public IVector FindDistances(IReadOnlyList <IVector> data, DistanceMetric distance)
{
Debug.Assert(IsValid && data.All(v => v.IsValid));
if (distance == DistanceMetric.Cosine)
{
var norm = DotProduct(this);
var dataNorm = data.Select(d => d.DotProduct(d)).ToList();
var ret = new float[data.Count];
for (var i = 0; i < data.Count; i++)
{
ret[i] = Convert.ToSingle(1d - DotProduct(data[i]) / Math.Sqrt(norm * dataNorm[i]));
}
return(_cuda.CreateVector(data.Count, i => ret[i]));
}
if (distance == DistanceMetric.Euclidean || distance == DistanceMetric.Manhattan)
{
var ret = _cuda.CalculateDistances(new[] { this }, data, distance);
return(ret.ReshapeAsVector());
}
else
{
var distanceFunc = _GetDistanceFunc(distance);
var ret = new float[data.Count];
for (var i = 0; i < data.Count; i++)
{
ret[i] = distanceFunc(data[i]);
}
return(_cuda.CreateVector(data.Count, i => ret[i]));
}
}
/// <summary>
/// Initializes a new instance of the FastMarching2dTest class.
/// </summary>
public GeodesicDistance()
: base("Geodesic Distance", "GeoDist",
"Computes the geodesic distance field for a set of sources.",
"SpatialSlur", "Field")
{
Metric = DistanceMetric.Euclidean;
}
public void TestRestrictiveBoxMethod(string path, DistanceMetric dist, bool useBoxMethod)
{
var features = ReadFeatures(path);
var clusterer = new UMCAverageLinkageClusterer <UMCLight, UMCClusterLight>
{
ShouldTestClustersWithinTolerance = useBoxMethod,
Parameters =
{
CentroidRepresentation = ClusterCentroidRepresentation.Mean,
DistanceFunction = DistanceFactory <UMCLight> .CreateDistanceFunction(dist),
OnlyClusterSameChargeStates = true,
Tolerances =
{
Mass = 10,
DriftTime = .3,
Net = .03
}
}
};
var clusters = clusterer.Cluster(features);
var i = 0;
clusters.ForEach(x => x.Id = i++);
WriteClusters(clusters);
}
public void TestDistancesEuclidean(string path, DistanceMetric dist)
{
var func = DistanceFactory <UMCClusterLight> .CreateDistanceFunction(DistanceMetric.Euclidean);
var oldClusters = ReadClusters(path);
var clusters = CreateSingletonClustersFromClusteredFeatures(new List <UMCClusterLight> {
oldClusters[1]
});
Console.WriteLine("Distance, Mass, NET, DT, Mass, Net, DT");
for (var i = 0; i < clusters.Count; i++)
{
for (var j = i + 1; j < clusters.Count; j++)
{
var distance = func(clusters[i], clusters[j]);
Console.WriteLine("{0},{1},{2},{3},{4},{5},{6}",
distance,
clusters[i].MassMonoisotopic,
clusters[i].Net,
clusters[i].DriftTime,
clusters[j].MassMonoisotopic,
clusters[j].Net,
clusters[j].DriftTime);
}
}
}
public KMeans(int k, IReadOnlyList <IVector> data, DistanceMetric distanceMetric = DistanceMetric.Euclidean, int?randomSeed = null)
{
_k = k;
_distanceMetric = distanceMetric;
_cluster = new ClusterData();
_data = data;
// use kmeans++ to find best initial positions
// https://normaldeviate.wordpress.com/2012/09/30/the-remarkable-k-means/
var rand = randomSeed.HasValue ? new Random(randomSeed.Value) : new Random();
var data2 = data.ToList();
// pick the first at random
var firstIndex = rand.Next(0, data2.Count);
_cluster.Add(data2[firstIndex]);
data2.RemoveAt(firstIndex);
// create a categorical distribution for each subsequent pick
for (var i = 1; i < _k && data2.Count > 0; i++)
{
var probabilityList = new List <double>();
foreach (var item in data2)
{
using (var distance = _cluster.CalculateDistance(item, _distanceMetric)) {
var minIndex = distance.MinimumIndex();
probabilityList.Add(distance.AsIndexable()[minIndex]);
}
}
var distribution = new Categorical(probabilityList.ToArray());
var nextIndex = distribution.Sample();
_cluster.Add(data2[nextIndex]);
data2.RemoveAt(nextIndex);
}
}
/// <summary>
/// Calculates the distance between two matrices
/// </summary>
/// <param name="distance"></param>
/// <param name="matrix1"></param>
