private List <IsoEnvelop> Deconvolute_BU(IMsScan scan)
{
var spectrum = new MzSpectrumXY(scan.Centroids.Select(p => p.Mz).ToArray(), scan.Centroids.Select(p => p.Intensity).ToArray(), false);
List <IsoEnvelop> isoEnvelops = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, Parameters.DeconvolutionParameter);
return(isoEnvelops);
}
public static void Test_ChargeDeconv()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/2076.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
Stopwatch stopwatch0 = new Stopwatch();
stopwatch0.Start();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
stopwatch0.Stop();
Stopwatch stopwatch_iso = new Stopwatch();
stopwatch_iso.Start();
var iso = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, deconvolutionParameter);
stopwatch_iso.Stop();
Stopwatch stopwatch1 = new Stopwatch();
stopwatch1.Start();
var x = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
stopwatch1.Stop();
//Stopwatch stopwatch2 = new Stopwatch();
//stopwatch2.Start();
var stopwatch2 = Stopwatch.StartNew();
var x2 = ChargeDecon.QuickFindChargesForScan(spectrum, deconvolutionParameter);
stopwatch2.Stop();
// Stopwatch stopwatch3 = new Stopwatch();
// stopwatch3.Start();
// int indUp = spectrum.ExtractIndicesByY().First();
// double mass_up = spectrum.XArray[indUp];
// var highest = ChargeDecon.FindChargesForPeak(spectrum, indUp, new DeconvolutionParameter());
// stopwatch3.Stop();
// var Parameters = Program.AddParametersFromFile("");
// List<double> masses = highest.Select(p => p.Value.Mz).ToList();
// string dynamicTargets;
// string dynamicMaxITs;
// Stopwatch stopwatch4 = new Stopwatch();
// stopwatch4.Start();
// var test = BoxCarScan.BuildDynamicBoxString(Parameters, masses, out dynamicTargets, out dynamicMaxITs);
// stopwatch4.Stop();
// Assert.That(test == "[(400.0,522.8),(524.8,542.2),(544.2,563.1),(565.1,585.6),(587.6,610.0),(612.0,636.5),(638.5,665.4),(667.4,697.1),(699.1,732.0),(734.0,770.5),(772.5,813.3),(815.3,861.1),(863.1,915.0),(917.0,976.0),(978.0,1045.7),(1047.7,1126.1),(1128.1,1200.0)]");
}
public static void BU_dynamicBoxCarRange()
{
string FilepathMZML = Path.Combine(TestContext.CurrentContext.TestDirectory, @"Data/20170802_QEp1_FlMe_SA_BOX0_SILAC_BoxCar_SLICED.mzML");
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList();
var spectrum = new MzSpectrumXY(scans.First().MassSpectrum.XArray, scans.First().MassSpectrum.YArray, true);
Parameters parameters = Program.AddParametersFromFile("");
var isos = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, parameters.DeconvolutionParameter);
List <List <Tuple <double, double, double> > > Boxes = new List <List <Tuple <double, double, double> > >();
BoxCarScan.GenerateDynamicBoxes_BU(isos, parameters, Boxes);
Assert.That(Boxes.Count == 2);
}
//This is not really a test, but could help to kown the deconvolution speed.
//[Test]
public static void Test_ChargeDeconvFile()
{
//string FilepathMZML = "E:\\MassData\\20190912_TD_yeast_DBC\\20190912_Yeast7_DBC_FullScanFirst_T3_TopDown.mzML";
string FilepathMZML = "E:\\MassData\\20191009_TD_F4\\20191009_J1-F4_DDA4.mzML";
MsDataFile file = Mzml.LoadAllStaticData(FilepathMZML, null);
var scans = file.GetAllScansList().Where(p => p.MsnOrder == 1).ToArray();
DeconvolutionParameter deconvolutionParameter = new DeconvolutionParameter();
//Stopwatch stopwatch0 = new Stopwatch();
//stopwatch0.Start();
//var spectrum = new MzSpectrumXY(scans[2167].MassSpectrum.XArray, scans[2167].MassSpectrum.YArray, true);
//stopwatch0.Stop();
//Stopwatch stopwatch_iso = new Stopwatch();
//stopwatch_iso.Start();
//var iso = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, deconvolutionParameter);
//stopwatch_iso.Stop();
//Stopwatch stopwatch1 = new Stopwatch();
//stopwatch1.Start();
//var x = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
//stopwatch1.Stop();
////Stopwatch stopwatch2 = new Stopwatch();
////stopwatch2.Start();
//var stopwatch2 = Stopwatch.StartNew();
//var x2 = ChargeDecon.QuickFindChargesForScan(spectrum, deconvolutionParameter);
//stopwatch2.Stop();
Tuple <int, double, long, long, long, long>[] watches = new Tuple <int, double, long, long, long, long> [scans.Length];
for (int i = 0; i < scans.Length; i++)
{
Stopwatch stopwatch0 = new Stopwatch();
stopwatch0.Start();
var spectrum = new MzSpectrumXY(scans[i].MassSpectrum.XArray, scans[i].MassSpectrum.YArray, true);
stopwatch0.Stop();
Stopwatch stopwatch_iso = new Stopwatch();
stopwatch_iso.Start();
var iso = IsoDecon.MsDeconv_Deconvolute(spectrum, spectrum.Range, deconvolutionParameter);
var test1 = iso.ToList();
stopwatch_iso.Stop();
Stopwatch stopwatch1 = new Stopwatch();
stopwatch1.Start();
//var x = ChargeDecon.FindChargesForScan(spectrum, deconvolutionParameter);
stopwatch1.Stop();
//Stopwatch stopwatch2 = new Stopwatch();
//stopwatch2.Start();
var stopwatch2 = Stopwatch.StartNew();
var isoEnvelops = new List <IsoEnvelop>();
var x2 = ChargeDecon.ChargeDeconIsoForScan(spectrum, deconvolutionParameter, out isoEnvelops);
stopwatch2.Stop();
watches[i] = new Tuple <int, double, long, long, long, long>(scans[i].OneBasedScanNumber, scans[i].RetentionTime, stopwatch0.ElapsedMilliseconds, stopwatch_iso.ElapsedMilliseconds, stopwatch1.ElapsedMilliseconds, stopwatch2.ElapsedMilliseconds);
}
var writtenFile = Path.Combine(Path.GetDirectoryName(FilepathMZML), "watches.mytsv");
using (StreamWriter output = new StreamWriter(writtenFile))
{
output.WriteLine("ScanNum\tRT\tConstruct\tIsoTime\tChargeDeconTime\tQuickChargeDeconTime");
foreach (var theEvaluation in watches.OrderBy(p => p.Item1))
{
output.WriteLine(theEvaluation.Item1.ToString() + "\t" + theEvaluation.Item2 + "\t" + theEvaluation.Item3.ToString() + "\t" + theEvaluation.Item4.ToString() + "\t" + theEvaluation.Item5 + "\t" + +theEvaluation.Item6);
}
}
}