/// <summary>
/// Gets specified centre.
/// </summary>
public List <IReadOnlyList <double> > GetCentre(ECentreMode mode, ECandidateMode iMode)
{
List <IReadOnlyList <double> > centre = new List <IReadOnlyList <double> >();
this.GetCentre(mode, iMode, centre);
return(centre);
}
/// <summary>
/// Assigns peaks to clusters
/// A single k-means iteration.
/// </summary>
public static bool Assign(IntensityMatrix vmatrix, IReadOnlyList <Cluster> toChoose, ECandidateMode source, ConfigurationMetric distanceMetric, ProgressReporter prog)
{
// Get the current cluster centres
prog.SetProgress(0, vmatrix.NumRows);
for (int index = 0; index < toChoose.Count; index++)
{
prog.SetProgress(index, toChoose.Count);
toChoose[index].SetCentre(ECentreMode.Average, source);
}
// Clear the previous assignments
Dictionary <Cluster, List <Vector> > previousAssignments = new Dictionary <Cluster, List <Vector> >();
for (int index = 0; index < toChoose.Count; index++)
{
previousAssignments.Add(toChoose[index], toChoose[index].Assignments.Vectors.ToList());
toChoose[index].Assignments.ClearAll();
}
// Detect changes so we know when the algorithm has converged
bool somethingChanged = false;
// Assign peaks to centres
for (int index = 0; index < vmatrix.NumRows; index++)
{
Vector vec = vmatrix.Vectors[index];
prog.SetProgress(index, vmatrix.NumRows);
ClusterScore best = FindClosestCluster(vec.Values, toChoose, distanceMetric);
// Something changed?
if (!previousAssignments[best.Cluster].Contains(vec))
{
somethingChanged = true;
}
// Create new assignment
best.Cluster.Assignments.Add(new Assignment(vec, best.Cluster, best.Score));
}
return(somethingChanged);
}
/// <summary>
/// Calculates cluster centre.
/// </summary>
private void GetCentre(ECentreMode mode, ECandidateMode iMode, List <IReadOnlyList <double> > centres)
{
centres.Clear();
IEnumerable <IReadOnlyList <double> > list;
int listCount;
switch (iMode)
{
case ECandidateMode.Exemplars:
list = this.Exemplars;
listCount = this.Exemplars.Count;
break;
case ECandidateMode.Assignments:
list = this.Assignments.Vectors.Select(z => z.Values);
listCount = this.Assignments.List.Count;
break;
default:
throw new InvalidOperationException("Invalid switch. 9B5EF96B-53F3-4651-AF7D-60B27475C7B5");
}
if (list.IsEmpty()) // check this function
{
return;
}
switch (mode)
{
case ECentreMode.All:
//////////////////
// ALL EXEMPLARS
{
foreach (IReadOnlyList <double> e in list)
{
centres.Add(e);
}
}
break;
case ECentreMode.Average:
////////////////////////////
// AVERGE OF ALL EXEMPLARS
{
int numPoints = list.First().Count;
double[] centre = new double[numPoints];
for (int o = 0; o < numPoints; o++)
{
double total = 0;
foreach (IReadOnlyList <double> v in list)
{
total += v[o];
}
centre[o] = total / listCount;
}
centres.Add(centre);
}
break;
}
}
/// <summary>
/// Calculates cluster centre.
/// </summary>
public void SetCentre(ECentreMode mode, ECandidateMode iMode)
{
this.GetCentre(mode, iMode, this.Centres);
}
