public void WatersMzXmlTest1() { var testfile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Waters\LC_MS_pHis_Caulo_meth_110207.mzXML"; var run = new RunFactory().CreateRun(testfile); Console.WriteLine(TestUtilities.DisplayRunInformation(run)); run.ScanSetCollection = new ScanSetCollection(); run.ScanSetCollection.Create(run, 500, 600, 1, 1); foreach (var scanSet in run.ScanSetCollection.ScanSetList) { var level = run.GetMSLevel(scanSet.PrimaryScanNumber); Console.WriteLine(scanSet + "\t" + level); } }
public void msgenTest1() { var run = new RunFactory().CreateRun(_testdatafile); var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); ScanSet scan = new ScanSet(1); run.CurrentScanSet = scan; msGen.Execute(run.ResultCollection); Console.WriteLine("scan\tmsLevel"); for (int i = run.MinLCScan; i < run.MaxLCScan; i++) { Console.WriteLine(i + "\t" + run.GetMSLevel(i)); } //TestUtilities.DisplayXYValues(run.XYData); }
public void Test1() { var run = new RunFactory().CreateRun( @"\\proto-7\VOrbiETD01\2012_3\QC_Shew_12_02_Run-03_26Jul12_Roc_12-04-08\QC_Shew_12_02_Run-03_26Jul12_Roc_12-04-08.raw"); Assert.IsNotNull(run); var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); run.CurrentScanSet = new ScanSet(20000); run.ScanSetCollection.Create(run, 3000, 3010, 1, 1, true); Console.WriteLine("scan\tz\tinfo"); foreach (var scanSet in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scanSet; msGen.Execute(run.ResultCollection); Console.WriteLine(scanSet.PrimaryScanNumber + "\t" + run.GetMSLevel(scanSet.PrimaryScanNumber) + "\t" + run.GetScanInfo(scanSet.PrimaryScanNumber)); } }
public void Test1() { var run = new RunFactory().CreateRun( @"D:\Data\From_Joe\MyDeconToolsTester\RawFiles\Transition_Selection_Orbitrap_HCD_8Mar13_Cougar_12-12-36.raw"); Assert.IsNotNull(run); var msGen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); int testScan = 2448; run.CurrentScanSet = new ScanSet(testScan); DeconToolsPeakDetectorV2 ms1PeakDetector = new DeconToolsPeakDetectorV2(); ms1PeakDetector.PeakToBackgroundRatio = 1.3; ms1PeakDetector.SignalToNoiseThreshold = 2; ms1PeakDetector.IsDataThresholded = true; DeconToolsPeakDetectorV2 ms2PeakDetectorForCentroidedData = new DeconToolsPeakDetectorV2(); DeconToolsPeakDetectorV2 ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2(); ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2(); ms2PeakDetectorForProfileData.PeakToBackgroundRatio = ms1PeakDetector.PeakToBackgroundRatio; ms2PeakDetectorForProfileData.SignalToNoiseThreshold = ms1PeakDetector.SignalToNoiseThreshold; ms2PeakDetectorForProfileData.IsDataThresholded = ms1PeakDetector.IsDataThresholded; ms2PeakDetectorForCentroidedData = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true); ms2PeakDetectorForCentroidedData.RawDataType = Globals.RawDataType.Centroided; run.ScanSetCollection.Create(run, testScan, testScan, 1, 1, true); Console.WriteLine("scan\tz\tinfo"); foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msGen.Execute(run.ResultCollection); if (run.GetMSLevel(scan.PrimaryScanNumber) == 1) { ms1PeakDetector.Execute(run.ResultCollection); } else { var dataIsCentroided = run.IsDataCentroided(scan.PrimaryScanNumber); Console.WriteLine("Scan " + scan.PrimaryScanNumber + "centroided=" + dataIsCentroided); TestUtilities.DisplayXYValues(run.XYData); if (dataIsCentroided) { ms2PeakDetectorForCentroidedData.Execute(run.ResultCollection); } else { ms2PeakDetectorForProfileData.Execute(run.ResultCollection); } } Console.WriteLine("---- peaks for Scan " + scan); TestUtilities.DisplayPeaks(run.PeakList); } }
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()); }