/// <param name="matrix2"></param>
/// <returns></returns>
public static IVector Calculate(this DistanceMetric distance, IMatrix matrix1, IMatrix matrix2)
{
switch (distance)
{
case DistanceMetric.Euclidean:
using (var diff = matrix1.Subtract(matrix2))
{
using var diffSquared = diff.PointwiseMultiply(diff);
using var rowSums = diffSquared.RowSums();
return(rowSums.Sqrt());
}
case DistanceMetric.SquaredEuclidean:
using (var diff = matrix1.Subtract(matrix2))
{
using var diffSquared = diff.PointwiseMultiply(diff);
return(diffSquared.RowSums());
}
case DistanceMetric.Cosine:
case DistanceMetric.Manhattan:
case DistanceMetric.MeanSquared:
default:
throw new NotImplementedException();
}
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="lap">Linear algebra provider</param>
/// <param name="data">List of vectors to compare</param>
/// <param name="distanceMetric">Distance metric for comparison</param>
public VectorDistanceHelper(ILinearAlgebraProvider lap, IReadOnlyList <IVector> data,
DistanceMetric distanceMetric = DistanceMetric.Euclidean)
{
_lap = lap;
Metric = distanceMetric;
_data = data;
}
/// <summary>
/// K Means uses coordinate descent and a distance metric between randomly selected centroids to cluster the data
/// </summary>
/// <param name="data">The list of vectors to cluster</param>
/// <param name="lap">Linear algebra provider</param>
/// <param name="k">The number of clusters to find</param>
/// <param name="maxIterations">The maximum number of iterations</param>
/// <param name="distanceMetric">Distance metric to use to compare centroids</param>
/// <returns>A list of k clusters</returns>
public static IReadOnlyList <IReadOnlyList <IVector> > KMeans(this IReadOnlyList <IVector> data,
ILinearAlgebraProvider lap, int k, int maxIterations = 1000,
DistanceMetric distanceMetric = DistanceMetric.Euclidean)
{
using var clusterer = new KMeans(lap, k, data, distanceMetric);
clusterer.ClusterUntilConverged(maxIterations);
return(clusterer.Clusters);
}
public IVector FindDistances(IReadOnlyList <IVector> data, DistanceMetric distance)
{
var distanceFunc = _GetDistanceFunc(distance);
var ret = new float[data.Count];
Parallel.ForEach(data, (vec, ps, ind) => ret[ind] = distanceFunc(vec));
return(new CpuVector(DenseVector.Create(data.Count, i => ret[i])));
}
public static void Print(Position first, Position second, double distance, DistanceMetric metric)
{
Console.WriteLine("--------------------------------");
Console.WriteLine("Distance Metric: " + metric.ToString());
Console.WriteLine("Point 1: (" + first.X + "," + first.Y + ")");
Console.WriteLine("Point 2: (" + second.X + "," + second.Y + ")");
Console.WriteLine("Distance: " + distance);
Console.WriteLine("--------------------------------");
}
/// <summary>
/// Computes the distance between singleton clusters.
/// </summary>
/// <param name="cluster1">The cluster1.</param>
/// <param name="cluster2">The cluster2.</param>
/// <param name="distanceMetric">The distance metric.</param>
/// <returns>Distance between singleton clusters</returns>
public static double ComputeDistance(Cluster cluster1, Cluster cluster2, DistanceMetric distanceMetric)
{
double distance = 0;
// check if clusters are singleton
if (cluster1.QuantityOfDataPoints == 1 && cluster2.QuantityOfDataPoints == 1)
distance = Distance.GetDistance(cluster1.DataPoints[0], cluster2.DataPoints[0], distanceMetric);
return distance;
}
public KNNClassifier(ILinearAlgebraProvider lap, KNearestNeighbours model, int k, DistanceMetric distanceMetric = DistanceMetric.Euclidean)
{
_k = k;
_lap = lap;
_model = model;
_distanceMetric = distanceMetric;
for (int i = 0, len = model.Instance.Length; i < len; i++)
{
_instance.Add(lap.Create(model.Instance[i].Data));
}
}
/// <summary>
/// Gets the distance.
