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 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);
}
protected override void IterateOverScans()
{
const int CONSOLE_INTERVAL_SECONDS = 15;
const bool SKIP_DECONVOLUTION = false;
var uimfRun = (UIMFRun)Run;
var startTime = DateTime.UtcNow;
var dtLastProgress = DateTime.UtcNow.Subtract(new TimeSpan(1, 0, 0));
var frameCountProcessed = 0;
var maxRuntimeHours = NewDeconToolsParameters.MiscMSProcessingParameters.MaxHoursPerDataset;
// uimfRun.IMSScanSetCollection.ScanSetList =uimfRun.IMSScanSetCollection.ScanSetList.Where(p => p.PrimaryScanNumber == 153).ToList();
// Iterate over unsummed data and fix saturated isotopic profiles. Unsummed will be used during a second iteration (over summed data)
foreach (var lcScanSet in uimfRun.ScanSetCollection.ScanSetList)
{
uimfRun.ResultCollection.MSPeakResultList.Clear();
_unsummedMSFeatures.Clear();
var unsummedFrameSet = new ScanSet(lcScanSet.PrimaryScanNumber);
// Get saturated MSFeatures for unsummed data
uimfRun.CurrentScanSet = unsummedFrameSet;
var forceProgressMessage = true;
var imsScanCountProcessed = 0;
var maxMinutesPerFrame = NewDeconToolsParameters.MiscMSProcessingParameters.MaxMinutesPerFrame;
if (uimfRun.GetNumFrames() <= 10)
{
// Disable the per-frame timeout if we have 10 or fewer frames
maxMinutesPerFrame = int.MaxValue;
}
var frameStartTime = DateTime.UtcNow;
var timeoutReached = false;
foreach (var scanset in uimfRun.IMSScanSetCollection.ScanSetList)
{
if (DateTime.UtcNow.Subtract(dtLastProgress).TotalSeconds >= CONSOLE_INTERVAL_SECONDS || forceProgressMessage)
{
dtLastProgress = DateTime.UtcNow;
forceProgressMessage = false;
Console.WriteLine("Processing frame " + lcScanSet.PrimaryScanNumber + ", scan " + scanset.PrimaryScanNumber + " (Unsummed)");
}
if (DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes >= maxMinutesPerFrame)
{
Console.WriteLine(
"Aborted processing of frame {0} because {1} minutes have elapsed (processing unsummed features); IMSScanCount processed = {2}",
lcScanSet.PrimaryScanNumber,
(int)DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes,
imsScanCountProcessed);
timeoutReached = true;
break;
}
uimfRun.ResultCollection.IsosResultBin.Clear(); //clear any previous MSFeatures
var unsummedIMSScanset = new IMSScanSet(scanset.PrimaryScanNumber);
uimfRun.CurrentIMSScanSet = unsummedIMSScanset;
_msGenerator.Execute(Run.ResultCollection);
_zeroFiller.Execute(Run.ResultCollection);
// For debugging....
// if (scanset.PrimaryScanNumber == 123)
// {
// Console.WriteLine(scanset + "\t being processed!");
// }
_peakDetector.Execute(Run.ResultCollection);
imsScanCountProcessed++;
if (SKIP_DECONVOLUTION)
{
continue;
}
// Deconvolute Unsummed MSFeatures
// This is a preliminary step for Saturation Detection
//#if Disable_DeconToolsV2
// throw new NotImplementedException("Cannot use class SaturationIMSScanBasedWorkflow since support for C++ based DeconToolsV2 is disabled");
//#else
_deconvolutor.Deconvolute(uimfRun.ResultCollection); //adds to IsosResultBin
//#endif
// Note: the deconvolutor automatically increases the MSFeatureCounter.
// Here, we don't want this, since this data is used only for saturation correction,
// not for generating the official MSFeatures list. So we need to
// correct the MSFeatureCounter value.
Run.ResultCollection.MSFeatureCounter = Run.ResultCollection.MSFeatureCounter -
Run.ResultCollection.IsosResultBin.Count;
_unsummedMSFeatures.AddRange(Run.ResultCollection.IsosResultBin);
// Iterate over unsummed MSFeatures and check for saturation
foreach (var isosResult in uimfRun.ResultCollection.IsosResultBin)
{
var msFeatureXYData = Run.XYData.TrimData(isosResult.IsotopicProfile.MonoPeakMZ - 10,
isosResult.IsotopicProfile.MonoPeakMZ + 10);
var tempMZ = isosResult.IsotopicProfile.MonoPeakMZ;
var currentScan = scanset.PrimaryScanNumber;
var isPossiblySaturated = isosResult.IntensityAggregate >
NewDeconToolsParameters.MiscMSProcessingParameters.SaturationThreshold;
// For debugging...
