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-rw-r--r--src/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java68
1 files changed, 27 insertions, 41 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java b/src/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java
index f61874dd..bf9ecdb0 100644
--- a/src/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java
+++ b/src/de/lmu/ifi/dbs/elki/application/cache/CacheDoubleDistanceRangeQueries.java
@@ -4,7 +4,7 @@ package de.lmu.ifi.dbs.elki.application.cache;
This file is part of ELKI:
Environment for Developing KDD-Applications Supported by Index-Structures
- Copyright (C) 2013
+ Copyright (C) 2014
Ludwig-Maximilians-Universität München
Lehr- und Forschungseinheit für Datenbanksysteme
ELKI Development Team
@@ -33,20 +33,17 @@ import java.nio.channels.FileLock;
import de.lmu.ifi.dbs.elki.application.AbstractApplication;
import de.lmu.ifi.dbs.elki.database.Database;
import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
-import de.lmu.ifi.dbs.elki.database.ids.distance.DistanceDBIDList;
-import de.lmu.ifi.dbs.elki.database.ids.distance.DistanceDBIDListIter;
-import de.lmu.ifi.dbs.elki.database.ids.distance.DoubleDistanceDBIDList;
-import de.lmu.ifi.dbs.elki.database.ids.distance.DoubleDistanceDBIDListIter;
+import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDList;
+import de.lmu.ifi.dbs.elki.database.ids.DoubleDBIDListIter;
import de.lmu.ifi.dbs.elki.database.query.DatabaseQuery;
import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
import de.lmu.ifi.dbs.elki.database.query.range.RangeQuery;
import de.lmu.ifi.dbs.elki.database.relation.Relation;
import de.lmu.ifi.dbs.elki.distance.distancefunction.DistanceFunction;
-import de.lmu.ifi.dbs.elki.distance.distancevalue.DoubleDistance;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.logging.progress.FiniteProgress;
-import de.lmu.ifi.dbs.elki.persistent.ByteArrayUtil;
import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
+import de.lmu.ifi.dbs.elki.utilities.io.ByteArrayUtil;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.constraints.CommonConstraints;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
@@ -78,7 +75,7 @@ public class CacheDoubleDistanceRangeQueries<O> extends AbstractApplication {
/**
* Distance function that is to be cached.
*/
- private DistanceFunction<O, DoubleDistance> distance;
+ private DistanceFunction<O> distance;
/**
* Query radius.
@@ -106,7 +103,7 @@ public class CacheDoubleDistanceRangeQueries<O> extends AbstractApplication {
* @param radius Query radius
* @param out Matrix output file
*/
- public CacheDoubleDistanceRangeQueries(InputStep input, DistanceFunction<O, DoubleDistance> distance, double radius, File out) {
+ public CacheDoubleDistanceRangeQueries(InputStep input, DistanceFunction<O> distance, double radius, File out) {
super();
this.input = input;
this.distance = distance;
@@ -118,11 +115,10 @@ public class CacheDoubleDistanceRangeQueries<O> extends AbstractApplication {
public void run() {
Database database = input.getDatabase();
Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
- DistanceQuery<O, DoubleDistance> distanceQuery = database.getDistanceQuery(relation, distance);
- DoubleDistance rad = new DoubleDistance(radius);
- RangeQuery<O, DoubleDistance> rangeQ = database.getRangeQuery(distanceQuery, rad, DatabaseQuery.HINT_HEAVY_USE);
+ DistanceQuery<O> distanceQuery = database.getDistanceQuery(relation, distance);
+ RangeQuery<O> rangeQ = database.getRangeQuery(distanceQuery, radius, DatabaseQuery.HINT_HEAVY_USE);
- LOG.verbose("Performing range queries with radius " + rad);
+ LOG.verbose("Performing range queries with radius " + radius);
// open file.