/// </summary>
/// <param name="x">The x.</param>
/// <param name="y">The y.</param>
/// <param name="distanceMetric">The distance metric.</param>
/// <returns>Datapoints distance</returns>
/// <exception cref="ArgumentException">Неравное колличество точек.</exception>
public static double GetDistance(DataPoint x, DataPoint y, DistanceMetric distanceMetric)
{
double distance = 0;
double diff;
// checks for dimensions match
if (x.Count != y.Count)
{
throw new ArgumentException("Неравное колличество точек.");
}
switch (distanceMetric)
{
case DistanceMetric.EuclidianDistance: // calculates by using Euclidian Distance
for (var i = 0; i < x.Count; i++)
{
diff = x[i] - y[i];
distance += diff * diff;
}
distance = Math.Sqrt(distance);
break;
case DistanceMetric.SquareEuclidianDistance: // calculates by using Square of Euclidian Distance
for (var i = 0; i < x.Count; i++)
{
diff = x[i] - y[i];
distance += diff * diff;
}
break;
case DistanceMetric.ManhattanDistance: // calculates by using Manhattan Distance
for (var i = 0; i < x.Count; i++)
{
diff = x[i] - y[i];
distance += Math.Abs(diff);
}
break;
case DistanceMetric.ChebyshevDistance: // calculates by using Chebyshev Distance
for (var i = 0; i < x.Count; i++)
{
diff = Math.Abs(x[i] - y[i]);
distance = distance > diff ? distance : diff;
}
break;
}
return(distance);
}
public static IEnumerable <Place> CalculateDendrogram(List <Place> places, DistanceMetric metric)
{
AGNESDendrogram agnesDendrogram = new AGNESDendrogram();
List <Place> toRet = agnesDendrogram.FitTrnaform(places, metric);
// Generate visual representation of the dendrogram
//Application.EnableVisualStyles();
//Application.SetCompatibleTextRenderingDefault(false);
//Application.Run(new DendrogramForm(agnesDendrogram.Dendrogram));
return(toRet);
}
/// <summary>
/// Gets the sum of squared error.
/// </summary>
/// <param name="distanceMetric">The distance metric.</param>
/// <returns>Sum of squared error of cluster</returns>
public double GetSumOfSquaredError(DistanceMetric distanceMetric)
{
double squaredErrorSum = 0;
//distance of each element to clustercenter
foreach (var pattern in DataPoints)
{
var distToCenter = Distance.GetDistance(Centroid, pattern, distanceMetric);
squaredErrorSum += Math.Pow(distToCenter, 2);
}
return(squaredErrorSum);
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="dm">distance metric</param>
public BKTree(DistanceMetric dm)
{
if (dm == DistanceMetric.Hamming)
{
metric = DistanceMetric.Hamming;
DistanceMethod = HammingDistance;
}
else
{
metric = DistanceMetric.Levenshtein;
DistanceMethod = LevenshteinDistance;
}
}
/// <summary>
/// Initializes a new instance of the <see cref="Agnes"/> class.
