public void weirdZeroValuesForMZsAtEarlyFramesTest1()
{
UIMFRun run = new UIMFRun(uimfTestfile1);
FrameSetCollectionCreator framecreator = new FrameSetCollectionCreator(run, 1, 10, 5, 1);
framecreator.Create();
ScanSetCollectionCreator scanCreator = new ScanSetCollectionCreator(run, 1, 1);
scanCreator.Create();
Task msgen = new UIMF_MSGenerator(0, 5000);
Task peakDet = new DeconToolsPeakDetector();
int scanstop = 599;
int scanstart = 0;
for (int i = scanstart; i < scanstop; i++)
{
run.CurrentFrameSet = run.FrameSetCollection.GetFrameSet(1);
run.CurrentScanSet = run.ScanSetCollection.GetScanSet(i);
msgen.Execute(run.ResultCollection);
if (run.XYData != null && run.XYData.Xvalues != null && run.XYData.Xvalues[0] == 0)
{
reportXYValues(run);
}
}
}
public void outputToSqlite_uimf_test1()
{
List <Run> runcoll = new List <Run>();
Run run = new UIMFRun(uimfFile1);
runcoll.Add(run);
FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 809, 3, 1);
fsc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 220, 9, 1);
sscc.Create();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new RapidDeconvolutor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor();
Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor();
Task scanResultUpdater = new ScanResultUpdater();
Task sqliteExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.ScanResultExporters.UIMFScanResult_SqliteExporter(uimf_Sqlite_ScanResultOutputFile1);
Stopwatch sw;
foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
ticExtractor.Execute(run.ResultCollection);
scanResultUpdater.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
origIntensExtr.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
sqliteExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("SqliteExporter execution time = \t" + sw.ElapsedMilliseconds);
}
}
}
}
public void serializeUIMFDataTest1()
{
Run run = new UIMFRun(uimfFilepath2);
List <Run> runCollection = new List <Run>();
runCollection.Add(run);
int startFrame = 1200;
int stopFrame = 1205;
int numFramesSummed = 3;
int numScansSummed = 3;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, numScansSummed, 1);
scanSetCreator.Create();
Task msgen = new UIMF_MSGenerator();
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 3;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = true;
Task peakdetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new RapidDeconvolutor();
TaskCollection taskcollection = new TaskCollection();
taskcollection.TaskList.Add(msgen);
taskcollection.TaskList.Add(peakdetector);
taskcollection.TaskList.Add(decon);
TaskController taskcontroller = new UIMF_TaskController(taskcollection);
taskcontroller.IsosResultThresholdNum = 50;
taskcontroller.Execute(runCollection);
ResultCollection results;
IsosResultDeSerializer deserializer = new IsosResultDeSerializer(run.Filename + "_tmp.bin");
int counter = 0;
do
{
counter++;
results = deserializer.GetNextSetOfResults();
} while (results != null);
Assert.AreEqual(8, counter);
}
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());
}
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 void test1_summing()
{
Project.Reset();
Project project = Project.getInstance();
UIMFRun run = new UIMFRun(uimfFilepath, 1201, 1201);
project.RunCollection.Add(run);
int numFramesSummed = 3;
int numScansSummed = 3;
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 250, 270, numScansSummed, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, numFramesSummed, 1);
fscc.Create();
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;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new HornDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
Task originalIntensitiesExtractor = new OriginalIntensitiesExtractor();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(decon);
project.TaskCollection.TaskList.Add(scanResultsUpdater);
project.TaskCollection.TaskList.Add(originalIntensitiesExtractor);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
ResultCollection rc = project.RunCollection[0].ResultCollection;
