private static void TestReader(string rawFilePath, bool centroid = false, bool testSumming = false, int scanStart = 0, int scanEnd = 0)
{
try
{
var rawFile = ResolveDataFile(rawFilePath);
if (rawFile == null)
{
return;
}
var options = new ThermoReaderOptions {
LoadMSMethodInfo = mLoadMethods
};
using (var reader = new XRawFileIO(rawFile.FullName, options, mTraceMode))
{
RegisterEvents(reader);
var numScans = reader.GetNumScans();
var collisionEnergyList = string.Empty;
ShowMethod(reader);
var scanStep = 1;
if (scanStart < 1)
{
scanStart = 1;
}
if (scanEnd < 1)
{
scanEnd = numScans;
scanStep = 21;
}
else
{
if (scanEnd < scanStart)
{
scanEnd = scanStart;
}
}
if (scanEnd > numScans)
{
scanEnd = numScans;
}
var msLevelStats = new Dictionary <int, int>();
Console.WriteLine();
Console.WriteLine("Reading data for scans {0} to {1}, step {2}", scanStart, scanEnd, scanStep);
for (var scanNum = scanStart; scanNum <= scanEnd; scanNum += scanStep)
{
if (scanNum > reader.ScanEnd)
{
ConsoleMsgUtils.ShowWarning("Exiting for loop since scan number {0} is greater than the max scan number, {1}", scanNum, reader.ScanEnd);
break;
}
if (mOnlyLoadMSLevelInfo)
{
var msLevel = reader.GetMSLevel(scanNum);
if (msLevelStats.TryGetValue(msLevel, out var msLevelObsCount))
{
msLevelStats[msLevel] = msLevelObsCount + 1;
}
else
{
msLevelStats.Add(msLevel, 1);
}
if (mScanInfoInterval <= 0 || scanNum % mScanInfoInterval == 0)
{
Console.WriteLine("Scan " + scanNum);
}
continue;
}
var success = reader.GetScanInfo(scanNum, out clsScanInfo scanInfo);
if (!success)
{
continue;
}
if (mScanInfoInterval <= 0 || scanNum % mScanInfoInterval == 0)
{
Console.WriteLine("Scan " + scanNum + " at " + scanInfo.RetentionTime.ToString("0.00") + " minutes: " + scanInfo.FilterText);
}
if (mLoadCollisionEnergies)
{
var collisionEnergies = reader.GetCollisionEnergy(scanNum);
if (collisionEnergies.Count == 0)
{
collisionEnergyList = string.Empty;
}
else if (collisionEnergies.Count >= 1)
{
collisionEnergyList = collisionEnergies[0].ToString("0.0");
if (collisionEnergies.Count > 1)
{
for (var index = 1; index <= collisionEnergies.Count - 1; index++)
{
collisionEnergyList += ", " + collisionEnergies[index].ToString("0.0");
}
}
}
if (string.IsNullOrEmpty(collisionEnergyList))
{
Console.WriteLine();
}
else
{
Console.WriteLine("; CE " + collisionEnergyList);
}
}
if (mGetScanEvents)
{
if (scanInfo.TryGetScanEvent("Monoisotopic M/Z:", out var monoMZ))
{
Console.WriteLine("Monoisotopic M/Z: " + monoMZ);
}
if (scanInfo.TryGetScanEvent("Charge State", out var chargeState, true))
{
Console.WriteLine("Charge State: " + chargeState);
}
if (scanInfo.TryGetScanEvent("MS2 Isolation Width", out var isolationWidth, true))
{
Console.WriteLine("MS2 Isolation Width: " + isolationWidth);
}
}
if (!mLoadScanData || (scanNum % 50 != 0 && scanEnd - scanStart > 50))
{
continue;
}
// Get the data for scan scanNum
Console.WriteLine();
Console.WriteLine("Spectrum for scan " + scanNum);
reader.GetScanData(scanNum, out var mzList, out var intensityList, 0, centroid);
var mzDisplayStepSize = 50;
if (centroid)
{
mzDisplayStepSize = 1;
}
for (var i = 0; i <= mzList.Length - 1; i += mzDisplayStepSize)
{
Console.WriteLine(" " + mzList[i].ToString("0.000") + " mz " + intensityList[i].ToString("0"));
}
Console.WriteLine();
const int scansToSum = 15;
if (scanNum + scansToSum < numScans && testSumming)
{
// Get the data for scan scanNum through scanNum + 15
#pragma warning disable 618
reader.GetScanDataSumScans(scanNum, scanNum + scansToSum, out var massIntensityPairs, 0, centroid);
#pragma warning restore 618
Console.WriteLine("Summed spectrum, scans " + scanNum + " through " + (scanNum + scansToSum));
for (var i = 0; i <= massIntensityPairs.GetLength(1) - 1; i += 50)
{
Console.WriteLine(" " + massIntensityPairs[0, i].ToString("0.000") + " mz " +
massIntensityPairs[1, i].ToString("0"));
}
Console.WriteLine();
}
if (!scanInfo.IsFTMS)
{
continue;
}
