private static void TestScanFilterParsing()
{
// Note: See also the unit test classes in the ThermoRawFileReaderUnitTests project
var filterList = new List <string>
{
"ITMS + c ESI Full ms [300.00-2000.00]",
"FTMS + p NSI Full ms [400.00-2000.00]",
"ITMS + p ESI d Z ms [579.00-589.00]",
"ITMS + c ESI d Full ms2 [email protected] [150.00-1180.00]",
"ITMS + c NSI d Full ms2 [email protected] [50.00-2000.00]",
"FTMS + c NSI d Full ms2 [email protected] [100.00-2000.00]",
"ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]",
"+ c d Full ms2 [email protected] [ 350.00-2000.00]",
"+ c d Full ms3 [email protected] [email protected] [ 350.00-2000.00]",
"ITMS + c NSI d Full ms10 [email protected]",
"+ p ms2 [email protected] [210.00-1200.00]",
"+ c NSI SRM ms2 [email protected] [507.259-507.261, 635-319-635.32]",
"+ c NSI SRM ms2 748.371 [701.368-701.370, 773.402-773.404, 887.484-887.486, 975.513-975.515]",
"+ p NSI Q1MS [179.652-184.582, 505.778-510.708, 994.968-999.898]",
"+ p NSI Q3MS [150.070-1500.000]",
"c NSI Full cnl 162.053 [300.000-1200.000]",
"- p NSI Full ms2 168.070 [300.000-1500.00]",
"+ c NSI Full ms2 1083.000 [300.000-1500.00]",
"- p NSI Full ms2 247.060 [300.000-1500.00]",
"- c NSI d Full ms2 921.597 [300.000-1500.00]",
"+ c NSI SRM ms2 965.958 [300.000-1500.00]",
"+ p NSI SRM ms2 1025.250 [300.000-1500.00]",
"+ c EI SRM ms2 247.000 [300.000-1500.00]",
"+ p NSI Full ms2 589.840 [300.070-1200.000]",
"+ p NSI ms [0.316-316.000]",
"ITMS + p NSI SIM ms",
"ITMS + c NSI d SIM ms",
"FTMS + p NSI SIM ms",
"FTMS + p NSI d SIM ms"
};
foreach (var filterItem in filterList)
{
var genericFilter = XRawFileIO.MakeGenericFinniganScanFilter(filterItem);
var scanType = XRawFileIO.GetScanTypeNameFromFinniganScanFilterText(filterItem);
Console.WriteLine(filterItem);
Console.WriteLine(" {0,-12} {1}", scanType, genericFilter);
var validMS1Scan = XRawFileIO.ValidateMSScan(filterItem, out var msLevel, out var simScan, out var mrmScanType, out var zoomScan);
if (validMS1Scan)
{
if (mrmScanType == MRMScanTypeConstants.NotMRM)
{
Console.Write(" MSLevel={0}", msLevel);
}
else
{
Console.Write(" MSLevel={0}, MRMScanType={1}", msLevel, mrmScanType);
}
if (simScan)
{
Console.Write(", SIM Scan");
}
if (zoomScan)
{
Console.Write(", Zoom Scan");
}
Console.WriteLine();
}
else
{
Console.WriteLine(" Not an MS1, SRM, MRM, or SIM scan");
}
Console.WriteLine();
}
Console.WriteLine();
}
private List <udtScansDataType> LoadScansFile(string strScansFilePath)
{
const string FILTERED_SCANS_SUFFIX = "_filtered_scans.csv";
var dctColumnInfo = new Dictionary <string, int>
{
{ "type", -1 },
{ "bpi", -1 },
{ "bpi_mz", -1 },
{ "tic", -1 },
{ "num_peaks", -1 },
{ "num_deisotoped", -1 }
};
var intColIndexScanOrFrameNum = -1;
var intColIndexScanOrFrameTime = -1;
var lstScanData = new List <udtScansDataType>();
var intRowNumber = 0;
var intColIndexScanInfo = -1;
if (!File.Exists(strScansFilePath) && strScansFilePath.ToLower().EndsWith(FILTERED_SCANS_SUFFIX))
{
strScansFilePath = strScansFilePath.Substring(0, strScansFilePath.Length - FILTERED_SCANS_SUFFIX.Length) + "_scans.csv";
}
if (!File.Exists(strScansFilePath))
{
OnWarningEvent("Warning: _scans.csv file is missing; will plot vs. scan number instead of vs. elution time");