/// </summary>
/// <param name="clusters">The clusters.</param>
/// <param name="distanceMetric">The distance metric.</param>
/// <param name="strategy">The strategy.</param>
public Agnes(ClusterSet clusters, DistanceMetric distanceMetric, MergeStrategy strategy)
{
_clusters = clusters;
_initialNumberOfClusters = clusters.Count;
_distanceMetric = distanceMetric;
_strategy = strategy;
// creating initial dissimilarity matrix from _clusters
BuildDissimilarityMatrix();
_chValue = new List <double>();
_chIndex = new List <int>();
}
private void CheckMaxCapacity()
{
if (this.ChildrenCount > this.Tree.MaxChildren)
{
DistanceMetric <T> distanceMetric = this.Tree.distanceMetric;
Tuple <T, T> promotions = this.Tree.splitPolicy.Promote(this.Children.Keys, distanceMetric);
Tuple <ISet <T>, ISet <T> > partitions = this.Tree.splitPolicy.Partition(promotions, this.Children.Keys, distanceMetric);
Node newNode0 = this.GetNewNode(promotions.Item1, partitions.Item1);
Node newNode1 = this.GetNewNode(promotions.Item2, partitions.Item2);
throw new SplitNodeReplacement(newNode0, newNode1);
}
}
public static (Position, Position, double) Calculate(List <Position> points, DistanceMetric metric)
{
Position closestA = null, closestB = null;
double minDistance = double.MaxValue;
for (int i = 0; i < points.Count - 1; i++)
{
for (int j = i + 1; j < points.Count; j++)
{
Position point1 = points[i];
Position point2 = points[j];
double distance;
switch (metric)
{
case DistanceMetric.EuclideanDistance:
distance = DistanceMetricFunctions.EuclideanDistance(point1, point2);
break;
case DistanceMetric.MeanAbsoluteError:
distance = DistanceMetricFunctions.MeanAbsoluteError(point1, point2);
break;
case DistanceMetric.MeanSquaredError:
distance = DistanceMetricFunctions.MeanSquaredError(point1, point2);
break;
case DistanceMetric.SumOfAbsoluteDistance:
distance = DistanceMetricFunctions.SumOfAbsoluteDistance(point1, point2);
break;
case DistanceMetric.SumOfSquaredDifference:
distance = DistanceMetricFunctions.SumOfSquaredDifference(point1, point2);
break;
default:
throw new NotSupportedException("Metric type not supported");
}
if (distance < minDistance)
{
closestA = point1;
closestB = point2;
minDistance = distance;
}
}
}
return(closestA, closestB, minDistance);
}
/// <summary>
/// Constructor (Add to subtree)
/// </summary>
/// <param name="w">word</param>
/// <param name="dist">distance</param>
/// <param name="dm">distance metric</param>
public BKTree(string w, int dist, DistanceMetric dm)
{
w = w.ToLower();
metric = dm;
if (dm == DistanceMetric.Hamming)
{
DistanceMethod = HammingDistance;
}
else
{
DistanceMethod = LevenshteinDistance;
}
word = w;
distParent = dist;
}
public IVector CalculateDistance(IVector vector, DistanceMetric distanceMetric)
{
if (_curr == null)
{
_curr = _centroid.Select(c => c.Current).ToArray();
}
if (distanceMetric == DistanceMetric.Cosine)
{
return(vector.CosineDistance(_curr, ref _clusterNorm));
}
else
{
return(vector.FindDistances(_curr, distanceMetric));
}
}
/// <summary>
/// Handles the Click event of the calculateClusterCountButton control.
