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The Waikato Environment for Knowledge Analysis (WEKA), a machine
learning workbench. This is the stable version. Apart from bugfixes, this version
does not receive any other updates.
/*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* CheckClusterer.java
* Copyright (C) 2006 University of Waikato, Hamilton, New Zealand
*
*/
package weka.clusterers;
import weka.core.CheckScheme;
import weka.core.FastVector;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.MultiInstanceCapabilitiesHandler;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SerializationHelper;
import weka.core.TestInstances;
import weka.core.Utils;
import weka.core.WeightedInstancesHandler;
import java.util.Enumeration;
import java.util.Random;
import java.util.Vector;
/**
* Class for examining the capabilities and finding problems with
* clusterers. If you implement a clusterer using the WEKA.libraries,
* you should run the checks on it to ensure robustness and correct
* operation. Passing all the tests of this object does not mean
* bugs in the clusterer don't exist, but this will help find some
* common ones.
*
* Typical usage:
* java weka.clusterers.CheckClusterer -W clusterer_name
* -- clusterer_options
*
* CheckClusterer reports on the following:
*
* - Clusterer abilities
*
* - Possible command line options to the clusterer
* - Whether the clusterer can predict nominal, numeric, string,
* date or relational class attributes.
* - Whether the clusterer can handle numeric predictor attributes
* - Whether the clusterer can handle nominal predictor attributes
* - Whether the clusterer can handle string predictor attributes
* - Whether the clusterer can handle date predictor attributes
* - Whether the clusterer can handle relational predictor attributes
* - Whether the clusterer can handle multi-instance data
* - Whether the clusterer can handle missing predictor values
* - Whether the clusterer can handle instance weights
*
*
* - Correct functioning
*
* - Correct initialisation during buildClusterer (i.e. no result
* changes when buildClusterer called repeatedly)
* - Whether the clusterer alters the data pased to it
* (number of instances, instance order, instance weights, etc)
*
*
* - Degenerate cases
*
* - building clusterer with zero training instances
* - all but one predictor attribute values missing
* - all predictor attribute values missing
* - all but one class values missing
* - all class values missing
*
*
*
* Running CheckClusterer with the debug option set will output the
* training dataset for any failed tests.
*
* The weka.clusterers.AbstractClustererTest uses this
* class to test all the clusterers. Any changes here, have to be
* checked in that abstract test class, too.
*
* Valid options are:
*
* -D
* Turn on debugging output.
*
* -S
* Silent mode - prints nothing to stdout.
*
* -N <num>
* The number of instances in the datasets (default 20).
*
* -nominal <num>
* The number of nominal attributes (default 2).
*
* -nominal-values <num>
* The number of values for nominal attributes (default 1).
*
* -numeric <num>
* The number of numeric attributes (default 1).
*
* -string <num>
* The number of string attributes (default 1).
*
* -date <num>
* The number of date attributes (default 1).
*
* -relational <num>
* The number of relational attributes (default 1).
*
* -num-instances-relational <num>
* The number of instances in relational/bag attributes (default 10).
*
* -words <comma-separated-list>
* The words to use in string attributes.
*
* -word-separators <chars>
* The word separators to use in string attributes.
*
* -W
* Full name of the clusterer analyzed.
* eg: weka.clusterers.SimpleKMeans
* (default weka.clusterers.SimpleKMeans)
*
*
* Options specific to clusterer weka.clusterers.SimpleKMeans:
*
*
* -N <num>
* number of clusters.
* (default 2).
*
* -V
* Display std. deviations for centroids.
*
*
* -M
* Replace missing values with mean/mode.
*
*
* -S <num>
* Random number seed.
* (default 10)
*
*
* Options after -- are passed to the designated clusterer.