return(lstScanData);
}
Console.WriteLine(" Reading the _scans.csv file");
using (var srIsosFile = new StreamReader(new FileStream(strScansFilePath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)))
{
while (!srIsosFile.EndOfStream)
{
intRowNumber += 1;
var strLineIn = srIsosFile.ReadLine();
if (strLineIn == null)
{
continue;
}
var lstData = strLineIn.Split(',').ToList();
if (intRowNumber == 1)
{
// Parse the header row
ParseColumnHeaders(dctColumnInfo, lstData, "_scans.csv");
intColIndexScanOrFrameNum = GetScanOrFrameColIndex(lstData, "_scans.csv");
intColIndexScanOrFrameTime = lstData.IndexOf("frame_time");
if (intColIndexScanOrFrameTime < 0)
{
intColIndexScanOrFrameTime = lstData.IndexOf("scan_time");
}
// The info column will have data of the form "FTMS + p NSI Full ms [400.00-2000.00]" for Thermo datasets
// For .mzXML files, this fill will simply have an integer (and thus isn't useful)
// It may not be present in older _scancs.csv files and is thus optional
intColIndexScanInfo = lstData.IndexOf("info");
continue;
}
try
{
var udtScanData = new udtScansDataType();
int.TryParse(lstData[intColIndexScanOrFrameNum], out udtScanData.Scan);
float.TryParse(lstData[intColIndexScanOrFrameTime], out udtScanData.ElutionTime);
int.TryParse(lstData[dctColumnInfo["type"]], out udtScanData.MSLevel);
double.TryParse(lstData[dctColumnInfo["bpi"]], out udtScanData.BasePeakIntensity);
double.TryParse(lstData[dctColumnInfo["bpi_mz"]], out udtScanData.BasePeakMZ);
double.TryParse(lstData[dctColumnInfo["tic"]], out udtScanData.TotalIonCurrent);
int.TryParse(lstData[dctColumnInfo["num_peaks"]], out udtScanData.NumPeaks);
int.TryParse(lstData[dctColumnInfo["num_deisotoped"]], out udtScanData.NumDeisotoped);
if (intColIndexScanInfo > 0)
{
var infoText = lstData[intColIndexScanInfo];
// Only store infoText in .FilterText if infoText is not simply an integer
if (!int.TryParse(infoText, out _))
{
udtScanData.FilterText = infoText;
}
}
lstScanData.Add(udtScanData);
if (mSaveTICAndBPI)
{
mTICandBPIPlot.AddData(udtScanData.Scan, udtScanData.MSLevel, udtScanData.ElutionTime, udtScanData.BasePeakIntensity, udtScanData.TotalIonCurrent);
}
string scanTypeName;
if (string.IsNullOrWhiteSpace(udtScanData.FilterText))
{
udtScanData.FilterText = udtScanData.MSLevel > 1 ? "HMSn" : "HMS";
scanTypeName = udtScanData.FilterText;
}
else
{
scanTypeName = XRawFileIO.GetScanTypeNameFromFinniganScanFilterText(udtScanData.FilterText);
}
var objScanStatsEntry = new clsScanStatsEntry
{
ScanNumber = udtScanData.Scan,
ScanType = udtScanData.MSLevel,
ScanTypeName = scanTypeName,
ScanFilterText = XRawFileIO.MakeGenericFinniganScanFilter(udtScanData.FilterText),
ElutionTime = udtScanData.ElutionTime.ToString("0.0###"),
TotalIonIntensity = StringUtilities.ValueToString(udtScanData.TotalIonCurrent, 5),
BasePeakIntensity = StringUtilities.ValueToString(udtScanData.BasePeakIntensity, 5),
BasePeakMZ = udtScanData.BasePeakMZ.ToString("0.0###"),
BasePeakSignalToNoiseRatio = "0",
IonCount = udtScanData.NumDeisotoped,
IonCountRaw = udtScanData.NumPeaks,
ExtendedScanInfo =
{
CollisionMode = string.Empty,
ScanFilterText = udtScanData.FilterText
}
};