Assert.AreEqual(180, rc.ResultList.Count);
StringBuilder sb = new StringBuilder();
IsosResultUtilities.DisplayResults(sb, rc.ResultList);
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();
}
public void examineFPGAFileTest1()
{
UIMFRun run = new UIMFRun(uimfFPGAFilePath);
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;
Task peakDetector = new DeconToolsPeakDetector(detectorParams);
Task decon = new HornDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
Task originalIntensitiesExtractor = new OriginalIntensitiesExtractor();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 300, 300, 1, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, 5, 5, 1, 1);
fscc.Create();
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msGen.Execute(run.ResultCollection);
//TestUtilities.DisplayXYValues(run.XYData);
originalIntensitiesExtractor.Execute(run.ResultCollection);
TestUtilities.DisplayXYValues(run.XYData);
}
}
}
public void GenerateUIMFSpectrumTest2()
{
Run run = new UIMFRun(uimfTestfile1);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(300);
run.ScanSetCollection = new ScanSetCollection();
run.ScanSetCollection.ScanSetList.Add(run.CurrentScanSet);
((UIMFRun)run).CurrentFrameSet = new FrameSet(1206);
Task msGen = new UIMF_MSGenerator(200, 2000);
msGen.Execute(results);
Assert.AreEqual(578, results.Run.XYData.Xvalues.Length);
Assert.AreEqual(578, results.Run.XYData.Yvalues.Length);
}
public void test1()
{
Project project = Project.getInstance();
//TODO: add project parameters (for summing)
Run run = new UIMFRun(uimfFilepath, 1200, 1202, 300, 400);
project.RunCollection.Add(run);
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, ((UIMFRun)run).MinFrame, ((UIMFRun)run).MaxFrame, 1, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetcreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1, false);
scanSetcreator.Create();
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 rapidDecon = new RapidDeconvolutor();
Task scanresultUpdater = new ScanResultUpdater();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(rapidDecon);
project.TaskCollection.TaskList.Add(scanresultUpdater);
TaskController controller = new UIMF_TaskController(project.TaskCollection);
controller.Execute(project.RunCollection);
UIMFScansExporter scansExporter = new UIMFScansExporter(uimfScansExporterTest1output);
scansExporter.Export(project.RunCollection[0].ResultCollection);
}
private void createPeaks(Run run)
{
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.StorePeakData = true;
peakDet.SigNoiseThreshold = 3;
peakDet.PeakBackgroundRatio = 4;
for (int i = 0; i < run.ScanSetCollection.ScanSetList.Count; i++)
{
ScanSet s = run.ScanSetCollection.ScanSetList[i];
run.CurrentScanSet = s;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
}
}
public void GenerateMassSpectraForRanges(Backend.Runs.UIMFRun run, int startFrame, int stopFrame, int startScan, int stopScan)
{
StringBuilder sb = new StringBuilder();
run.ScanSetCollection.Create(run, startFrame, stopFrame, 1, 1);
run.IMSScanSetCollection.Create(run, startScan, stopScan, 1, 1);
UIMF_MSGenerator msgen = new UIMF_MSGenerator();
foreach (var frame in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
sb.Append(frame.PrimaryScanNumber);
sb.Append("\t");
sb.Append(scan.PrimaryScanNumber);
sb.Append("\t");
try
{
msgen.Execute(run.ResultCollection);
sb.Append("Passed");
}
catch (Exception ex)
{
sb.Append("FAILED. \t" + ex.Message);
}
sb.Append(Environment.NewLine);
}
}
Console.WriteLine(sb.ToString());
}
public void uimfPeakDetectionErrorTest1()
{
UIMFRun run = new UIMFRun(uimfTestfile1);
FrameSetCollectionCreator framecreator = new FrameSetCollectionCreator(run, 1, 10, 3, 1);
framecreator.Create();
ScanSetCollectionCreator scanCreator = new ScanSetCollectionCreator(run, 1, 1);
scanCreator.Create();
Task msgen = new UIMF_MSGenerator(10, 5000);
Task peakDet = new DeconToolsPeakDetector();
int scanstop = 599;
int scanstart = 0;
for (int i = scanstart; i < scanstop; i++)
