Changeset 15130 for stable/HeuristicLab.ExtLibs/HeuristicLab.Igraph/0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers

Timestamp:

07/06/17 10:09:53 (8 years ago)

Author:

gkronber

Message:

#2651: merged r14234,r14244:14247,r14250,r14256,r14257,r14272 from trunk to stable

Location:

stable/HeuristicLab.ExtLibs/HeuristicLab.Igraph

Files:

• . (copied) (copied from trunk/sources/HeuristicLab.ExtLibs/HeuristicLab.Igraph)
• 0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Datatypes.cs (copied) (copied from trunk/sources/HeuristicLab.ExtLibs/HeuristicLab.Igraph/0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Datatypes.cs)
• 0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Graph.cs (modified) (2 diffs)
• 0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Matrix.cs (modified) (3 diffs)
• 0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Vector.cs (copied) (copied from trunk/sources/HeuristicLab.ExtLibs/HeuristicLab.Igraph/0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Vector.cs)

stable/HeuristicLab.ExtLibs/HeuristicLab.Igraph/0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Graph.cs

@@ -1 @@
-using System;
+#region License Information
+/* HeuristicLab
+ * Copyright (C) 2002-2016 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ *
+ * This file is part of HeuristicLab.
+ *
+ * HeuristicLab is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * HeuristicLab is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
+ */
+#endregion
+
+using System;
 using System.Collections.Generic;
 
-namespace HeuristicLab.igraph.Wrappers {
-  public class Graph : IDisposable {
+namespace HeuristicLab.IGraph.Wrappers {
+  public sealed class Graph : IDisposable {
     private igraph_t graph;
+    internal igraph_t NativeInstance { get { return graph; } }
+
     public int Vertices { get { return graph.n; } }
+    public bool IsDirected { get { return graph.directed; } }
 
     public Graph() : this(0) { }
@@ -39 +63 @@
     }
 
-    public double[,] LayoutWithFruchtermanReingold() {
-      return LayoutWithFruchtermanReingold(500, Math.Sqrt(Vertices));
+    public double Density() {
+      double density;
+      DllImporter.igraph_density(graph, out density, false);
+      return density;
     }
-    public double[,] LayoutWithFruchtermanReingold(int niter, double startTemp) {
-      using (var coords = new Matrix(graph.n, 2)) {
-        DllImporter.igraph_layout_fruchterman_reingold(graph, coords.NativeInstance, false, niter, startTemp, igraph_layout_grid_t.IGRAPH_LAYOUT_AUTOGRID, null, null, null, null, null);
-        return coords.ToMatrix();
+
+    public Vector PageRank(double damping = 0.85, Vector weights = null) {
+      var vec = new Vector(Vertices);
+      var all = new igraph_vs_t();
+      DllImporter.igraph_vs_all(ref all);
+      try {
+        double eigenv = 0;
+        DllImporter.igraph_pagerank(graph, igraph_pagerank_algo_t.IGRAPH_PAGERANK_ALGO_PRPACK, vec.NativeInstance, out eigenv, all, IsDirected, damping, weights != null ? weights.NativeInstance : null);
+      } finally {
+        DllImporter.igraph_vs_destroy(ref all);
       }
+      return vec;
+    }
+
+    public Matrix LayoutWithFruchtermanReingold(Matrix initialCoords = null) {
+      return LayoutWithFruchtermanReingold(500, Math.Sqrt(Vertices), initialCoords);
+    }
+    public Matrix LayoutWithFruchtermanReingold(int niter, double startTemp, Matrix initialCoords = null) {
+      if (initialCoords != null && (initialCoords.Rows != Vertices || initialCoords.Columns != 2))
+        throw new ArgumentException("Initial coordinate matrix does not contain the required number of rows and columns.", "initialCoords");
+      var coords = initialCoords != null ? new Matrix(initialCoords) : new Matrix(Vertices, 2);
+      DllImporter.igraph_layout_fruchterman_reingold(graph, coords.NativeInstance, initialCoords != null, niter, startTemp, igraph_layout_grid_t.IGRAPH_LAYOUT_AUTOGRID, null, null, null, null, null);
+      return coords;
+    }
+
+    public Matrix LayoutWithKamadaKawai(Matrix initialCoords = null) {
+      return LayoutWithKamadaKawai(50 * Vertices, 0, Vertices, initialCoords);
+    }
+    public Matrix LayoutWithKamadaKawai(int maxiter, double epsilon, double kkconst, Matrix initialCoords = null) {
+      if (initialCoords != null && (initialCoords.Rows != Vertices || initialCoords.Columns != 2))
+        throw new ArgumentException("Initial coordinate matrix does not contain the required number of rows and columns.", "initialCoords");
+      var coords = initialCoords != null ? new Matrix(initialCoords) : new Matrix(Vertices, 2);
+      DllImporter.igraph_layout_kamada_kawai(graph, coords.NativeInstance, initialCoords != null, maxiter, epsilon, kkconst, null, null, null, null, null);
+      return coords;
+    }
+
+    public Matrix LayoutWithDavidsonHarel(Matrix initialCoords = null) {
+      var density = Density();
+      return LayoutWithDavidsonHarel(10, Math.Max(10, (int)Math.Log(Vertices, 2)), 0.75, 1.0, 0.0, density / 10.0, 1.0 - Math.Sqrt(density), 0.2 * (1 - density), initialCoords);
+    }
+    public Matrix LayoutWithDavidsonHarel(int maxiter, int fineiter, double cool_fact, double weight_node_dist, double weight_border, double weight_edge_lengths, double weight_edge_crossings, double weight_node_edge_dist, Matrix initialCoords = null) {
+      if (initialCoords != null && (initialCoords.Rows != Vertices || initialCoords.Columns != 2))
+        throw new ArgumentException("Initial coordinate matrix does not contain the required number of rows and columns.", "initialCoords");
+      var coords = initialCoords != null ? new Matrix(initialCoords) : new Matrix(Vertices, 2);
+      DllImporter.igraph_layout_davidson_harel(graph, coords.NativeInstance, initialCoords != null, maxiter, fineiter, cool_fact, weight_node_dist, weight_border, weight_edge_lengths, weight_edge_crossings, weight_node_edge_dist);
+      return coords;
+    }
+
+    /// <summary>
+    /// Use multi-dimensional scaling to layout vertices. 
+    /// A distance matrix can be used to specify the distances between the vertices.
+    /// Otherwise the distances will be calculated by shortest-path-length.
+    /// </summary>
+    /// <remarks>
+    /// For disconnected graphs, dimension must be 2.
+    /// </remarks>
+    /// <param name="dist">The distance matrix to layout the vertices.</param>
+    /// <param name="dim">How many dimensions should be used.</param>
+    /// <returns>The coordinates matrix of the aligned vertices.</returns>
+    public Matrix LayoutWithMds(Matrix dist = null, int dim = 2) {
+      var coords = new Matrix(Vertices, dim);
+      DllImporter.igraph_layout_mds(graph, coords.NativeInstance, dist != null ? dist.NativeInstance : null, dim);
+      return coords;
+    }
+
+    public void BreadthFirstWalk(BreadthFirstHandler handler, int root, DirectedWalkMode mode, bool includeUnreachableFromRoot = false, object tag = null) {
+      igraph_bfshandler_t wrapper = (t, vid, pred, succ, rank, dist, extra) => handler != null && handler(this, vid, pred, succ, rank, dist, tag);
+      DllImporter.igraph_bfs(graph, root, null, (igraph_neimode_t)mode, includeUnreachableFromRoot, null, null, null, null, null, null, null, wrapper, tag);
+    }
+
+    public void DepthFirstWalk(DepthFirstHandler inHandler, DepthFirstHandler outHandler, int root, DirectedWalkMode mode, bool includeUnreachableFromRoot = false, object tag = null) {
+      igraph_dfshandler_t inWrapper = (t, vid, dist, extra) => inHandler != null && inHandler(this, vid, dist, tag);
+      igraph_dfshandler_t outWrapper = (t, vid, dist, extra) => outHandler != null && outHandler(this, vid, dist, tag);
+      DllImporter.igraph_dfs(graph, root, (igraph_neimode_t)mode, includeUnreachableFromRoot, null, null, null, null, inWrapper, outWrapper, tag);
     }
   }

