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Refactor kNNClusterer for serialization

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This commit is contained in:
Antonin Delpeuch 2018-09-05 17:39:31 +01:00
parent 31954862e8
commit c9436f563d
2 changed files with 143 additions and 27 deletions
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123
main/src/com/google/refine/clustering/knn/kNNClusterer.java
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@ -51,10 +51,12 @@ import org.json.JSONWriter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.refine.Jsonizable;
import com.google.refine.browsing.Engine;
import com.google.refine.browsing.FilteredRows;
import com.google.refine.browsing.RowVisitor;
import com.google.refine.clustering.Clusterer;
import com.google.refine.clustering.ClustererConfig;
import com.google.refine.model.Cell;
import com.google.refine.model.Project;
import com.google.refine.model.Row;
@ -73,7 +75,83 @@ import edu.mit.simile.vicino.distances.PPMDistance;
public class kNNClusterer extends Clusterer {
public static class kNNClustererConfig extends ClustererConfig {
private String _distanceStr;
private Distance _distance;
private kNNClustererConfigParameters _parameters;
@Override
public void write(JSONWriter writer, Properties options)
throws JSONException {
writer.object();
writer.key("function"); writer.value(_distanceStr);
writer.key("type"); writer.value("knn");
writer.key("column"); writer.value(getColumnName());
if(_parameters != null) {
writer.key("params");
_parameters.write(writer, options);
}
writer.endObject();
}
public void initializeFromJSON(JSONObject o) {
super.initializeFromJSON(o);
_distanceStr = o.getString("function");
_distance = _distances.get(_distanceStr.toLowerCase());
if(o.has("params")) {
_parameters = kNNClustererConfigParameters.reconstruct(o.getJSONObject("params"));
} else {
_parameters = null;
}
}
public Distance getDistance() {
return _distance;
}
public kNNClustererConfigParameters getParameters() {
return _parameters;
}
@Override
public kNNClusterer apply(Project project) {
kNNClusterer clusterer = new kNNClusterer();
clusterer.initializeFromConfig(project, this);
return clusterer;
}
}
public static class kNNClustererConfigParameters implements Jsonizable {
public static final double defaultRadius = 1.0d;
public static final int defaultBlockingNgramSize = 6;
public double radius = defaultRadius;
public int blockingNgramSize = defaultBlockingNgramSize;
@Override
public void write(JSONWriter writer, Properties options)
throws JSONException {
writer.object();
writer.key("radius"); writer.value(radius);
writer.key("blocking-ngram-size");
writer.value(blockingNgramSize);
writer.endObject();
}
public static kNNClustererConfigParameters reconstruct(JSONObject o) {
kNNClustererConfigParameters params = new kNNClustererConfigParameters();
if(o.has("radius")) {
params.radius = o.getDouble("radius");
}
if(o.has("blocking-ngram-size")) {
params.blockingNgramSize = o.getInt("blocking-ngram-size");
}
return params;
}
}
private Distance _distance;
private kNNClustererConfigParameters _params;
static final protected Map<String, Distance> _distances = new HashMap<String, Distance>();
@ -97,20 +175,13 @@ public class kNNClusterer extends Clusterer {
class VPTreeClusteringRowVisitor implements RowVisitor {
Distance _distance;
JSONObject _config;
kNNClustererConfigParameters _params;
VPTreeClusterer _clusterer;
double _radius = 1.0f;
public VPTreeClusteringRowVisitor(Distance d, JSONObject o) {
public VPTreeClusteringRowVisitor(Distance d, kNNClustererConfigParameters params) {
_distance = d;
_config = o;
_clusterer = new VPTreeClusterer(_distance);
try {
JSONObject params = o.getJSONObject("params");
