/// <summary>
/// Determines what needs calculating.
/// </summary>
private void Thread_AddFilterToCalculationList([Const] Core core, [Const] ConfigurationMetric metric, [Const] IntensityMatrix vmatrix, [Const] DistanceMatrix dmatrix, [Const] EClustererStatistics statistics, [Const] Cluster[] realClusters, [Const] ObsFilter obsFilter, [MutableUnsafe] List <ForStat> needsCalculating, [MutableSafe] ProgressParallelHandler progP)
{
progP.SafeIncrement();
IntensityMatrix vmatFiltered;
DistanceMatrix dmatFiltered;
int[] filteredIndices;
if (obsFilter == null)
{
vmatFiltered = vmatrix;
dmatFiltered = dmatrix;
filteredIndices = null;
}
else
{
filteredIndices = vmatrix.Columns.Which(z => obsFilter.Test(z.Observation)).ToArray(); // TODO: Multuple iteration
vmatFiltered = vmatrix.Subset(null, obsFilter, ESubsetFlags.None);
dmatFiltered = null;
}
Dictionary <Cluster, IReadOnlyList <double> > centreVectors = new Dictionary <Cluster, IReadOnlyList <double> >();
foreach (Cluster cluster in realClusters)
{
/////////////////////
// ASSIGNMENT STATS
var centre = cluster.GetCentre(ECentreMode.Average, ECandidateMode.Assignments);
IReadOnlyList <double> centreVector = centre.Count != 0 ? centre[0] : null;
if (filteredIndices != null)
{
centreVector = centreVector.Extract(filteredIndices);
}
centreVectors.Add(cluster, centreVector);
}
foreach (Assignment ass in Assignments)
{
ForStat f = new ForStat();
f.Assignment = ass;
f.ObsFilter = obsFilter;
if (filteredIndices != null)
{
f.AssignmentVector = vmatFiltered.Vectors[ass.Vector.Index];
}
else
{
f.AssignmentVector = ass.Vector;
}
f.ClusterVector = centreVectors[ass.Cluster];
if (statistics.HasFlag(EClustererStatistics.SilhouetteWidth))
{
if (dmatFiltered == null)
{
dmatFiltered = DistanceMatrix.Create(core, vmatrix, metric, ProgressReporter.GetEmpty());
}
}
f.DistanceMatrix = dmatFiltered;
lock (needsCalculating)
{
needsCalculating.Add(f);
}
}
}
public ResultClusterer ExecuteAlgorithm(Core core, int isPreview, bool doNotCluster, ArgsClusterer args, ConfigurationClusterer tag, ProgressReporter prog, out IntensityMatrix vmatrixOut, out DistanceMatrix dmatrixOut)
{
IReadOnlyList <Peak> peaks;
if (isPreview > 0 && isPreview < core.Peaks.Count)
{
List <Peak> p = core.Peaks.ToList();
p.Shuffle();
p = p.GetRange(0, Math.Min(isPreview, p.Count)).ToList();
// Make sure any seed peaks are in the list
foreach (Peak peak in tag.Args.Parameters.OfType <WeakReference <Peak> >().Select(par => (par).GetTargetOrThrow()))
{
p.Insert(0, peak);
p.RemoveAt(p.Count - 1);
}
peaks = p;
}
else
{
peaks = core.Peaks;
}
// FILTER PEAKS
PeakFilter pfilter = args.PeakFilter ?? PeakFilter.Empty;
IntensityMatrix src = args.SourceMatrix;
Filter <Peak> .Results filter = pfilter.Test(peaks);
Cluster insigs;
if (filter.Failed.Count == 0)
{
insigs = null;
}
else
{
insigs = new Cluster("Insig", tag);
insigs.States |= Session.Main.Cluster.EStates.Insignificants;
// We still need the vmatrix for plotting later
IntensityMatrix operational = src.Subset(args.PeakFilter, args.ObsFilter, ESubsetFlags.InvertPeakFilter);
if (args.SplitGroups)
{
operational = operational.SplitGroups();
}
for (int index = 0; index < operational.NumRows; index++)
{
Vector p = new Vector(operational, index);
insigs.Assignments.Add(new Assignment(p, insigs, double.NaN));
}
}
// CREATE VMATRIX AND FILTER OBSERVATIONS
PeakFilter temp = new PeakFilter("filtered in", null, new[] { new PeakFilter.ConditionPeak(Filter.ELogicOperator.And, false, filter.Failed, Filter.EElementOperator.IsNot) });
IntensityMatrix vmatrix = src.Subset(args.PeakFilter, args.ObsFilter, ESubsetFlags.None);
if (args.SplitGroups)
