr+PCr).')
+    optional.add_argument('--h2o_scale', type=float, default=1.0,
+                          help='Additional scaling modifier for external water referencing.')
     optional.add_argument('--central_frequency', default=None, type=float,
                           help='central frequency in Hz')
     optional.add_argument('--dwell_time', default=None, type=float,
@@ -329,20 +331,23 @@ def main():
                           ' no absolute quantification will be performed.',
                           UserWarning)
         res.calculateConcScaling(mrs, referenceMetab=args.internal_ref)
-    elif args.tissue_frac is None:
+    elif args.tissue_frac is not None:
         res.calculateConcScaling(mrs,
                                  referenceMetab=args.internal_ref,
                                  waterRefFID=mrs.H2O,
-                                 tissueFractions=None,
+                                 tissueFractions=args.tissue_frac,
                                  TE=echotime,
-                                 verbose=args.verbose)
+                                 verbose=args.verbose,
+                                 add_scale=args.h2o_scale)
     else:
         res.calculateConcScaling(mrs,
                                  referenceMetab=args.internal_ref,
                                  waterRefFID=mrs.H2O,
-                                 tissueFractions=args.tissue_frac,
+                                 tissueFractions=None,
                                  TE=echotime,
-                                 verbose=args.verbose)
+                                 verbose=args.verbose,
+                                 add_scale=args.h2o_scale)
+
     # Combine metabolites.
     if args.combine is not None:
         res.combine(args.combine)

fsl_mrs/utils/results.py

@@ -93,9 +93,18 @@ class FitRes(object):
             self.combine([['Cr','PCr']])        
             self.calculateConcScaling(mrs)
 
-
-
-    def calculateConcScaling(self,mrs,referenceMetab=['Cr','PCr'],waterRefFID=None,tissueFractions=None,TE=None,T2='Default',waterReferenceMetab='Cr',wRefMetabProtons=5,reflimits=(2,5),verbose=False,Q=None):
+    def calculateConcScaling(self, mrs,
+                             referenceMetab=['Cr', 'PCr'],
+                             waterRefFID=None,
+                             tissueFractions=None,
+                             TE=None,
+                             T2='Default',
+                             waterReferenceMetab='Cr',
+                             wRefMetabProtons=5,
+                             reflimits=(2, 5),
+                             verbose=False,
+                             Q=None,
+                             add_scale=None):
 
         self.intrefstr = '+'.join(referenceMetab)
         self.referenceMetab = referenceMetab
@@ -111,6 +120,10 @@ class FitRes(object):
                     Q = quant.loadDefaultQuantificationInfo(TE,tissueFractions,mrs.centralFrequency/1E6)
                 else:
                     Q = quant.QuantificationInfo(TE,T2,tissueFractions)
+
+            if add_scale is not None:
+                Q.additionalCorr *= add_scale
+
             molalityScaling,molarityScaling,quant_info = quant.quantifyWater(mrs,
                                                             waterRefFID,
                                                             refFID,