public static (ScanIndex, PrecursorScanCollection, ScanDependentsCollections) ScanIndicesPrecursorsDependents(IRawFileThreadManager rawFileAccessor)
{
Log.Information("Extracting scan indices");
ConcurrentDictionary <int, ScanData> allScans;
allScans = new ConcurrentDictionary <int, ScanData>();
Dictionary <int, ScanData> orphanScans = new Dictionary <int, ScanData>();
MSOrderType AnalysisOrder;
ConcurrentBag <int> ms1 = new ConcurrentBag <int>();
ConcurrentBag <int> ms2 = new ConcurrentBag <int>();
ConcurrentBag <int> ms3 = new ConcurrentBag <int>();
ConcurrentBag <int> msAny = new ConcurrentBag <int>();
ConcurrentDictionary <int, PrecursorScanData> precursorScans = new ConcurrentDictionary <int, PrecursorScanData>();
ConcurrentDictionary <int, IScanDependents> dependents = new ConcurrentDictionary <int, IScanDependents>();
var staticRawFile = rawFileAccessor.CreateThreadAccessor();
staticRawFile.SelectMsData();
// populate the scan indices
IEnumerable <int> scans = staticRawFile.GetFilteredScanEnumerator(staticRawFile.GetFilterFromString("")); // get all scans
// get ms order of experiment
Console.Write("Determing MS analysis order... ");
AnalysisOrder = (from x in scans select staticRawFile.GetScanEventForScanNumber(x).MSOrder).Max();
Console.WriteLine("Done!");
object lockTarget = new object();
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan indices");
int chunkSize = Constants.MultiThreading.ChunkSize(scans.Count());
var batches = scans.Chunk(chunkSize);
Parallel.ForEach(batches, batch =>
{
ScanData ms1ScanData;
ScanData ms2ScanData;
ScanData ms3ScanData;
foreach (int scan in batch)
{
//var rawFile = rawFileAccessor.CreateThreadAccessor();
using (var rawFile = rawFileAccessor.CreateThreadAccessor())
{
rawFile.SelectMsData();
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
ms1ScanData = new ScanData();
ms2ScanData = new ScanData();
ms3ScanData = new ScanData();
ms1ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms1ScanData.MSOrder = scanEvent.MSOrder;
if (ms1ScanData.MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
msAny.Add(scan);
var scanDependents = rawFile.GetScanDependents(scan, 4);
dependents.TryAdd(scan, scanDependents);
// check if the ms1 scan has dependent scans
if (scanDependents == null)
{
// there are no scan dependents
ms1ScanData.HasDependents = false;
allScans.TryAdd(scan, ms1ScanData);
return;
}
else
{
ms1ScanData.HasDependents = true;
allScans.TryAdd(scan, ms1ScanData);
}
for (int i = 0; i < scanDependents.ScanDependentDetailArray.Length; i++)
{
int ms2Scan = scanDependents.ScanDependentDetailArray[i].ScanIndex;
ms2.Add(ms2Scan);
msAny.Add(ms2Scan);
if (AnalysisOrder == MSOrderType.Ms2) // it is ms2
{
ms2ScanData = new ScanData();
scanEvent = rawFile.GetScanEventForScanNumber(ms2Scan);
ms2ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms2ScanData.MSOrder = scanEvent.MSOrder;
ms2ScanData.HasDependents = false;
ms2ScanData.HasPrecursors = true;
allScans.TryAdd(ms2Scan, ms2ScanData);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
}
else // it is ms3
{
var ms2Dependents = rawFile.GetScanDependents(ms2Scan, 4).ScanDependentDetailArray;
ms2ScanData = new ScanData();
scanEvent = rawFile.GetScanEventForScanNumber(ms2Scan);
ms2ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms2ScanData.MSOrder = scanEvent.MSOrder;
ms2ScanData.HasPrecursors = true;
