public void peakDetectionOnXCaliburTest1()
{
Run run = new XCaliburRun(xcaliburTestfile, 6000, 7000);
ScanSetCollection scansetCollection = new ScanSetCollection();
for (int i = 6000; i < 6015; i++)
{
scansetCollection.ScanSetList.Add(new ScanSet(i));
}
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in scansetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator();
msgen.Execute(results);
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(results);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
}
Assert.AreEqual(2, results.ScanResultList.Count);
}
private ScanSetCollection CreateLcScanSetCollection()
{
var scanSetCollection = new ScanSetCollection();
scanSetCollection.Create(Run, WorkflowParameters.LCScanMin, WorkflowParameters.LCScanMax,
WorkflowParameters.Num_LC_TimePointsSummed, 1, WorkflowParameters.ProcessMSMS);
return(scanSetCollection);
}
public void ExportMultipleScansTest1()
{
Run run = new IMFRun(imfFilepath);
ScanSetCollection scanSetCollection = new ScanSetCollection();
scanSetCollection.ScanSetList.Add(new ScanSet(232));
scanSetCollection.ScanSetList.Add(new ScanSet(233));
scanSetCollection.ScanSetList.Add(new ScanSet(234));
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in scanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
Task msGen = new GenericMSGenerator();
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
Task decon = new RapidDeconvolutor();
decon.Execute(results);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
}
Assert.AreEqual(3, results.ScanResultList.Count);
Assert.AreEqual(92, results.ScanResultList[0].NumPeaks);
Assert.AreEqual(82, results.ScanResultList[1].NumPeaks);
Assert.AreEqual(72, results.ScanResultList[2].NumPeaks);
Assert.AreEqual(11, results.ScanResultList[0].NumIsotopicProfiles);
Assert.AreEqual(9, results.ScanResultList[1].NumIsotopicProfiles);
Assert.AreEqual(9, results.ScanResultList[2].NumIsotopicProfiles);
Assert.AreEqual(830.045752112968, (Decimal)results.ScanResultList[0].BasePeak.XValue);
Assert.AreEqual(10438, results.ScanResultList[0].BasePeak.Height);
Assert.AreEqual(0.09454554, (Decimal)results.ScanResultList[0].BasePeak.Width);
Assert.AreEqual(434.9167, (Decimal)results.ScanResultList[0].BasePeak.SN);
Exporter <ResultCollection> exporter = new BasicScansExporter(scansExporterTest1output);
exporter.Export(results);
}
public void updateScanResultsOnXCaliburFileTest1()
{
Run run = new XCaliburRun(xcaliburTestfile, 6000, 7000);
ScanSetCollection scansetCollection = new ScanSetCollection();
for (int i = 6000; i < 6015; i++)
{
scansetCollection.ScanSetList.Add(new ScanSet(i));
}
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in scansetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator(0, 2000);
msgen.Execute(results);
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(results);
Task rapid = new RapidDeconvolutor();
rapid.Execute(results);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(results);
}
Assert.AreEqual(2, results.ScanResultList.Count);
Assert.AreEqual(1, results.ScanResultList[0].SpectrumType);
Assert.AreEqual(481.274105402604, (decimal)results.ScanResultList[0].BasePeak.XValue);
Assert.AreEqual(353, results.ScanResultList[0].NumIsotopicProfiles);
Assert.AreEqual(2052, results.ScanResultList[0].NumPeaks);
//Assert.AreEqual(2132, results.ScanResultList[0].NumPeaks);
Assert.AreEqual(32.6941466666667, (decimal)results.ScanResultList[0].ScanTime);
Assert.AreEqual(6005, results.ScanResultList[0].ScanSet.PrimaryScanNumber);
Assert.AreEqual(362, results.ScanResultList[1].NumIsotopicProfiles);
//Assert.AreEqual(370, results.ScanResultList[1].NumIsotopicProfiles);
Assert.AreEqual(715, results.ResultList.Count);
}
public void MSGeneratorOnXCaliburFileTest2()
{
Run run = new XCaliburRun(xcaliburTestfile, 6000, 7000);
ScanSetCollection scansetCollection = new ScanSetCollection();
for (int i = 6000; i < 6015; i++)
{
scansetCollection.ScanSetList.Add(new ScanSet(i));
}
ResultCollection results = new ResultCollection(run);
foreach (ScanSet scanset in scansetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator();
msgen.Execute(results);
}
Assert.AreEqual(0, results.ScanResultList.Count); //Scan results are now created by the ScanResultUpdaterTask
}
public XYData GetBaseChromXYData(Run run, int startScan, int stopScan, double baseMZValue)
{
//note: currently 'GenerateChromatogram' results in 0's being padded on both sides of start and stop scans.
