private static void FillMatrixDontKeep(int groupColInd, int validVals, IMatrixData mdata,
Func <IList <double>, double> func)
{
string[][] groupCol = mdata.GetCategoryRowAt(groupColInd);
string[] groupNames = ArrayUtils.UniqueValuesPreserveOrder(groupCol);
int[][] colInds = PerseusPluginUtils.GetMainColIndices(groupCol, groupNames);
double[,] newExCols = new double[mdata.RowCount, groupNames.Length];
double[,] newQuality = new double[mdata.RowCount, groupNames.Length];
bool[,] newImputed = new bool[mdata.RowCount, groupNames.Length];
for (int i = 0; i < newExCols.GetLength(0); i++)
{
for (int j = 0; j < newExCols.GetLength(1); j++)
{
List <double> vals = new List <double>();
List <bool> imps = new List <bool>();
foreach (int ind in colInds[j])
{
double val = mdata.Values.Get(i, ind);
if (!double.IsNaN(val) && !double.IsInfinity(val))
{
vals.Add(val);
imps.Add(mdata.IsImputed[i, ind]);
}
}
bool imp = false;
double xy = double.NaN;
if (vals.Count >= validVals)
{
xy = func(vals);
imp = ArrayUtils.Or(imps);
}
newExCols[i, j] = xy;
newQuality[i, j] = double.NaN;
newImputed[i, j] = imp;
}
}
mdata.ColumnNames = new List <string>(groupNames);
mdata.ColumnDescriptions = GetEmpty(groupNames);
mdata.Values.Set(newExCols);
mdata.Quality.Set(newQuality);
mdata.IsImputed.Set(newImputed);
mdata.RemoveCategoryRowAt(groupColInd);
for (int i = 0; i < mdata.CategoryRowCount; i++)
{
mdata.SetCategoryRowAt(AverageCategoryRow(mdata.GetCategoryRowAt(i), colInds), i);
}
for (int i = 0; i < mdata.NumericRows.Count; i++)
{
mdata.NumericRows[i] = AverageNumericRow(mdata.NumericRows[i], colInds);
}
}
private static void AddStandardDeviation(int groupColInd, int validVals, IMatrixData mdata, int varInd)
{
string[][] groupCol = mdata.GetCategoryRowAt(groupColInd);
string[] groupNames = ArrayUtils.UniqueValuesPreserveOrder(groupCol);
int[][] colInds = PerseusPluginUtils.GetMainColIndices(groupCol, groupNames);
double[][] newNumCols = new double[groupNames.Length][];
for (int i = 0; i < newNumCols.Length; i++)
{
newNumCols[i] = new double[mdata.RowCount];
}
for (int i = 0; i < mdata.RowCount; i++)
{
for (int j = 0; j < groupNames.Length; j++)
{
List <double> vals = new List <double>();
foreach (int ind in colInds[j])
{
double val = mdata.Values.Get(i, ind);
if (!double.IsNaN(val) && !double.IsInfinity(val))
{
vals.Add(val);
}
}
double xy = double.NaN;
if (vals.Count >= validVals)
{
if (varInd == 0)
{
xy = ArrayUtils.StandardDeviation(vals);
}
else
{
xy = ArrayUtils.StandardDeviation(vals) / Math.Sqrt(vals.Count);
}
}
newNumCols[j][i] = xy;
}
}
for (int i = 0; i < groupNames.Length; i++)
{
string name = "stddev " + groupNames[i];
mdata.AddNumericColumn(name, name, newNumCols[i]);
}
}
private static void FillMatrixKeep(int groupColInd, int validVals, IMatrixData mdata, Func <IList <double>, double> func)
{
string[][] groupCol = mdata.GetCategoryRowAt(groupColInd);
string[] groupNames = ArrayUtils.UniqueValuesPreserveOrder(groupCol);
int[][] colInds = PerseusPluginUtils.GetMainColIndices(groupCol, groupNames);