*
* @author Len Trigg ([email protected])
* @author FracPete (fracpete at waikato dot ac dot nz)
* @version $Revision: 1.11 $
* @see TestInstances
*/
public class CheckClusterer
extends CheckScheme {
/*
* Note about test methods:
* - methods return array of booleans
* - first index: success or not
* - second index: acceptable or not (e.g., Exception is OK)
*
* FracPete (fracpete at waikato dot ac dot nz)
*/
/*** The clusterer to be examined */
protected Clusterer m_Clusterer = new SimpleKMeans();
/**
* default constructor
*/
public CheckClusterer() {
super();
setNumInstances(40);
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector result = new Vector();
Enumeration en = super.listOptions();
while (en.hasMoreElements())
result.addElement(en.nextElement());
result.addElement(new Option(
"\tFull name of the clusterer analyzed.\n"
+"\teg: weka.clusterers.SimpleKMeans\n"
+ "\t(default weka.clusterers.SimpleKMeans)",
"W", 1, "-W"));
if ((m_Clusterer != null)
&& (m_Clusterer instanceof OptionHandler)) {
result.addElement(new Option("", "", 0,
"\nOptions specific to clusterer "
+ m_Clusterer.getClass().getName()
+ ":"));
Enumeration enu = ((OptionHandler)m_Clusterer).listOptions();
while (enu.hasMoreElements())
result.addElement(enu.nextElement());
}
return result.elements();
}
/**
* Parses a given list of options.
*
* Valid options are:
*
* -D
* Turn on debugging output.
*
* -S
* Silent mode - prints nothing to stdout.
*
* -N <num>
* The number of instances in the datasets (default 20).
*
* -nominal <num>
* The number of nominal attributes (default 2).
*
* -nominal-values <num>
* The number of values for nominal attributes (default 1).
*
* -numeric <num>
* The number of numeric attributes (default 1).
*
* -string <num>
* The number of string attributes (default 1).
*
* -date <num>
* The number of date attributes (default 1).
*
* -relational <num>
* The number of relational attributes (default 1).
*
* -num-instances-relational <num>
* The number of instances in relational/bag attributes (default 10).
*
* -words <comma-separated-list>
* The words to use in string attributes.
*
* -word-separators <chars>
* The word separators to use in string attributes.
*
* -W
* Full name of the clusterer analyzed.
* eg: weka.clusterers.SimpleKMeans
* (default weka.clusterers.SimpleKMeans)
*
*
* Options specific to clusterer weka.clusterers.SimpleKMeans:
*
*
* -N <num>
* number of clusters.
* (default 2).
*
* -V
* Display std. deviations for centroids.
*
*
* -M
* Replace missing values with mean/mode.
*
*
* -S <num>
* Random number seed.
* (default 10)
*
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String tmpStr;
tmpStr = Utils.getOption('N', options);
super.setOptions(options);
if (tmpStr.length() != 0)
setNumInstances(Integer.parseInt(tmpStr));
else
setNumInstances(40);
tmpStr = Utils.getOption('W', options);
if (tmpStr.length() == 0)
tmpStr = weka.clusterers.SimpleKMeans.class.getName();
setClusterer(
(Clusterer) forName(
"weka.clusterers",
Clusterer.class,
tmpStr,
Utils.partitionOptions(options)));
}
/**
* Gets the current settings of the CheckClusterer.
*
* @return an array of strings suitable for passing to setOptions
*/
public String[] getOptions() {
Vector result;
String[] options;
int i;
result = new Vector();
options = super.getOptions();
for (i = 0; i < options.length; i++)
result.add(options[i]);
if (getClusterer() != null) {
result.add("-W");
result.add(getClusterer().getClass().getName());
}
if ((m_Clusterer != null) && (m_Clusterer instanceof OptionHandler))
options = ((OptionHandler) m_Clusterer).getOptions();
else
options = new String[0];
if (options.length > 0) {
result.add("--");
for (i = 0; i < options.length; i++)
result.add(options[i]);
}
return (String[]) result.toArray(new String[result.size()]);
}
/**
* Begin the tests, reporting results to System.out
*/
public void doTests() {
if (getClusterer() == null) {
println("\n=== No clusterer set ===");
return;
}
println("\n=== Check on Clusterer: "
+ getClusterer().getClass().getName()
+ " ===\n");
// Start tests
println("--> Checking for interfaces");
canTakeOptions();
boolean updateable = updateableClusterer()[0];
boolean weightedInstancesHandler = weightedInstancesHandler()[0];
boolean multiInstanceHandler = multiInstanceHandler()[0];
println("--> Clusterer tests");
declaresSerialVersionUID();
runTests(weightedInstancesHandler, multiInstanceHandler, updateable);
}
/**
* Set the clusterer for testing.
*
* @param newClusterer the Clusterer to use.
