public void peak_interference_UIMF_expectInterference_test1()
{
var uimfFrame1200_142 = FileRefs.RawDataBasePath + @"\UIMF\Sarc_MS_90_21Aug10_Cheetah_10-08-02_0000_frame1200_scan142.txt";
Run run = new DeconTools.Backend.Runs.MSScanFromTextFileRun(uimfFrame1200_142);
var scanSet = new ScanSet(0);
run.CurrentScanSet = scanSet;
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
msgen.MinMZ = 200;
msgen.MaxMZ = 2000;
var peakDetector = new DeconToolsPeakDetectorV2(4, 3, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
var decon = new HornDeconvolutor();
decon.MinIntensityForScore = 10;
decon.DeleteIntensityThreshold = 10;
decon.MaxFitAllowed = 0.4;
decon.MinMZ = 200;
decon.MaxMZ = 2000;
decon.IsMZRangeUsed = false;
var zeroFiller = new DeconToolsZeroFiller();
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
//Assert.AreEqual(93, run.ResultCollection.ResultList.Count);
var testResult = run.ResultCollection.ResultList.Where(p => p.IsotopicProfile.MonoPeakMZ > 428 && p.IsotopicProfile.MonoPeakMZ < 430).First();
var monoPeak = testResult.IsotopicProfile.getMonoPeak();
var lastPeak = testResult.IsotopicProfile.Peaklist[testResult.IsotopicProfile.Peaklist.Count - 1];
var startIndexOfXYData = MathUtils.BinarySearchWithTolerance(run.XYData.Xvalues, monoPeak.XValue - 3, 0, (run.XYData.Xvalues.Length - 1), 2);
//interference scorer
var interferenceScorer = new InterferenceScorer();
var stopwatch = new Stopwatch();
stopwatch.Start();
var scanPeaks = run.PeakList.Select <Peak, MSPeak>(i => (MSPeak)i).ToList();
var interferenceScore = interferenceScorer.GetInterferenceScore(scanPeaks, testResult.IsotopicProfile.Peaklist, monoPeak.XValue - 1.1,
lastPeak.XValue + lastPeak.Width);
stopwatch.Stop();
Console.WriteLine("interference= " + interferenceScore);
Console.WriteLine("Time taken = " + stopwatch.ElapsedMilliseconds);
}
public void ZeroFillerCompareNewAndOld()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var zeroFiller = new DeconToolsZeroFiller(3);
msgen.Execute(run.ResultCollection);
var numZerosToFill = 3;
var newZeroFilled = zeroFiller.ZeroFill(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
// var oldZeroFilled = zeroFiller.ZeroFillOld(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
var lowerMZ = 625.48;
var upperMZ = 626.18;
run.XYData = run.XYData.TrimData(lowerMZ, upperMZ);
newZeroFilled = newZeroFilled.TrimData(lowerMZ, upperMZ);
// oldZeroFilled = oldZeroFilled.TrimData(lowerMZ, upperMZ);
Console.WriteLine("---------- before zerofilling ---------------");
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("---------- after zerofilling ---------------");
TestUtilities.DisplayXYValues(newZeroFilled);
// Console.WriteLine("---------- after zerofilling using DeconEngine ---------------");
// TestUtilities.DisplayXYValues(oldZeroFilled);
}
public SaturationIMSScanBasedWorkflow(DeconToolsParameters parameters, Run run, string outputFolderPath = null, BackgroundWorker backgroundWorker = null)
: base(parameters, run, outputFolderPath, backgroundWorker)
{
Check.Require(run is UIMFRun, "Cannot create workflow. Run is required to be a UIMFRun for this type of workflow");
PeakBRSaturatedPeakDetector = parameters.PeakDetectorParameters.PeakToBackgroundRatio * 0.75;
_msGenerator = new UIMF_MSGenerator();
_peakDetector = new DeconToolsPeakDetectorV2(5, 3, Globals.PeakFitType.QUADRATIC, false);
_zeroFiller = new DeconToolsZeroFiller();
//#if Disable_DeconToolsV2
// throw new NotImplementedException("Cannot use class SaturationIMSScanBasedWorkflow since support for C++ based DeconToolsV2 is disabled");
//#else
_deconvolutor = new HornDeconvolutor(parameters)
{
MaxFitAllowed = 0.9,
MinPeptideBackgroundRatio = _peakDetector.PeakToBackgroundRatio
};
//#endif
AdjustMonoIsotopicMasses = true;