stable/HeuristicLab.ExtLibs/HeuristicLab.Igraph/0.8.0-pre/HeuristicLab.Igraph-0.8.0-pre/Wrappers/Matrix.cs

@@ -1 @@
-using System;
-using System.Runtime.InteropServices;
+#region License Information
+/* HeuristicLab
+ * Copyright (C) 2002-2016 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ *
+ * This file is part of HeuristicLab.
+ *
+ * HeuristicLab is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * HeuristicLab is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
+ */
+#endregion
 
-namespace HeuristicLab.igraph.Wrappers {
-  [StructLayout(LayoutKind.Sequential, CharSet = CharSet.Ansi)]
-  public class Matrix : IDisposable {
+using System;
+
+namespace HeuristicLab.IGraph.Wrappers {
+  public sealed class Matrix : IDisposable {
     igraph_matrix_t matrix;
     internal igraph_matrix_t NativeInstance { get { return matrix; } }
@@ -11 +30 @@
 
     public Matrix(int nrow, int ncol) {
+      if (nrow < 0 || ncol < 0) throw new ArgumentException("Rows and Columns must be >= 0");
       matrix = new igraph_matrix_t();
       DllImporter.igraph_matrix_init(matrix, nrow, ncol);
+    }
+    public Matrix(Matrix other) {
+      if (other == null) throw new ArgumentNullException("other");
+      matrix = new igraph_matrix_t();
+      DllImporter.igraph_matrix_copy(matrix, other.NativeInstance);
+    }
+    public Matrix(double[,] mat) {
+      if (mat == null) throw new ArgumentNullException("mat");
+      matrix = new igraph_matrix_t();
+      var nrows = mat.GetLength(0);
+      var ncols = mat.GetLength(1);
+      DllImporter.igraph_matrix_init(matrix, nrows, ncols);
+      var colwise = new double[ncols * nrows];
+      for (var j = 0; j < ncols; j++)
+        for (var i = 0; i < nrows; i++)
+          colwise[j * nrows + i] = mat[i, j];
+      DllImporter.igraph_vector_init_copy(matrix.data, colwise);
     }
     ~Matrix() {
@@ -23 +60 @@
       matrix = null;
       GC.SuppressFinalize(this);
+    }
+
+    public void Fill(double v) {
+      DllImporter.igraph_matrix_fill(matrix, v);
+    }
+
+    public void Transpose() {
+      DllImporter.igraph_matrix_transpose(matrix);
+    }
+
+    public void Scale(double by) {
+      DllImporter.igraph_matrix_scale(matrix, by);
     }