*/
public void setClusterer(Clusterer newClusterer) {
m_Clusterer = newClusterer;
}
/**
* Get the clusterer used as the clusterer
*
* @return the clusterer used as the clusterer
*/
public Clusterer getClusterer() {
return m_Clusterer;
}
/**
* Run a battery of tests
*
* @param weighted true if the clusterer says it handles weights
* @param multiInstance true if the clusterer is a multi-instance clusterer
* @param updateable true if the classifier is updateable
*/
protected void runTests(boolean weighted, boolean multiInstance, boolean updateable) {
boolean PNom = canPredict(true, false, false, false, false, multiInstance)[0];
boolean PNum = canPredict(false, true, false, false, false, multiInstance)[0];
boolean PStr = canPredict(false, false, true, false, false, multiInstance)[0];
boolean PDat = canPredict(false, false, false, true, false, multiInstance)[0];
boolean PRel;
if (!multiInstance)
PRel = canPredict(false, false, false, false, true, multiInstance)[0];
else
PRel = false;
if (PNom || PNum || PStr || PDat || PRel) {
if (weighted)
instanceWeights(PNom, PNum, PStr, PDat, PRel, multiInstance);
canHandleZeroTraining(PNom, PNum, PStr, PDat, PRel, multiInstance);
boolean handleMissingPredictors = canHandleMissing(PNom, PNum, PStr, PDat, PRel,
multiInstance, true, 20)[0];
if (handleMissingPredictors)
canHandleMissing(PNom, PNum, PStr, PDat, PRel, multiInstance, true, 100);
correctBuildInitialisation(PNom, PNum, PStr, PDat, PRel, multiInstance);
datasetIntegrity(PNom, PNum, PStr, PDat, PRel, multiInstance, handleMissingPredictors);
if (updateable)
updatingEquality(PNom, PNum, PStr, PDat, PRel, multiInstance);
}
}
/**
* Checks whether the scheme can take command line options.
*
* @return index 0 is true if the clusterer can take options
*/
protected boolean[] canTakeOptions() {
boolean[] result = new boolean[2];
print("options...");
if (m_Clusterer instanceof OptionHandler) {
println("yes");
if (m_Debug) {
println("\n=== Full report ===");
Enumeration enu = ((OptionHandler)m_Clusterer).listOptions();
while (enu.hasMoreElements()) {
Option option = (Option) enu.nextElement();
print(option.synopsis() + "\n"
+ option.description() + "\n");
}
println("\n");
}
result[0] = true;
}
else {
println("no");
result[0] = false;
}
return result;
}
/**
* Checks whether the scheme can build models incrementally.
*
* @return index 0 is true if the clusterer can train incrementally
*/
protected boolean[] updateableClusterer() {
boolean[] result = new boolean[2];
print("updateable clusterer...");
if (m_Clusterer instanceof UpdateableClusterer) {
println("yes");
result[0] = true;
}
else {
println("no");
result[0] = false;
}
return result;
}
/**
* Checks whether the scheme says it can handle instance weights.
*
* @return true if the clusterer handles instance weights
*/
protected boolean[] weightedInstancesHandler() {
boolean[] result = new boolean[2];
print("weighted instances clusterer...");
if (m_Clusterer instanceof WeightedInstancesHandler) {
println("yes");
result[0] = true;
}
else {
println("no");
result[0] = false;
}
return result;
}
/**
* Checks whether the scheme handles multi-instance data.
*
* @return true if the clusterer handles multi-instance data
*/
protected boolean[] multiInstanceHandler() {
boolean[] result = new boolean[2];
print("multi-instance clusterer...");
if (m_Clusterer instanceof MultiInstanceCapabilitiesHandler) {
println("yes");
result[0] = true;
}
else {
println("no");
result[0] = false;
}
return result;
}
/**
* tests for a serialVersionUID. Fails in case the scheme doesn't declare
* a UID.
*
* @return index 0 is true if the scheme declares a UID
*/
protected boolean[] declaresSerialVersionUID() {
boolean[] result = new boolean[2];
print("serialVersionUID...");
result[0] = !SerializationHelper.needsUID(m_Clusterer.getClass());
if (result[0])
println("yes");
else
println("no");
return result;
}
/**
* Checks basic prediction of the scheme, for simple non-troublesome
* datasets.