var xydata = PeakChromGen.GenerateChromatogram(run, startScan, stopScan, baseMZValue, ChromTolerance, ChromToleranceUnit);
XYData basePeakChromXYData;
if (xydata == null || xydata.Xvalues.Length < 3)
{
basePeakChromXYData = new XYData();
if (xydata == null)
{
basePeakChromXYData.Xvalues = new double[0];
basePeakChromXYData.Yvalues = new double[0];
}
else
{
basePeakChromXYData.Xvalues = xydata.Xvalues;
basePeakChromXYData.Yvalues = xydata.Yvalues;
}
}
else
{
basePeakChromXYData = Smoother.Smooth(xydata);
}
var scanSetCollection = new ScanSetCollection();
scanSetCollection.Create(run, startScan, stopScan, 1, 1, false);
var validScanNums = scanSetCollection.ScanSetList.Select(p => (double)p.PrimaryScanNumber).ToArray();
basePeakChromXYData = FillInAnyMissingValuesInChromatogram(validScanNums, basePeakChromXYData);
return(basePeakChromXYData);
}
public void ChromAnalysisForAllSelectedPrecursors()
{
var isDataSmoothed = true;
var numPointsInSmoothing = 9;
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(numPointsInSmoothing, 2);
var graphGenerator = new BasicGraphControl();
var thermoFile1 = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(thermoFile1);
var outputFolderForChromGraphs = @"\\protoapps\DataPkgs\Public\2012\684_DeconMSn_research1\ChromatogramImages";
if (!Directory.Exists(outputFolderForChromGraphs))
{
Directory.CreateDirectory(outputFolderForChromGraphs);
}
var scanSetCollection = new ScanSetCollection();
var scanStart = run.MinLCScan;
var scanStop = run.MaxLCScan;
scanSetCollection.Create(run, scanStart, scanStop, 1, 1, true);
var sb = new StringBuilder();
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (!File.Exists(expectedPeaksFile))
{
var peakCreatorParams = new PeakDetectAndExportWorkflowParameters();
peakCreatorParams.PeakBR = 1.75;
var peakCreator = new PeakDetectAndExportWorkflow(run, peakCreatorParams);
peakCreator.Execute();
}
var peakImporter = new PeakImporterFromText(expectedPeaksFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
double ppmTol = 50;
var peakChromatogramGenerator = new PeakChromatogramGenerator(ppmTol, Globals.ChromatogramGeneratorMode.MZ_BASED);
var scansetList = scanSetCollection.ScanSetList;
var scanCounter = 0;
var currentBin = 0;
foreach (var scanSet in scansetList)
{
run.CurrentScanSet = scanSet;
var currentScanLevel = run.GetMSLevel(scanSet.PrimaryScanNumber);
if (currentScanLevel > 1)
{
scanCounter++;
var precursorInfo = run.GetPrecursorInfo(scanSet.PrimaryScanNumber);
var scanInfo = run.GetScanInfo(scanSet.PrimaryScanNumber);
var scanWindowSize = 400;
var startScan = scanSet.PrimaryScanNumber - scanWindowSize / 2;
var stopScan = scanSet.PrimaryScanNumber + scanWindowSize / 2;
run.XYData = peakChromatogramGenerator.GenerateChromatogram(run, startScan, stopScan, precursorInfo.PrecursorMZ, ppmTol);
if (run.XYData == null)
{
run.XYData = new XYData();
run.XYData.Xvalues = new double[] { 0, 1, 2 };
run.XYData.Yvalues = new double[] { 0, 1, 2 };
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan + "--------- NO XYData!!! -------------");
}
else
{
if (isDataSmoothed)
{
run.XYData = smoother.Smooth(run.XYData);
}
}
Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + precursorInfo.MSLevel + "\t" + precursorInfo.PrecursorMZ +
"\t" + precursorInfo.PrecursorScan);
graphGenerator.GenerateGraph(run.XYData.Xvalues, run.XYData.Yvalues);
var line = graphGenerator.GraphPane.CurveList[0] as LineItem;
line.Line.IsVisible = true;
line.Symbol.Size = 2;
line.Symbol.Type = SymbolType.Circle;
graphGenerator.GraphPane.XAxis.Title.Text = "scan";
graphGenerator.GraphPane.YAxis.Title.Text = "intensity";
graphGenerator.GraphPane.XAxis.Scale.MinAuto = true;
graphGenerator.GraphPane.YAxis.Scale.MinAuto = false;
graphGenerator.GraphPane.YAxis.Scale.Min = 0;
graphGenerator.GraphPane.XAxis.Scale.FontSpec.Size = 12;
graphGenerator.AddVerticalLineToGraph(scanSet.PrimaryScanNumber, 3);
graphGenerator.AddAnnotationRelativeAxis(scanInfo, 0.3, 0.1);
if (scanCounter > 500)
{
currentBin++;
scanCounter = 0;
}
var currentOutputFolder = Path.Combine(outputFolderForChromGraphs, "bin" + currentBin);
if (!Directory.Exists(currentOutputFolder))
{
Directory.CreateDirectory(currentOutputFolder);
}
var baseFilename = Path.Combine(currentOutputFolder,
scanSet.PrimaryScanNumber.ToString().PadLeft(5, '0') + "_mz" + precursorInfo.PrecursorMZ);