var dataCount = reader.GetScanLabelData(scanNum, out var ftLabelData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", "Mass", "Intensity", "Resolution", "Baseline", "Noise", "Charge");
for (var i = 0; i <= dataCount - 1; i += 50)
{
Console.WriteLine("{0,12:F3}{1,12:0}{2,12:0}{3,12:F1}{4,12:0}{5,12:0}",
ftLabelData[i].Mass,
ftLabelData[i].Intensity,
ftLabelData[i].Resolution,
ftLabelData[i].Baseline,
ftLabelData[i].Noise,
ftLabelData[i].Charge);
}
dataCount = reader.GetScanPrecisionData(scanNum, out var ftPrecisionData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", "Mass", "Intensity", "AccuracyMMU", "AccuracyPPM", "Resolution");
for (var i = 0; i <= dataCount - 1; i += 50)
{
Console.WriteLine("{0,12:F3}{1,12:0}{2,12:F3}{3,12:F3}{4,12:0}",
ftPrecisionData[i].Mass,
ftPrecisionData[i].Intensity, ftPrecisionData[i].AccuracyMMU,
ftPrecisionData[i].AccuracyPPM,
ftPrecisionData[i].Resolution);
}
}
if (mOnlyLoadMSLevelInfo)
{
Console.WriteLine();
Console.WriteLine("{0,-10} {1}", "MSLevel", "Scans");
foreach (var item in msLevelStats)
{
Console.WriteLine("{0, -10} {1}", item.Key, item.Value);
}
}
}
}
catch (Exception ex)
{
ShowError("Error in TestReader: " + ex.Message, ex);
}
}
public override XYData GetMassSpectrum(ScanSet scanSet, double minMZ, double maxMZ)
{
Check.Require(scanSet != null, "Can't get mass spectrum; inputted set of scans is null");
if (scanSet == null)
{
return(null);
}
Check.Require(scanSet.IndexValues.Count > 0, "Can't get mass spectrum; no scan numbers inputted");
if (Math.Abs(minMZ) < float.Epsilon && Math.Abs(maxMZ) < float.Epsilon)
{
maxMZ = 10000000;
}
double[,] massIntensityPairs;
var spectraAreSummed = scanSet.IndexValues.Count > 1;
var scanNumFirst = scanSet.IndexValues[0];
var scanNumLast = scanSet.IndexValues[scanSet.IndexValues.Count - 1];
string scanDescription;
if (spectraAreSummed)
{
scanDescription = "scan " + scanSet.PrimaryScanNumber + " ( summing scans " + scanNumFirst + " to " + scanNumLast + ")";
}
else
{
scanDescription = "scan " + scanSet.PrimaryScanNumber;
}
try
{
if (spectraAreSummed)
{
// Note that GetScanDataSumScans uses the scan filter of the first scan to assure that similar scans are summed
mRawFileReader.GetScanDataSumScans(scanNumFirst, scanNumLast, out massIntensityPairs, 0, false);
}
else
{
var scanNum = scanSet.PrimaryScanNumber;
mRawFileReader.GetScanData2D(scanNum, out massIntensityPairs);
}
}
catch (AccessViolationException)
{
var errorMessage = "XCaliburRun2.GetMassSpectrum: Unable to load data for " + scanDescription +
"; possibly a corrupt .Raw file";
Console.WriteLine(errorMessage);
Logger.Instance.AddEntry(errorMessage);
return(new XYData());
}
catch (Exception ex)
{
Logger.Instance.AddEntry("XCaliburRun2.GetMassSpectrum: Unable to load data for " + scanDescription +
": " + ex.Message + "; possibly a corrupt .Raw file");
return(new XYData());
}
var dataPointCount = massIntensityPairs.GetLength(1);
var xVals = new List <double>();
var yVals = new List <double>();
// Note from MEM (October 2013)
// GetMassListFromScanNum generally returns the data sorted by m/z ascending
// However, there are edge cases for certain spectra in certain datasets where adjacent data points are out of order and need to be swapped
// Therefore, we must validate that the data is truly sorted, and if we find a discrepancy, sort it after populating xyData.Xvalues and xyData.Yvalues
var sortRequired = false;
for (var i = 0; i < dataPointCount; i++)
{
var xValue = massIntensityPairs[0, i];
if (xValue < minMZ || xValue > maxMZ)
{
continue;
}
var yValue = massIntensityPairs[1, i];
if (i > 0 && xValue < massIntensityPairs[0, i - 1])
{
// Points are out of order; this rarely occurs but it is possible and has been observed
sortRequired = true;
}
xVals.Add(xValue);
yVals.Add(yValue);
}
var xyData = new XYData
{
Xvalues = xVals.ToArray(),
Yvalues = yVals.ToArray()
};
if (sortRequired)
{
Array.Sort(xyData.Xvalues, xyData.Yvalues);
}
return(xyData);
}