/// </summary>
/// <param name="sender">The source of the event.</param>
/// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
/// <exception cref="Clusterizer.CustomException">Не было выбрано ни одного показателя. - Ощибка при выборе показателей</exception>
private void calculateClusterCountButton_Click(object sender, EventArgs e)
{
// gets selected parameters of clustering
distanceMetric = (DistanceMetric)distanceSelectComboBox.SelectedIndex;
strategy = (MergeStrategy)strategySelectComboBox.SelectedIndex;
normalizeMethod = (NormalizeMethod)normalizeMethodSelectComboBox.SelectedIndex;
// gets selected datapoints
var isChosen = new bool[Tools.NumericDataHeadings.Length];
bool isAllFalse = true;
int ind = 0;
for (int i = 0; i < pointsSelectTreeView.Nodes.Count; i++)
{
for (int j = 0; j < pointsSelectTreeView.Nodes[i].Nodes.Count; j++)
{
isChosen[ind] = pointsSelectTreeView.Nodes[i].Nodes[j].Checked;
if (isAllFalse)
{
isAllFalse = !isChosen[ind];
}
ind++;
}
}
// check if no datapoint is selected
if (isAllFalse)
{
throw new CustomException("Не было выбрано ни одного показателя.", "Ощибка при выборе показателей");
}
// gets cluster set from data
var clusters = Tools.Data.GetClusterSet(Tools.isChosen);
clusters.Normalize(normalizeMethod);
// executes clustering for determining recomended count of clusters
Agnes agnes = new Agnes(clusters,
distanceMetric, strategy);
agnes.ExecuteClustering(2, true);
// gets recomended count of clusters
countOfClusters = agnes.GetRecommendedCountOfClusters();
clusterCountTextBox.Text = $"{countOfClusters}";
}
public void TestDistanceDistributions(string path, DistanceMetric dist)
{
var features = ReadFeatures(path);
var clusterer = new UMCAverageLinkageClusterer <UMCLight, UMCClusterLight>
{
ShouldTestClustersWithinTolerance = false,
Parameters =
{
CentroidRepresentation = ClusterCentroidRepresentation.Mean,
DistanceFunction = DistanceFactory <UMCLight> .CreateDistanceFunction(dist),
OnlyClusterSameChargeStates = true,
Tolerances =
{
Mass = 10,
DriftTime = .3,
Net = .03
}
}
};
var clusters = clusterer.Cluster(features);
var distances = new List <double>();
foreach (var cluster in clusters)
{
var centroid = new UMCLight();
centroid.MassMonoisotopicAligned = cluster.MassMonoisotopic;
centroid.Net = cluster.Net;
centroid.DriftTime = cluster.DriftTime;
var func = clusterer.Parameters.DistanceFunction;
foreach (var feature in cluster.Features)
{
var distance = func(feature, centroid);
distances.Add(distance);
}
distances.Sort();
var sum = 0;
foreach (var distance in distances)
{
sum++;
Console.WriteLine("{0},{1}", distance, sum);
}
}
}
/*
* To use BKTree:
* 1. Create a class dervied from BKTreeNode
* 2. Add a member variable of your data to be sorted / retrieved
* 3. Override the calculateDistance method to calculate the distance metric
* between two nodes for the data to be sorted / retrieved.
* 4. Instantiate a BKTree with the type name of the class created in (1).
*/
static void Main(string[] args)
{
/*
* NOTE: More comprehensive examples of BK-Tree methods in unit tests
*/
// Exercise static distance metric methods -- just because
Console.WriteLine(
DistanceMetric.calculateHammingDistance(
new byte[] { 0xEF, 0x35, 0x20 },
new byte[] { 0xAD, 0x13, 0x87 }));
Console.WriteLine(
DistanceMetric.calculateLeeDistance(
new int[] { 196, 105, 48 },
new int[] { 201, 12, 51 }));
Console.WriteLine(
DistanceMetric.calculateLevenshteinDistance(
"kitten",
"sitting"));
// Create BKTree with derived node class from top of file
BKTree <ExampleNodeRecord> tree = new BKTree <ExampleNodeRecord>();
// Add some nodes
tree.add(new ExampleNodeRecord(1, new int[] { 100, 200, 300 }));
tree.add(new ExampleNodeRecord(2, new int[] { 110, 210, 310 }));
tree.add(new ExampleNodeRecord(3, new int[] { 120, 220, 320 }));
tree.add(new ExampleNodeRecord(4, new int[] { 130, 230, 330 }));
tree.add(new ExampleNodeRecord(5, new int[] { 140, 240, 340 }));
// Get best node from our tree with best distance
Dictionary <ExampleNodeRecord, Int32> results =
tree.findBestNodeWithDistance(
new ExampleNodeRecord(new int[] { 103, 215, 303 }));
// Get best nodes below threshold
results = tree.query(
new ExampleNodeRecord(new int[] { 103, 215, 303 }),
10); // arbitrary threshold
// Dictionaries don't print well; so invent your own handy print routine
}
/// <summary>
/// Handles the Click event of the doClusteringButton control.