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @return index 0 is true if the test was passed, index 1 is true if test
* was acceptable
*/
protected boolean[] canPredict(
boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance) {
print("basic predict");
printAttributeSummary(
nominalPredictor, numericPredictor, stringPredictor, datePredictor, relationalPredictor, multiInstance);
print("...");
FastVector accepts = new FastVector();
accepts.addElement("unary");
accepts.addElement("binary");
accepts.addElement("nominal");
accepts.addElement("numeric");
accepts.addElement("string");
accepts.addElement("date");
accepts.addElement("relational");
accepts.addElement("multi-instance");
accepts.addElement("not in classpath");
int numTrain = getNumInstances(), missingLevel = 0;
boolean predictorMissing = false;
return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
datePredictor, relationalPredictor,
multiInstance,
missingLevel, predictorMissing,
numTrain,
accepts);
}
/**
* Checks whether the scheme can handle zero training instances.
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @return index 0 is true if the test was passed, index 1 is true if test
* was acceptable
*/
protected boolean[] canHandleZeroTraining(
boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance) {
print("handle zero training instances");
printAttributeSummary(
nominalPredictor, numericPredictor, stringPredictor, datePredictor, relationalPredictor, multiInstance);
print("...");
FastVector accepts = new FastVector();
accepts.addElement("train");
accepts.addElement("value");
int numTrain = 0, missingLevel = 0;
boolean predictorMissing = false;
return runBasicTest(
nominalPredictor, numericPredictor, stringPredictor,
datePredictor, relationalPredictor,
multiInstance,
missingLevel, predictorMissing,
numTrain,
accepts);
}
/**
* Checks whether the scheme correctly initialises models when
* buildClusterer is called. This test calls buildClusterer with
* one training dataset. buildClusterer is then called on a training set
* with different structure, and then again with the original training set.
* If the equals method of the ClusterEvaluation class returns
* false, this is noted as incorrect build initialisation.
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @return index 0 is true if the test was passed
*/
protected boolean[] correctBuildInitialisation(
boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance) {
boolean[] result = new boolean[2];
print("correct initialisation during buildClusterer");
printAttributeSummary(
nominalPredictor, numericPredictor, stringPredictor, datePredictor, relationalPredictor, multiInstance);
print("...");
int numTrain = getNumInstances(), missingLevel = 0;
boolean predictorMissing = false;
Instances train1 = null;
Instances train2 = null;
Clusterer clusterer = null;
ClusterEvaluation evaluation1A = null;
ClusterEvaluation evaluation1B = null;
ClusterEvaluation evaluation2 = null;
boolean built = false;
int stage = 0;
try {
// Make two train sets with different numbers of attributes
train1 = makeTestDataset(42, numTrain,
nominalPredictor ? getNumNominal() : 0,
numericPredictor ? getNumNumeric() : 0,
stringPredictor ? getNumString() : 0,
datePredictor ? getNumDate() : 0,
relationalPredictor ? getNumRelational() : 0,
multiInstance);
train2 = makeTestDataset(84, numTrain,
nominalPredictor ? getNumNominal() + 1 : 0,
numericPredictor ? getNumNumeric() + 1 : 0,
stringPredictor ? getNumString() : 0,
datePredictor ? getNumDate() : 0,
relationalPredictor ? getNumRelational() : 0,
multiInstance);
if (nominalPredictor && !multiInstance) {
train1.deleteAttributeAt(0);
train2.deleteAttributeAt(0);
}
if (missingLevel > 0) {
addMissing(train1, missingLevel, predictorMissing);
addMissing(train2, missingLevel, predictorMissing);
}
clusterer = AbstractClusterer.makeCopies(getClusterer(), 1)[0];
evaluation1A = new ClusterEvaluation();
evaluation1B = new ClusterEvaluation();
evaluation2 = new ClusterEvaluation();
} catch (Exception ex) {
throw new Error("Error setting up for tests: " + ex.getMessage());
}
try {
stage = 0;
clusterer.buildClusterer(train1);
built = true;
evaluation1A.setClusterer(clusterer);
evaluation1A.evaluateClusterer(train1);
stage = 1;
built = false;
clusterer.buildClusterer(train2);
built = true;
evaluation2.setClusterer(clusterer);
evaluation2.evaluateClusterer(train2);
stage = 2;
built = false;
clusterer.buildClusterer(train1);
built = true;
evaluation1B.setClusterer(clusterer);
