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-rw-r--r--src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java77
1 files changed, 26 insertions, 51 deletions
diff --git a/src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java b/src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java
index 144b4b70..5499415b 100644
--- a/src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.java
+++ b/src/de/lmu/ifi/dbs/elki/application/cache/CacheFloatDistanceInOnDiskMatrix.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) 2012
+ Copyright (C) 2013
Ludwig-Maximilians-Universität München
Lehr- und Forschungseinheit für Datenbanksysteme
ELKI Development Team
@@ -28,7 +28,6 @@ import java.io.IOException;
import de.lmu.ifi.dbs.elki.application.AbstractApplication;
import de.lmu.ifi.dbs.elki.database.Database;
-import de.lmu.ifi.dbs.elki.database.StaticArrayDatabase;
import de.lmu.ifi.dbs.elki.database.ids.DBIDIter;
import de.lmu.ifi.dbs.elki.database.ids.DBIDUtil;
import de.lmu.ifi.dbs.elki.database.query.distance.DistanceQuery;
@@ -39,14 +38,13 @@ import de.lmu.ifi.dbs.elki.distance.distancevalue.NumberDistance;
import de.lmu.ifi.dbs.elki.logging.Logging;
import de.lmu.ifi.dbs.elki.persistent.OnDiskUpperTriangleMatrix;
import de.lmu.ifi.dbs.elki.utilities.exceptions.AbortException;
-import de.lmu.ifi.dbs.elki.utilities.optionhandling.OptionID;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameterization.Parameterization;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.FileParameter;
import de.lmu.ifi.dbs.elki.utilities.optionhandling.parameters.ObjectParameter;
+import de.lmu.ifi.dbs.elki.workflow.InputStep;
/**
- * Wrapper to convert a traditional text-serialized result into a on-disk matrix
- * for random access.
+ * Precompute an on-disk distance matrix, using double precision.
*
* @author Erich Schubert
*
@@ -63,22 +61,6 @@ public class CacheFloatDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>>
private static final Logging LOG = Logging.getLogger(CacheFloatDistanceInOnDiskMatrix.class);
/**
- * Parameter that specifies the name of the directory to be re-parsed.
- * <p>
- * Key: {@code -loader.diskcache}
- * </p>
- */
- public static final OptionID CACHE_ID = new OptionID("loader.diskcache", "File name of the disk cache to create.");
-
- /**
- * Parameter that specifies the name of the directory to be re-parsed.
- * <p>
- * Key: {@code -loader.distance}
- * </p>
- */
- public static final OptionID DISTANCE_ID = new OptionID("loader.distance", "Distance function to cache.");
-
- /**
* Debug flag, to double-check all write operations.
*/
private static final boolean debugExtraCheckSymmetry = false;
@@ -89,9 +71,9 @@ public class CacheFloatDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>>
private static final int FLOAT_SIZE = 4;
/**
- * Holds the database connection to have the algorithm run with.
+ * Data source to process.
*/
- private Database database;
+ private InputStep input;
/**
* Distance function that is to be cached.
@@ -106,28 +88,28 @@ public class CacheFloatDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>>
/**
* Constructor.
