/// <summary>
/// Creates RetentionTimeRasterItem from XICTraceGenerator.
/// </summary>
private RetentionTimeRasterItem MakeRetentionTimeRasterItem(XICTraceGenerator <UnknownFeatureIonInstanceItem> tracer, int fileID)
{
// get raster points
var raster = tracer.RetentionTimeRaster;
// get raster info
var info = tracer.RetentionTimeRasterInfo;
// make RetentionTimeRasterItem
return(new RetentionTimeRasterItem
{
ID = EntityDataService.NextId <RetentionTimeRasterItem>(),
FileID = fileID,
MSOrder = info.MSOrder,
Polarity = info.Polarity,
IonizationSource = info.IonizationSource,
MassAnalyzer = info.MassAnalyzer,
MassRange = info.MassRange,
ResolutionAtMass200 = info.ResolutionAtMass200,
ScanRate = info.ScanRate,
ScanType = info.ScanType,
ActivationTypes = info.ActivationTypes,
ActivationEnergies = info.ActivationEnergies,
IsolationWindow = info.IsolationWindow,
IsolationMass = info.IsolationMass,
IsolationWidth = info.IsolationWidth,
IsolationOffset = info.IsolationOffset,
IsMultiplexed = info.IsMultiplexed,
Trace = new TraceData(raster),
});
}
/// <summary>
/// Creates and persists XIC traces for all compound ion items.
/// </summary>
private void RebuildAndPersistCompoundIonTraces(
int fileID,
IEnumerable <SpectrumDescriptor> spectrumDescriptors,
Dictionary <UnknownFeatureIonInstanceItem, List <ChromatogramPeakItem> > ionInstanceToPeaksMap)
{
SendAndLogTemporaryMessage("Re-creating XIC traces...");
var time = Stopwatch.StartNew();
// init XICPattern builder
var xicPatternBuilder = new Func <List <ChromatogramPeakItem>, XICPattern>(
peaks =>
{
var masks = peaks.Select(
peak => new XICMask(
peak.IsotopeNumber,
peak.Mass,
MassTolerance.Value)
).ToList();
return(new XICPattern(masks));
});
// make XIC patterns
var xicPatterns = ionInstanceToPeaksMap.ToDictionary(item => item.Key, item => xicPatternBuilder(item.Value));
// init XIC tracer
var tracer = new XICTraceGenerator <UnknownFeatureIonInstanceItem>(xicPatterns);
// get sprectrum IDs
var spectrumIds = spectrumDescriptors
.Where(s => s.ScanEvent.MSOrder == MSOrderType.MS1)
.OrderBy(o => o.Header.RetentionTimeRange.LowerLimit)
.Select(s => s.Header.SpectrumID)
.ToList();
// add spectrum to tracer
foreach (var spectrum in ProcessingServices.SpectrumProcessingService.ReadSpectraFromCache(spectrumIds))
{
tracer.AddSpectrum(spectrum);
}
// make trace items
var ionInstanceToTraceMap = new Dictionary <UnknownFeatureIonInstanceItem, XicTraceItem>();
foreach (var item in ionInstanceToPeaksMap)
{
// get trace
var trace = tracer.GetXICTrace(item.Key, useFullRange: true, useFullRaster: false);
// make XicTraceItem
ionInstanceToTraceMap.Add(
item.Key,
new XicTraceItem
{
ID = EntityDataService.NextId <XicTraceItem>(),
FileID = fileID,
Trace = new TraceData(trace),
});
}
// make raster
var rasterItem = MakeRetentionTimeRasterItem(tracer, fileID);
// persist traces
EntityDataService.InsertItems(ionInstanceToTraceMap.Values);
EntityDataService.ConnectItems(ionInstanceToTraceMap.Select(s => Tuple.Create(s.Key, s.Value)));
// persist raster
EntityDataService.InsertItems(new[] { rasterItem });
EntityDataService.ConnectItems(ionInstanceToTraceMap.Select(s => Tuple.Create(s.Value, rasterItem)));
time.Stop();
SendAndLogVerboseMessage("Re-creating and persisting {0} XIC traces took {1:F2} s.", ionInstanceToTraceMap.Values.Count, time.Elapsed.TotalSeconds);
m_currentStep += 4;
ReportTotalProgress((double)m_currentStep / m_numSteps);
}