if (ms2Dependents.Length != 0) // make sure there is ms3 data
{
int ms3Scan = ms2Dependents[0].ScanIndex;
ms3.Add(ms3Scan);
msAny.Add(ms3Scan);
scanEvent = rawFile.GetScanEventForScanNumber(ms3Scan);
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
precursorScans.TryAdd(ms3Scan, new PrecursorScanData(ms3scan: ms3Scan, ms2Scan: ms2Scan, masterScan: scan));
ms2ScanData.HasDependents = true;
ms3ScanData = new ScanData();
ms3ScanData.HasPrecursors = true;
ms3ScanData.MassAnalyzer = scanEvent.MassAnalyzer;
ms3ScanData.MSOrder = scanEvent.MSOrder;
allScans.TryAdd(ms3Scan, ms3ScanData);
}
else
{
// there is no ms3 scan, so we only add the ms2 scan
precursorScans.TryAdd(ms2Scan, new PrecursorScanData(ms2scan: ms2Scan, masterScan: scan));
ms2ScanData.HasDependents = false;
}
allScans.TryAdd(ms2Scan, ms2ScanData);
}
}
}
lock (lockTarget)
{
P.Update();
}
}
}
});
P.Done();
HashSet <int> allKeys = new HashSet <int>(allScans.Keys);
P = new ProgressIndicator(scans.Count(), "Checking for orphaned scans");
foreach (int scan in scans)
{
if (allKeys.Contains(scan))
{
continue;
}
else
{
ScanData scanData = new ScanData();
var scanEvent = staticRawFile.GetScanEventForScanNumber(scan);
scanData.MassAnalyzer = scanEvent.MassAnalyzer;
scanData.MSOrder = scanEvent.MSOrder;
orphanScans.Add(scan, scanData);
}
P.Update();
}
P.Done();
Console.WriteLine();
Console.WriteLine("================ Scan indexing report ================");
Console.WriteLine($"Total scans in file: {staticRawFile.RunHeaderEx.SpectraCount}");
Console.WriteLine($"Scans linked: {allScans.Count()}");
Console.WriteLine();
Console.WriteLine("Orphan scans:");
if (orphanScans.Count() > 0)
{
foreach (var scan in orphanScans)
{
Console.WriteLine($"\tScan: {scan.Key}, MSOrder: {scan.Value.MSOrder}");
}
Console.WriteLine("\nThe above scans will not be present in the output data. You should");
Console.WriteLine("manually check them to ensure they are not critical to you analysis.");
}
else
{
Console.WriteLine("None!");
}
Console.WriteLine();
if (staticRawFile.RunHeaderEx.SpectraCount == allScans.Count() + orphanScans.Count())
{
Console.WriteLine("All scans accounted for!");
}
else
{
Console.WriteLine($"Number of scans unaccounted for: {staticRawFile.RunHeaderEx.SpectraCount - (allScans.Count() + orphanScans.Count())}");
Console.WriteLine("If this number is alarming, please contact the RawTools authors\n" +
"by posting an issue at:\n" +
"https://github.com/kevinkovalchik/RawTools/issues");
}
Console.WriteLine("======================================================");
Console.WriteLine();
// we need to order the scan enumerators before sending them out
var orderedMs1 = ms1.ToList();
var orderedMs2 = ms2.ToList();
var orderedMs3 = ms3.ToList();
var orderedMsAny = msAny.ToList();
orderedMs1.Sort();
orderedMs2.Sort();
orderedMs3.Sort();
orderedMsAny.Sort();
ScanIndex scanIndex = new ScanIndex();
scanIndex.allScans = allScans.ConvertToDictionary();
scanIndex.AnalysisOrder = AnalysisOrder;
scanIndex.ScanEnumerators.Add(MSOrderType.Any, orderedMsAny.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms, orderedMs1.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, orderedMs2.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, orderedMs3.ToArray());
scanIndex.TotalScans = staticRawFile.RunHeaderEx.SpectraCount;
return(scanIndex, new PrecursorScanCollection(precursorScans), new ScanDependentsCollections(dependents));
}