/// </summary>
/// <param name="sender">The source of the event.</param>
/// <param name="e">The <see cref="EventArgs"/> instance containing the event data.</param>
/// <exception cref="Clusterizer.CustomException">
/// Введите правилное количество кластеров. - Ошибка при вводе числа кластеров
/// or
/// Не было выбрано не одного показателя. - Ощибка при выборе показателей
/// </exception>
private void doClusteringButton_Click(object sender, EventArgs e)
{
// Gets selected parameters of clustering
distanceMetric = (DistanceMetric)distanceSelectComboBox.SelectedIndex;
strategy = (MergeStrategy)strategySelectComboBox.SelectedIndex;
normalizeMethod = (NormalizeMethod)normalizeMethodSelectComboBox.SelectedIndex;
// checks for correct cluster number
if (int.TryParse(clusterCountTextBox.Text, out var tmp) && tmp > 0 && tmp < Tools.Data.Rows.Count)
{
countOfClusters = tmp;
}
else
{
throw new CustomException("Введите правилное количество кластеров.", "Ошибка при вводе числа кластеров");
}
// gets selected datapoints
var isChosen = new bool[Tools.NumericDataHeadings.Length];
bool isAllFalse = true;
int ind = 0;
for (int i = 0; i < pointsSelectTreeView.Nodes.Count; i++)
{
for (int j = 0; j < pointsSelectTreeView.Nodes[i].Nodes.Count; j++)
{
isChosen[ind] = pointsSelectTreeView.Nodes[i].Nodes[j].Checked;
if (isAllFalse)
{
isAllFalse = !isChosen[ind];
}
ind++;
}
}
// check if no datapoint is selected
if (isAllFalse)
{
throw new CustomException("Не было выбрано не одного показателя.", "Ощибка при выборе показателей");
}
Tools.isChosen = isChosen;
isParametersSelected = true;
Close();
}
public List <Place> FitTrnaform(List <Place> places, DistanceMetric metric)
{
List <Dendrogram> tempDendrograms = places.Select(place => new LeafNode(place)).ToList().ConvertAll(leaf => (Dendrogram)leaf);
while (tempDendrograms.Count > 1)
{
double minDist = double.MaxValue;
Dendrogram minDend1 = null, minDend2 = null;
foreach (Dendrogram dend1 in tempDendrograms)
{
foreach (Dendrogram dend2 in tempDendrograms)
{
if (dend1 == dend2)
{
continue;
}
double tempDist = dend1.DistanceTo(dend2, metric);
if (tempDist < minDist)
{
minDist = tempDist;
minDend1 = dend1;
minDend2 = dend2;
}
}
}
if (minDend1 is LeafNode)
{
this.placesByRemoteness.Add(minDend1.Places[0]);
}
if (minDend2 is LeafNode)
{
this.placesByRemoteness.Add(minDend2.Places[0]);
}
Dendrogram combinedDend = new InternalNode(minDend1, minDend2, minDist);
tempDendrograms.Remove(minDend1);
tempDendrograms.Remove(minDend2);
tempDendrograms.Add(combinedDend);
}
this.Dendrogram = tempDendrograms[0];
this.placesByRemoteness.Reverse();
return(this.placesByRemoteness);
}
public IVector FindDistances(IReadOnlyList <IVector> data, DistanceMetric distance)
{
Debug.Assert(IsValid && data.All(v => v.IsValid));
if (distance == DistanceMetric.Cosine)
{
var norm = DotProduct(this);
var dataNorm = data.Select(d => d.DotProduct(d)).ToList();
var ret = new float[data.Count];
for (var i = 0; i < data.Count; i++)
{
ret[i] = Convert.ToSingle(1d - DotProduct(data[i]) / Math.Sqrt(norm * dataNorm[i]));
}
return(new GpuVector(_cuda, data.Count, i => ret[i]));
}
else if (distance == DistanceMetric.Euclidean)
{
var ptrArray = data.Cast <GpuVector>().Select(d => d._data.DevicePointer).ToArray();
var ret = _cuda.MultiEuclideanDistance(_data, ptrArray, _size);
using (var matrix = new GpuMatrix(_cuda, _size, data.Count, ret)) {
