public void SetOptions(clsPeakProcessorParameters parameters)
{
_parameters = parameters;
// the minimum intensity is not set till the actual data is available in DiscoverPeaks
_peakProcessor.SetOptions(_parameters.SignalToNoiseThreshold, 0, _parameters.ThresholdedData,
_parameters.PeakFitType);
}
public clsPeakProcessor()
{
_peakProcessor = new PeakProcessor();
_parameters = new clsPeakProcessorParameters();
_peakProcessor.SetOptions(_parameters.SignalToNoiseThreshold, 0, false,
_parameters.PeakFitType);
ProfileType = enmProfileType.PROFILE;
}
public clsPeakProcessorParameters Clone()
{
var newParams = new clsPeakProcessorParameters
{
SignalToNoiseThreshold = this.SignalToNoiseThreshold,
PeakBackgroundRatio = this.PeakBackgroundRatio,
PeakFitType = this.PeakFitType,
};
newParams.ThresholdedData = ThresholdedData;
return(newParams);
}
public void fitterOnRapidDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
bool isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 0.5;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetectorV2(detectorParams);
peakDetector.Execute(results);
Task decon = new RapidDeconvolutor();
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
// theorXYData.Display();
AreaFitter areafitter = new AreaFitter();
double fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0207350903681061m, (decimal)fitval);
}
public void WriteFile(string file_name, DeconToolsV2.Results.clsTransformResults results,
Peaks.clsPeakProcessorParameters peak_parameters,
HornTransform.clsHornTransformParameters transform_parameters)
{
using (var file = new StreamWriter(new FileStream(file_name, FileMode.Create, FileAccess.Write)))
{
// Write out descriptors. Some information is unavailable for now.
// i.e. what is the start position of the peaks data block and
// the transform data block. Fill in place holders for now.
// Once the data is actually written out, we can return to the stream and
// write it.
float version_num = 1;
file.Write("<Version>" + version_num + "</version>");
WritePeakParameters(file, peak_parameters);
WriteTransformParameters(file, transform_parameters);
WritePeaks(file, results);
}
}
private void WritePeakParameters(TextWriter file, Peaks.clsPeakProcessorParameters peak_parameters)
{
// In a wierd pseudo xml/raw file format, we will write out tags in text
// but keep all the data in binary.
// We will not use a specialized SAX parser because our vocabulary on the XML file
// will not be increasing to a point where we actually want to go through the effort
// of incorporating an XML parser with our binary data.
if (peak_parameters != null)
{
file.Write("<PeakParameters>");
file.Write("<MinBackgroundRatio>" + peak_parameters.PeakBackgroundRatio + "</MinBackgroundRatio>");
file.Write("<PeakFitType>");
switch (peak_parameters.PeakFitType)
{
case Peaks.PEAK_FIT_TYPE.APEX:
file.Write("APEX");
break;
case Peaks.PEAK_FIT_TYPE.QUADRATIC:
file.Write("QUADRATIC");
break;
case Peaks.PEAK_FIT_TYPE.LORENTZIAN:
file.Write("LORENTZIAN");
break;
default:
break;
}
file.Write("</PeakFitType>");
file.Write("<S2NThreshold>" + peak_parameters.SignalToNoiseThreshold + "</S2NThreshold>");
file.Write("</PeakParameters>");
}
}
public void ReadFile(string file_name, DeconToolsV2.Results.clsTransformResults results,
Peaks.clsPeakProcessorParameters peak_parameters,
HornTransform.clsHornTransformParameters transform_parameters)
{
}