Java tutorial
/** * Licensed to the Apache Software Foundation (ASF) under one or more * contributor license agreements. See the NOTICE file distributed with * this work for additional information regarding copyright ownership. * The ASF licenses this file to You under the Apache License, Version 2.0 * (the "License"); you may not use this file except in compliance with * the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.apache.mahout.utils.clustering; import java.io.IOException; import java.io.Writer; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Random; import java.util.regex.Pattern; import org.apache.mahout.clustering.Cluster; import org.apache.mahout.clustering.classify.WeightedPropertyVectorWritable; import org.apache.mahout.clustering.classify.WeightedVectorWritable; import org.apache.mahout.clustering.iterator.ClusterWritable; import org.apache.mahout.common.RandomUtils; import org.apache.mahout.common.StringUtils; import org.apache.mahout.common.distance.DistanceMeasure; import org.apache.mahout.math.NamedVector; import org.apache.mahout.math.Vector; /** * GraphML -- see http://gephi.org/users/supported-graph-formats/graphml-format/ */ public class GraphMLClusterWriter extends AbstractClusterWriter { private static final Pattern VEC_PATTERN = Pattern.compile("\\{|\\:|\\,|\\}"); private final Map<Integer, Color> colors = new HashMap<>(); private Color lastClusterColor; private float lastX; private float lastY; private Random random; private int posStep; private final String[] dictionary; private final int numTopFeatures; private final int subString; public GraphMLClusterWriter(Writer writer, Map<Integer, List<WeightedPropertyVectorWritable>> clusterIdToPoints, DistanceMeasure measure, int numTopFeatures, String[] dictionary, int subString) throws IOException { super(writer, clusterIdToPoints, measure); this.dictionary = dictionary; this.numTopFeatures = numTopFeatures; this.subString = subString; init(writer); } private void init(Writer writer) throws IOException { writer.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>"); writer.append("<graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\"\n" + "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" + "xsi:schemaLocation=\"http://graphml.graphdrawing.org/xmlns\n" + "http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd\">"); //support rgb writer.append("<key attr.name=\"r\" attr.type=\"int\" for=\"node\" id=\"r\"/>\n" + "<key attr.name=\"g\" attr.type=\"int\" for=\"node\" id=\"g\"/>\n" + "<key attr.name=\"b\" attr.type=\"int\" for=\"node\" id=\"b\"/>" + "<key attr.name=\"size\" attr.type=\"int\" for=\"node\" id=\"size\"/>" + "<key attr.name=\"weight\" attr.type=\"float\" for=\"edge\" id=\"weight\"/>" + "<key attr.name=\"x\" attr.type=\"float\" for=\"node\" id=\"x\"/>" + "<key attr.name=\"y\" attr.type=\"float\" for=\"node\" id=\"y\"/>"); writer.append("<graph edgedefault=\"undirected\">"); lastClusterColor = new Color(); posStep = (int) (0.1 * clusterIdToPoints.size()) + 100; random = RandomUtils.getRandom(); } /* <?xml version="1.0" encoding="UTF-8"?> <graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"> <graph id="G" edgedefault="undirected"> <node id="n0"/> <node id="n1"/> <edge id="e1" source="n0" target="n1"/> </graph> </graphml> */ @Override public void write(ClusterWritable clusterWritable) throws IOException { StringBuilder line = new StringBuilder(); Cluster cluster = clusterWritable.getValue(); Color rgb = getColor(cluster.getId()); String topTerms = ""; if (dictionary != null) { topTerms = getTopTerms(cluster.getCenter(), dictionary, numTopFeatures); } String clusterLabel = String.valueOf(cluster.getId()) + '_' + topTerms; //do some positioning so that items are visible and grouped together //TODO: put in a real layout algorithm float x = lastX + 1000; float y = lastY; if (x > (1000 + posStep)) { y = lastY + 1000; x = 0; } line.append(createNode(clusterLabel, rgb, x, y)); List<WeightedPropertyVectorWritable> points = clusterIdToPoints.get(cluster.getId()); if (points != null) { for (WeightedVectorWritable point : points) { Vector theVec = point.getVector(); double distance = 1; if (measure != null) { //scale the distance distance = measure.distance(cluster.getCenter().getLengthSquared(), cluster.getCenter(), theVec) * 500; } String vecStr; int angle = random.nextInt(360); //pick an angle at random and then scale along that angle double angleRads = Math.toRadians(angle); float targetX = x + (float) (distance * Math.cos(angleRads)); float targetY = y + (float) (distance * Math.sin(angleRads)); if (theVec instanceof NamedVector) { vecStr = ((NamedVector) theVec).getName(); } else { vecStr = theVec.asFormatString(); //do some basic manipulations for display vecStr = VEC_PATTERN.matcher(vecStr).replaceAll("_"); } if (subString > 0 && vecStr.length() > subString) { vecStr = vecStr.substring(0, subString); } line.append(createNode(vecStr, rgb, targetX, targetY)); line.append(createEdge(clusterLabel, vecStr, distance)); } } lastClusterColor = rgb; lastX = x; lastY = y; getWriter().append(line).append("\n"); } private Color getColor(int clusterId) { Color result = colors.get(clusterId); if (result == null) { result = new Color(); //there is probably some better way to color a graph int incR = 0; int incG = 0; int incB = 0; if (lastClusterColor.r + 20 < 256 && lastClusterColor.g + 20 < 256 && lastClusterColor.b + 20 < 256) { incR = 20; incG = 0; incB = 0; } else if (lastClusterColor.r + 20 >= 256 && lastClusterColor.g + 20 < 256 && lastClusterColor.b + 20 < 256) { incG = 20; incB = 0; } else if (lastClusterColor.r + 20 >= 256 && lastClusterColor.g + 20 >= 256 && lastClusterColor.b + 20 < 256) { incB = 20; } else { incR += 3; incG += 3; incR += 3; } result.r = (lastClusterColor.r + incR) % 256; result.g = (lastClusterColor.g + incG) % 256; result.b = (lastClusterColor.b + incB) % 256; colors.put(clusterId, result); } return result; } private static String createEdge(String left, String right, double distance) { left = StringUtils.escapeXML(left); right = StringUtils.escapeXML(right); return "<edge id=\"" + left + '_' + right + "\" source=\"" + left + "\" target=\"" + right + "\">" + "<data key=\"weight\">" + distance + "</data></edge>"; } private static String createNode(String s, Color rgb, float x, float y) { return "<node id=\"" + StringUtils.escapeXML(s) + "\"><data key=\"r\">" + rgb.r + "</data>" + "<data key=\"g\">" + rgb.g + "</data>" + "<data key=\"b\">" + rgb.b + "</data>" + "<data key=\"x\">" + x + "</data>" + "<data key=\"y\">" + y + "</data>" + "</node>"; } @Override public void close() throws IOException { getWriter().append("</graph>").append("</graphml>"); super.close(); } private static class Color { int r; int g; int b; } }