// UIMFIsosResult tempIsosResult = (UIMFIsosResult) isosResult;
// if (tempIsosResult.IMSScanSet.PrimaryScanNumber == 123)
// {
// Console.WriteLine(tempIsosResult + "\t being processed!");
// }
if (isPossiblySaturated)
{
RebuildSaturatedIsotopicProfile(msFeatureXYData, isosResult, uimfRun.PeakList, out var theorIso);
AdjustSaturatedIsotopicProfile(isosResult.IsotopicProfile, theorIso, AdjustMonoIsotopicMasses, true);
}
}
}
// DisplayMSFeatures(_unsummedMSFeatures);
// Now sum across IMSScans, deconvolute and adjust using saturation detection
forceProgressMessage = true;
imsScanCountProcessed = 0;
// Compute a buffer using .MaxMinutesPerFrame times 20%
double maxFrameMinutesAddon = 0;
var bufferMinutes = maxMinutesPerFrame * 0.2;
if (bufferMinutes < 1)
{
bufferMinutes = 1;
}
if (timeoutReached ||
DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes + bufferMinutes >= maxMinutesPerFrame)
{
// Maximum time per frame has been reached (or has almost been reached)
// Allow the next step to run for an additional bufferMinutes
maxFrameMinutesAddon = bufferMinutes;
}
foreach (var scanSet in uimfRun.IMSScanSetCollection.ScanSetList)
{
var scanset = (IMSScanSet)scanSet;
if (DateTime.UtcNow.Subtract(dtLastProgress).TotalSeconds >= CONSOLE_INTERVAL_SECONDS || forceProgressMessage)
{
dtLastProgress = DateTime.UtcNow;
forceProgressMessage = false;
Console.WriteLine("Processing frame " + lcScanSet.PrimaryScanNumber + ", scan " + scanset.PrimaryScanNumber + " (Summed)");
}
if (DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes >= maxMinutesPerFrame + maxFrameMinutesAddon)
{
Console.WriteLine(
"Aborted processing of frame {0} because {1} minutes have elapsed (processing summed features); IMSScanCount processed = {2}",
lcScanSet.PrimaryScanNumber,
(int)DateTime.UtcNow.Subtract(frameStartTime).TotalMinutes,
imsScanCountProcessed);
break;
}
uimfRun.ResultCollection.IsosResultBin.Clear(); //clear any previous MSFeatures
// Get the summed isotopic profile
uimfRun.CurrentScanSet = lcScanSet;
uimfRun.CurrentIMSScanSet = scanset;
ExecuteTask(MSGenerator);
if (NewDeconToolsParameters.MiscMSProcessingParameters.UseZeroFilling)
{
ExecuteTask(ZeroFiller);
}
if (NewDeconToolsParameters.MiscMSProcessingParameters.UseSmoothing)
{
ExecuteTask(Smoother);
}
ExecuteTask(PeakDetector);
imsScanCountProcessed++;
if (!SKIP_DECONVOLUTION)
{
ExecuteTask(Deconvolutor);
foreach (var isosResult in Run.ResultCollection.IsosResultBin)
{
var isPossiblySaturated = isosResult.IntensityAggregate >
NewDeconToolsParameters.MiscMSProcessingParameters.SaturationThreshold;
if (isPossiblySaturated)
{
var msFeatureXYData = Run.XYData.TrimData(isosResult.IsotopicProfile.MonoPeakMZ - 10,
isosResult.IsotopicProfile.MonoPeakMZ + 10);
RebuildSaturatedIsotopicProfile(msFeatureXYData, isosResult, Run.PeakList, out var theorIso);
AdjustSaturatedIsotopicProfile(isosResult.IsotopicProfile, theorIso, AdjustMonoIsotopicMasses, false);
var currentScan = scanset.PrimaryScanNumber;
var currentMZ = isosResult.IsotopicProfile.MonoPeakMZ;
UpdateReportedSummedPeakIntensities(isosResult, lcScanSet, scanset);
}
else
{
}
if (isosResult.IsotopicProfile.IsSaturated)
{
GetRebuiltFitScore(isosResult);
}
}
}
// Need to remove any duplicate MSFeatures (this occurs when incorrectly deisotoped profiles are built).
// Will do this by making the MSFeatureID the same. Then the Exporter will ensure that only one MSFeature per MSFeatureID
// is exported. This isn't ideal. Better to remove the features but this proves to be quite hard to do without large performance hits.
foreach (var isosResult in Run.ResultCollection.IsosResultBin)
{
double ppmToleranceForDuplicate = 20;
var massTolForDuplicate = ppmToleranceForDuplicate *
isosResult.IsotopicProfile.MonoIsotopicMass / 1e6;
var isosResultLocal = isosResult;
var duplicateIsosResults = (from n in Run.ResultCollection.IsosResultBin
where
Math.Abs(n.IsotopicProfile.MonoIsotopicMass -
isosResultLocal.IsotopicProfile.MonoIsotopicMass) <
massTolForDuplicate && n.IsotopicProfile.ChargeState == isosResultLocal.IsotopicProfile.ChargeState
select n);
var minMSFeatureID = int.MaxValue;
foreach (var dup in duplicateIsosResults)
{
if (dup.MSFeatureID < minMSFeatureID)
{
minMSFeatureID = dup.MSFeatureID;
}
else
{
//here we have found a duplicate
dup.MSFeatureID = minMSFeatureID;
//because there are duplicates, we need to maintain the MSFeatureCounter so it doesn't skip values, as will
//happen when there are duplicates
//Run.ResultCollection.MSFeatureCounter--;
}
}
}
ExecuteTask(ResultValidator);
ExecuteTask(ScanResultUpdater);
if (NewDeconToolsParameters.ScanBasedWorkflowParameters.IsRefittingPerformed)
{
ExecuteTask(FitScoreCalculator);
}
// Allows derived classes to execute additional tasks
ExecuteOtherTasksHook();
if (ExportData)
{
// The following exporting tasks should be last
if (NewDeconToolsParameters.ScanBasedWorkflowParameters.ExportPeakData)
{
ExecuteTask(PeakToMSFeatureAssociator);
ExecuteTask(PeakListExporter);
}
ExecuteTask(IsosResultExporter);
ExecuteTask(ScanResultExporter);
}
ReportProgress();
}
frameCountProcessed++;
if (DateTime.UtcNow.Subtract(startTime).TotalHours >= maxRuntimeHours)
{
Console.WriteLine(
"Aborted processing because {0} hours have elapsed; Frames processed = {1}",
(int)DateTime.UtcNow.Subtract(startTime).TotalHours,
frameCountProcessed);
break;
}
}
}
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());
}
}
}
}