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 LoadData(FileInfo fiIsosFile, clsDatasetFileInfo datasetFileInfo)
{
// Cache the data in the _isos.csv and _scans.csv files
if (mSaveTICAndBPI)
{
// Initialize the TIC and BPI arrays
InitializeTICAndBPI();
}
if (mSaveLCMS2DPlots)
{
InitializeLCMS2DPlot();
}
var lstIsosData = LoadIsosFile(fiIsosFile.FullName, MaxFit);
if (lstIsosData.Count == 0)
{
OnErrorEvent("No data found in the _isos.csv file: " + fiIsosFile.FullName);
return;
}
var strScansFilePath = GetDatasetNameViaPath(fiIsosFile.Name) + DECONTOOLS_SCANS_FILE_SUFFIX;
if (fiIsosFile.Directory != null)
{
strScansFilePath = Path.Combine(fiIsosFile.Directory.FullName, strScansFilePath);
}
var lstScanData = LoadScansFile(strScansFilePath);
var scansFileIsMissing = false;
if (lstScanData.Count > 0)
{
datasetFileInfo.AcqTimeEnd = datasetFileInfo.AcqTimeStart.AddMinutes(lstScanData.Last().ElutionTime);
datasetFileInfo.ScanCount = lstScanData.Last().Scan;
}
else
{
scansFileIsMissing = true;
datasetFileInfo.ScanCount = (from item in lstIsosData select item.Scan).Max();
for (var intScanIndex = 1; intScanIndex <= datasetFileInfo.ScanCount; intScanIndex++)
{
var udtScanData = new udtScansDataType
{
Scan = intScanIndex,
ElutionTime = intScanIndex,
MSLevel = 1
};
lstScanData.Add(udtScanData);
}
}
// Step through the isos data and call mLCMS2DPlot.AddScan() for each scan
var lstIons = new List <clsLCMSDataPlotter.udtMSIonType>();
var intCurrentScan = 0;
// Note: we only need to update mLCMS2DPlot
// The options for mLCMS2DPlotOverview will be cloned from mLCMS2DPlot.Options
mLCMS2DPlot.Options.PlottingDeisotopedData = true;
var dblMaxMonoMass = mLCMS2DPlot.Options.MaxMonoMassForDeisotopedPlot;
for (var intIndex = 0; intIndex <= lstIsosData.Count - 1; intIndex++)
{
if (lstIsosData[intIndex].Scan > intCurrentScan || intIndex == lstIsosData.Count - 1)
{
// Store the cached values
if (lstIons.Count > 0)
{
var udtCurrentScan = (from item in lstScanData where item.Scan == intCurrentScan select item).ToList().FirstOrDefault();
lstIons.Sort(new clsLCMSDataPlotter.udtMSIonTypeComparer());
mLCMS2DPlot.AddScan(intCurrentScan, udtCurrentScan.MSLevel, udtCurrentScan.ElutionTime, lstIons);
if (scansFileIsMissing && mSaveTICAndBPI)
{
// Determine the TIC and BPI values using the data from the .isos file
double tic = 0;
double bpi = 0;
for (var dataIndex = 0; dataIndex <= lstIons.Count - 1; dataIndex++)
{
tic += lstIons[dataIndex].Intensity;
if (lstIons[dataIndex].Intensity > bpi)
{
bpi = lstIons[dataIndex].Intensity;
}
}
mTICandBPIPlot.AddData(intCurrentScan, udtCurrentScan.MSLevel, udtCurrentScan.ElutionTime, bpi, tic);
}
}
intCurrentScan = lstIsosData[intIndex].Scan;
lstIons.Clear();
}
if (lstIsosData[intIndex].MonoMass <= dblMaxMonoMass)
{
var udtIon = new clsLCMSDataPlotter.udtMSIonType
{
// Note that we store .MonoMass in a field called .mz; we'll still be plotting monoisotopic mass
MZ = lstIsosData[intIndex].MonoMass,
Intensity = lstIsosData[intIndex].Abundance,
Charge = lstIsosData[intIndex].Charge
};
lstIons.Add(udtIon);
}
}
}