using (var temp = matrix.ColumnSums())
return(temp.Sqrt());
}
}
else if (distance == DistanceMetric.Manhattan)
{
var ptrArray = data.Cast <GpuVector>().Select(d => d._data.DevicePointer).ToArray();
var ret = _cuda.MultiManhattanDistance(_data, ptrArray, _size);
using (var matrix = new GpuMatrix(_cuda, _size, data.Count, ret)) {
return(matrix.ColumnSums());
}
}
else
{
var distanceFunc = _GetDistanceFunc(distance);
var ret = new float[data.Count];
for (var i = 0; i < data.Count; i++)
{
ret[i] = distanceFunc(data[i]);
}
return(new GpuVector(_cuda, data.Count, i => ret[i]));
}
}
/// <summary>
/// Calculates the distance between two vectors
/// </summary>
/// <param name="distance"></param>
/// <param name="vector1"></param>
/// <param name="vector2"></param>
public static float Calculate(this DistanceMetric distance, IVector vector1, IVector vector2)
{
switch (distance)
{
case DistanceMetric.Cosine:
return(vector1.CosineDistance(vector2));
case DistanceMetric.Euclidean:
return(vector1.EuclideanDistance(vector2));
case DistanceMetric.Manhattan:
return(vector1.ManhattanDistance(vector2));
case DistanceMetric.SquaredEuclidean:
return(vector1.SquaredEuclidean(vector2));
default:
return(vector1.MeanSquaredDistance(vector2));
}
}
/// <summary>
/// Initializes a new instance of the <see cref="MTree{T}"/> class.
/// </summary>
/// <param name="minChildren">The minimum number of children nodes for a node.</param>
/// <param name="maxChildren">The maximum number of children nodes for a node.</param>
/// <param name="distanceMetric">
/// The distance metric to be used to calculate distances between data points.
///
/// The distance metric must satisfy the following properties:
/// <list type="bullet">
/// <item>
/// <description><c>d(a,b) = d(b,a)</c> for every <c>a</c> and <c>b</c> points (symmetry)</description>
/// </item>
/// <item>
/// <description><c>d(a,a) = 0</c> and <c>d(a,b) > 0</c> for every <c>a != b</c> points (non-negativity)</description>
/// </item>
/// <item>
/// <description><c>d(a,b) <= d(a,c) + d(c,b)</c> for every <c>a</c>, <c>b</c> and <c>c</c> points (triangle inequality)</description>
/// </item>
/// </list>
/// </param>
/// <param name="splitPolicy">The split policy to use. It consist of a partition and a promotion policy. <see cref="SplitPolicy{DATA}"/></param>
/// <exception cref="ArgumentOutOfRangeException">
/// <c>minChildren</c> is less than 1
/// or
/// <c>maxChildren</c> is less than <c>minChildren</c>
/// </exception>
/// <exception cref="ArgumentNullException">
/// <c>distanceMetric</c> is missing
/// or
/// <c>splitPolicy</c> is missing
/// </exception>
public MTree(
Int32 minChildren,
Int32 maxChildren,
DistanceMetric <T> distanceMetric,
ISplitPolicy <T> splitPolicy)
{
if (minChildren < 1)
{
throw new ArgumentOutOfRangeException(nameof(minChildren), CoreMessages.MinimumNumberOfChildNodesIsLessThan1);
}
if (minChildren >= maxChildren)
{
throw new ArgumentOutOfRangeException(nameof(maxChildren), CoreMessages.MaximumNumberOfChildNodesIsEqualToMinimum);
}
this.MinChildren = minChildren;
this.MaxChildren = maxChildren;
this.distanceMetric = distanceMetric ?? throw new ArgumentNullException(nameof(distanceMetric));
this.splitPolicy = splitPolicy ?? throw new ArgumentNullException(nameof(splitPolicy));
this.NumberOfDataItems = 0;
}
