fix endpoints

Author: z3rone

native/ThermoNativeReader/NativeApi.cs

@@ -551,7 +551,40 @@ public static unsafe int GetMs1ScanNumberFromRt(long arg0, double arg1)
         }
 
         [UnmanagedCallersOnly(EntryPoint = "get_chromatogram")]
-        public static unsafe int GetChromatogram(long arg0, int arg1, byte* arg2, double* arg3, double* arg4, int arg5, int arg6, int arg7, double* arg8, double* arg9, int arg10) { return RunOnWorker(() => { if (!_openFiles.TryGetValue(arg0, out var f)) return 0; try { return 0; } catch { return 0; } }); }
+        public static unsafe int GetChromatogram(long arg0, int arg1, byte* arg2, double* arg3, double* arg4, int arg5, int arg6, int arg7, double* arg8, double* arg9, int arg10)
+        {
+            return RunOnWorker(() => {
+                if (!_openFiles.TryGetValue(arg0, out var f)) return 0;
+                try { 
+                    string filter = Marshal.PtrToStringAnsi((IntPtr)arg2) ?? "";
+                    var settings = new ChromatogramTraceSettings((TraceType)arg1) { Filter = filter };
+                    
+                    if (arg5 > 0)
+                    {
+                        settings.MassRangeCount = arg5;
+                        for (int i = 0; i < arg5; i++)
+                        {
+                            settings.SetMassRange(i, new Range(arg3[i], arg4[i]));
+                        }
+                    }
+
+                    var data = f.GetChromatogramData(new[] { settings }, arg6, arg7);
+                    
+                    if (data == null || data.PositionsArray == null || data.PositionsArray.Length == 0) 
+                    {
+                        return 0;
+                    }
+                    
+                    int count = Math.Min(data.PositionsArray[0].Length, arg10);
+                    for (int i = 0; i < count; i++)
+                    {
+                        arg8[i] = data.PositionsArray[0][i];
+                        arg9[i] = data.IntensitiesArray[0][i];
+                    }
+                    return count;
+                } catch { return 0; }
+            });
+        }
 
         [UnmanagedCallersOnly(EntryPoint = "get_filters")]
         public static unsafe int GetFilters(long arg0, byte* arg1, int arg2) { return RunOnWorker(() => { if (!_openFiles.TryGetValue(arg0, out var f)) return 0; try { return 0; } catch { return 0; } }); }

native_fisher_py/python/native_fisher_py/raw_file.py

@@ -367,10 +367,10 @@ def get_scan_ms1(self, scan_number: int):
 
     def get_scan_ms2(self, *args):
         if len(args) == 1:
-            return self.get_scan_from_scan_number(self._handle, args[0])
+            return self.get_scan_from_scan_number(args[0])
         elif len(args) >= 2:
-            scan, _ = self.get_ms2_scan_number_from_retention_time(self._handle, args[0], args[1])
-            return self.get_scan_from_scan_number(self._handle, scan)
+            scan, _ = self.get_ms2_scan_number_from_retention_time(args[0], args[1])
+            return self.get_scan_from_scan_number(scan)
         return np.array([]), np.array([]), np.array([]), ""
 
     def get_tic_ms2(self):
@@ -394,9 +394,9 @@ def get_precursor_mz(self, scan_number: int) -> float:
 
     def get_scan_from_scan_number(self, scan_number: int):
         # Use get_centroid_stream to match behavior for parity
-        masses, intensities = get_centroid_stream(self._handle, scan_number, 1000000)
+        masses, intensities, _, _, _, _, _ = get_centroid_stream(self._handle, scan_number, 1000000)
         charges = np.zeros_like(masses)
-        event_str = self.get_scan_event_string_for_scan_number(self._handle, scan_number)
+        event_str = self.get_scan_event_string_for_scan_number(scan_number)
         return np.array(masses), np.array(intensities), charges, event_str
 
     def get_scan_number_from_retention_time(self, rt: float) -> int: