Merge pull request #16 from MannLabs/faims

add CV support for FAIMS

alpharaw/thermo.py

@@ -50,6 +50,8 @@ def _import_batch(
     precursor_charges = []
     ms_order_list = []
     ce_list = []
+    cv_list = []
+
     for i in range(
         start,
         stop
@@ -68,12 +70,18 @@ def _import_batch(
 
         if ms_order == 1:
             ce_list.append(0)
+            cv_list.append(0)
             precursor_mz_values.append(-1.0)
             isolation_mz_lowers.append(-1.0)
             isolation_mz_uppers.append(-1.0)
             precursor_charges.append(0)
         else:
             ce_list.append(rawfile.GetCollisionEnergyForScanNum(i))
+            n_cvs = rawfile.GetNumberOfSourceFragmentsFromScanNum(i)
+            if n_cvs > 0:
+                cv_list.append(rawfile.GetSourceFragmentValueFromScanNum(i,0))
+            else:
+                cv_list.append(0)
 
             isolation_center = rawfile.GetPrecursorMassForScanNum(i)
             isolation_width = rawfile.GetIsolationWidthForScanNum(i)
@@ -95,6 +103,7 @@ def _import_batch(
                 isolation_mz_uppers.append(isolation_center + isolation_width / 2)
                 precursor_charges.append(charge)
     rawfile.Close()
+
     return {
         '_peak_indices': _peak_indices,
         'peak_mz': np.concatenate(mz_values),
@@ -106,6 +115,7 @@ def _import_batch(
         'isolation_upper_mz': np.array(isolation_mz_uppers),
         'ms_level': np.array(ms_order_list, dtype=np.int8),
         'nce': np.array(ce_list, dtype=np.float32),
+        'cv': np.array(cv_list, dtype=np.float32),
     }
 class ThermoRawData(MSData_Base):
     """
@@ -173,6 +183,42 @@ def _import(self,
         rawfile.Close()
 
         return output_dict
+
+    def _set_dataframes(self, raw_data:dict):
+        self.create_spectrum_df(len(raw_data['rt']))
+        self.set_peak_df_by_indexed_array(
+            raw_data['peak_mz'],
+            raw_data['peak_intensity'],
+            raw_data['peak_indices'][:-1],
+            raw_data['peak_indices'][1:],
+        )
+        self.add_column_in_spec_df(
+            'rt', raw_data['rt']
+        )
+        self.add_column_in_spec_df(
+            'ms_level', raw_data['ms_level'],
+            dtype=np.int8
+        )
+        self.set_precursor_mz(
+            raw_data['precursor_mz']
+        )
+        self.add_column_in_spec_df(
+            'charge', raw_data['precursor_charge'],
+            dtype=np.int8
+        )
+        self.set_isolation_mz_windows(
+            raw_data['isolation_mz_lower'],
+            raw_data['isolation_mz_upper'],
+        )
+        self.add_column_in_spec_df(
+            "nce", raw_data["nce"],
+            dtype=np.float32,
+        )
+        self.add_column_in_spec_df(
+            "cv", raw_data["cv"],
+            dtype=np.float32,
+        )
+
 
     def import_raw(self, _path: str):
         super().import_raw(_path)