public IMatrix CalculateDistances(IReadOnlyList <IVector> vectors,
IReadOnlyList <IVector> compareTo, DistanceMetric distanceMetric)
{
var rows = compareTo.Count;
var columns = vectors.Count;
Debug.Assert(vectors[0].Count == compareTo[0].Count);
var ret = new float[rows * columns];
Parallel.ForEach(vectors,
(column1, _, i) =>
{
Parallel.ForEach(compareTo,
(column2, __, j) =>
{
ret[i * rows + j] = column1.FindDistance(column2, distanceMetric);
});
});
return(new CpuMatrix(DenseMatrix.Build.Dense(rows, columns, ret)));
}
public static DistanceFunc GetDistanceFunction(DistanceMetric distanceMetric)
{
DistanceFunc ret;
switch(distanceMetric)
{
case DistanceMetric.EuclidianSq:
ret = new DistanceFunc(EuclidianSq);
break;
case DistanceMetric.Euclidian:
ret = new DistanceFunc(Euclidian);
break;
case DistanceMetric.Manhattan:
ret = new DistanceFunc(Manhattan);
break;
case DistanceMetric.Chebyshev:
ret = new DistanceFunc(Chebyshev);
break;
default:
ret = new DistanceFunc(EuclidianSq);
break;
}
return ret;
}
public void TestDistanceDistributions(string path, DistanceMetric dist)
{
var features = ReadFeatures(path);
var clusterer = new UMCAverageLinkageClusterer<UMCLight, UMCClusterLight>
{
ShouldTestClustersWithinTolerance = false,
Parameters =
{
CentroidRepresentation = ClusterCentroidRepresentation.Mean,
DistanceFunction = DistanceFactory<UMCLight>.CreateDistanceFunction(dist),
OnlyClusterSameChargeStates = true,
Tolerances =
{
Mass = 10,
DriftTime = .3,
Net = .03
}
}
};
var clusters = clusterer.Cluster(features);
var distances = new List<double>();
foreach (var cluster in clusters)
{
var centroid = new UMCLight();
centroid.MassMonoisotopicAligned = cluster.MassMonoisotopic;
centroid.Net = cluster.Net;
centroid.DriftTime = cluster.DriftTime;
var func = clusterer.Parameters.DistanceFunction;
foreach (var feature in cluster.Features)
{
var distance = func(feature, centroid);
distances.Add(distance);
}
distances.Sort();
var sum = 0;
foreach (var distance in distances)
{
sum++;
Console.WriteLine("{0},{1}", distance, sum);
}
}
}
public void TestDistancesEuclidean(string path, DistanceMetric dist)
{
var func = DistanceFactory<UMCClusterLight>.CreateDistanceFunction(DistanceMetric.Euclidean);
var oldClusters = ReadClusters(path);
var clusters = CreateSingletonClustersFromClusteredFeatures(new List<UMCClusterLight> {oldClusters[1]});
Console.WriteLine("Distance, Mass, NET, DT, Mass, Net, DT");
for (var i = 0; i < clusters.Count; i++)
{
for (var j = i + 1; j < clusters.Count; j++)
{
var distance = func(clusters[i], clusters[j]);
Console.WriteLine("{0},{1},{2},{3},{4},{5},{6}",
distance,
clusters[i].MassMonoisotopic,
clusters[i].Net,
clusters[i].DriftTime,
clusters[j].MassMonoisotopic,
clusters[j].Net,
clusters[j].DriftTime);
}
}
}
public void TestRestrictiveBoxMethod(string path, DistanceMetric dist, bool useBoxMethod)
{
var features = ReadFeatures(path);
var clusterer = new UMCAverageLinkageClusterer<UMCLight, UMCClusterLight>
{
ShouldTestClustersWithinTolerance = useBoxMethod,
Parameters =
{
CentroidRepresentation = ClusterCentroidRepresentation.Mean,
DistanceFunction = DistanceFactory<UMCLight>.CreateDistanceFunction(dist),
OnlyClusterSameChargeStates = true,
Tolerances =
{
Mass = 10,
DriftTime = .3,
Net = .03
}
}
};
var clusters = clusterer.Cluster(features);
var i = 0;
clusters.ForEach(x => x.Id = i++);
WriteClusters(clusters);
}