string outputGraphFilename;
string outputXYData;
if (isDataSmoothed)
{
outputGraphFilename = baseFilename + "_smoothed_chrom.png";
outputXYData = baseFilename + "_smoothed_xydata.txt";
}
else
{
outputXYData = baseFilename + "_xydata.txt";
outputGraphFilename = baseFilename + "_chrom.png";
}
graphGenerator.SaveGraph(outputGraphFilename);
TestUtilities.WriteToFile(run.XYData, outputXYData);
}
}
Console.WriteLine(sb.ToString());
}
public void BasePeakChromatogramTests()
{
var filename = @"D:\Data\UIMF\Sarc_P13_C10_1186_23Sep11_Cheetah_11-09-06.uimf";
var run = new RunFactory().CreateRun(filename);
var scanSetCollection = new ScanSetCollection();
//scanSetCollection.Create(run, 500, 550,1,1);
scanSetCollection.Create(run, run.MinLCScan, run.MaxLCScan, 1, 1);
var imsScanSetCollection = new IMSScanSetCollection();
imsScanSetCollection.Create(run, 60, 250, 1, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 4;
peakDet.SignalToNoiseThreshold = 2;
peakDet.IsDataThresholded = true;
var outputFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2013\Saturation_Correction\chromOuput.txt";
using (var writer = new StreamWriter(outputFile))
{
for (var lcscan = 0; lcscan < scanSetCollection.ScanSetList.Count; lcscan++)
{
Console.WriteLine("lcscan= " + lcscan);
var scanSet = scanSetCollection.ScanSetList[lcscan];
run.CurrentScanSet = scanSet;
var sb = new StringBuilder();
var numImsScans = imsScanSetCollection.ScanSetList.Count;
for (var imsScan = 0; imsScan < numImsScans; imsScan++)
{
var imsscanSet = (IMSScanSet)imsScanSetCollection.ScanSetList[imsScan];
((UIMFRun)run).CurrentIMSScanSet = imsscanSet;
var basePeakIntensity = 0;
try
{
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
basePeakIntensity = GetMaxPeak(run.PeakList);
}
catch (Exception ex)
{
Console.WriteLine("skipping lcscan " + lcscan + " --- it is empty");
}
sb.Append(basePeakIntensity);
if (imsScan != numImsScans - 1) // if not the last value, add delimiter
{
sb.Append("\t");
}
}
writer.WriteLine(sb.ToString());
}
}
}
public void Get3DElutionProfileFromPeakLevelData(Run run, int minScan, int maxScan, double minMZ, double maxMZ, out int[] scans, out double[] mzBins, out float[] intensities, double binWidth = 0.01, bool applyLogTransform = false)
{
var msPeakList = run.ResultCollection.MSPeakResultList;
Check.Require(msPeakList != null && msPeakList.Count > 0, "Run is missing peaks. Elution profile is based on peak-level info");
Check.Require(binWidth > 0, "Binwidth must be greater than 0");
var scanSetCollection = new ScanSetCollection();
scanSetCollection.Create(run, minScan, maxScan, 1, 1, false);
//create bins
var numBins = (int)Math.Round((maxMZ - minMZ) / binWidth);
mzBins = new double[numBins];
var firstBinMZ = minMZ;
for (var i = 0; i < numBins; i++)
{
mzBins[i] = firstBinMZ + i * binWidth;
}
//iterate over scans and collected MzIntensityArray for each scan
var intensityList = new List <float>();
scans = scanSetCollection.ScanSetList.Select(p => p.PrimaryScanNumber).ToArray();
//gather relevant peaks.
var scanTolerance = 5; // TODO: keep an eye on this
minScan = scans.First();
maxScan = scans.Last();
var indexOfLowerScan = getIndexOfClosestScanValue(msPeakList, minScan, 0, msPeakList.Count - 1, scanTolerance);
var indexOfUpperScan = getIndexOfClosestScanValue(msPeakList, maxScan, 0, msPeakList.Count - 1, scanTolerance);
var currentIndex = indexOfLowerScan;
var filteredPeakList = new List <MSPeakResult>();
while (currentIndex <= indexOfUpperScan)
{
var currentPeak = msPeakList[currentIndex];
if (currentPeak.XValue >= minMZ && currentPeak.XValue <= maxMZ)
{
filteredPeakList.Add(currentPeak);
}
currentIndex++;
}
foreach (var scan in scans)
{
var peaksForScan = filteredPeakList.Where(n => n.Scan_num == scan).ToList();
var intensitiesForScan = new float[numBins];
foreach (var msPeakResult in peaksForScan)
{
var targetBin = (int)Math.Round((msPeakResult.XValue - firstBinMZ) / binWidth);
if (targetBin < intensitiesForScan.Length)
{
intensitiesForScan[targetBin] += (float)Math.Round(msPeakResult.Height);
}
}
intensityList.AddRange(intensitiesForScan);
}
if (applyLogTransform)
{
intensities = intensityList.Select(p => (float)Math.Log(p)).ToArray();
}
else
{
intensities = intensityList.ToArray();
}
Scans = scans;
Intensities = intensities;
MzBins = mzBins;
}