{
vmatrix = vmatrix.SplitGroups();
}
prog.Enter("Creating distance matrix");
DistanceMatrix dmatrix = RequiresDistanceMatrix ? DistanceMatrix.Create(core, vmatrix, args.Distance, prog) : null;
prog.Leave();
IEnumerable <Cluster> clusters;
if (doNotCluster)
{
vmatrixOut = vmatrix;
dmatrixOut = dmatrix;
return(null);
}
// CLUSTER USING VMATRIX OR DMATRIX
prog.Enter("Clustering");
clusters = Cluster(vmatrix, dmatrix, args, tag, prog);
prog.Leave();
vmatrixOut = vmatrix;
dmatrixOut = dmatrix;
List <Cluster> result = new List <Cluster>();
if (insigs != null)
{
result.Add(insigs);
}
result.AddRange(clusters);
return(new ResultClusterer(result));
}
private void UpdateScores()
{
StringBuilder title = new StringBuilder();
IntensityMatrix sourceMatrix = this._selectedCorrection.Provide;
IntensityMatrix source = sourceMatrix.Subset(this._peakFilter, this._obsFilter, ESubsetFlags.None);
double[] plsrResponseMatrix = null;
this._lblPcaSource.Text = this._transposeToShowPeaks ? "Peaks" : "Observations";
this.transposeToShowObservationsToolStripMenuItem.Checked = !this._transposeToShowPeaks;
this.transposeToShowPeaksToolStripMenuItem.Checked = this._transposeToShowPeaks;
this._lblObs.Text = this._obsFilter.ToString();
this._lblPeaks.Text = this._peakFilter.ToString();
this._lblCorrections.Text = this._selectedCorrection.ToString();
this._lblMethod.Text = this._method.ToString().ToUpper();
this.ctlTitleBar1.Text = this._method.ToUiString();
this._lblPlsrSource.Visible = this._mnuPlsrSource.Visible = this._method == EMethod.Plsr;
int corIndex = IVisualisableExtensions.WhereEnabled(this._core.Corrections).IndexOf(this._selectedCorrection);
Column plsrColumn;
this.GetSource(this._regressAgainst, out plsrColumn);
this._lblPlsrSource.Text = plsrColumn.DisplayName;
double[,] valueMatrix = this._transposeToShowPeaks ? new double[source.NumRows, source.NumCols] : new double[source.NumCols, source.NumRows];
for (int row = 0; row < source.NumRows; row++)
{
Vector vector = source.Vectors[row];
int obsIndex = 0;
for (int col = 0; col < source.NumCols; col++)
{
if (this._transposeToShowPeaks)
{
valueMatrix[row, col] = source.Values[row, col];
}
else
{
valueMatrix[col, row] = source.Values[row, col];
}
++obsIndex;
}
}
this._pcaPeaks = source.Rows.Select(z => z.Peak).ToArray();
this._pcaObservations = source.Columns.Select(z => z.Observation).ToArray();
if (this._method == EMethod.Plsr)
{
plsrResponseMatrix = new double[valueMatrix.GetLength(0)];
IEnumerable rows;
if (this._transposeToShowPeaks)
{
rows = this._pcaPeaks;
}
else
{
rows = this._pcaObservations;
}
IEnumerator en = rows.GetEnumerator();
Factoriser fac = new Factoriser();
for (int n = 0; n < plsrResponseMatrix.Length; n++)
{
en.MoveNext();
object row = plsrColumn.GetRow((Visualisable)en.Current);
plsrResponseMatrix[n] = fac.Factor(row);
}
}
try
{
switch (this._method)
{
case EMethod.Pca:
FrmWait.Show(this, "PCA", "Updating scores", () =>
Arr.Instance.Pca(valueMatrix, out this._scores, out this._loadings));
break;
case EMethod.Plsr:
FrmWait.Show(this, "PLSR", "Updating scores", () =>
Arr.Instance.Plsr(valueMatrix, plsrResponseMatrix, out this._scores, out this._loadings));
break;
default:
throw new SwitchException(this._method);
}
this._errorMessage = null;
}
catch (Exception ex)
{
if (ex.Message.Contains("there is no package called 'pls'"))
{
this._errorMessage = "The 'pls' library for R is not installed on your system. Please install that library to use the PLS feature.";
FrmMsgBox.ShowError(this, this._errorMessage);
}
else
{
this._errorMessage = ex.Message;
}
this._scores = null;
this._loadings = null;
}
this.UpdatePlot();
}
