public static IInterpolation GetLinearInterpolationMethod(Peak peak)
{
var xValues = new List <double>();
var yValues = new List <double>();
peak.GetXAndYValuesAsLists(out xValues, out yValues);
IInterpolation interpolation = LinearSpline.Interpolate(xValues, yValues);
return(interpolation);
}
/*
* public static List<int> DetectGaussianPeaks(List<double> peak)
* {
* int peakWindow = 5;
* int halfWindow = (int)Math.Floor(peakWindow / 2.0);
*
* List<double> gaussianPeak = CreateTheoreticalGaussianPeak(peakWindow / 2.0, peakWindow, peakWindow);
*
* Dictionary<int, double> peakIndexToScoreMap = new Dictionary<int, double>();
*
* for (int i = peakWindow - halfWindow - 1; i + peakWindow < peak.Count; i++)
* {
* List<double> currentPeakPoints = peak.GetRange(i, peakWindow);
*
* //double maximumValue = double.NaN;
* //FindPositionOfMaximum(currentPeakPoints, out maximumValue);
*
* double fitScore = CalculatePeakFit(currentPeakPoints, gaussianPeak, 0.05);
* peakIndexToScoreMap.Add(i, fitScore);
* }
*
* // TODO: Use the scores to find peaks??
* int referenceIndex = -99;
* double referenceScore = -99;
* bool movingUp = false;
* List<int> peakIndices = new List<int>();
*
* foreach (KeyValuePair<int, double> kvp in peakIndexToScoreMap)
* {
* Console.WriteLine(kvp.Key + ": " + kvp.Value);
*
* int index = kvp.Key;
* double score = kvp.Value;
*
* if (score > referenceScore)
* {
* movingUp = true;
* }
* else
* {
* if (movingUp)
* {
* peakIndices.Add(referenceIndex);
* }
*
* movingUp = false;
* }
*
* referenceScore = score;
* referenceIndex = index;
* }
*
* Console.WriteLine("*******************************************************************");
*
* Console.Write("Peaks found at: ");
* foreach (int index in peakIndices)
* {
* Console.Write(index + "\t");
* }
* Console.Write("\n");
*
* Console.WriteLine("===================================================================");
*
* return null;
* }
*/
// TODO: Verify this actually works --- Da's code, slightly modified by me
public static Peak KDESmooth(Peak peak, double bandwidth)
{
var xValueList = new List <double>();
var yValueList = new List <double>();
peak.GetXAndYValuesAsLists(out xValueList, out yValueList);
var numPoints = xValueList.Count;
var numBins = numPoints;
var newYValueList = new List <double>();
foreach (var point in xValueList)
{
double sumWInv = 0;
double sumXoW = 0;
double sumX2oW = 0;
double sumYoW = 0;
double sumXYoW = 0;
for (var j = 0; j < numPoints; j++)
{
var x = xValueList[j];
var y = yValueList[j];
var standardized = Math.Abs(x - point) / bandwidth;
double w = 0;
if (standardized < 6)
{
w = 2 * Math.Sqrt(2 * Math.PI) * Math.Exp(-2 * standardized * standardized);
sumWInv += 1 / w;
}
sumXoW += x * w;
sumX2oW += x * x * w;
sumYoW += y * w;
sumXYoW += x * y * w;
}
var intercept = 1 / (sumWInv * sumX2oW - sumXoW * sumXoW) * (sumX2oW * sumYoW - sumXoW * sumXYoW);
var slope = 1 / (sumWInv * sumX2oW - sumXoW * sumXoW) * (sumWInv * sumXYoW - sumXoW * sumYoW);
newYValueList.Add(intercept + slope * point);
}
var newPeak = new Peak(xValueList, newYValueList);
return(newPeak);
}