{
run.CurrentFrameSet = run.FrameSetCollection.GetFrameSet(1);
run.CurrentScanSet = run.ScanSetCollection.GetScanSet(i);
msgen.Execute(run.ResultCollection);
try
{
peakDet.Execute(run.ResultCollection);
}
catch (Exception)
{
Console.WriteLine("--------Report of scan " + run.CurrentScanSet.PrimaryScanNumber + "-------------------------");
reportXYValues(run);
}
}
}
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 msGeneratorSummingTest1()
{
Run run = new UIMFRun(uimfFilePath3);
int startFrame = 800;
int stopFrame = 802;
int numFramesSummed = 3;
int numScansSummed = 9;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(run, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, numScansSummed, 1);
scanSetCreator.Create();
ResultCollection results = new ResultCollection(run);
List <timingResult> timingResults = new List <timingResult>();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task scanResultUpdater = new ScanResultUpdater();
Task uimfTicExtractor = new UIMF_TICExtractor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
((HornDeconvolutor)decon).MinPeptideBackgroundRatio = 4;
foreach (FrameSet frameset in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
((UIMFRun)run).CurrentFrameSet = frameset;
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
sw.Reset();
timingResult timeresult = new timingResult();
timeresult.frameNum = frameset.PrimaryFrame;
timeresult.scanNum = scanset.PrimaryScanNumber;
sw.Start();
run.CurrentScanSet = scanset;
msgen.Execute(results);
timeresult.msGenTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
peakDetector.Execute(results);
timeresult.peakDetectorTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
decon.Execute(results);
timeresult.deconTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
scanResultUpdater.Execute(results);
timeresult.resultUpdaterTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
uimfTicExtractor.Execute(results);
timeresult.ticExtractorTime = sw.ElapsedMilliseconds;
sw.Reset();
sw.Start();
driftTimeExtractor.Execute(results);
timeresult.driftTimeExtractorTime = sw.ElapsedMilliseconds;
timingResults.Add(timeresult);
}
}
//reportTimingEachFrameEachScan(timingResults);
Console.WriteLine("Total _isos = " + results.ResultList.Count);
Console.WriteLine("PeptideBR = " + ((HornDeconvolutor)decon).MinPeptideBackgroundRatio);
Console.WriteLine();
Console.WriteLine();
Console.WriteLine();
reportTiming_FrameAggregate(timingResults, startFrame, stopFrame);
Project.Reset();
}
public void outputToText_uimf_test1()
{
if (File.Exists(uimf_text_IsosResultOutputFile1))
{
File.Delete(uimf_text_IsosResultOutputFile1);
}
List <Run> runcoll = new List <Run>();
Run run = new UIMFRun(uimfFile1);
runcoll.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 240, 9, 1, false);
sscc.Create();
FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 801, 3, 1);
fsc.Create();
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task decon = new HornDeconvolutor();
Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor();
Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor();
Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.UIMFIsosResultTextFileExporter(uimf_text_IsosResultOutputFile1, 1000000);
Task flagger = new ResultValidatorTask();
Stopwatch sw;
foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frame;
foreach (ScanSet scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
flagger.Execute(run.ResultCollection);
driftTimeExtractor.Execute(run.ResultCollection);
origIntensExtr.Execute(run.ResultCollection);
sw = new Stopwatch();
sw.Start();
isosExporter.Execute(run.ResultCollection);
sw.Stop();
if (sw.ElapsedMilliseconds > 10)
{
Console.WriteLine("execution time = \t" + sw.ElapsedMilliseconds);
}
}
}
Assert.AreEqual(true, File.Exists(uimf_text_IsosResultOutputFile1));
FileInfo fi = new FileInfo(uimf_text_IsosResultOutputFile1);
Assert.AreEqual(99743, fi.Length);
Console.Write(fi.Length);
}
public void updateScanResultsUIMFFileTest1()
{
UIMFRun run = new UIMFRun(uimfFilepath);
