public void criticalErrorInPeakDetectorTest1()
{
UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2);
FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 425, 432, 3, 1);
ffcc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 1, 500, 9, 1);
sscc.Create();
MSGeneratorFactory factory = new MSGeneratorFactory();
Task msgen = factory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 4;
peakDet.SigNoiseThreshold = 3;
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
}
}
}
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 checkIntegrityOfUIMF_RawDataTest1()
{
UIMFRun run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath2);
FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 696, 696, 3, 1);
ffcc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 350, 500, 9, 1);
sscc.Create();
MSGeneratorFactory factory = new MSGeneratorFactory();
Task msgen = factory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
StringBuilder sb = new StringBuilder();
sb.Append("frame\tscan\tmaxIntens\tnumZeros\n");
foreach (var frame in run.FrameSetCollection.FrameSetList)
{
run.CurrentFrameSet = frame;
foreach (var scan in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
List <int> indices = getIndicesOf0MZValues(run.XYData.Xvalues);
double maxY = run.XYData.GetMaxY();
if (indices.Count > -1)
{
sb.Append(frame.PrimaryFrame);
sb.Append("\t");
sb.Append(scan.PrimaryScanNumber);
sb.Append("\t");
sb.Append(maxY);
sb.Append("\t");
sb.Append(indices.Count);
sb.Append("\n");
}
}
}
Console.WriteLine(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 basicCreatorTest2()
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator creator = new FrameSetCollectionCreator(run, 1200, 1300, 3, 1);
creator.Create();
UIMFRun uimfRun = (UIMFRun)run;
Assert.AreEqual(101, uimfRun.FrameSetCollection.FrameSetList.Count);
Assert.AreEqual(1200, uimfRun.FrameSetCollection.FrameSetList[0].PrimaryFrame);
Assert.AreEqual(new int[] { 1199, 1200, 1201 }, uimfRun.FrameSetCollection.FrameSetList[0].IndexValues.ToArray());
}
public void basicCreatorTest1()
{
Run run = new UIMFRun(uimfFilepath);
FrameSetCollectionCreator creator = new FrameSetCollectionCreator(run, 3, 1);
creator.Create();
UIMFRun uimfRun = (UIMFRun)run;
Assert.AreEqual(1950, uimfRun.FrameSetCollection.FrameSetList.Count);
Assert.AreEqual(3, uimfRun.FrameSetCollection.FrameSetList[2].PrimaryFrame);
Assert.AreEqual(new int[] { 2, 3, 4 }, uimfRun.FrameSetCollection.FrameSetList[2].IndexValues.ToArray());
Assert.AreEqual(new int[] { 1, 2 }, uimfRun.FrameSetCollection.FrameSetList[0].IndexValues.ToArray());
Assert.AreEqual(new int[] { 1949, 1950 }, uimfRun.FrameSetCollection.FrameSetList.Last().IndexValues.ToArray());
}
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 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);
}
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 void examineFPGAUIMFTest1()
{
Run run = new DeconTools.Backend.Runs.UIMFRun(fpgaUIMFFilePath);
FrameSetCollectionCreator ffcc = new FrameSetCollectionCreator(run, 1, 1, 1, 1);
ffcc.Create();
ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 285, 285, 9, 1);
sscc.Create();
MSGeneratorFactory factory = new MSGeneratorFactory();
Task msgen = factory.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector();
peakDet.PeakBackgroundRatio = 6;
peakDet.SigNoiseThreshold = 3;
HornDeconvolutor decon = new HornDeconvolutor();
decon.MinPeptideBackgroundRatio = 5;
foreach (var scanset in run.ScanSetCollection.ScanSetList)
{
run.CurrentScanSet = scanset;
((UIMFRun)run).CurrentFrameSet = new FrameSet(1);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
decon.Execute(run.ResultCollection);
}
}
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 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 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()
{
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 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");
}
}
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);
}
