let's try with another knn method

git-svn-id: http://google-refine.googlecode.com/svn/trunk@254 7d457c2a-affb-35e4-300a-418c747d4874

src/main/java/com/metaweb/gridworks/clustering/knn/kNNClusterer.java

@@ -5,6 +5,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Properties;
@@ -21,6 +22,9 @@ import com.metaweb.gridworks.clustering.Clusterer;
 import com.metaweb.gridworks.model.Cell;
 import com.metaweb.gridworks.model.Project;
 import com.metaweb.gridworks.model.Row;
+import com.wcohen.ss.expt.ClusterNGramBlocker;
+import com.wcohen.ss.expt.MatchData;
+import com.wcohen.ss.expt.Blocker.Pair;
 
 import edu.mit.simile.vicino.Distance;
 import edu.mit.simile.vicino.distances.BZip2Distance;
@@ -39,7 +43,7 @@ public class kNNClusterer extends Clusterer {
     
     static protected Map<String, Distance> _distances = new HashMap<String, Distance>();
 
-    List<List<? extends Serializable>> _clusters;
+    List<List<Serializable>> _clusters;
     
     static {
         _distances.put("levenshtein", new LevenshteinDistance());
@@ -52,14 +56,14 @@ public class kNNClusterer extends Clusterer {
         _distances.put("ppm", new PPMDistance());
     }
 
-    class kNNClusteringRowVisitor implements RowVisitor {
+    class VPTreeClusteringRowVisitor implements RowVisitor {
 
         Distance _distance;
         JSONObject _config;
         VPTreeBuilder _treeBuilder;
         float _radius;
         
-        public kNNClusteringRowVisitor(Distance d, JSONObject o) {
+        public VPTreeClusteringRowVisitor(Distance d, JSONObject o) {
             _distance = d;
             _config = o;
             _treeBuilder = new VPTreeBuilder(_distance);
@@ -85,9 +89,68 @@ public class kNNClusterer extends Clusterer {
             return _treeBuilder.getClusters(_radius);
         }
     }
+
+    class BlockingClusteringRowVisitor implements RowVisitor {
+
+        Distance _distance;
+        JSONObject _config;
+        MatchData _data;
+        float _radius;
+        HashSet<String> _set;
+        
+        public BlockingClusteringRowVisitor(Distance d, JSONObject o) {
+            _distance = d;
+            _config = o;
+            _data = new MatchData();
+            _set = new HashSet<String>();
+            try {
+                _radius = (float) o.getJSONObject("params").getDouble("radius");
+            } catch (JSONException e) {
+                Gridworks.warn("No radius found, using default");
+                _radius = 0.1f;
+            }
+        }
+        
+        public boolean visit(Project project, int rowIndex, Row row, boolean contextual) {
+            Cell cell = row.cells.get(_colindex);
+            if (cell != null && cell.value != null) {
+                Object v = cell.value;
+                String s = (v instanceof String) ? ((String) v) : v.toString().intern();
+                if (!_set.contains(s)) {
+                    _set.add(s);
+                    _data.addInstance("", "", s);
+                }
+            }
+            return false;
+        }
+        
+        public Map<Serializable,List<Serializable>> getClusters() {
+            Map<Serializable,List<Serializable>> map = new HashMap<Serializable,List<Serializable>>();
+            ClusterNGramBlocker blocker = new ClusterNGramBlocker();
+            blocker.block(_data);
+            for (int i = 0; i < blocker.numCorrectPairs(); i++) {
+                Pair p = blocker.getPair(i);
+                String a = p.getA().unwrap();
+                String b = p.getB().unwrap();
+                List<Serializable> l = null; 
+                if (!map.containsKey(a)) {
+                    l = new ArrayList<Serializable>(); 
+                    map.put(a, l);
+                } else {
+                    l = map.get(a);
+                }
+                double d = _distance.d(a,b);
+                System.out.println(a + " | " + b + ": " + d);
+                if (d <= _radius) {
+                    l.add(b);
+                }
+            }
+            return map;
+        }
+    }
     
-    public class SizeComparator implements Comparator<List<? extends Serializable>> {
-        public int compare(List<? extends Serializable> o1, List<? extends Serializable> o2) {
+    public class SizeComparator implements Comparator<List<Serializable>> {
+        public int compare(List<Serializable> o1, List<Serializable> o2) {
             return o2.size() - o1.size();
         }
     }
@@ -98,18 +161,19 @@ public class kNNClusterer extends Clusterer {
     }
 
     public void computeClusters(Engine engine) {
-        kNNClusteringRowVisitor visitor = new kNNClusteringRowVisitor(_distance,_config);
+        //VPTreeClusteringRowVisitor visitor = new VPTreeClusteringRowVisitor(_distance,_config);
+        BlockingClusteringRowVisitor visitor = new BlockingClusteringRowVisitor(_distance,_config);
         FilteredRows filteredRows = engine.getAllFilteredRows(true);
         filteredRows.accept(_project, visitor);
      
-        Map<Serializable,List<? extends Serializable>> clusters = visitor.getClusters();
-        _clusters = new ArrayList<List<? extends Serializable>>(clusters.values());
+        Map<Serializable,List<Serializable>> clusters = visitor.getClusters();
+        _clusters = new ArrayList<List<Serializable>>(clusters.values());
         Collections.sort(_clusters, new SizeComparator());
     }
     
     public void write(JSONWriter writer, Properties options) throws JSONException {
         writer.array();        
-        for (List<? extends Serializable> m : _clusters) {
+        for (List<Serializable> m : _clusters) {
             if (m.size() > 1) {
                 writer.array();        
                 for (Serializable s : m) {

src/main/java/edu/mit/simile/vicino/distances/BZip2Distance.java

@@ -9,7 +9,7 @@ public class BZip2Distance extends PseudoMetricDistance {
 
     public double d2(String x, String y) {
         String str = x + y;
-        float result = 0.0f;
+        double result = 0.0f;
         try {
             ByteArrayOutputStream baos = new ByteArrayOutputStream(str.length());
             CBZip2OutputStream os = new CBZip2OutputStream(baos);

src/main/java/edu/mit/simile/vicino/distances/GZipDistance.java

@@ -8,7 +8,7 @@ public class GZipDistance extends PseudoMetricDistance {
 
     public double d2(String x, String y) {
         String str = x + y;
-        float result = 0.0f;
+        double result = 0.0f;
         try {
             ByteArrayOutputStream baos = new ByteArrayOutputStream(str.length());
             GZIPOutputStream os = new GZIPOutputStream(baos);

src/main/java/edu/mit/simile/vicino/distances/PPMDistance.java

@@ -10,7 +10,7 @@ public class PPMDistance extends PseudoMetricDistance {
 
     public double d2(String x, String y) {
         String str = x + y;
-        float result = 0.0f;
+        double result = 0.0f;
         try {
             ByteArrayOutputStream baos = new ByteArrayOutputStream(str.length());
             ArithCodeOutputStream os = new ArithCodeOutputStream(baos,new PPMModel(8));

src/main/java/edu/mit/simile/vicino/distances/PseudoMetricDistance.java

@@ -9,9 +9,8 @@ public abstract class PseudoMetricDistance implements Distance {
         double cyy = d2(y, y);
         double cxy = d2(x, y);
         double cyx = d2(y, x);
-        double result1 = (cxy + cyx) / (cxx + cyy) - 1.0d;
-        return result1;
+        return (cxy + cyx) / (cxx + cyy) - 1.0d;
     }
-
+    
     protected abstract double d2(String x, String y);
 }