public void TestEuclideanDistanceForSpatialVectors()
{
var v1 = FeatureUtil.makeSpatialVector(0.0, 0.0, 0.0, 0.0, 0.0, 0.0);
var v2 = FeatureUtil.makeSpatialVector(1.0, -1.0, 1.0, -1.0, 1.0, -1.0);
var dist = SpectralModelBuilder.euclideanDistance(v1, v2);
Assert.AreEqual(dist, Math.Sqrt(6.0));
}
public void TestEuclideanDistanceForScalars()
{
var h1 = FeatureUtil.makeNum(1.0);
var h2 = FeatureUtil.makeNum(0.0);
var dist = SpectralModelBuilder.euclideanDistance(h1, h2);
Assert.AreEqual(dist, 1.0);
}
public void SimpleCountableHashTest()
{
var o = BigInteger.One;
var c = FeatureUtil.makeFullCVR(1, 1, 1, 1, 1, 1, 1);
var bvbi = o | (o << 1) | (o << 2) | (o << 3) | (o << 4) | (o << (20 * 5)) | (o << (20 * 5 + 1));
var bv = UInt128.FromBigInteger(bvbi);
var bv_is = LSHCalc.h7(c);
Assert.AreEqual(bv, bv_is);
}
public static IEnumerable <LCIMSMSFeature> CorrectLCIMSMSFeatures(List <LCIMSMSFeature> lcImsMsFeatureEnumerable)
{
var massToleranceBase = Settings.MassMonoisotopicConstraint;
// ReSharper disable once NotAccessedVariable
var totalFound = 0;
foreach (var lcimsmsFeature in lcImsMsFeatureEnumerable)
{
if (lcimsmsFeature.imsMsFeatureList.Count == 0)
{
continue;
}
var averageMass = lcimsmsFeature.CalculateAverageMonoisotopicMass();
var massTolerance = massToleranceBase * averageMass / 1000000.0;
var errorFlagPercentage = lcimsmsFeature.GetFlaggedPercentage();
var searchForDaErrorQuery = from otherLCIMSMSFeature in lcImsMsFeatureEnumerable
where
Math.Abs(averageMass - otherLCIMSMSFeature.CalculateAverageMonoisotopicMass()) >= (1 - massTolerance) &&
Math.Abs(averageMass - otherLCIMSMSFeature.CalculateAverageMonoisotopicMass()) <= (1 + massTolerance) &&
otherLCIMSMSFeature.imsMsFeatureList.Count > 0
orderby Math.Abs(errorFlagPercentage - otherLCIMSMSFeature.GetFlaggedPercentage()) descending
select otherLCIMSMSFeature;
foreach (var lcimsmsFeatureToCheck in searchForDaErrorQuery.AsParallel().Where(lcimsmsFeatureToCheck => Math.Abs(errorFlagPercentage - lcimsmsFeatureToCheck.GetFlaggedPercentage()) > 0.3))
{
//bool featuresFitTogether = FeatureUtil.DoLCIMSMSFeaturesFitTogether(lcimsmsFeature, lcimsmsFeatureToCheck);
//if (featuresFitTogether)
//{
if (errorFlagPercentage > lcimsmsFeatureToCheck.GetFlaggedPercentage())
{
FeatureUtil.MergeLCIMSMSFeatures(lcimsmsFeatureToCheck, lcimsmsFeature);
}
else
{
FeatureUtil.MergeLCIMSMSFeatures(lcimsmsFeature, lcimsmsFeatureToCheck);
}
totalFound++;
break;
//}
}
}
var newFeatureListQuery = lcImsMsFeatureEnumerable.Where(lcimsmsFeature => lcimsmsFeature.imsMsFeatureList.Count > 0);
return(newFeatureListQuery.AsEnumerable());
}
public void AddImsMsFeature(imsMsFeature imsMsFeature)
{
var lcScan = imsMsFeature.ScanLC;
foreach (var otherImsMsFeature in imsMsFeatureList.Where(otherImsMsFeature => otherImsMsFeature.ScanLC == lcScan))
{
FeatureUtil.MergeImsMsFeatures(imsMsFeature, otherImsMsFeature);
imsMsFeatureList.Add(imsMsFeature);
imsMsFeatureList.Remove(otherImsMsFeature);
return;
}
imsMsFeatureList.Add(imsMsFeature);
}
public void AddIMSMSFeature(IMSMSFeature imsmsFeature)
{
var lcScan = imsmsFeature.ScanLC;
foreach (var otherIMSMSFeature in IMSMSFeatureList.Where(otherIMSMSFeature => otherIMSMSFeature.ScanLC == lcScan))
{
FeatureUtil.MergeIMSMSFeatures(imsmsFeature, otherIMSMSFeature);