_radius = params.getDouble("radius");
} catch (JSONException e) {
//Refine.warn("No parameters found, using defaults");
}
_params = params;
}
@Override
@ -136,32 +207,23 @@ public class kNNClusterer extends Clusterer {
}
public List<Set<Serializable>> getClusters() {
return _clusterer.getClusters(_radius);
return _clusterer.getClusters(_params.radius);
}
}
class BlockingClusteringRowVisitor implements RowVisitor {
Distance _distance;
JSONObject _config;
double _radius = 1.0d;
int _blockingNgramSize = 6;
HashSet<String> _data;
NGramClusterer _clusterer;
public BlockingClusteringRowVisitor(Distance d, JSONObject o) {
public BlockingClusteringRowVisitor(Distance d, kNNClustererConfigParameters params) {
_distance = d;
_config = o;
_data = new HashSet<String>();
try {
JSONObject params = o.getJSONObject("params");
_radius = params.getDouble("radius");
logger.debug("Use radius: {}", _radius);
_blockingNgramSize = params.getInt("blocking-ngram-size");
logger.debug("Use blocking ngram size: {}",_blockingNgramSize);
} catch (JSONException e) {
logger.debug("No parameters found, using defaults");
}
_blockingNgramSize = params.blockingNgramSize;
_radius = params.radius;
_clusterer = new NGramClusterer(_distance, _blockingNgramSize);
}
@ -192,16 +254,23 @@ public class kNNClusterer extends Clusterer {
}
}
@Override
@Deprecated
public void initializeFromJSON(Project project, JSONObject o) throws Exception {
super.initializeFromJSON(project, o);
_distance = _distances.get(o.getString("function").toLowerCase());
kNNClustererConfig config = new kNNClustererConfig();
config.initializeFromJSON(o);
initializeFromConfig(project, config);
}
public void initializeFromConfig(Project project, kNNClustererConfig config) {
super.initializeFromConfig(project, config);
_distance = config.getDistance();
_params = config.getParameters();
}
@Override
public void computeClusters(Engine engine) {
//VPTreeClusteringRowVisitor visitor = new VPTreeClusteringRowVisitor(_distance,_config);
BlockingClusteringRowVisitor visitor = new BlockingClusteringRowVisitor(_distance,_config);
BlockingClusteringRowVisitor visitor = new BlockingClusteringRowVisitor(_distance,_params);
FilteredRows filteredRows = engine.getAllFilteredRows();
filteredRows.accept(_project, visitor);

47
main/tests/server/src/com/google/refine/tests/clustering/kNNClustererTests.java Normal file
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@ -0,0 +1,47 @@
package com.google.refine.tests.clustering;
import org.json.JSONObject;
import org.testng.annotations.Test;
import com.google.refine.browsing.Engine;
import com.google.refine.clustering.knn.kNNClusterer;
import com.google.refine.clustering.knn.kNNClusterer.kNNClustererConfig;
import com.google.refine.model.Project;
import com.google.refine.tests.RefineTest;
import com.google.refine.tests.util.TestUtils;
public class kNNClustererTests extends RefineTest {
public static String configJson = "{"
+ "\"type\":\"knn\","
+ "\"function\":\"PPM\","
+ "\"column\":\"values\","
+ "\"params\":{\"radius\":1,\"blocking-ngram-size\":2}"
+ "}";
public static String clustererJson = "["
+ " [{\"v\":\"ab\",\"c\":1},{\"v\":\"abc\",\"c\":1}]"
+ "]";
@Test
public void serializekNNClustererConfig() {
kNNClustererConfig config = new kNNClustererConfig();
config.initializeFromJSON(new JSONObject(configJson));
TestUtils.isSerializedTo(config, configJson);
}
@Test
public void serializekNNClusterer() {
Project project = createCSVProject("column\n"
+ "ab\n"
+ "abc\n"
+ "c\n"
+ "ĉ\n");
kNNClustererConfig config = new kNNClustererConfig();
config.initializeFromJSON(new JSONObject(configJson));
kNNClusterer clusterer = config.apply(project);
clusterer.computeClusters(new Engine(project));
TestUtils.isSerializedTo(clusterer, clustererJson);
}
}