Run.PeakList = new List <Peak>();
}
public void examineIMFFile_Scan233MZ630()
{
Run run = new IMFRun(imfFilepath);
run.MSParameters = new DeconTools.Backend.Parameters.MSParameters();
run.CurrentScanSet = new ScanSet(233, 229, 237);
run.MSParameters.MinMZ = 100;
run.MSParameters.MaxMZ = 631.5;
int numPeaks = 0;
for (double n = 629; n < 630; n = n + 0.01)
{
ResultCollection rc = new ResultCollection(run);
Task msGen = new GenericMSGenerator(n, run.MSParameters.MaxMZ);
msGen.Execute(rc);
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 zeroFiller = new DeconToolsZeroFiller(3);
//zeroFiller.Execute(rc);
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(rc);
Task decon = new RapidDeconvolutor();
decon.Execute(rc);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < rc.ResultList.Count; i++)
{
IsosResult result = rc.ResultList[i];
if (result.IsotopicProfile.Peaklist[0].XValue > 629 && result.IsotopicProfile.Peaklist[0].XValue < 631)
{
sb.Append(n.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Peaklist[0].XValue.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Score.ToString("0.00"));
sb.Append("\t");
sb.Append(result.Run.PeakList.Count);
sb.Append("\t");
sb.Append(result.Run.XYData.Xvalues.Length);
sb.Append("\n");
}
}
Console.Write(sb.ToString());
}
}
public void examineRAWFile_Scan6757()
{
Run run = new XCaliburRun(xcaliburTestfile);
run.MSParameters = new DeconTools.Backend.Parameters.MSParameters();
run.CurrentScanSet = new ScanSet(6757);
run.MSParameters.MinMZ = 0;
run.MSParameters.MaxMZ = 10000;
ResultCollection rc = new ResultCollection(run);
Task msGen = new GenericMSGenerator(run.MSParameters.MinMZ, run.MSParameters.MaxMZ);
msGen.Execute(rc);
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 zeroFiller = new DeconToolsZeroFiller(3);
//zeroFiller.Execute(rc);
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(rc);
Task decon = new RapidDeconvolutor();
decon.Execute(rc);
StringBuilder sb = new StringBuilder();
for (int i = 0; i < rc.ResultList.Count; i++)
{
IsosResult result = rc.ResultList[i];
if (result.IsotopicProfile.Peaklist[0].XValue > 0 && result.IsotopicProfile.Peaklist[0].XValue < 10000)
{
sb.Append(result.IsotopicProfile.Peaklist[0].XValue.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Score.ToString("0.00"));
sb.Append("\t");
sb.Append(result.IsotopicProfile.Peaklist[0].SN.ToString("0.0"));
sb.Append("\t");
sb.Append(result.Run.PeakList.Count);
sb.Append("\t");
sb.Append(result.Run.XYData.Xvalues.Length);
sb.Append("\n");
}
}
Console.Write(sb.ToString());
}
public void multipleFrames_horn_test1()
{
Project.Reset();
Project project = Project.getInstance();
project.LoadOldDecon2LSParameters(uimfParameters1);
UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1203);
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(0, 5000);
Task zeroFiller = new DeconToolsZeroFiller(3);
Task peakDetector = new DeconToolsPeakDetector(project.Parameters.OldDecon2LSParameters.PeakProcessorParameters);
Task decon = new HornDeconvolutor(project.Parameters.OldDecon2LSParameters.HornTransformParameters);
Task scanResultsUpdater = new ScanResultUpdater();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(zeroFiller);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
sw.Stop();
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + project.RunCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Peaks found = " + project.RunCollection[0].ResultCollection.ScanResultList[0].NumPeaks);
StringBuilder sb = new StringBuilder();
}
protected override void InitializeProcessingTasks()
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters);
var moreSensitivePeakToBackgroundRatio = NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio / 2;
var moreSensitiveSigNoiseThresh = NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold;
_moreSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(moreSensitivePeakToBackgroundRatio,
moreSensitiveSigNoiseThresh, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
_superSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(0, 0, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters);
//Will initialize these but whether or not they are used are determined elsewhere
ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill);
Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth,
NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder);
FitScoreCalculator = new DeconToolsFitScoreCalculator();
ResultValidator = new ResultValidatorTask();
PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator();
_ms2PeakDetectorForCentroidData = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true)
{
RawDataType = Globals.RawDataType.Centroided
};
_ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2(NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio,
NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold,
NewDeconToolsParameters.PeakDetectorParameters.PeakFitType,
NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded);
Check.Ensure(Deconvolutor is ThrashDeconvolutorV2, "Error. Currently the DeconMSn workflow only works with the ThrashV2 deconvolutor. Selected deconvolutor= " + Deconvolutor);
}
public void ZeroFillerTest1()
{
Run run = new MSScanFromTextFileRun(FileRefs.RawDataMSFiles.TextFileMS_std1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var zeroFiller = new DeconToolsZeroFiller(3);
msgen.Execute(run.ResultCollection);
// Delete data points such that we only retain 50% of the data
var fractionToKeep = 0.50;
var distanceBetweenPoints = (int)(run.XYData.Xvalues.Length / (run.XYData.Xvalues.Length * fractionToKeep));
var newXVals = new List <double>();
var newYVals = new List <double>();
for (var i = 0; i < run.XYData.Xvalues.Length; i += distanceBetweenPoints)
{
if (i < run.XYData.Xvalues.Length)
{
newXVals.Add(run.XYData.Xvalues[i]);
newYVals.Add(run.XYData.Yvalues[i]);
}
}
run.XYData.Xvalues = newXVals.ToArray();
run.XYData.Yvalues = newYVals.ToArray();
var numZerosToFill = 3;
var newZeroFilled = zeroFiller.ZeroFill(run.XYData.Xvalues, run.XYData.Yvalues, numZerosToFill);
double lowerMZ = 1000;
double upperMZ = 1300;
run.XYData = run.XYData.TrimData(lowerMZ, upperMZ);
newZeroFilled = newZeroFilled.TrimData(lowerMZ, upperMZ);
Console.WriteLine("---------- before zerofilling ---------------");
TestUtilities.DisplayXYValues(run.XYData, lowerMZ, upperMZ);
Console.WriteLine("---------- after zerofilling ---------------");
TestUtilities.DisplayXYValues(newZeroFilled, lowerMZ, upperMZ);
Assert.IsTrue(newZeroFilled.Xvalues.Length > run.XYData.Xvalues.Length);
}
public SaturationIMSScanBasedWorkflow(DeconToolsParameters parameters, Run run, string outputDirectoryPath = null, BackgroundWorker backgroundWorker = null)
: base(parameters, run, outputDirectoryPath, backgroundWorker)
{
Check.Require(run is UIMFRun, "Cannot create workflow. Run is required to be a UIMFRun for this type of workflow");
PeakBRSaturatedPeakDetector = parameters.PeakDetectorParameters.PeakToBackgroundRatio * 0.75;
_msGenerator = new UIMF_MSGenerator();
_peakDetector = new DeconToolsPeakDetectorV2(5, 3);
_zeroFiller = new DeconToolsZeroFiller();
_deconvolutor = new HornDeconvolutor(parameters)
{
MaxFitAllowed = 0.9,
MinPeptideBackgroundRatio = _peakDetector.PeakToBackgroundRatio
};
AdjustMonoIsotopicMasses = true;
Run.PeakList = new List <Peak>();
}
public void Test1()
{
var saturationDetector = new SaturationDetector();
var testFile = FileRefs.RawDataMSFiles.UIMFStdFile3;
var run = (UIMFRun) new RunFactory().CreateRun(testFile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var zeroFiller = new DeconToolsZeroFiller();