*
- * @param database Database
+ * @param input Data source
* @param distance Distance function
* @param out Matrix output file
*/
- public CacheFloatDistanceInOnDiskMatrix(Database database, DistanceFunction<O, D> distance, File out) {
+ public CacheFloatDistanceInOnDiskMatrix(InputStep input, DistanceFunction<O, D> distance, File out) {
super();
- this.database = database;
+ this.input = input;
this.distance = distance;
this.out = out;
}
@Override
public void run() {
- database.initialize();
+ Database database = input.getDatabase();
Relation<O> relation = database.getRelation(distance.getInputTypeRestriction());
DistanceQuery<O, D> distanceQuery = database.getDistanceQuery(relation, distance);
int matrixsize = 0;
- for(DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
+ for (DBIDIter iditer = relation.iterDBIDs(); iditer.valid(); iditer.advance()) {
final int intid = DBIDUtil.asInteger(iditer);
matrixsize = Math.max(matrixsize, intid + 1);
- if(intid < 0) {
+ if (intid < 0) {
throw new AbortException("OnDiskMatrixCache does not allow negative DBIDs.");
}
}
@@ -135,25 +117,23 @@ public class CacheFloatDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>>
OnDiskUpperTriangleMatrix matrix;
try {
matrix = new OnDiskUpperTriangleMatrix(out, DiskCacheBasedFloatDistanceFunction.FLOAT_CACHE_MAGIC, 0, FLOAT_SIZE, matrixsize);
- }
- catch(IOException e) {
+ } catch (IOException e) {
throw new AbortException("Error creating output matrix.", e);
}
- for(DBIDIter id1 = relation.iterDBIDs(); id1.valid(); id1.advance()) {
- for(DBIDIter id2 = relation.iterDBIDs(); id2.valid(); id2.advance()) {
- if(DBIDUtil.asInteger(id2) >= DBIDUtil.asInteger(id1)) {
+ for (DBIDIter id1 = relation.iterDBIDs(); id1.valid(); id1.advance()) {
+ for (DBIDIter id2 = relation.iterDBIDs(); id2.valid(); id2.advance()) {
+ if (DBIDUtil.asInteger(id2) >= DBIDUtil.asInteger(id1)) {
float d = distanceQuery.distance(id1, id2).floatValue();
- if(debugExtraCheckSymmetry) {
+ if (debugExtraCheckSymmetry) {
float d2 = distanceQuery.distance(id2, id1).floatValue();
- if(Math.abs(d - d2) > 0.0000001) {
+ if (Math.abs(d - d2) > 0.0000001) {
LOG.warning("Distance function doesn't appear to be symmetric!");
}
}
try {
matrix.getRecordBuffer(DBIDUtil.asInteger(id1), DBIDUtil.asInteger(id2)).putFloat(d);
- }
- catch(IOException e) {
+ } catch (IOException e) {
throw new AbortException("Error writing distance record " + id1 + "," + id2 + " to matrix.", e);
}
}
@@ -170,9 +150,9 @@ public class CacheFloatDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>>
*/
public static class Parameterizer<O, D extends NumberDistance<D, ?>> extends AbstractApplication.Parameterizer {
/**
- * Holds the database connection to have the algorithm run with.
+ * Data source to process.
*/
- private Database database = null;
+ private InputStep input = null;
/**
* Distance function that is to be cached.
@@ -187,27 +167,22 @@ public class CacheFloatDistanceInOnDiskMatrix<O, D extends NumberDistance<D, ?>>
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
- // Database connection parameter
- final ObjectParameter<Database> dbpar = new ObjectParameter<Database>(OptionID.DATABASE_CONNECTION, Database.class, StaticArrayDatabase.class);
- if(config.grab(dbpar)) {
- database = dbpar.instantiateClass(config);
- }
+ input = config.tryInstantiate(InputStep.class);
// Distance function parameter
- final ObjectParameter<DistanceFunction<O, D>> dpar = new ObjectParameter<DistanceFunction<O, D>>(DISTANCE_ID, DistanceFunction.class);
- if(config.grab(dpar)) {
+ final ObjectParameter<DistanceFunction<O, D>> dpar = new ObjectParameter<>(CacheDoubleDistanceInOnDiskMatrix.Parameterizer.DISTANCE_ID, DistanceFunction.class);
+ if (config.grab(dpar)) {
distance = dpar.instantiateClass(config);
}
// Output file parameter
- final FileParameter cpar = new FileParameter(CACHE_ID, FileParameter.FileType.OUTPUT_FILE);
- if(config.grab(cpar)) {
+ final FileParameter cpar = new FileParameter(CacheDoubleDistanceInOnDiskMatrix.Parameterizer.CACHE_ID, FileParameter.FileType.OUTPUT_FILE);
+ if (config.grab(cpar)) {
out = cpar.getValue();
}
-
}
@Override
protected CacheFloatDistanceInOnDiskMatrix<O, D> makeInstance() {
- return new CacheFloatDistanceInOnDiskMatrix<O, D>(database, distance, out);
+ return new CacheFloatDistanceInOnDiskMatrix<>(input, distance, out);
}
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-21 01:51:53 +0000