/// <summary>
/// Get data in Xvalues and Yvalues where the y value is positive
/// </summary>
/// <returns></returns>
public XYData GetNonZeroXYData()
{
var yDataCount = Yvalues.Length;
var data = new XYData();
var tempXVals = new List <double>();
var tempYVals = new List <double>();
for (var i = 0; i < Xvalues.Length; i++)
{
if (i == yDataCount)
{
break;
}
if (Yvalues[i] > 0)
{
tempXVals.Add(Xvalues[i]);
tempYVals.Add(Yvalues[i]);
}
}
data.Xvalues = tempXVals.ToArray();
data.Yvalues = tempYVals.ToArray();
return(data);
}
public void GetSpectrumTest1()
{
Run run = new DeconTools.Backend.Runs.AgilentDRun(agilentDataset1);
var scanset = new ScanSet(25);
var xydata = new XYData();
xydata = run.GetMassSpectrum(scanset, 0, 6000);
//TestUtilities.DisplayXYValues(xydata);
Console.WriteLine("numPoints = " + xydata.Xvalues.Length);
Assert.AreEqual(156723, xydata.Xvalues.Length);
}
/// Writes three spectra files to disk so that the data can be compared before and after summing
public void GetSummedSpectrumTestWriteToDisk()
{
var testfile =
@"\\proto-5\BionetXfer\People\ScottK\2012_01_12 SPIN QTOF3\GLY06_11JAN12_LYNX_SN7980_TOP4wList_75000_SPIN_2.d";
Run run = new DeconTools.Backend.Runs.AgilentDRun(testfile);
var primaryScan = 10000;
//Scan A
var scansetA = new ScanSet(primaryScan - 1);
var xydata = new XYData();
xydata = run.GetMassSpectrum(scansetA, 0, 6000);
TestUtilities.WriteToFile(xydata, @"P:\ScanA.txt");
TestUtilities.DisplayXYValues(xydata);
Console.WriteLine("numPoints = " + run.XYData.Xvalues.Length);
Assert.AreEqual(258899, run.XYData.Xvalues.Length);
//Scan B
var scansetB = new ScanSet(primaryScan);
xydata = run.GetMassSpectrum(scansetB, 0, 6000);
TestUtilities.WriteToFile(run.XYData, @"P:\ScanB.txt");
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("numPoints = " + run.XYData.Xvalues.Length);
Assert.AreEqual(258899, run.XYData.Xvalues.Length);
//Scan C
var scansetC = new ScanSet(primaryScan + 1);
xydata = run.GetMassSpectrum(scansetC, 0, 6000);
TestUtilities.WriteToFile(run.XYData, @"P:\ScanC.txt");
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("numPoints = " + run.XYData.Xvalues.Length);
Assert.AreEqual(258899, run.XYData.Xvalues.Length);
//Scan ABC summed
var scansetSum = new ScanSet(primaryScan, primaryScan - 1, primaryScan + 1);//primary, min, max
xydata = run.GetMassSpectrum(scansetSum, 0, 6000);
TestUtilities.WriteToFile(run.XYData, @"P:\ScanABC.txt");
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("numPoints = " + run.XYData.Xvalues.Length);
Assert.AreEqual(258899, run.XYData.Xvalues.Length);
}
/// <summary>
/// Filter the data to only keep data with x values between minX and maxX, optionally specifying a startingIndex
/// If startingIndex is greater than or equal to data.Xvalues.Length, returns null
/// </summary>
/// <param name="data"></param>
/// <param name="minX"></param>
/// <param name="maxX"></param>
/// <param name="startingIndex"></param>
/// <returns></returns>
/// <remarks>Assumes the data in Xvalues is sorted</remarks>
public static XYData GetFilteredXYValues(XYData data, double minX, double maxX, int startingIndex = 0)
{
if (data == null || startingIndex >= data.Xvalues.Length)
{
return(null);
}
if (startingIndex < 0)
{
startingIndex = 0;
}
var yDataCount = data.Yvalues.Length;
var xVals = new List <double>();
var yVals = new List <double>();
for (var i = startingIndex; i < data.Xvalues.Length; i++)
{
if (i == yDataCount)
{
break;
}
if (data.Xvalues[i] < minX)
{
continue;
}
if (data.Xvalues[i] > maxX)
{
break;
}
xVals.Add(data.Xvalues[i]);
yVals.Add(data.Yvalues[i]);
}
if (xVals.Count == 0)
{
return(null);
}
var returnedData = new XYData
{
Xvalues = xVals.ToArray(),
Yvalues = yVals.ToArray()
};
return(returnedData);
}
public static XYData ConvertDrawingPoints(System.Drawing.PointF[] points)
{
var xydata = new XYData();
xydata.Xvalues = new double[points.Length];
xydata.Yvalues = new double[points.Length];
for (var i = 0; i < points.Length; i++)
{
xydata.Xvalues[i] = (double)points[i].X;
xydata.Yvalues[i] = (double)points[i].Y;
}
return(xydata);
}
public static XYData GetFilteredXYValues(XYData data, double minX, double maxX, int startingIndex)
{
//this assumes XY pairs with ordered x-values.
