IsoDec incorporated!

smith-chem-wisc · Aug 5, 2024 · b626f41 · b626f41
1 parent 6720fc5
commit b626f41
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Showing 5 changed files with 101 additions and 47 deletions.
diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs b/mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs
@@ -0,0 +1,96 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Numerics;
+using System.Runtime.InteropServices;
+using System.Text;
+using System.Threading.Tasks;
+using MassSpectrometry.MzSpectra;
+using MzLibUtil;
+using MathNet.Numerics.Statistics;
+
+namespace MassSpectrometry
+{
+    public class IsoDecAlgorithm(DeconvolutionParameters deconParameters)
+        : DeconvolutionAlgorithm(deconParameters)
+    {
+        [StructLayout(LayoutKind.Sequential, Pack =1)]
+        public struct MatchedPeak
+        {
+            public float mz;
+            public int z;
+            public float monoiso;
+            public float peakmass;
+            public float avgmass;
+            public float area;
+            public float peakint;
+            [MarshalAs(UnmanagedType.ByValArray, SizeConst = 64)]
+            public int[] matchedindsiso;
+            [MarshalAs(UnmanagedType.ByValArray, SizeConst = 64)]
+            public int[] matchedindsexp;
+            [MarshalAs(UnmanagedType.ByValArray, SizeConst = 128)]
+            public float[] isomz;
+            [MarshalAs(UnmanagedType.ByValArray, SizeConst = 128)]
+            public float[] isodist;
+            [MarshalAs(UnmanagedType.ByValArray, SizeConst = 128)]
+            public float[] isomass;
+            public int startindex;
+            public int endindex;
+        }
+
+
+        [DllImport(@"C:\Python\UniDec3\unidec\IsoDec\src\isodec\x64\Release\isodeclib.dll", CallingConvention = CallingConvention.Cdecl)]
+        public static extern int process_spectrum(float[] mz, float[] intensity, int len, string modelpath, IntPtr matchedpeaks);
+
+
+        public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range)
+        {
+            var firstIndex = spectrum.GetClosestPeakIndex(range.Minimum);
+            var lastIndex = spectrum.GetClosestPeakIndex(range.Maximum);
+
+            var mzs = spectrum.XArray[firstIndex..lastIndex]
+                .Select(p => (float)p)
+                .ToArray();
+            var intensities = spectrum.YArray[firstIndex..lastIndex]
+                .Select(p => (float)p)
+                .ToArray();
+
+            IntPtr matchedPeaksPtr = Marshal.AllocHGlobal(Marshal.SizeOf(typeof(MatchedPeak)) * intensities.Length);
+
+            int result = process_spectrum(mzs, intensities, intensities.Length,  @"C:\Python\UniDec3\unidec\IsoDec\phase_model.bin", matchedPeaksPtr);
+            if(result > 0)
+            {
+                MatchedPeak[] matchedpeaks = new MatchedPeak[result];
+                for(int i = 0;i<result;i++)
+                {
+                    matchedpeaks[i] = Marshal.PtrToStructure<MatchedPeak>(matchedPeaksPtr + i * Marshal.SizeOf(typeof(MatchedPeak)));
+                }
+                return ConvertToIsotopicEnvelopes(matchedpeaks, mzs, intensities);
+            }
+
+            else return new List<IsotopicEnvelope>();
+        }
+
+        private List<IsotopicEnvelope> ConvertToIsotopicEnvelopes(MatchedPeak[] matchedpeaks, float[] mzs, float[] intensities)
+        {
+            List<IsotopicEnvelope> result = new List<IsotopicEnvelope>();
+            foreach(MatchedPeak peak in matchedpeaks)
+            {
+                List<(double,double)> peaks = new List<(double,double)> ();
+                List<double> listofratios = new List<double>();
+                for(int i = 0;i<peak.matchedindsexp.Length;i++)
+                {
+                    if (i > 0 && peak.matchedindsexp[i] == 0)
+                        break;
+                    else
+                    {
+                        listofratios.Add(peak.isodist[i] / intensities[peak.startindex + i]);
+                        peaks.Add((mzs[peak.startindex + i], intensities[peak.startindex + i]));
+                    }
+                }
+                result.Add(new IsotopicEnvelope(peaks, peak.monoiso, peak.z, peak.peakint, Statistics.StandardDeviation(listofratios), 0));
+            }
+            return result;
+        }
+    }
+}
diff --git a/mzLib/MassSpectrometry/Deconvolution/Algorithms/JohnnyDeconvolutionAlgorithm.cs b/mzLib/MassSpectrometry/Deconvolution/Algorithms/JohnnyDeconvolutionAlgorithm.cs
diff --git a/mzLib/MassSpectrometry/Deconvolution/Deconvoluter.cs b/mzLib/MassSpectrometry/Deconvolution/Deconvoluter.cs
@@ -65,7 +65,7 @@ public static IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum,
             {
                 DeconvolutionType.ClassicDeconvolution => new ClassicDeconvolutionAlgorithm(deconvolutionParameters),
                 DeconvolutionType.ExampleNewDeconvolutionTemplate => new ExampleNewDeconvolutionAlgorithmTemplate(deconvolutionParameters),
-                DeconvolutionType.JohnnyDeconvolution => new JohnnyDeconvolutionAlgorithm(deconvolutionParameters),
+                DeconvolutionType.IsoDecDeconvolution => new IsoDecAlgorithm(deconvolutionParameters),
                 _ => throw new MzLibException("DeconvolutionType not yet supported")
             };
 

diff --git a/mzLib/MassSpectrometry/Deconvolution/DeconvolutionType.cs b/mzLib/MassSpectrometry/Deconvolution/DeconvolutionType.cs
@@ -10,6 +10,6 @@ public enum DeconvolutionType
     {
         ClassicDeconvolution,
         ExampleNewDeconvolutionTemplate,
-        JohnnyDeconvolution,
+        IsoDecDeconvolution,
     }
 }
diff --git a/...rameters/JohnnyDeconvolutionParameters.cs → ...rameters/IsoDecDeconvolutionParameters.cs b/...rameters/JohnnyDeconvolutionParameters.cs → ...rameters/IsoDecDeconvolutionParameters.cs
@@ -6,12 +6,12 @@
 
 namespace MassSpectrometry
 {
-    public class JohnnyDeconvolutionParameters : DeconvolutionParameters
+    public class IsoDecDeconvolutionParameters : DeconvolutionParameters
     {
         public override DeconvolutionType DeconvolutionType { get; protected set; } =
-            DeconvolutionType.JohnnyDeconvolution;
+            DeconvolutionType.IsoDecDeconvolution;
 
-        public JohnnyDeconvolutionParameters(Polarity polarity = Polarity.Positive) 
+        public IsoDecDeconvolutionParameters(Polarity polarity = Polarity.Positive) 
             : base(1, 100, polarity)
         {