evaluation1B.evaluateClusterer(train1);
stage = 3;
if (!evaluation1A.equals(evaluation1B)) {
if (m_Debug) {
println("\n=== Full report ===\n");
println("First buildClusterer()");
println(evaluation1A.clusterResultsToString() + "\n\n");
println("Second buildClusterer()");
println(evaluation1B.clusterResultsToString() + "\n\n");
}
throw new Exception("Results differ between buildClusterer calls");
}
println("yes");
result[0] = true;
if (false && m_Debug) {
println("\n=== Full report ===\n");
println("First buildClusterer()");
println(evaluation1A.clusterResultsToString() + "\n\n");
println("Second buildClusterer()");
println(evaluation1B.clusterResultsToString() + "\n\n");
}
}
catch (Exception ex) {
println("no");
result[0] = false;
if (m_Debug) {
println("\n=== Full Report ===");
print("Problem during");
if (built) {
print(" testing");
} else {
print(" training");
}
switch (stage) {
case 0:
print(" of dataset 1");
break;
case 1:
print(" of dataset 2");
break;
case 2:
print(" of dataset 1 (2nd build)");
break;
case 3:
print(", comparing results from builds of dataset 1");
break;
}
println(": " + ex.getMessage() + "\n");
println("here are the datasets:\n");
println("=== Train1 Dataset ===\n"
+ train1.toString() + "\n");
println("=== Train2 Dataset ===\n"
+ train2.toString() + "\n");
}
}
return result;
}
/**
* Checks basic missing value handling of the scheme. If the missing
* values cause an exception to be thrown by the scheme, this will be
* recorded.
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @param predictorMissing true if the missing values may be in
* the predictors
* @param missingLevel the percentage of missing values
* @return index 0 is true if the test was passed, index 1 is true if test
* was acceptable
*/
protected boolean[] canHandleMissing(
boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance,
boolean predictorMissing,
int missingLevel) {
if (missingLevel == 100)
print("100% ");
print("missing");
if (predictorMissing) {
print(" predictor");
}
print(" values");
printAttributeSummary(
nominalPredictor, numericPredictor, stringPredictor, datePredictor, relationalPredictor, multiInstance);
print("...");
FastVector accepts = new FastVector();
accepts.addElement("missing");
accepts.addElement("value");
accepts.addElement("train");
int numTrain = getNumInstances();
return runBasicTest(nominalPredictor, numericPredictor, stringPredictor,
datePredictor, relationalPredictor,
multiInstance,
missingLevel, predictorMissing,
numTrain,
accepts);
}
/**
* Checks whether the clusterer can handle instance weights.
* This test compares the clusterer performance on two datasets
* that are identical except for the training weights. If the
* results change, then the clusterer must be using the weights. It
* may be possible to get a false positive from this test if the
* weight changes aren't significant enough to induce a change
* in clusterer performance (but the weights are chosen to minimize
* the likelihood of this).
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @return index 0 true if the test was passed
*/
protected boolean[] instanceWeights(
boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance) {
print("clusterer uses instance weights");
printAttributeSummary(
nominalPredictor, numericPredictor, stringPredictor, datePredictor, relationalPredictor, multiInstance);
print("...");
int numTrain = 2*getNumInstances(), missingLevel = 0;
boolean predictorMissing = false;
boolean[] result = new boolean[2];
Instances train = null;
Clusterer [] clusterers = null;
ClusterEvaluation evaluationB = null;
ClusterEvaluation evaluationI = null;
boolean built = false;
boolean evalFail = false;
try {
train = makeTestDataset(42, numTrain,
nominalPredictor ? getNumNominal() + 1 : 0,
numericPredictor ? getNumNumeric() + 1 : 0,
stringPredictor ? getNumString() : 0,
datePredictor ? getNumDate() : 0,
relationalPredictor ? getNumRelational() : 0,
multiInstance);
if (nominalPredictor && !multiInstance)
train.deleteAttributeAt(0);
if (missingLevel > 0)
addMissing(train, missingLevel, predictorMissing);
clusterers = AbstractClusterer.makeCopies(getClusterer(), 2);
evaluationB = new ClusterEvaluation();
evaluationI = new ClusterEvaluation();
clusterers[0].buildClusterer(train);
evaluationB.setClusterer(clusterers[0]);
} catch (Exception ex) {
throw new Error("Error setting up for tests: " + ex.getMessage());
}
try {
// Now modify instance weights and re-built/test