if (data == null || startingIndex > data.Xvalues.Length - 1)
{
return(null);
}
var xvals = new List <double>();
var yvals = new List <double>();
for (var i = startingIndex; i < data.Xvalues.Length; i++)
{
if (data.Xvalues[i] >= minX)
{
if (data.Xvalues[i] <= maxX)
{
xvals.Add(data.Xvalues[i]);
yvals.Add(data.Yvalues[i]);
}
else
{
break;
}
}
else
{
}
}
if (xvals.Count == 0)
{
return(null);
}
var returnedData = new XYData();
returnedData.Xvalues = xvals.ToArray();
returnedData.Yvalues = yvals.ToArray();
return(returnedData);
}
///checks the length of a non-summed and summed spectra
public void GetSummedSpectrumTest1()
{
var testfile =
@"\\proto-5\BionetXfer\People\ScottK\2012_01_12 SPIN QTOF3\GLY06_11JAN12_LYNX_SN7980_TOP4wList_75000_SPIN_2.d";
var stopWatch = new Stopwatch();
Run run = new DeconTools.Backend.Runs.AgilentDRun(testfile);
var scanset = new ScanSet(25);
stopWatch.Start();
var xydata = new XYData();
xydata = run.GetMassSpectrum(scanset);
stopWatch.Stop();
var singleSpectraLoadTime = stopWatch.Elapsed;
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("numPoints = " + run.XYData.Xvalues.Length);
Assert.AreEqual(258899, run.XYData.Xvalues.Length);
var scansetSum = new ScanSet(25, 24, 26);
stopWatch.Start();
xydata = run.GetMassSpectrum(scansetSum);
stopWatch.Stop();
var threeScanSumSpectraLoadTime = stopWatch.Elapsed;
TestUtilities.DisplayXYValues(run.XYData);
Console.WriteLine("numPoints = " + run.XYData.Xvalues.Length);
Console.WriteLine("This took " + singleSpectraLoadTime + " seconds to load one scan");
Console.WriteLine("This took " + threeScanSumSpectraLoadTime + " seconds to load and sum three scans");
Assert.AreEqual(258899, run.XYData.Xvalues.Length);
}
public XYData GetNonZeroXYData()
{
var data = new XYData();
var tempxvals = new List <double>();
var tempyvals = new List <double>();
for (var i = 0; i < xvalues.Length; i++)
{
if (yvalues[i] > 0)
{
tempxvals.Add(xvalues[i]);
tempyvals.Add(yvalues[i]);
}
}
data.Xvalues = tempxvals.ToArray();
data.Yvalues = tempyvals.ToArray();
return(data);
}
public XYData TrimData(double xmin, double xmax, double tolerance = 0.1)
{
if (xvalues == null || yvalues == null || xvalues.Length == 0 || yvalues.Length == 0)
{
return(this);
}
var currentMinXValue = xvalues[0];
var currentMaxXValue = xvalues[xvalues.Length - 1];
//if it doesn't need trimming, return it.
if (xmin < currentMinXValue && xmax > currentMaxXValue)
{
return(this);
}
var data = new XYData();
var indexClosestXValMin = MathUtils.GetClosest(xvalues, xmin, tolerance);
var indexClosestXValMax = MathUtils.GetClosest(xvalues, xmax, tolerance);
var numPoints = indexClosestXValMax - indexClosestXValMin + 1;
if (numPoints <= 0)
{
throw new InvalidOperationException("indexClosestXValMin > indexClosestXValMax in XYData.TrimData; xvalues are likely not sorted");
}
data.Xvalues = new double[numPoints];
data.Yvalues = new double[numPoints];
for (var i = indexClosestXValMin; i <= indexClosestXValMax; i++)
{
data.Xvalues[i - indexClosestXValMin] = xvalues[i];
data.Yvalues[i - indexClosestXValMin] = yvalues[i];
}
return(data);
}
/// <summary>
/// Trim the Xvalues and Yvalues properties to only keep the data between xMin and xMax
/// </summary>
/// <param name="xMin"></param>
/// <param name="xMax"></param>
/// <param name="tolerance"></param>
/// <returns></returns>
/// <remarks>Assumes the data in Xvalues is sorted</remarks>
public XYData TrimData(double xMin, double xMax, double tolerance = 0.1)
{
if (Xvalues == null || Yvalues == null || Xvalues.Length == 0 || Yvalues.Length == 0)
{
return(this);
}
var currentMinXValue = Xvalues[0];
var currentMaxXValue = Xvalues[Xvalues.Length - 1];
if (xMin < currentMinXValue && xMax > currentMaxXValue)
{
// Nothing to trim
return(this);
}
var data = new XYData();
var indexClosestXValMin = MathUtils.GetClosest(Xvalues, xMin, tolerance);
var indexClosestXValMax = MathUtils.GetClosest(Xvalues, xMax, tolerance);
var numPoints = indexClosestXValMax - indexClosestXValMin + 1;
if (numPoints <= 0)
{
throw new InvalidOperationException("indexClosestXValMin > indexClosestXValMax in XYData.TrimData; Xvalues is likely not sorted");
}
data.Xvalues = new double[numPoints];
data.Yvalues = new double[numPoints];
for (var i = indexClosestXValMin; i <= indexClosestXValMax; i++)
{
data.Xvalues[i - indexClosestXValMin] = Xvalues[i];
data.Yvalues[i - indexClosestXValMin] = Yvalues[i];
}
return(data);
}
public static XYData GetFilteredXYValues(XYData data, double minX, double maxX)
{
return(GetFilteredXYValues(data, minX, maxX, 0));
}