public void UIMFTest1()
{
var uimffile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31.uimf";
var rf = new RunFactory();
var run = rf.CreateRun(uimffile);
var expectedPeaksFile =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\UIMF\Sarc_P09_B06_0786_20Jul11_Cheetah_11-05-31_peaks.txt";
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var parameters = new PeakDetectAndExportWorkflowParameters();
parameters.LCScanMin = 500;
parameters.LCScanMax = 510;
parameters.NumIMSScansSummed = -1;
var workflow = new PeakDetectAndExportWorkflow(run, parameters);
workflow.Execute();
Assert.IsTrue(File.Exists(expectedPeaksFile));
}
public void testPeakGeneration()
{
var fileName =
@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.raw";
var run = new RunFactory().CreateRun(fileName);
var parameters = new PeakDetectAndExportWorkflowParameters();
parameters.LCScanMin = 5000;
parameters.LCScanMax = 7000;
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var workflow = new PeakDetectAndExportWorkflow(run, parameters);
workflow.Execute();
var fileinfo = new FileInfo(expectedPeaksFile);
Assert.IsTrue(fileinfo.Exists);
Assert.IsTrue(fileinfo.Length > 1000000);
}
public void peakexporterTest1()
{
var rf = new RunFactory();
var run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var parameters = new PeakDetectAndExportWorkflowParameters();
parameters.LCScanMin = 5500;
parameters.LCScanMax = 6500;
parameters.OutputFolder = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TempOutput";
var expectedPeaksFile = Path.Combine(parameters.OutputFolder, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var workflow = new PeakDetectAndExportWorkflow(run, parameters);
workflow.Execute();
var fileinfo = new FileInfo(expectedPeaksFile);
Assert.IsTrue(fileinfo.Exists);
Assert.IsTrue(fileinfo.Length > 1000000);
}
public void createPeaksTest1()
{
var testFile =
@"D:\Data\Orbitrap\BrianIQTesting\QC_Shew_11_02_pt5-b_6Jun11_Sphinx_11-03-27.RAW";
var run = new RunFactory().CreateRun(testFile);
var parameters = new PeakDetectAndExportWorkflowParameters();
TargetedWorkflowParameters deconParam = new BasicTargetedWorkflowParameters();
deconParam.ChromGenSourceDataPeakBR = 3;
parameters.PeakBR = deconParam.ChromGenSourceDataPeakBR;
parameters.PeakFitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
parameters.SigNoiseThreshold = deconParam.ChromGenSourceDataSigNoise;
var peakCreator = new PeakDetectAndExportWorkflow(run, parameters);
peakCreator.Execute();
}
public void stolen_peakexporterTest1()
{
//RunFactory rf = new RunFactory();
//Run run = rf.CreateRun(DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var fileName = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
//@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.raw";
//@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\Orbitrap\Vorbi\Yellow_C12_099_18Mar10_Griffin_10-01-13.raw";
//
//Run run = RunUtilities.CreateAndLoadPeaks(fileName);
var run = new RunFactory().CreateRun(fileName);
var parameters = new PeakDetectAndExportWorkflowParameters();
parameters.LCScanMin = 5500;
parameters.LCScanMax = 6500;
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var workflow = new PeakDetectAndExportWorkflow(run, parameters);
workflow.Execute();
var fileinfo = new FileInfo(expectedPeaksFile);
Assert.IsTrue(fileinfo.Exists);
Assert.IsTrue(fileinfo.Length > 1000000);
}
public void exportPeaksFromMixedProfileAndCentroidMS2Data()
{
//TODO: finish off this test
var testFile = @"D:\Data\From_Matt\XGA121_lipid_pt5uM_1.raw";
var rf = new RunFactory();
var run = rf.CreateRun(testFile);
var parameters = new PeakDetectAndExportWorkflowParameters();
parameters.LCScanMin = 1;
parameters.LCScanMax = 20;
parameters.ProcessMSMS = true;
parameters.IsDataThresholded = true;
parameters.MS2PeakDetectorDataIsThresholded = true;
var expectedPeaksFile = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt");
if (File.Exists(expectedPeaksFile))
{
File.Delete(expectedPeaksFile);
}
var workflow = new PeakDetectAndExportWorkflow(run, parameters);
workflow.Execute();
var fileinfo = new FileInfo(expectedPeaksFile);
Assert.IsTrue(fileinfo.Exists);
}
private void LoadPeaks()
{
try
{
_peaksFilename = this.Run.DataSetPath + "\\" + this.Run.DatasetName + "_peaks.txt";
if (!File.Exists(_peaksFilename))
{
GeneralStatusMessage =
"Creating chromatogram data (_peaks.txt file); this is only done once. It takes 1 - 5 min .......";
var deconParam = (TargetedWorkflowParameters)Workflow.WorkflowParameters;