IMSMSFeatureList.Add(imsmsFeature);
IMSMSFeatureList.Remove(otherIMSMSFeature);
return;
}
IMSMSFeatureList.Add(imsmsFeature);
}
public async void SetUpVM(IVideoFrameInputController controller)
{
// WinML requires Windows 10 build 17728 or higher to run: https://docs.microsoft.com/en-us/windows/ai/
if (!MLHelper.IsMLAvailable())
{
IsEnabled = false;
AppService.DisplayDialog(FeatureUtil.GetLocalizedText("WinMLNotAvailableTitle"), FeatureUtil.GetLocalizedText("WinMLNotAvailableDescription"));
return;
}
LogService.Write($"Loading model {ModelFileName}...");
var modelFile = await FileUtil.GetFileFromInstalledLocationAsync(MLHelper.ModelBasePath + ModelFileName);
_model = await mnistModel.CreateFromStreamAsync(modelFile);
_controller = controller;
_controller.InputReady += Controller_InputReady;
IsEnabled = true;
}
public void Execute()
{
{
Logger.Log("Total number of MS Features in _isos.csv file = " + m_isosReader.NumOfUnfilteredMSFeatures);
Logger.Log("Total number of MS Features we'll consider = " + m_isosReader.MSFeatureList.Count);
Logger.Log("Creating IMS-MS Features...");
var filteredMSFeatureList = m_isosReader.MSFeatureList;
var imsmsfeatureBag = new ConcurrentBag <IMSMSFeature>();
if (Settings.UseCharge)
{
var groupByScanLCAndChargeQuery = from msFeature in filteredMSFeatureList
group msFeature by new { msFeature.ScanLC, msFeature.Charge } into newGroup
select newGroup;
Parallel.ForEach(groupByScanLCAndChargeQuery, msFeatureGroup =>
{
var imsmsFeatureList = ClusterMSFeatures.ClusterByMass(msFeatureGroup);
foreach (var imsmsFeature in imsmsFeatureList)
{
imsmsfeatureBag.Add(imsmsFeature);
}
});
}
else
{
var groupByScanLCQuery = from msFeature in filteredMSFeatureList
group msFeature by msFeature.ScanLC into newGroup
select newGroup;
Parallel.ForEach(groupByScanLCQuery, msFeatureGroup =>
{
var imsmsFeatureList = ClusterMSFeatures.ClusterByMass(msFeatureGroup);
foreach (var imsmsFeature in imsmsFeatureList)
{
imsmsfeatureBag.Add(imsmsFeature);
}
});
}
Logger.Log("Total Number of Unfiltered IMS-MS Features = " + imsmsfeatureBag.Count);
//Logger.Log("Filtering out short IMS-MS Features...");
//IEnumerable<IMSMSFeature> imsmsFeatureEnumerable = FeatureUtil.FilterByMemberCount(imsmsfeatureBag);
//imsmsfeatureBag = null;
//Logger.Log("Total Number of Filtered IMS-MS Features = " + imsmsFeatureEnumerable.Count());
Logger.Log("Creating LC-IMS-MS Features...");
var lcimsmsFeatureBag = new ConcurrentBag <LCIMSMSFeature>();
if (Settings.UseCharge)
{
var groupByChargeQuery = from imsmsFeature in imsmsfeatureBag
group imsmsFeature by imsmsFeature.Charge into newGroup
select newGroup;
Parallel.ForEach(groupByChargeQuery, imsmsFeatureGroup =>
{
var lcimsmsFeatureList = ClusterIMSMSFeatures.ClusterByMassAndScanLC(imsmsFeatureGroup);
foreach (var lcimsmsFeature in lcimsmsFeatureList)
{
lcimsmsFeatureBag.Add(lcimsmsFeature);
}
});
}
else
{
var lcimsmsFeatureList = ClusterIMSMSFeatures.ClusterByMassAndScanLC(imsmsfeatureBag);
foreach (var lcimsmsFeature in lcimsmsFeatureList)
{
lcimsmsFeatureBag.Add(lcimsmsFeature);
}
}
Logger.Log("Total Number of LC-IMS-MS Features = " + lcimsmsFeatureBag.Count);
IEnumerable <LCIMSMSFeature> lcimsmsFeatureEnumerable;
