public IClusterer <T, U> Create(GenericClusteringAlgorithmType clusterType)
{
IClusterer <T, U> clusterer = null;
switch (clusterType)
{
case GenericClusteringAlgorithmType.AverageLinkage:
clusterer = new UMCAverageLinkageClusterer <T, U>();
break;
case GenericClusteringAlgorithmType.Centroid:
clusterer = new UMCCentroidClusterer <T, U>();
break;
case GenericClusteringAlgorithmType.SingleLinkage:
clusterer = new UMCSingleLinkageClusterer <T, U>();
break;
case GenericClusteringAlgorithmType.Prims:
clusterer = new UMCPrimsClustering <T, U>();
break;
case GenericClusteringAlgorithmType.BinarySearchTree:
clusterer = new Clustering.MsFeatureTreeClusterer <T, U>();
break;
default:
throw new ArgumentOutOfRangeException(string.Format("Cannot create generic {0} clusterer.", clusterType));
}
return(clusterer);
}
public static IClusterer<UMCLight, UMCClusterLight> Create(LcmsFeatureClusteringAlgorithmType clusterType)
{
IClusterer<UMCLight, UMCClusterLight> clusterer = null;
switch (clusterType)
{
case LcmsFeatureClusteringAlgorithmType.AverageLinkage:
clusterer = new UMCAverageLinkageClusterer<UMCLight, UMCClusterLight>();
break;
case LcmsFeatureClusteringAlgorithmType.Centroid:
clusterer = new UMCCentroidClusterer<UMCLight, UMCClusterLight>();
break;
case LcmsFeatureClusteringAlgorithmType.SingleLinkage:
clusterer = new UMCSingleLinkageClusterer<UMCLight, UMCClusterLight>();
break;
case LcmsFeatureClusteringAlgorithmType.Prims:
clusterer = new UMCPrimsClustering<UMCLight, UMCClusterLight>();
break;
}
return clusterer;
}
//[TestCase(@"ClusterData\clusterData-merged-nodelin.txt")]
public void TestPrims(string path)
{
Console.WriteLine("Test: " + path);
var features = GetClusterData(Path.Combine(TestPathSingleton.TestDirectory, path));
Assert.IsNotEmpty(features);
var cluster = new UMCClusterLight();
cluster.Id = features[0].Id;
features.ForEach(x => cluster.AddChildFeature(x));
var maps = new Dictionary <int, UMCClusterLight>();
var prims = new UMCPrimsClustering <UMCLight, UMCClusterLight>();
prims.Parameters = new FeatureClusterParameters <UMCLight>();
prims.Parameters.CentroidRepresentation = ClusterCentroidRepresentation.Mean;
prims.Parameters.Tolerances = new FeatureTolerances();
var clusters = prims.Cluster(features);
var counts = new Dictionary <int, Dictionary <int, int> >();
var cid = 0;
foreach (var clusterx in clusters)
{
clusterx.Id = cid++;
foreach (var feature in clusterx.Features)
{
if (!counts.ContainsKey(feature.GroupId))
{
counts.Add(feature.GroupId, new Dictionary <int, int>());
}
if (!counts[feature.GroupId].ContainsKey(feature.Id))
{
counts[feature.GroupId].Add(feature.Id, 0);
}
if (feature.Id == 51 || feature.Id == 37)
{
Console.WriteLine("Found it {0} cluster {1}", feature.Id, clusterx.Id);
}
counts[feature.GroupId][feature.Id]++;
Console.WriteLine("Found {0}", clusterx.Id);
if (counts[feature.GroupId][feature.Id] > 1)
{
Console.WriteLine("Duplicate!!!! cluster {0} feature {1}", clusterx.Id, feature.Id);
}
}
}
Console.WriteLine("Group\tFeature\tCount");
foreach (var group in counts.Keys)
{
foreach (var id in counts[group].Keys)
{
Console.WriteLine("{0}\t{1}\t{2}", group, id, counts[group][id]);
}
}
Console.WriteLine("Clusters = {0}", clusters.Count);
}
//[TestCase(@"ClusterData\clusterData-single-1500.txt", 4)]
//[TestCase(@"ClusterData\clusterData-single-1500-two.txt", 4)]
public void TestPrimsWeighted(string path, double sigma)
{
sigma = 1;
Console.WriteLine();
Console.WriteLine("Tests: " + path);
Console.WriteLine("Sigma Cutoff: {0}", sigma);
var features = GetClusterData(Path.Combine(TestPathSingleton.TestDirectory, path));
Assert.IsNotEmpty(features);
var cluster = new UMCClusterLight();
cluster.Id = features[0].Id;
features.ForEach(x => cluster.AddChildFeature(x));
var maps = new Dictionary <int, UMCClusterLight>();
var prims = new UMCPrimsClustering <UMCLight, UMCClusterLight>(sigma);
prims.Parameters = new FeatureClusterParameters <UMCLight>();
prims.Parameters.CentroidRepresentation = ClusterCentroidRepresentation.Mean;
prims.Parameters.Tolerances = new FeatureTolerances();
prims.Parameters.OnlyClusterSameChargeStates = false;
prims.Parameters.Tolerances.DriftTime = .3;
prims.Parameters.Tolerances.Mass = 15;
prims.Parameters.Tolerances.Net = .02;
prims.DumpLinearRelationship = false;
var distance = new WeightedEuclideanDistance <UMCLight>();
prims.Parameters.DistanceFunction = distance.EuclideanDistance;
var clusters = prims.Cluster(features);
Console.WriteLine();
Console.WriteLine("Clusters = {0}", clusters.Count);
var id = 1;
foreach (var testCluster in clusters)
{
testCluster.CalculateStatistics(ClusterCentroidRepresentation.Mean);
var distances = new List <double>();
// Show a sampling of 15 results
var threshold = (int)(testCluster.Features.Count / (double)15);
if (threshold < 1)
{
threshold = 1;
}
testCluster.Id = id++;
var featureID = 0;
foreach (var feature in testCluster.Features)
{
featureID++;
if (featureID % threshold == 0)
{
Console.WriteLine("{0},{1},{2},{3}",
feature.Net,
feature.MassMonoisotopicAligned,
feature.DriftTime,
testCluster.Id);
}
var newDistance = distance.EuclideanDistance(feature, testCluster);
distances.Add(newDistance);
}
//Console.WriteLine();
//Console.WriteLine("Distances");
//distances.ForEach(x => Console.WriteLine(x));
//Console.WriteLine();
}
Console.WriteLine();
Console.WriteLine("Test Done:");
Console.WriteLine();
}