var peakCreationParameters = new PeakDetectAndExportWorkflowParameters();
peakCreationParameters.PeakBR = deconParam.ChromGenSourceDataPeakBR;
peakCreationParameters.PeakFitType = Globals.PeakFitType.QUADRATIC;
peakCreationParameters.SigNoiseThreshold = deconParam.ChromGenSourceDataSigNoise;
var peakCreator = new PeakDetectAndExportWorkflow(Run, peakCreationParameters, _backgroundWorker);
peakCreator.Execute();
}
}
catch (Exception ex)
{
GeneralStatusMessage = ex.Message;
return;
}
GeneralStatusMessage = "Loading chromatogram data (_peaks.txt file) .......";
try
{
PeakImporterFromText peakImporter = new PeakImporterFromText(_peaksFilename, _backgroundWorker);
peakImporter.ImportPeaks(this.Run.ResultCollection.MSPeakResultList);
}
catch (Exception ex)
{
GeneralStatusMessage = ex.Message;
return;
//throw new ApplicationException("Peaks failed to load. Maybe the details below will help... \n\n" + ex.Message + "\nStacktrace: " + ex.StackTrace, ex);
}
if (Run.ResultCollection.MSPeakResultList != null && Run.ResultCollection.MSPeakResultList.Count > 0)
{
int numPeaksLoaded = Run.ResultCollection.MSPeakResultList.Count;
GeneralStatusMessage = "Chromatogram data LOADED. (# peaks= " + numPeaksLoaded + ")";
}
else
{
GeneralStatusMessage = "No Chromatogram data!!! Check your _peaks.txt file for correct format.";
}
}
private void CreatePeaksForChromSourceData()
{
PeakDetectAndExportWorkflowParameters parameters = new PeakDetectAndExportWorkflowParameters();
TargetedWorkflowParameters deconParam = (TargetedWorkflowParameters)this._workflowParameters;
parameters.PeakBR = deconParam.ChromGenSourceDataPeakBR;
parameters.PeakFitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
parameters.SigNoiseThreshold = deconParam.ChromGenSourceDataSigNoise;
PeakDetectAndExportWorkflow peakCreator = new PeakDetectAndExportWorkflow(this.Run, parameters, _backgroundWorker);
peakCreator.Execute();
}
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());
}
private void LoadPeaks()
{
try
{
_peaksFilename = Path.Combine(this.Run.DataSetPath, this.Run.DatasetName + "_peaks.txt");
var fiPeaksFile = new FileInfo(_peaksFilename);
if (!fiPeaksFile.Exists)
{
var alternatePeaksFilePath = Path.Combine(System.IO.Path.GetTempPath(), this.Run.DatasetName + "_peaks.txt");
if (File.Exists(alternatePeaksFilePath))
{
_peaksFilename = alternatePeaksFilePath;
fiPeaksFile = new FileInfo(_peaksFilename);
}
}
if (_recreatePeaksFile || !fiPeaksFile.Exists)
{
_recreatePeaksFile = false;
// Make sure we have write access to the folder with the dataset file
try
{
using (var swPeaksfile = new StreamWriter(new FileStream(fiPeaksFile.FullName, FileMode.Create, FileAccess.Write)))
{
swPeaksfile.WriteLine("Test");
}
}
catch (UnauthorizedAccessException)
{
// Create the _peaks.txt file in the user's temprorary folder
_peaksFilename = Path.Combine(System.IO.Path.GetTempPath(), this.Run.DatasetName + "_peaks.txt");
fiPeaksFile = new FileInfo(_peaksFilename);
}
fiPeaksFile.Refresh();
if (fiPeaksFile.Exists)
fiPeaksFile.Delete();
GeneralStatusMessage =
"Creating chromatogram data (_peaks.txt file); this is only done once. It takes 1 - 5 min .......";
var peakCreationParameters = new PeakDetectAndExportWorkflowParameters();
peakCreationParameters.PeakBR = ChromSourcePeakDetectorPeakBr;
peakCreationParameters.PeakFitType = Globals.PeakFitType.QUADRATIC;
peakCreationParameters.SigNoiseThreshold = ChromSourcePeakDetectorSigNoise;
peakCreationParameters.OutputFolder = fiPeaksFile.Directory.FullName;
var peakCreator = new PeakDetectAndExportWorkflow(Run, peakCreationParameters, _backgroundWorker);
peakCreator.Execute();
}
}
catch (Exception ex)
{
GeneralStatusMessage = ex.Message;
return;
}
GeneralStatusMessage = "Loading chromatogram data (_peaks.txt file) .......";
try
{
PeakImporterFromText peakImporter = new PeakImporterFromText(_peaksFilename, _backgroundWorker);
peakImporter.ImportPeaks(this.Run.ResultCollection.MSPeakResultList);
}
catch (Exception ex)
{
GeneralStatusMessage = ex.Message;
return;
//throw new ApplicationException("Peaks failed to load. Maybe the details below will help... \n\n" + ex.Message + "\nStacktrace: " + ex.StackTrace, ex);
}
if (Run.ResultCollection.MSPeakResultList != null && Run.ResultCollection.MSPeakResultList.Count > 0)
{
int numPeaksLoaded = Run.ResultCollection.MSPeakResultList.Count;
GeneralStatusMessage = "Chromatogram data LOADED. (# peaks= " + numPeaksLoaded + ")";
}
else
{
GeneralStatusMessage = "No Chromatogram data!!! Check your _peaks.txt file for correct format.";
}
}