if (Settings.IMSDaCorrectionMax > 0 && !Settings.FilterFlaggedData)
{
Logger.Log("Executing Dalton Correction Algorithm on LC-IMS-MS Features...");
var daCorrectedLCIMSMSFeatureBag = new ConcurrentBag <LCIMSMSFeature>();
var lcimsmsFeatureListBag = new ConcurrentBag <IEnumerable <LCIMSMSFeature> >();
if (Settings.UseCharge)
{
var groupByChargeQuery2 = from lcimsmsFeature in lcimsmsFeatureBag
group lcimsmsFeature by lcimsmsFeature.Charge into newGroup
select newGroup;
Parallel.ForEach(groupByChargeQuery2, lcimsmsFeatureGroup =>
{
IEnumerable <IEnumerable <LCIMSMSFeature> > returnList = FeatureUtil.PartitionFeaturesByMass(lcimsmsFeatureGroup);
foreach (var lcimsmsFeatureList in returnList)
{
lcimsmsFeatureListBag.Add(lcimsmsFeatureList);
}
});
}
else
{
IEnumerable <IEnumerable <LCIMSMSFeature> > returnList = FeatureUtil.PartitionFeaturesByMass(lcimsmsFeatureBag);
foreach (var lcimsmsFeatureList in returnList)
{
lcimsmsFeatureListBag.Add(lcimsmsFeatureList);
}
}
Parallel.ForEach(lcimsmsFeatureListBag, lcimsmsFeatureGroup =>
{
var lcimsmsFeatureList = DaltonCorrection.CorrectLCIMSMSFeatures(lcimsmsFeatureGroup);
foreach (var lcimsmsFeature in lcimsmsFeatureList)
{
daCorrectedLCIMSMSFeatureBag.Add(lcimsmsFeature);
}
});
lcimsmsFeatureEnumerable = daCorrectedLCIMSMSFeatureBag;
Logger.Log("Total Number of Dalton Corrected LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
}
else
{
lcimsmsFeatureEnumerable = lcimsmsFeatureBag;
}
Logger.Log("Filtering LC-IMS-MS features based on Member Count...");
lcimsmsFeatureEnumerable = FeatureUtil.FilterByMemberCount(lcimsmsFeatureEnumerable);
Logger.Log("Total Number of Filtered LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
Logger.Log("Splitting LC-IMS-MS Features by LC Scan...");
lcimsmsFeatureEnumerable = FeatureUtil.SplitLCIMSMSFeaturesByScanLC(lcimsmsFeatureEnumerable);
if (!Settings.UseConformationDetection)
{
lcimsmsFeatureEnumerable = FeatureUtil.FilterSingleLCScan(lcimsmsFeatureEnumerable);
}
Logger.Log("New Total Number of Filtered LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
if (Settings.UseConformationDetection)
{
Logger.Log("Conformation Detection...");
lcimsmsFeatureEnumerable = ConformationDetection.DetectConformationsUsingRawData(lcimsmsFeatureEnumerable.ToList());
//lcimsmsFeatureEnumerable = FeatureUtil.FilterSingleLCScan(lcimsmsFeatureEnumerable);
lcimsmsFeatureEnumerable = FeatureUtil.FilterByMemberCount(lcimsmsFeatureEnumerable);
Logger.Log("New Total Number of LC-IMS-MS Features = " + lcimsmsFeatureEnumerable.Count());
}
lcimsmsFeatureEnumerable = FeatureUtil.SortByMass(lcimsmsFeatureEnumerable);
Logger.Log("Creating filtered Isos file...");
var msFeatureListOutput = new List <MSFeature>();
foreach (var lcimsmsFeature in lcimsmsFeatureEnumerable)
{
if (Settings.FilterIsosToSinglePoint)
{
var msFeatureRep = lcimsmsFeature.GetMSFeatureRep();
msFeatureListOutput.Add(msFeatureRep);
}
else
{
foreach (var imsmsFeature in lcimsmsFeature.IMSMSFeatureList)
{
msFeatureListOutput.AddRange(imsmsFeature.MSFeatureList);
}
}
}
var isosWriter = new IsosWriter(msFeatureListOutput, m_isosReader.ColumnMap);
Logger.Log("Writing output files...");
FeatureUtil.WriteLCIMSMSFeatureToFile(lcimsmsFeatureEnumerable);
LCimsmsFeatures = lcimsmsFeatureEnumerable;
}
}
