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Averaging slight adjustement for ensured thread safety #810

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Averaging slight adjustement for ensured thread safety #810

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29 changes: 13 additions & 16 deletions mzLib/SpectralAveraging/Algorithms/SpectraAveraging.cs
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
using System;
using System.Collections.Concurrent;
using System.Collections.Generic;
using System.Linq;
using System.Threading.Tasks;
Expand Down Expand Up @@ -40,7 +41,7 @@ public static double[][] AverageSpectra(double[][] xArrays, double[][] yArrays,
/// <param name="parameters">how to perform the averaging</param>
/// <returns></returns>
private static double[][] MzBinning(double[][] xArrays, double[][] yArrays,
SpectralAveragingParameters parameters)
SpectralAveragingParameters parameters)
{
// get tics
var tics = yArrays.Select(p => p.Sum()).ToArray();
Expand All @@ -56,22 +57,18 @@ private static double[][] MzBinning(double[][] xArrays, double[][] yArrays,
var weights = SpectralWeighting.CalculateSpectraWeights(xArrays, yArrays, parameters.SpectralWeightingType);

// reject outliers and average bins
List<(double mz, double intensity)> averagedPeaks = new();
Parallel.ForEach(Enumerable.Range(0, parameters.MaxThreadsToUsePerFile), (iterationIndex) =>
var averagedPeaks = new ConcurrentBag<(double mz, double intensity)>();
var binIncidences = bins.Keys.ToArray();

Parallel.ForEach(binIncidences, new ParallelOptions { MaxDegreeOfParallelism = parameters.MaxThreadsToUsePerFile }, binIndex =>
{
// each bin index that contains peaks
var binIncidences = bins.Keys.ToList();

// iterate through each bin index which contains peaks
for (; iterationIndex < binIncidences.Count; iterationIndex += parameters.MaxThreadsToUsePerFile)
{
var peaksFromBin = bins[binIncidences[iterationIndex]];

peaksFromBin = OutlierRejection.RejectOutliers(peaksFromBin, parameters);
if (!peaksFromBin.Any()) continue;
lock (averagedPeaks)
averagedPeaks.Add(AverageBin(peaksFromBin, weights));
}
var peaksFromBin = bins[binIndex];
peaksFromBin = OutlierRejection.RejectOutliers(peaksFromBin, parameters);

if (peaksFromBin.Count == 0)
return;

averagedPeaks.Add(AverageBin(peaksFromBin, weights));
});

// return averaged
Expand Down
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