run.FrameSetCollection = new FrameSetCollection();
for (int i = 1200; i < 1203; i++)
{
run.FrameSetCollection.FrameSetList.Add(new FrameSet(i));
}
run.ScanSetCollection = new ScanSetCollection();
for (int i = 200; i < 304; i++)
{
run.ScanSetCollection.ScanSetList.Add(new ScanSet(i));
}
StreamWriter sw;
ResultCollection results = new ResultCollection(run);
Task msgen = new UIMF_MSGenerator();
Task peakDetector = new DeconToolsPeakDetector();
Task rapid = new RapidDeconvolutor();
Task scanResultUpdater = new ScanResultUpdater();
Task peakListExporter = new PeakListTextExporter(run.MSFileType, peakListoutputPath);
foreach (FrameSet frameset in run.FrameSetCollection.FrameSetList)
{
((UIMFRun)run).CurrentFrameSet = frameset;
foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
msgen.Execute(results);
peakDetector.Execute(results);
rapid.Execute(results);
scanResultUpdater.Execute(results);
peakListExporter.Execute(results);
}
}
peakListExporter.Cleanup();
Assert.AreEqual(3, results.ScanResultList.Count);
Assert.AreEqual(1, results.ScanResultList[0].SpectrumType);
Assert.AreEqual(670.990710325132, (decimal)results.ScanResultList[0].BasePeak.XValue);
Assert.AreEqual(183, results.ScanResultList[0].NumIsotopicProfiles);
Assert.AreEqual(7097, results.ScanResultList[0].NumPeaks);
Assert.AreEqual(-1, (decimal)results.ScanResultList[0].ScanTime);
UIMFScanResult uimfScanresult1 = (UIMFScanResult)(results.ScanResultList[0]);
Assert.AreEqual(4.0, uimfScanresult1.FramePressureFront);
Assert.AreEqual(4.016, uimfScanresult1.FramePressureBack);
Assert.AreEqual(1200, uimfScanresult1.Frameset.PrimaryFrame);
Assert.AreEqual(504, results.ResultList.Count);
}
public void test1()
{
Project.Reset();
Project project = Project.getInstance();
UIMFRun run = new UIMFRun(uimfFilepath, 1200, 1202);
project.RunCollection.Add(run);
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 1);
sscc.Create();
FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1);
fscc.Create();
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 rapidDecon = new RapidDeconvolutor();
Task scanResultsUpdater = new ScanResultUpdater();
project.TaskCollection.TaskList.Add(msGen);
project.TaskCollection.TaskList.Add(peakDetector);
project.TaskCollection.TaskList.Add(rapidDecon);
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);
Assert.AreEqual(1, Project.getInstance().RunCollection.Count);
Assert.AreEqual(4, project.TaskCollection.TaskList.Count);
Assert.AreEqual(600, project.RunCollection[0].ScanSetCollection.ScanSetList.Count);
UIMFRun uimfRun = (UIMFRun)(project.RunCollection[0]);
Assert.AreEqual(3, uimfRun.FrameSetCollection.FrameSetList.Count);
StringBuilder sb = new StringBuilder();
foreach (IsosResult result in project.RunCollection[0].ResultCollection.ResultList)
{
Assert.IsInstanceOfType(typeof(UIMFIsosResult), result);
UIMFIsosResult uimfResult = (UIMFIsosResult)result;
sb.Append(uimfResult.FrameSet.PrimaryFrame);
sb.Append("\t");
sb.Append(uimfResult.ScanSet.PrimaryScanNumber);
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.Peaklist[0].XValue);
sb.Append("\t");
sb.Append(uimfResult.IsotopicProfile.GetAbundance());
sb.Append("\t");
//sb.Append(uimfResult.IsotopicProfile.
sb.Append(Environment.NewLine);
}
Console.Write(sb.ToString());
}
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 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);
}
public void compareUIMF_and_IMF_XYDataPoints2()
{
Run uimfRun = new UIMFRun(uimfFilepath2);
ResultCollection uimfResults = new ResultCollection(uimfRun);
Run imfRun = new IMFRun(imf2Frame391);
ResultCollection imfResults = new ResultCollection(imfRun);
FrameSet uimfFrame = new FrameSet(391);
((UIMFRun)uimfRun).CurrentFrameSet = uimfFrame;
Task uimfMSGen = new UIMF_MSGenerator();
Task imfMSGen = new GenericMSGenerator();
ScanSetCollectionCreator scanSetCollectionCreator = new ScanSetCollectionCreator(uimfRun, 9, 1);
scanSetCollectionCreator.Create();
scanSetCollectionCreator = new ScanSetCollectionCreator(imfRun, 9, 1);
