/// <summary>
/// Each row should contain the correction factors in numbers that range from 1 to 100
/// The value for the monoisotopic should be entered as -1
/// </summary>
/// <param name="correctionTable"></param>
/// <returns></returns>
public static PatternTools.CSML.Matrix GenerateInverseCorrectionMatrix(List <List <double> > correctionTable)
{
//We now need to normalize the -1 so the sum adds to 100
foreach (List <double> l in correctionTable)
{
double sum = l.Sum() + 1;
int index = l.FindIndex(a => a == -1);
l[index] = 100 - sum;
}
//Generate Correction Matrix
//Prepare the coeficient matrix
double[,] coeficientMatrix = new double[correctionTable.Count, correctionTable.Count];
int counter = -1;
for (int i = 0; i < correctionTable.Count; i++)
{
counter++;
for (int j = 0; j < 5; j++)
{
try
{
coeficientMatrix[j - 2 + counter, i] = correctionTable[i][j];
}
catch (Exception e)
{
Console.WriteLine(e.Message + "\n i = {0}, j = {1}", i, j);
}
}
}
//Mcorrected = c^-1 * signal
PatternTools.CSML.Matrix c = new PatternTools.CSML.Matrix(coeficientMatrix);
PatternTools.CSML.Matrix cInverse = c.Inverse();
cInverse *= 100;
return(cInverse);
}
public double Evaluate(double[] pointA)
{
if (!alreadyEvaluated)
{
//Wi = -0.5 * inverseCovarianceMatrix;
//wi = inverseCovarianceMatrix * meanVector;
//w0Part1 = -0.5 * meanVector.Transpose() * inverseCovarianceMatrix * meanVector;
//w0Part2 = -(0.5 * Math.Log(covarianceMatrix.Determinant().Re, Math.E));
//w0 = w0Part1.Determinant().Re + w0Part2;
}
if (!alreadyEvaluated)
{
Wi = -0.5 * inverseCovarianceMatrix;
wi = inverseCovarianceMatrix * meanVector;
Matrix wi0Part1 = -0.5 * meanVector.Transpose() * inverseCovarianceMatrix * meanVector;
double wi0Part2 = -(0.5 * Math.Log(covarianceMatrix.Determinant().Re, Math.E));
double wi0Part3 = Math.Log(Prior);
wi0 = wi0Part1.Determinant().Re + wi0Part2 + wi0Part3;
}
alreadyEvaluated = true;
PatternTools.CSML.Matrix point = new PatternTools.CSML.Matrix(pointA);
//Term 1
PatternTools.CSML.Matrix t1 = point.Transpose() * Wi * point;
//Term 2
PatternTools.CSML.Matrix t2 = wi.Transpose() * point;
double gx = t1.Determinant().Re + t2.Determinant().Re + wi0;
return(gx);
}
public static List <int> Verify2(List <sparseMatrixRow> rows)
{
//We group rows by class, and then for each class we check if there is a dim that holds the same value for all
//We then eliminate these dims from all rows of all classes and report the eliminated dims
List <int> unstableDims = new List <int>();
var rowsGroupedByClasses = from r in rows
group r by r.Lable into g
select new { label = g.Key, rows = g };
Dictionary <int, List <sparseMatrixRow> > lableRowDict = rowsGroupedByClasses.ToDictionary(a => a.label, a => a.rows.ToList());
foreach (KeyValuePair <int, List <sparseMatrixRow> > kvp in lableRowDict)
{
SparseMatrix matrix = new SparseMatrix(rows);
Matrix meanVector = new PatternTools.CSML.Matrix(matrix.GetMeanVector().ToArray());
double[,] covMatrix = PatternTools.SparseMatrix.CovarianceMatrix(matrix.ToDoubleArrayMatrix(), matrix.GetMeanVector().ToArray());
unstableDims.AddRange(checkStability(covMatrix));
}
unstableDims = unstableDims.Distinct().ToList();
unstableDims.Sort((a, b) => b.CompareTo(a));
//Now we eliminate these dims from the sparse matrix
foreach (int d in unstableDims)
{
int index = rows[0].Dims.FindIndex(a => a == d);
foreach (sparseMatrixRow r in rows)
{
r.Values.RemoveAt(index);
}
rows[0].Dims.RemoveAt(index);
}
return(unstableDims);
}
/// <summary>
/// The method returns unstable dims that were elmininated from the sparse matrix and should be eliminated from future input vectors used for classification
/// </summary>
/// <param name="useRobustStatistics"></param>
/// <param name="regularizationFactor"></param>
/// <param name="saveMatrices"></param>
/// <returns></returns>
public List <int> ComputeMatrices(bool useRobustStatistics, bool saveMatrices)
{
//Get the mean vector
double[,] covMatrix;
if (useRobustStatistics)
{
meanVector = new PatternTools.CSML.Matrix(matrix.GetMedianVector().ToArray());
covMatrix = PatternTools.SparseMatrix.CovarianceMatrix(matrix.ToDoubleArrayMatrix(), matrix.GetMedianVector().ToArray());
}
else
{
meanVector = new PatternTools.CSML.Matrix(matrix.GetMeanVector().ToArray());
covMatrix = PatternTools.SparseMatrix.CovarianceMatrix(matrix.ToDoubleArrayMatrix(), matrix.GetMeanVector().ToArray());
}
unstableDims = checkStability(covMatrix);
if (unstableDims.Count > 0)
{
unstableDims.Sort((a, b) => b.CompareTo(a));
double perturbationCounter = 0;
if (unstableDims.Count > 0)
{
Console.WriteLine("**Warning:: I am adding a perturbation to the convariance matrix for stability reasons!!!");
foreach (int d in unstableDims)
{
foreach (sparseMatrixRow r in matrix.theMatrixInRows)
{
perturbationCounter += 0.0005;
r.Values[d] += perturbationCounter;
if (perturbationCounter > 0.05)
{
perturbationCounter = 0;
}
}
}
covMatrix = PatternTools.SparseMatrix.CovarianceMatrix(matrix.ToDoubleArrayMatrix(), matrix.GetMedianVector().ToArray());
}
if (useRobustStatistics)
{
covMatrix = PatternTools.SparseMatrix.CovarianceMatrix(matrix.ToDoubleArrayMatrix(), matrix.GetMedianVector().ToArray());
}
else
{
covMatrix = PatternTools.SparseMatrix.CovarianceMatrix(matrix.ToDoubleArrayMatrix(), matrix.GetMeanVector().ToArray());
}
}
covarianceMatrix = new CSML.Matrix(covMatrix);
inverseCovarianceMatrix = covarianceMatrix.Inverse();
if (saveMatrices)
{
matrix.saveMatrix(matrix.theMatrixInRows[0].Lable + "FullMatrix.txt");
StreamWriter sr = new StreamWriter(matrix.theMatrixInRows[0].Lable + "_covMatrix.txt");
int top = (int)Math.Sqrt(covMatrix.Length);
for (int i = 0; i < top; i++)
{
for (int j = 0; j < top; j++)
{
sr.Write(covMatrix[i, j] + "\t");
}
sr.WriteLine("");
}
sr.Close();
Console.WriteLine("Saving variance matrix and its inverse to disk.");
}
return(unstableDims);
}
public static List <double> CorrectForSignal(PatternTools.CSML.Matrix cInverse, double[] signal)
{
//Mcorrected = c^-1 * signal
PatternTools.CSML.Matrix correctedS = cInverse * new PatternTools.CSML.Matrix(signal);
return(correctedS.GetRow(0));
}