First pass at mega default mm.

fsl_mrs/core/basis.py

@@ -384,7 +384,7 @@ class Basis:
         self._names.pop(index)
         self._widths.pop(index)
 
-    def add_peak(self, ppm, amp, name, gamma=0.0, sigma=0.0):
+    def add_peak(self, ppm, amp, name, gamma=0.0, sigma=0.0, conj=False):
         """Add Voigt peak to basis at specified ppm
 
         :param ppm: The ppm position of the peak
@@ -397,12 +397,17 @@ class Basis:
         :type gamma: float, optional
         :param sigma: Guassian line broadening, defaults to 0
         :type sigma: float, optional
+        :param conj: Conjugate fid, defaults to False
+        :type conj: Bool, optional
         """
         # Calculate the time axis
         time_axis = self.original_time_axis
+        time_axis -= time_axis[0]
 
         fid = misc.create_peak(time_axis, self.cf, ppm, amp, gamma, sigma)[:, None]
         width = None  # TO DO
+        if conj:
+            fid = fid.conj()
         self.add_fid_to_basis(fid, name, width=width)
 
     def update_fid(self, new_fid, name):

fsl_mrs/core/mrs.py

@@ -591,18 +591,49 @@ class MRS(object):
 
         return 0
 
-    def add_MM_peaks(self, ppmlist=None, amplist=None, gamma=0, sigma=0):
-        """Add default MM spectra to basis set
-
-        By default will use the defined shifts and amplitudes
+    def add_default_MM_peaks(self, gamma=0, sigma=0):
+        """Add the default MM peaks to the basis set
+        These use the defined shifts and amplitudes
         ppmlist :  [0.9,1.2,1.4,1.7,[2.08,2.25,1.95,3.0]]
         amplist : [3.0,2.0,2.0,2.0,[1.33,0.33,0.33,0.4]]
-        but these can be overridden using the kwargs
 
-        :param ppmlist: List of shifts, nested lists group into single basis, defaults to None
-        :type ppmlist: List of floats, optional
-        :param amplist: List of amplitudes, nested lists group into single basis, defaults to None
-        :type amplist: List of floats, optional
+        :param gamma: Lorentzian broadening, defaults to 0
+        :type gamma: int, optional
+        :param sigma: Gaussian broadening, defaults to 0
+        :type sigma: int, optional
+        """
+        from fsl_mrs.utils.constants import DEFAULT_MM_AMP, DEFAULT_MM_PPM
+        return self.add_MM_peaks(
+            DEFAULT_MM_PPM,
+            DEFAULT_MM_AMP,
+            gamma=gamma,
+            sigma=sigma)
+
+    def add_default_MEGA_MM_peaks(self, gamma=0, sigma=0):
+        """Add the default MEGA-PRESS MM peaks to the basis set
+        These use the defined shifts and amplitudes
+        ppmlist : [[0.94, 3.0]]
+        amplist : [[3.0, 2.0]]
+
+        :param gamma: Lorentzian broadening, defaults to 0
+        :type gamma: int, optional
+        :param sigma: Gaussian broadening, defaults to 0
+        :type sigma: int, optional
+        """
+        from fsl_mrs.utils.constants import DEFAULT_MM_MEGA_AMP, DEFAULT_MM_MEGA_PPM
+        return self.add_MM_peaks(
+            DEFAULT_MM_MEGA_PPM,
+            DEFAULT_MM_MEGA_AMP,
+            gamma=gamma,
+            sigma=sigma)
+
+    def add_MM_peaks(self, ppmlist, amplist, gamma=0, sigma=0):
+        """Add extra Gaussian peaks (normal MM spectra) to basis set
+
+        :param ppmlist: List of shifts, nested lists group into single basis.
+        :type ppmlist: List of floats
+        :param amplist: List of amplitudes, nested lists group into single basis.
+        :type amplist: List of floats
         :param gamma: Lorentzian broadening, defaults to 0
         :type gamma: int, optional
         :param sigma: Gaussian broadening, defaults to 0
@@ -610,11 +641,6 @@ class MRS(object):
         :return: Number of basis sets added
         :rtype: int
         """
-        if ppmlist is None:
-            from fsl_mrs.utils.constants import DEFAULT_MM_AMP, DEFAULT_MM_PPM
-            ppmlist = DEFAULT_MM_PPM
-            amplist = DEFAULT_MM_AMP
-
         for idx, _ in enumerate(ppmlist):
             if isinstance(ppmlist[idx], (float, int)):
                 ppmlist[idx] = [float(ppmlist[idx]), ]
@@ -624,7 +650,7 @@ class MRS(object):
         names = [f'MM{i[0]*10:02.0f}' for i in ppmlist]
 
         for name, ppm, amp in zip(names, ppmlist, amplist):
-            self._basis.add_peak(ppm, amp, name, gamma, sigma)
+            self._basis.add_peak(ppm, amp, name, gamma, sigma, conj=self.conj_Basis)
 
         return len(ppmlist)
 

fsl_mrs/scripts/fsl_mrs

@@ -74,6 +74,8 @@ def main():
                                    ' or list of names for indept groups.')
     fitting_args.add_argument('--add_MM', action="store_true",
                               help="include default macromolecule peaks")
+    fitting_args.add_argument('--add_MM_MEGA', action="store_true",
+                              help="include default MEGA-PRESS macromolecule peaks")
     fitting_args.add_argument('--lorentzian', action="store_true",
                               help='Enable purely lorentzian broadening'
                                    ' (default is Voigt)')
@@ -255,7 +257,13 @@ def main():
     if args.add_MM:
         if args.verbose:
             print('Adding macromolecules')
-        nMM = mrs.add_MM_peaks(gamma=10, sigma=20)
+        nMM = mrs.add_default_MM_peaks(gamma=10, sigma=20)
+        G = [i + max(metab_groups) + 1 for i in range(nMM)]
+        metab_groups += G
+    if args.add_MM_MEGA:
+        if args.verbose:
+            print('Adding MEGA-PRESS macromolecules')
+        nMM = mrs.add_default_MEGA_MM_peaks(gamma=10, sigma=0)
         G = [i + max(metab_groups) + 1 for i in range(nMM)]
         metab_groups += G
 

fsl_mrs/utils/constants.py

@@ -119,3 +119,6 @@ Shift and amplitude values for the default macromolecule basis set
 '''
 DEFAULT_MM_PPM = [0.9, 1.2, 1.4, 1.7, [2.08, 2.25, 1.95, 3.0]]
 DEFAULT_MM_AMP = [3.0, 2.0, 2.0, 2.0, [1.33, 0.33, 0.33, 0.4]]
+
+DEFAULT_MM_MEGA_PPM = [[0.915, 3.000], ]
+DEFAULT_MM_MEGA_AMP = [[3.75, 2.0], ]