mDatasetStatsSummarizer.AddDatasetScan(objScanStatsEntry);
}
catch (Exception ex)
{
OnWarningEvent("Warning: Ignoring scan " + lstData[dctColumnInfo["scan_num"]] + " since data conversion error: " + ex.Message);
}
}
}
return(lstScanData);
}
private void LoadScanDetails(XRawFileIO objXcaliburAccessor)
{
OnStatusEvent(" Loading scan details");
if (mSaveTICAndBPI)
{
// Initialize the TIC and BPI arrays
InitializeTICAndBPI();
}
if (mSaveLCMS2DPlots)
{
InitializeLCMS2DPlot();
}
var dtLastProgressTime = DateTime.UtcNow;
var scanCount = objXcaliburAccessor.GetNumScans();
GetStartAndEndScans(scanCount, out var scanStart, out var scanEnd);
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
try
{
var blnSuccess = objXcaliburAccessor.GetScanInfo(scanNumber, out scanInfo);
if (blnSuccess)
{
if (mSaveTICAndBPI)
{
mTICandBPIPlot.AddData(
scanNumber,
scanInfo.MSLevel,
(float)scanInfo.RetentionTime,
scanInfo.BasePeakIntensity,
scanInfo.TotalIonCurrent);
}
var objScanStatsEntry = new clsScanStatsEntry
{
ScanNumber = scanNumber,
ScanType = scanInfo.MSLevel,
ScanTypeName = XRawFileIO.GetScanTypeNameFromFinniganScanFilterText(scanInfo.FilterText),
ScanFilterText = XRawFileIO.MakeGenericFinniganScanFilter(scanInfo.FilterText),
ElutionTime = scanInfo.RetentionTime.ToString("0.0###"),
TotalIonIntensity = StringUtilities.ValueToString(scanInfo.TotalIonCurrent, 5),
BasePeakIntensity = StringUtilities.ValueToString(scanInfo.BasePeakIntensity, 5),
BasePeakMZ = scanInfo.BasePeakMZ.ToString("0.0###"),
BasePeakSignalToNoiseRatio = "0",
IonCount = scanInfo.NumPeaks,
IonCountRaw = scanInfo.NumPeaks
};
// Store the ScanEvent values in .ExtendedScanInfo
StoreExtendedScanInfo(ref objScanStatsEntry.ExtendedScanInfo, scanInfo.ScanEvents);
// Store the collision mode and the scan filter text
objScanStatsEntry.ExtendedScanInfo.CollisionMode = scanInfo.CollisionMode;
objScanStatsEntry.ExtendedScanInfo.ScanFilterText = scanInfo.FilterText;
mDatasetStatsSummarizer.AddDatasetScan(objScanStatsEntry);
}
}
catch (Exception ex)
{
OnErrorEvent("Error loading header info for scan " + scanNumber + ": " + ex.Message);
continue;
}
try
{
if (mSaveLCMS2DPlots | mCheckCentroidingStatus)
{
// Also need to load the raw data
// Load the ions for this scan
var intIonCount = objXcaliburAccessor.GetScanData2D(scanNumber, out var dblMassIntensityPairs);
if (intIonCount > 0)
{
if (mSaveLCMS2DPlots)
{
mLCMS2DPlot.AddScan2D(scanNumber, scanInfo.MSLevel, (float)scanInfo.RetentionTime, intIonCount, dblMassIntensityPairs);
}
if (mCheckCentroidingStatus)
{
var mzCount = dblMassIntensityPairs.GetLength(1);
var lstMZs = new List <double>(mzCount);
for (var i = 0; i <= mzCount - 1; i++)
{
lstMZs.Add(dblMassIntensityPairs[0, i]);
}
var centroidingStatus = GetCentroidStatus(scanNumber, scanInfo);
mDatasetStatsSummarizer.ClassifySpectrum(lstMZs, scanInfo.MSLevel, centroidingStatus);
}
}
}
}
catch (Exception ex)
{
OnErrorEvent("Error loading m/z and intensity values for scan " + scanNumber + ": " + ex.Message);
}
var percentComplete = scanNumber / (float)scanCount * 100;
OnProgressUpdate("Scans processed: " + scanNumber, percentComplete);
ShowProgress(scanNumber, scanCount, ref dtLastProgressTime);
}
Console.WriteLine();
}