try (RandomAccessFile file = new RandomAccessFile(out, "rw");
@@ -139,16 +135,16 @@ public class CacheDoubleDistanceRangeQueries<O> extends AbstractApplication {
FiniteProgress prog = LOG.isVerbose() ? new FiniteProgress("Computing range queries", relation.size(), LOG) : null;
- for (DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
- final DistanceDBIDList<DoubleDistance> nn = rangeQ.getRangeForDBID(it, rad);
+ for(DBIDIter it = relation.iterDBIDs(); it.valid(); it.advance()) {
+ final DoubleDBIDList nn = rangeQ.getRangeForDBID(it, radius);
final int nnsize = nn.size();
// Grow the buffer when needed:
- if (nnsize * 12 + 10 > bufsize) {
- while (nnsize * 12 + 10 > bufsize) {
+ if(nnsize * 12 + 10 > bufsize) {
+ while(nnsize * 12 + 10 > bufsize) {
bufsize <<= 1;
}
- LOG.verbose("Resizing buffer to "+bufsize+" to store "+nnsize+" results:");
+ LOG.verbose("Resizing buffer to " + bufsize + " to store " + nnsize + " results:");
buffer = ByteBuffer.allocateDirect(bufsize);
}
@@ -156,32 +152,22 @@ public class CacheDoubleDistanceRangeQueries<O> extends AbstractApplication {
ByteArrayUtil.writeUnsignedVarint(buffer, it.internalGetIndex());
ByteArrayUtil.writeUnsignedVarint(buffer, nnsize);
int c = 0;
- if (nn instanceof DoubleDistanceDBIDList) {
- for (DoubleDistanceDBIDListIter ni = ((DoubleDistanceDBIDList) nn).iter(); ni.valid(); ni.advance(), c++) {
- ByteArrayUtil.writeUnsignedVarint(buffer, ni.internalGetIndex());
- buffer.putDouble(ni.doubleDistance());
- }
- } else {
- for (DistanceDBIDListIter<DoubleDistance> ni = nn.iter(); ni.valid(); ni.advance(), c++) {
- ByteArrayUtil.writeUnsignedVarint(buffer, ni.internalGetIndex());
- buffer.putDouble(ni.getDistance().doubleValue());
- }
+ for(DoubleDBIDListIter ni = nn.iter(); ni.valid(); ni.advance(), c++) {
+ ByteArrayUtil.writeUnsignedVarint(buffer, ni.internalGetIndex());
+ buffer.putDouble(ni.doubleValue());
}
- if (c != nn.size()) {
+ if(c != nn.size()) {
throw new AbortException("Sizes did not agree. Cache is invalid.");
}
buffer.flip();
channel.write(buffer);
- if (prog != null) {
- prog.incrementProcessed(LOG);
- }
- }
- if (prog != null) {
- prog.ensureCompleted(LOG);
+ LOG.incrementProcessed(prog);
}
+ LOG.ensureCompleted(prog);
lock.release();
- } catch (IOException e) {
+ }
+ catch(IOException e) {
LOG.exception(e);
}
// FIXME: close!
@@ -227,7 +213,7 @@ public class CacheDoubleDistanceRangeQueries<O> extends AbstractApplication {
/**
* Distance function that is to be cached.
*/
- private DistanceFunction<O, DoubleDistance> distance = null;
+ private DistanceFunction<O> distance = null;
/**
* Number of neighbors to precompute.
@@ -244,18 +230,18 @@ public class CacheDoubleDistanceRangeQueries<O> extends AbstractApplication {
super.makeOptions(config);
input = config.tryInstantiate(InputStep.class);
// Distance function parameter
- final ObjectParameter<DistanceFunction<O, DoubleDistance>> dpar = new ObjectParameter<>(DISTANCE_ID, DistanceFunction.class);
- if (config.grab(dpar)) {
+ final ObjectParameter<DistanceFunction<O>> dpar = new ObjectParameter<>(DISTANCE_ID, DistanceFunction.class);
+ if(config.grab(dpar)) {
distance = dpar.instantiateClass(config);
}
final DoubleParameter kpar = new DoubleParameter(RADIUS_ID);
kpar.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE);
- if (config.grab(kpar)) {
+ if(config.grab(kpar)) {
radius = kpar.doubleValue();
}
// Output file parameter
final FileParameter cpar = new FileParameter(CACHE_ID, FileParameter.FileType.OUTPUT_FILE);
- if (config.grab(cpar)) {
+ if(config.grab(cpar)) {
out = cpar.getValue();
}
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-08 01:37:19 +0000