double[][] newNumCols = new double[groupNames.Length][];
for (int i = 0; i < newNumCols.Length; i++)
{
newNumCols[i] = new double[mdata.RowCount];
}
for (int i = 0; i < mdata.RowCount; i++)
{
for (int j = 0; j < groupNames.Length; j++)
{
List <double> vals = new List <double>();
foreach (int ind in colInds[j])
{
double val = mdata.Values.Get(i, ind);
if (!double.IsNaN(val) && !double.IsInfinity(val))
{
vals.Add(val);
}
}
double xy = double.NaN;
if (vals.Count >= validVals)
{
xy = func(vals);
}
newNumCols[j][i] = xy;
}
}
for (int i = 0; i < groupNames.Length; i++)
{
mdata.AddNumericColumn(groupNames[i], groupNames[i], newNumCols[i]);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
ParameterWithSubParams <int> xp = param.GetParamWithSubParams <int>("Expression column selection");
bool groups = xp.Value == 2;
string[] groupNames = null;
int[][] colIndsGroups = null;
if (groups)
{
int groupRowInd = xp.GetSubParameters().GetParam <int>("Group").Value;
string[][] groupCol = mdata.GetCategoryRowAt(groupRowInd);
groupNames = ArrayUtils.UniqueValuesPreserveOrder(groupCol);
colIndsGroups = PerseusPluginUtils.GetMainColIndices(groupCol, groupNames);
}
int[] useCols = xp.Value == 1
? xp.GetSubParameters().GetParam <int[]>("Columns").Value
: ArrayUtils.ConsecutiveInts(mdata.ColumnCount);
HashSet <int> w = ArrayUtils.ToHashSet(param.GetParam <int[]>("Calculate").Value);
bool[] include = new bool[procs.Length];
double[][] columns = new double[procs.Length][];
double[][][] columnsG = null;
if (groups)
{
columnsG = new double[procs.Length][][];
for (int i = 0; i < columnsG.Length; i++)
{
columnsG[i] = new double[groupNames.Length][];
}
}
for (int i = 0; i < include.Length; i++)
{
include[i] = w.Contains(i);
if (include[i])
{
columns[i] = new double[mdata.RowCount];
if (groups)
{
for (int j = 0; j < groupNames.Length; j++)
{
columnsG[i][j] = new double[mdata.RowCount];
}
}
}
}
for (int i = 0; i < mdata.RowCount; i++)
{
List <double> v = new List <double>();
foreach (int j in useCols)
{
double x = mdata.Values.Get(i, j);
if (!double.IsNaN(x) && !double.IsInfinity(x))
{
v.Add(x);
}
}
for (int j = 0; j < include.Length; j++)
{
if (include[j])
{
columns[j][i] = procs[j].Item2(v);
}
}
if (groups)
{
List <double>[] vg = new List <double> [groupNames.Length];
for (int j = 0; j < colIndsGroups.Length; j++)
{
vg[j] = new List <double>();
for (int k = 0; k < colIndsGroups[j].Length; k++)
{
double x = mdata.Values.Get(i, colIndsGroups[j][k]);
if (!double.IsNaN(x) && !double.IsInfinity(x))
{
vg[j].Add(x);
}
}
}
for (int j = 0; j < include.Length; j++)
{
if (include[j])
{
for (int k = 0; k < groupNames.Length; k++)
{
columnsG[j][k][i] = procs[j].Item2(vg[k]);
}
}
}
}
}
for (int i = 0; i < include.Length; i++)
{
if (include[i])
{
mdata.AddNumericColumn(procs[i].Item1, procs[i].Item3, columns[i]);
if (groups)
{
for (int k = 0; k < groupNames.Length; k++)
{
mdata.AddNumericColumn(procs[i].Item1 + " " + groupNames[k], procs[i].Item3, columnsG[i][k]);
}
}
}
}
}
