protected override void InitializeProcessingTasks()
{
base.InitializeProcessingTasks();
UimfDriftTimeExtractor = new UIMFDriftTimeExtractor();
UimfTicExtractor = new UIMF_TICExtractor();
SaturationDetector = new SaturationDetector();
}
public void uimf_data_preLoaded() // in this case, data is preloaded, preventing re-accessing the same drifttimes over and over
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
((UIMFRun)run).GetFrameDataAllFrameSets(); // this is the key line... loads data necessary for drift time calc and correction
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
protected override void InitializeProcessingTasks()
{
base.InitializeProcessingTasks();
UimfDriftTimeExtractor = new UIMFDriftTimeExtractor();
UimfTicExtractor = new UIMF_TICExtractor();
SaturationDetector = new SaturationDetector();
mCachedProgressMessage = string.Empty;
mLastProgress = DateTime.UtcNow;
}
public void uimf_data_not_preLoaded() // in this case the drift time is calculated every time by looking up sqlite data from uimf file
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fscc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 220, 270, 9, 1);
sscc.Create();
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
UIMFDriftTimeExtractor driftTimeExtractor = new UIMFDriftTimeExtractor();
StringBuilder sb = new StringBuilder();
foreach (var frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
}
}
foreach (var item in run.ResultCollection.ResultList)
{
UIMFIsosResult isosresult = (UIMFIsosResult)item;
sb.Append(isosresult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(isosresult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(isosresult.IsotopicProfile.MonoPeakMZ.ToString("0.000"));
sb.Append("\t");
sb.Append(isosresult.DriftTime.ToString("0.000"));
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
public static Run CreateResultsFromTwoFramesOfStandardUIMFData()
{
var run = new UIMFRun(FileRefs.RawDataMSFiles.UIMFStdFile1);
run.ResultCollection.ResultType = Globals.ResultType.UIMF_TRADITIONAL_RESULT;
run.ScanSetCollection.Create(run, 500, 501, 3, 1);
run.IMSScanSetCollection.Create(run, 250, 270, 9, 1);
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetectorV2();
Task decon = new ThrashDeconvolutorV2();
Task msScanInfoCreator = new ScanResultUpdater();
Task flagger = new ResultValidatorTask();
Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor();
Task driftTimeextractor = new UIMFDriftTimeExtractor();
foreach (var frame in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = frame;
foreach (IMSScanSet scan in run.IMSScanSetCollection.ScanSetList)
{
run.CurrentIMSScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
driftTimeextractor.Execute(run.ResultCollection);
msScanInfoCreator.Execute(run.ResultCollection);
ticExtractor.Execute(run.ResultCollection);
}
}
return(run);
}
public void smallExportTest1()
{
Project project = Project.getInstance();
//TODO: add project parameters (for summing)
project.RunCollection.Add(new UIMFRun(uimfFilepath, 1200, 1202, 250, 300));
Task msGen = new UIMF_MSGenerator(200, 2000);
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);
Task decon = new HornDeconvolutor();
Task driftTimeExtractor = new UIMFDriftTimeExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(driftTimeExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
UIMFIsosExporter isosExporter = new UIMFIsosExporter(uimfIsosExporterTest1output);
isosExporter.Export(project.RunCollection[0].ResultCollection);
}
public void test1()
{
Run uimfrun = new UIMFRun(inputUIMFFile1);
int startFrame = 800;
int stopFrame = 800;
int numFramesSummed = 3;
int numScansSummed = 9;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(uimfrun, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scansetCreator = new ScanSetCollectionCreator(uimfrun, 230, 240, numScansSummed, 1, false);
scansetCreator.Create();
Project project = Project.getInstance();
project.RunCollection.Add(uimfrun);
Task msGen = new UIMF_MSGenerator(200, 2000);
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);
Task decon = new HornDeconvolutor();
Task driftTimeExtractor = new UIMFDriftTimeExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(driftTimeExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
Assert.AreEqual(252, project.RunCollection[0].ResultCollection.ResultList.Count);
if (File.Exists(outputFile1))
{
File.Delete(outputFile1);
}
Stopwatch sw = new Stopwatch();
sw.Start();
UIMFSQLiteIsosExporter isosExporter = new UIMFSQLiteIsosExporter(outputFile1);
isosExporter.Export(project.RunCollection[0].ResultCollection);
sw.Stop();
Console.Write("\n\n----------- Time taken for UIMFSQLiteIsosExporter (milliseconds) = \t" + sw.ElapsedMilliseconds);
}
