Added a add_water_peak method to mrs.

CHANGELOG.rst

@@ -8,6 +8,7 @@ This document contains the FSL-MRS release history in reverse chronological orde
 - fsl_mrsi now outputs fitting nuisance parameters: phases, and shifts & linewidths for each metabolite group.
 - Add NIfTI-MRS reshape command
 - Add basis_tools remove_peak option to run HLSVD, typical usage for removing TMS peak.
+- Added an add_water_peak method to MRS class.
 
 1.1.3 (Tuesday 29th June 2021)
 ------------------------------

fsl_mrs/core/mrs.py

@@ -656,6 +656,25 @@ class MRS(object):
 
         return len(ppmlist)
 
+    def add_water_peak(self, gamma=0.0, sigma=0.0, ppm=4.65, amp=1.0, name='H2O'):
+        """Add a peak at 4.65 ppm to capture (residual) water.
+
+        :param gamma: Lorentzian broadening, defaults to 0
+        :type gamma: float, optional
+        :param sigma: Gaussian broadening, defaults to 0
+        :type sigma: float, optional
+        :param ppm: Peak position, defaults to 4.65
+        :type ppm: float, optional
+        :param amp: Peak amplitude, defaults to 1.0
+        :type amp: float, optional
+        :param name: Basis name, defaults to 'H2O'
+        :type name: str, optional
+        :return: Number of basis spectra added (1).
+        :rtype: int
+        """
+        self._basis.add_peak(ppm, amp, name, gamma, sigma, conj=self.conj_Basis)
+        return 1
+
     # Plotting functions
     def plot(self, ppmlim=(0.2, 4.2)):
         """Plot the spectrum in the mrs object

fsl_mrs/tests/test_core_mrs.py

@@ -148,22 +148,29 @@ def test_basis_manipulations(synth_data):
     assert mrs.numBasis == 6
     assert mrs.names == ['ppm_2', 'MM09', 'MM12', 'MM14', 'MM17', 'MM21']
 
-    mrs.ignore = ['MM09']
+    mrs.add_water_peak(gamma=10, sigma=10, name='myh2o')
+    assert mrs.basis.shape == (2048, 7)
+    assert mrs.numBasis == 7
+    assert mrs.names == ['ppm_2', 'MM09', 'MM12', 'MM14', 'MM17', 'MM21', 'myh2o']
 
-    assert mrs.basis.shape == (2048, 5)
-    assert mrs.numBasis == 5
+    mrs.ignore = ['MM09']
 
+    assert mrs.basis.shape == (2048, 6)
+    assert mrs.numBasis == 6
+    
     mrs.ignore = []
+    # This suprising result is because mrs.keep is still populated.
     assert mrs.basis.shape == (2048, 1)
     assert mrs.numBasis == 1
+
     mrs.keep = []
-    assert mrs.basis.shape == (2048, 7)
-    assert mrs.numBasis == 7
+    assert mrs.basis.shape == (2048, 8)
+    assert mrs.numBasis == 8
 
     mrs.keep = None
     mrs.ignore = None
-    assert mrs.basis.shape == (2048, 7)
-    assert mrs.numBasis == 7
+    assert mrs.basis.shape == (2048, 8)
+    assert mrs.numBasis == 8
 
 
 def test_nucleus_identification():