private static IChromatogramData GetChromatogramData(IRawDataPlus rawFile, IChromatogramSettings settings,
int firstScanNumber, int lastScanNumber)
{
IChromatogramData data = null;
try
{
data = rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, firstScanNumber,
lastScanNumber);
}
catch (InvalidFilterFormatException ex)
{
Log.Warn($"Invalid filter string {settings.Filter}");
}
catch (InvalidFilterCriteriaException ex)
{
Log.Warn($"Invalid filter string {settings.Filter}");
}
return(data);
}
public static void ReadXic(string rawFilePath, bool base64, XicData xicData)
{
IRawDataPlus rawFile;
using (rawFile = RawFileReaderFactory.ReadFile(rawFilePath))
{
if (!rawFile.IsOpen)
{
throw new RawFileParserException("Unable to access the RAW file using the native Thermo library.");
}
// Check for any errors in the RAW file
if (rawFile.IsError)
{
throw new RawFileParserException(
$"Error opening ({rawFile.FileError}) - {rawFilePath}");
}
// Check if the RAW file is being acquired
if (rawFile.InAcquisition)
{
throw new RawFileParserException("RAW file still being acquired - " + rawFilePath);
}
// Get the number of instruments (controllers) present in the RAW file and set the
// selected instrument to the MS instrument, first instance of it
rawFile.SelectInstrument(Device.MS, 1);
// Get the first and last scan from the RAW file
var firstScanNumber = rawFile.RunHeaderEx.FirstSpectrum;
var lastScanNumber = rawFile.RunHeaderEx.LastSpectrum;
// Get the start and end time from the RAW file
var startTime = rawFile.RunHeaderEx.StartTime;
var endTime = rawFile.RunHeaderEx.EndTime;
// Get the mass range from the RAW file
var minMass = rawFile.RunHeaderEx.LowMass;
var maxMass = rawFile.RunHeaderEx.HighMass;
// Update global metadata
xicData.OutputMeta.base64 = base64;
xicData.OutputMeta.timeunit = "minutes";
foreach (var xicUnit in xicData.Content)
{
IChromatogramSettings settings = null;
if (!xicUnit.Meta.MzStart.HasValue && !xicUnit.Meta.MzEnd.HasValue)
{
settings = new ChromatogramTraceSettings()
{
Filter = xicUnit.Meta.Filter ?? "ms"
};
}
if (!xicUnit.Meta.MzStart.HasValue)
{
xicUnit.Meta.MzStart = minMass;
}
if (!xicUnit.Meta.MzEnd.HasValue)
{
xicUnit.Meta.MzEnd = maxMass;
}
if (settings == null)
{
settings = new ChromatogramTraceSettings(TraceType.MassRange)
{
Filter = xicUnit.Meta.Filter ?? "ms",
MassRanges = new[]
{
new Range(xicUnit.Meta.MzStart.Value,
xicUnit.Meta.MzEnd.Value)
}
};
}
List <int> rtFilteredScans = null;
if (!xicUnit.Meta.RtStart.HasValue && !xicUnit.Meta.RtEnd.HasValue)
{
rtFilteredScans = new List <int>();
}
if (!xicUnit.Meta.RtStart.HasValue)
{
xicUnit.Meta.RtStart = startTime;
}
if (!xicUnit.Meta.RtEnd.HasValue)
{
xicUnit.Meta.RtEnd = endTime;
}
IChromatogramData data = null;
if (rtFilteredScans == null)
{
rtFilteredScans = rawFile.GetFilteredScansListByTimeRange(MsFilter,
xicUnit.Meta.RtStart.Value, xicUnit.Meta.RtEnd.Value);
if (rtFilteredScans.Count != 0)
{
data = GetChromatogramData(rawFile, settings, rtFilteredScans[0],
rtFilteredScans[rtFilteredScans.Count - 1]);
if (data != null && data.PositionsArray.Length == 1 && data.PositionsArray[0].Length == 1 &&
(Math.Abs(data.PositionsArray[0][0] - startTime) < 0.001 ||
Math.Abs(data.PositionsArray[0][0] - endTime) < 0.001))
{
Log.Warn(
$"Only the minimum or maximum retention time was returned. This is an indication that the provided retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}] lies outside the max. window [{startTime}-{endTime}]");
}
}
else
{
Log.Warn(
$"No scans found in retention time range [{xicUnit.Meta.RtStart}-{xicUnit.Meta.RtEnd}]. This is an indication that the provided retention time window lies outside the max. window [{startTime}-{endTime}]");
}
}
else
{
data = GetChromatogramData(rawFile, settings, firstScanNumber, lastScanNumber);
}
if (data != null)
{
var chromatogramTrace = ChromatogramSignal.FromChromatogramData(data);
if (chromatogramTrace[0].Scans.Count != 0)
{
if (!base64)
{
xicUnit.RetentionTimes = chromatogramTrace[0].Times;
xicUnit.Intensities = chromatogramTrace[0].Intensities;
}
else
{
xicUnit.RetentionTimes = GetBase64String(chromatogramTrace[0].Times);
xicUnit.Intensities = GetBase64String(chromatogramTrace[0].Intensities);
}
}
}
}
}
}