var peakDetector = new DeconToolsPeakDetectorV2(4, 3, Globals.PeakFitType.QUADRATIC, false);
var decon = new HornDeconvolutor();
decon.LeftFitStringencyFactor = 2.5;
decon.RightFitStringencyFactor = 0.5;
var startScan = 100;
var stopScan = 200;
for (var i = startScan; i < stopScan; i++)
{
var frame = new ScanSet(500);
var primaryScan = i;
var scan = new ScanSet(primaryScan, primaryScan - 3, primaryScan + 3);
run.CurrentScanSet = frame;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
zeroFiller.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
saturationDetector.GetUnsummedIntensitiesAndDetectSaturation(run, run.ResultCollection.IsosResultBin);
}
var msfeatureElution = (from n in run.ResultCollection.ResultList
where
n.IsotopicProfile.MonoIsotopicMass > 1253.71 &&
n.IsotopicProfile.MonoIsotopicMass < 1253.73
select n);
foreach (var result in msfeatureElution)
{
if (result.IsotopicProfile.IsSaturated || true)
{
Console.WriteLine(result.ScanSet.PrimaryScanNumber + "\t" +
result.IsotopicProfile.MonoPeakMZ.ToString("0.0000") + "\t" +
result.IntensityAggregate + "\t" +
result.IsotopicProfile.IntensityAggregateAdjusted);
}
}
//TestUtilities.DisplayIsotopicProfileData(testIso1);
//TestUtilities.DisplayPeaks(run.PeakList);
}
public void multipleFrames_horn_test4()
{
Project.Reset();
//Project.getInstance().LoadOldDecon2LSParameters(uimfParameters1);
UIMFRun run = new UIMFRun(uimfFilepath, 1202, 1202);
Project.getInstance().RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
Task msGen = new UIMF_MSGenerator(0, 5000);
Task zeroFiller = new DeconToolsZeroFiller(3);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 4;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParams.CompleteFit = true;
hornParams.LeftFitStringencyFactor = 2.5;
hornParams.RightFitStringencyFactor = 0.5;
hornParams.PeptideMinBackgroundRatio = 4;
hornParams.MaxFit = 0.4;
hornParams.UseMZRange = false;
hornParams.UseMercuryCaching = true;
Task decon = new HornDeconvolutor(hornParams);
Task scanResultsUpdater = new ScanResultUpdater();
Project.getInstance().TaskCollection.TaskList.Add(msGen);
Project.getInstance().TaskCollection.TaskList.Add(zeroFiller);
Project.getInstance().TaskCollection.TaskList.Add(peakDetector);
Project.getInstance().TaskCollection.TaskList.Add(decon);
Project.getInstance().TaskCollection.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new UIMF_TaskController(Project.getInstance().TaskCollection);
controller.Execute(Project.getInstance().RunCollection);
sw.Stop();
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + Project.getInstance().RunCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Peaks found = " + Project.getInstance().RunCollection[0].ResultCollection.ScanResultList[0].NumPeaks);
StringBuilder sb = new StringBuilder();
}
public void imf_multipleFrames_horn_test2()
{
List <Run> runCollection = new List <Run>();
Run run = new IMFRun(imfFilePath);
runCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1);
sscc.Create();
Task msGen = new GenericMSGenerator(0, 5000);
Task zeroFiller = new DeconToolsZeroFiller(3);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 4;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParams.CompleteFit = true;
hornParams.LeftFitStringencyFactor = 2.5;
hornParams.RightFitStringencyFactor = 0.5;
hornParams.PeptideMinBackgroundRatio = 4;
hornParams.MaxFit = 0.4;
Task decon = new HornDeconvolutor(hornParams);
Task scanResultsUpdater = new ScanResultUpdater();
TaskCollection tc = new TaskCollection();
tc.TaskList.Add(msGen);
tc.TaskList.Add(zeroFiller);
tc.TaskList.Add(peakDetector);
tc.TaskList.Add(decon);
tc.TaskList.Add(scanResultsUpdater);
Stopwatch sw = new Stopwatch();
sw.Start();