scanSetCollectionCreator.Create();
int scanStart = 200;
int scanStop = 400;
StringBuilder sb = new StringBuilder();
for (int n = scanStart; n < scanStop; n++)
{
uimfRun.CurrentScanSet = uimfRun.ScanSetCollection.ScanSetList[n];
imfRun.CurrentScanSet = imfRun.ScanSetCollection.ScanSetList[n + 1];
uimfMSGen.Execute(uimfResults);
imfMSGen.Execute(imfResults);
Assert.AreEqual(imfResults.Run.XYData.Xvalues.Length, uimfResults.Run.XYData.Xvalues.Length);
double[] ppmDiffValues = new double[imfResults.Run.XYData.Xvalues.Length];
for (int i = 0; i < uimfResults.Run.XYData.Xvalues.Length; i++)
{
double imfXval = imfResults.Run.XYData.Xvalues[i];
double uimfXval = uimfResults.Run.XYData.Xvalues[i];
double imfYval = imfResults.Run.XYData.Yvalues[i];
double uimfYval = uimfResults.Run.XYData.Yvalues[i];
Assert.AreEqual(imfYval, uimfYval);
Assert.AreEqual(Math.Round(imfXval, 8), Math.Round(uimfXval, 8));
//double ppmDiff = Math.Abs(imfXval - uimfXval) / imfXval * 1e6;
//ppmDiffValues[i] = ppmDiff;
//Assert.Less(ppmDiff, 0.25);
}
for (int i = 0; i < imfResults.Run.XYData.Xvalues.Length; i++)
{
sb.Append(n);
sb.Append("\t");
sb.Append(imfResults.Run.XYData.Xvalues[i].ToString("0.00000"));
sb.Append("\t");
sb.Append(uimfResults.Run.XYData.Xvalues[i].ToString("0.00000"));
sb.Append("\t");
sb.Append(ppmDiffValues[i].ToString("0.00"));
sb.Append("\t");
sb.Append(imfResults.Run.XYData.Yvalues[i]);
sb.Append("\t");
sb.Append(uimfResults.Run.XYData.Yvalues[i]);
sb.Append("\n");
}
}
Console.Write(sb.ToString());
}
public void UIMF_and_IMF_Nosumming_Test1()
{
Run uimfrun = new UIMFRun(uimfFilepath);
Run imfRun = new IMFRun(imfFrame1200filepath);
int startFrame = 1200;
int stopFrame = 1200;
int numFramesSummed = 1;
int numScansSummed = 1;
FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(uimfrun, startFrame, stopFrame, numFramesSummed, 1);
framesetCreator.Create();
ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(uimfrun, numScansSummed, 1);
scanSetCreator.Create();
ResultCollection uimfResults = new ResultCollection(uimfrun);
//first analyze the UIMF file....
foreach (FrameSet frameset in ((UIMFRun)uimfrun).FrameSetCollection.FrameSetList)
{
System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch();
((UIMFRun)uimfrun).CurrentFrameSet = frameset;
foreach (ScanSet scanset in uimfrun.ScanSetCollection.ScanSetList)
{
uimfrun.CurrentScanSet = scanset;
Task msgen = new UIMF_MSGenerator(0, 2000);
msgen.Execute(uimfResults);
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(uimfResults);
Task rapid = new RapidDeconvolutor();
rapid.Execute(uimfResults);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(uimfResults);
}
}
//next analyze the IMF file for the corresponding frame
scanSetCreator = new ScanSetCollectionCreator(imfRun, 0, 599, numScansSummed, 1);
scanSetCreator.Create();
ResultCollection imfResults = new ResultCollection(imfRun);
foreach (ScanSet scanset in imfRun.ScanSetCollection.ScanSetList)
{
imfRun.CurrentScanSet = scanset;
Task msgen = new GenericMSGenerator(0, 2000);
msgen.Execute(imfResults);
Task peakDetector = new DeconToolsPeakDetector();
peakDetector.Execute(imfResults);
Task rapid = new RapidDeconvolutor();
rapid.Execute(imfResults);
Task scanResultUpdater = new ScanResultUpdater();
scanResultUpdater.Execute(imfResults);
}
Console.WriteLine("imfScanSetCount = " + imfResults.Run.ScanSetCollection.ScanSetList.Count);
Console.WriteLine("UIMFScanSetCount = " + uimfResults.Run.ScanSetCollection.ScanSetList.Count);
Console.WriteLine("IMF scan0 peaks = " + imfResults.ScanResultList.Sum(p => p.NumPeaks));
Console.WriteLine("UIMF scan0 peaks = " + uimfResults.ScanResultList[0].NumPeaks);
Console.WriteLine("imfResultCount = " + imfResults.ResultList.Count);
Console.WriteLine("UIMFResultCount = " + uimfResults.ResultList.Count);
for (int i = 0; i < uimfResults.ResultList.Count; i++)
{
Console.Write(getResultSummary(uimfResults.ResultList[i]));
Console.Write(getResultSummary(imfResults.ResultList[i]));
Console.Write("\n");
}
}
