re-add calibration reference masses

Author: wkew-pnnl

corems/mass_spectrum/calc/Calibration.py

@@ -427,8 +427,8 @@ def recalibrate_mass_spectrum(self, cal_peaks_mz : list[float], cal_refs_mz : li
             self.mass_spectrum.calibration_order = order
             self.mass_spectrum.calibration_RMS = float(res['fun'])
             self.mass_spectrum.calibration_points = int(len(cal_refs_mz))
-            self.mass_spectrum.calib_ref_mzs = cal_refs_mz
-            #self.mass_spectrum.calib_meas_mzs = cal_refs_mz
+            self.mass_spectrum.calibration_ref_mzs = cal_refs_mz
+            self.mass_spectrum.calibration_meas_mzs = cal_peaks_mz
 
             self.mass_spectrum.calibration_segment = self.mzsegment
 

corems/mass_spectrum/factory/MassSpectrumClasses.py

@@ -59,6 +59,10 @@ class MassSpecBase(MassSpecCalc, KendrickGrouping):
         The order of the mass spectrum's calibration.
     calibration_points : None or ndarray
         The calibration points of the mass spectrum.
+    calibration_ref_mzs: None or ndarray
+        The reference m/z values of the mass spectrum's calibration.
+    calibration_meas_mzs : None or ndarray
+        The measured m/z values of the mass spectrum's calibration.
     calibration_RMS : None or float
         The root mean square of the mass spectrum's calibration.
     calibration_segment : None or CalibrationSegment
@@ -117,6 +121,8 @@ def __init__(self, mz_exp, abundance, d_params, **kwargs):
 
         self.calibration_order = None
         self.calibration_points = None
+        self.calibration_ref_mzs = None
+        self.calibration_meas_mzs = None
         self.calibration_RMS = None
         self.calibration_segment = None
         self.calibration_raw_error_median = None