TaskController controller = new BasicTaskController(tc);
controller.Execute(runCollection);
sw.Stop();
Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds);
Console.WriteLine("Scans analyzed = " + runCollection[0].ScanSetCollection.ScanSetList.Count);
Console.WriteLine("Features found = " + runCollection[0].ResultCollection.ResultList.Count);
Console.WriteLine("Peaks found = " + runCollection[0].ResultCollection.ScanResultList.Sum(p => p.NumPeaks));
StringBuilder sb = new StringBuilder();
}
public void BPISaturationCorrectedTest1()
{
var filename = @"D:\Data\UIMF\Sarc_P13_C10_1186_23Sep11_Cheetah_11-09-06.uimf";
var run = new RunFactory().CreateRun(filename);
run.ScanSetCollection = new ScanSetCollection();
//scanSetCollection.Create(run, 500, 550,1,1);
var startFrame = 477;
var stopFrame = 477;
//startFrame = run.MinLCScan;
//stopFrame = run.MaxLCScan;
run.ScanSetCollection.Create(run, startFrame, stopFrame, 1, 1);
((UIMFRun)run).IMSScanSetCollection = new IMSScanSetCollection();
((UIMFRun)run).IMSScanSetCollection.Create(run, 122, 122, 1, 1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDet = new DeconToolsPeakDetectorV2();
peakDet.PeakToBackgroundRatio = 2;
peakDet.SignalToNoiseThreshold = 2;
peakDet.IsDataThresholded = true;
var _zeroFiller = new DeconToolsZeroFiller();
var _deconvolutor = new ThrashDeconvolutorV2();
_deconvolutor.UseAutocorrelationChargeDetermination = true;
_deconvolutor.Parameters.MaxFit = 0.8;
var saturationWorkflow = new SaturationIMSScanBasedWorkflow(new DeconToolsParameters(), run);
var outputFile = @"C:\Users\d3x720\Documents\PNNL\My_DataAnalysis\2013\Saturation_Correction\chromOuputSatCorrected.txt";
using (var writer = new StreamWriter(outputFile))
{
var uimfRun = (UIMFRun)run;
var _unsummedMSFeatures = new List <IsosResult>();
foreach (var lcScanSet in run.ScanSetCollection.ScanSetList)
{
Console.WriteLine("Scanset= " + lcScanSet);
uimfRun.ResultCollection.MSPeakResultList.Clear();
_unsummedMSFeatures.Clear();
var unsummedFrameSet = new ScanSet(lcScanSet.PrimaryScanNumber);
//get saturated MSFeatures for unsummed data
uimfRun.CurrentScanSet = unsummedFrameSet;
var sb = new StringBuilder();
var errorInFrame = false;
var numIMSScans = uimfRun.IMSScanSetCollection.ScanSetList.Count;
for (var imsScanNum = 0; imsScanNum < numIMSScans; imsScanNum++)
{
var imsScanSet = uimfRun.IMSScanSetCollection.ScanSetList[imsScanNum];
uimfRun.ResultCollection.IsosResultBin.Clear(); //clear any previous MSFeatures
var unsummedIMSScanset = new IMSScanSet(imsScanSet.PrimaryScanNumber);
uimfRun.CurrentIMSScanSet = unsummedIMSScanset;
try
{
msgen.Execute(run.ResultCollection);
_zeroFiller.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
_deconvolutor.Deconvolute(uimfRun.ResultCollection); //adds to IsosResultBin
}
catch (Exception ex)
{
errorInFrame = true;
}
_unsummedMSFeatures.AddRange(run.ResultCollection.IsosResultBin);
var basePeakIntensity = 0;
//iterate over unsummed MSFeatures and check for saturation
foreach (var isosResult in uimfRun.ResultCollection.IsosResultBin)
{
var isPossiblySaturated = isosResult.IntensityAggregate > 1e7;
if (isPossiblySaturated)
{
var theorIso = new IsotopicProfile();
saturationWorkflow.RebuildSaturatedIsotopicProfile(run.XYData, isosResult, uimfRun.PeakList, out theorIso);
saturationWorkflow.AdjustSaturatedIsotopicProfile(isosResult.IsotopicProfile, theorIso, true, true);
}
TestUtilities.DisplayIsotopicProfileData(isosResult.IsotopicProfile);
var height = (int)isosResult.IsotopicProfile.getMostIntensePeak().Height;
if (height > basePeakIntensity)
{
basePeakIntensity = height;
}
}
sb.Append(basePeakIntensity);
var isNotLastIMSScan = imsScanNum != numIMSScans - 1;
if (isNotLastIMSScan)
{
sb.Append("\t");
}
}
if (errorInFrame)
{
}
else
{
writer.WriteLine(sb.ToString());
}
}
}
}
