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Averaging slight adjustement for ensured thread safety #810

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merged 5 commits into from
Dec 12, 2024
Merged

Averaging slight adjustement for ensured thread safety #810

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094da3d
Refactor for thread safety and performance
nbollis Nov 26, 2024
95c213c
Test Project cleanup
nbollis Dec 4, 2024
a283aee
used a partitioner
nbollis Dec 4, 2024
dd4ee58
Oopsie
nbollis Dec 4, 2024
3bfed73
Removed bag as it was an unnecessry structure
nbollis Dec 4, 2024
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24 changes: 11 additions & 13 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 @@ -39,8 +40,7 @@ public static double[][] AverageSpectra(double[][] xArrays, double[][] yArrays,
/// <param name="yArrays">yArrays of spectra to be averaged</param>
/// <param name="parameters">how to perform the averaging</param>
/// <returns></returns>
private static double[][] MzBinning(double[][] xArrays, double[][] yArrays,
SpectralAveragingParameters parameters)
private static double[][] MzBinning(double[][] xArrays, double[][] yArrays, SpectralAveragingParameters parameters)
{
// get tics
var tics = yArrays.Select(p => p.Sum()).ToArray();
Expand All @@ -56,21 +56,20 @@ 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) =>
{
// each bin index that contains peaks
var binIncidences = bins.Keys.ToList();
var binIncidences = bins.Keys.ToList();
(double mz, double intensity)[] averagedPeaks = new (double, double)[binIncidences.Count];
var partitioner = Partitioner.Create(0, binIncidences.Count);

// iterate through each bin index which contains peaks
for (; iterationIndex < binIncidences.Count; iterationIndex += parameters.MaxThreadsToUsePerFile)
Parallel.ForEach(partitioner, new ParallelOptions { MaxDegreeOfParallelism = parameters.MaxThreadsToUsePerFile }, (range, state) =>
{
for (int i = range.Item1; i < range.Item2; i++)
{
var peaksFromBin = bins[binIncidences[iterationIndex]];
var peaksFromBin = bins[binIncidences[i]];

peaksFromBin = OutlierRejection.RejectOutliers(peaksFromBin, parameters);
if (!peaksFromBin.Any()) continue;
lock (averagedPeaks)
averagedPeaks.Add(AverageBin(peaksFromBin, weights));

averagedPeaks[i] = AverageBin(peaksFromBin, weights);
}
});

Expand All @@ -86,7 +85,6 @@ private static double[][] MzBinning(double[][] xArrays, double[][] yArrays,
};
}


#region Helpers

/// <summary>
Expand Down
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