private static void WritePScans(string fileName,
IRawDataPlus raw,
List <PScan> scans)
{
var enumerator = raw.GetFilteredScanEnumerator(" ");
foreach (var scanNumber in enumerator) // note in my tests serial is faster than Parallel.Foreach() (this involves disk access, so it makes sense)
{
//trailer iinformation is extracted via index
var trailers = raw.GetTrailerExtraValues(scanNumber);
var trailerLabels = raw.GetTrailerExtraInformation(scanNumber);
object chargeState = 0;
for (int i = 0; i < trailerLabels.Labels.Length; i++)
{
if (trailerLabels.Labels[i] == "Charge State:")
{
chargeState = raw.GetTrailerExtraValue(scanNumber, i);
break;
}
}
var scanFilter = raw.GetFilterForScanNumber(scanNumber);
var scanStats = raw.GetScanStatsForScanNumber(scanNumber);
CentroidStream centroidStream = new CentroidStream();
//check for FT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerFTMS)
{
centroidStream = raw.GetCentroidStream(scanNumber, false);
}
//check for IT mass analyzer data
if (scanFilter.MassAnalyzer == MassAnalyzerType.MassAnalyzerITMS)
{
var scanData = raw.GetSimplifiedScan(scanNumber);
centroidStream.Masses = scanData.Masses;
centroidStream.Intensities = scanData.Intensities;
}
var msOrder = raw.GetScanEventForScanNumber(scanNumber).MSOrder;
if (msOrder == MSOrderType.Ms)
{
var pscan = GetPScan(scanStats, centroidStream, 1, fileName, Convert.ToInt32(chargeState));
scans.Add(pscan);
}
if (msOrder == MSOrderType.Ms2)
{
var precursorMz = raw.GetScanEventForScanNumber(scanNumber).GetReaction(0).PrecursorMass;
var pscan = GetPScan(scanStats, centroidStream, 2, fileName, precursorMz, Convert.ToInt32(chargeState));
scans.Add(pscan);
}
var t = raw.GetTrailerExtraValues(scanNumber);
}
WriteScans(scans, fileName);
}
public double[] GetScanFrequency(string filterString = "", int n = 100)
{
List <double> rv = new List <double>();
var filter = rawFile.GetFilterFromString(filterString);
if (filter == null)
{
return(null);
}
var filteredScanNumbers = rawFile.GetFilteredScanEnumerator(filter).ToArray();
if (n > filteredScanNumbers.Length)
{
n = filteredScanNumbers.Length;
}
int stepsize = filteredScanNumbers.Length / n;
double ortime = 0.0;
for (int scanNumber = filteredScanNumbers[0];
scanNumber < filteredScanNumbers[filteredScanNumbers.Length - 1];
scanNumber += stepsize)
{
var scanStatistics = rawFile.GetScanStatsForScanNumber(scanNumber);
var rtime = Math.Round(scanStatistics.StartTime * 60 * 1000) / 1000;
rv.Add(rtime);
rv.Add(stepsize / (rtime - ortime));
ortime = rtime;
}
return(rv.ToArray());
}
public static ScanIndex ScanIndices(IRawDataPlus rawFile)
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Extracting scan indices");
Dictionary <int, ScanData> allScans;
allScans = new Dictionary <int, ScanData>();
MSOrderType AnalysisOrder;
List <int> ms1 = new List <int>();
List <int> ms2 = new List <int>();
List <int> ms3 = new List <int>();
List <int> msAny = new List <int>();
// populate the scan indices
IEnumerable <int> scans = rawFile.GetFilteredScanEnumerator(rawFile.GetFilterFromString("")); // get all scans
ProgressIndicator P = new ProgressIndicator(scans.Count(), "Extracting scan indices");
foreach (int scan in scans)
{
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
ScanData scanData = new ScanData();
scanData.MassAnalyzer = scanEvent.MassAnalyzer;
scanData.MSOrder = scanEvent.MSOrder;
allScans.Add(scan, scanData);
msAny.Add(scan);
if (allScans[scan].MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms2)
{
ms2.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms3)
{
ms3.Add(scan);
}
P.Update();
}
P.Done();
// determine the msorder of the experiment
if ((ms1.Count > 0) & (ms2.Count == 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms;
}
else
{
if ((ms1.Count > 0) & (ms2.Count > 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms2;
}
else
{
AnalysisOrder = MSOrderType.Ms3;
}
}
ScanIndex scanIndex = new ScanIndex();
scanIndex.allScans = allScans;
scanIndex.AnalysisOrder = AnalysisOrder;
scanIndex.ScanEnumerators.Add(MSOrderType.Any, msAny.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms, ms1.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, ms2.ToArray());
scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, ms3.ToArray());
return(scanIndex);
}
public static void ExtractScanIndex(this RawDataCollection rawData, IRawDataPlus rawFile)
{
Log.Information("Extracting scan indices");
Dictionary <int, (MSOrderType MSOrder, MassAnalyzerType MassAnalyzer)> allScans;
allScans = new Dictionary <int, (MSOrderType MSOrder, MassAnalyzerType MassAnalyzer)>();
MSOrderType AnalysisOrder;
List <int> ms1 = new List <int>();
List <int> ms2 = new List <int>();
List <int> ms3 = new List <int>();
List <int> msAny = new List <int>();
// populate the scan indices
IEnumerable <int> scans = rawFile.GetFilteredScanEnumerator(rawFile.GetFilterFromString("")); // get all scans
foreach (int scan in scans)
{
IScanEvent scanEvent = rawFile.GetScanEventForScanNumber(scan);
allScans.Add(scan, (scanEvent.MSOrder, scanEvent.MassAnalyzer));
msAny.Add(scan);
if (allScans[scan].MSOrder == MSOrderType.Ms)
{
ms1.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms2)
{
ms2.Add(scan);
}
if (allScans[scan].MSOrder == MSOrderType.Ms3)
{
ms3.Add(scan);
}
}
// determine the msorder of the experiment
if ((ms1.Count > 0) & (ms2.Count == 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms;
}
else
{
if ((ms1.Count > 0) & (ms2.Count > 0) & (ms3.Count == 0))
{
AnalysisOrder = MSOrderType.Ms2;
}
else
{
AnalysisOrder = MSOrderType.Ms3;
}
}
rawData.scanIndex = new ScanIndex();
rawData.scanIndex.allScans = allScans;
rawData.scanIndex.AnalysisOrder = AnalysisOrder;
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Any, msAny.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms, ms1.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms2, ms2.ToArray());
rawData.scanIndex.ScanEnumerators.Add(MSOrderType.Ms3, ms3.ToArray());
// we need to check if it is a boxcar file because those have some scan index issues
bool isBoxCar = rawFile.GetScanEventForScanNumber(1).MassRangeCount > 1;
rawData.Performed.Add(Operations.ScanIndex);
if (isBoxCar)
{
Log.Information("Raw file looks like a boxcar run. Scan indices being adjusted to account for missing scan dependents.");
rawData.ExtractPrecursorScans(rawFile);
rawData.scanIndex.ScanEnumerators[rawData.scanIndex.AnalysisOrder] = rawData.precursorScans.Keys.ToArray();
}
}
