Merge branch '243_non_ms_data_fix' into 'corems_4_0'

Add filter on scan_df to remove non-mass spec scans

See merge request mass-spectrometry/corems!223

Author: corilo

corems/mass_spectra/input/mzml.py

@@ -167,6 +167,9 @@ def get_scan_df(self, data=None, time_range: Optional[Union[Tuple[float, float],
                 scan_dict["ms_format"][i] = None
 
         scan_df = pd.DataFrame(scan_dict)
+
+        # Remove any non-mass spectra scans (e.g., MS level 0 or None)
+        scan_df = scan_df[scan_df.ms_level.notnull() & (scan_df.ms_level > 0)].reset_index(drop=True)
 
         # Apply time range filtering if specified
         if time_range is not None:

corems/mass_spectra/input/rawFileReader.py

@@ -1436,7 +1436,10 @@ def get_scan_df(self, time_range: Optional[Union[Tuple[float, float], List[Tuple
                 scan_df.loc[scan_df.scan == i, "ms_format"] = "centroid"
             else:
                 scan_df.loc[scan_df.scan == i, "ms_format"] = "profile"
-
+        
+        # Remove any non-mass spectra scans (e.g., MS level 0 or None)
+        scan_df = scan_df[scan_df.ms_level.notnull() & (scan_df.ms_level > 0)].reset_index(drop=True)
+        
         # Filter by time range if specified
         if time_range is not None:
             time_ranges = self._normalize_time_range(time_range)