for (int i = 0; i < train.numInstances(); i++) {
train.instance(i).setWeight(0);
}
Random random = new Random(1);
for (int i = 0; i < train.numInstances() / 2; i++) {
int inst = Math.abs(random.nextInt()) % train.numInstances();
int weight = Math.abs(random.nextInt()) % 10 + 1;
train.instance(inst).setWeight(weight);
}
clusterers[1].buildClusterer(train);
built = true;
evaluationI.setClusterer(clusterers[1]);
if (evaluationB.equals(evaluationI)) {
// println("no");
evalFail = true;
throw new Exception("evalFail");
}
println("yes");
result[0] = true;
} catch (Exception ex) {
println("no");
result[0] = false;
if (m_Debug) {
println("\n=== Full Report ===");
if (evalFail) {
println("Results don't differ between non-weighted and "
+ "weighted instance models.");
println("Here are the results:\n");
println("\nboth methods\n");
println(evaluationB.clusterResultsToString());
} else {
print("Problem during");
if (built) {
print(" testing");
} else {
print(" training");
}
println(": " + ex.getMessage() + "\n");
}
println("Here is the dataset:\n");
println("=== Train Dataset ===\n"
+ train.toString() + "\n");
println("=== Train Weights ===\n");
for (int i = 0; i < train.numInstances(); i++) {
println(" " + (i + 1)
+ " " + train.instance(i).weight());
}
}
}
return result;
}
/**
* Checks whether the scheme alters the training dataset during
* training. If the scheme needs to modify the training
* data it should take a copy of the training data. Currently checks
* for changes to header structure, number of instances, order of
* instances, instance weights.
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @param predictorMissing true if we know the clusterer can handle
* (at least) moderate missing predictor values
* @return index 0 is true if the test was passed
*/
protected boolean[] datasetIntegrity(
boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance,
boolean predictorMissing) {
print("clusterer doesn't alter original datasets");
printAttributeSummary(
nominalPredictor, numericPredictor, stringPredictor, datePredictor, relationalPredictor, multiInstance);
print("...");
int numTrain = getNumInstances(), missingLevel = 20;
boolean[] result = new boolean[2];
Instances train = null;
Clusterer clusterer = null;
try {
train = makeTestDataset(42, numTrain,
nominalPredictor ? getNumNominal() : 0,
numericPredictor ? getNumNumeric() : 0,
stringPredictor ? getNumString() : 0,
datePredictor ? getNumDate() : 0,
relationalPredictor ? getNumRelational() : 0,
multiInstance);
if (nominalPredictor && !multiInstance)
train.deleteAttributeAt(0);
if (missingLevel > 0)
addMissing(train, missingLevel, predictorMissing);
clusterer = AbstractClusterer.makeCopies(getClusterer(), 1)[0];
} catch (Exception ex) {
throw new Error("Error setting up for tests: " + ex.getMessage());
}
try {
Instances trainCopy = new Instances(train);
clusterer.buildClusterer(trainCopy);
compareDatasets(train, trainCopy);
println("yes");
result[0] = true;
} catch (Exception ex) {
println("no");
result[0] = false;
if (m_Debug) {
println("\n=== Full Report ===");
print("Problem during training");
println(": " + ex.getMessage() + "\n");
println("Here is the dataset:\n");
println("=== Train Dataset ===\n"
+ train.toString() + "\n");
}
}
return result;
}
/**
* Checks whether an updateable scheme produces the same model when
* trained incrementally as when batch trained. The model itself
* cannot be compared, so we compare the evaluation on test data
* for both models. It is possible to get a false positive on this
* test (likelihood depends on the classifier).
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @return index 0 is true if the test was passed
*/
protected boolean[] updatingEquality(
boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance) {
print("incremental training produces the same results"
+ " as batch training");
printAttributeSummary(
nominalPredictor, numericPredictor, stringPredictor, datePredictor, relationalPredictor, multiInstance);
print("...");
int numTrain = getNumInstances(), missingLevel = 0;
boolean predictorMissing = false, classMissing = false;
boolean[] result = new boolean[2];
Instances train = null;
Clusterer[] clusterers = null;
ClusterEvaluation evaluationB = null;
ClusterEvaluation evaluationI = null;
boolean built = false;
try {
train = makeTestDataset(42, numTrain,
nominalPredictor ? getNumNominal() : 0,
numericPredictor ? getNumNumeric() : 0,
stringPredictor ? getNumString() : 0,
datePredictor ? getNumDate() : 0,
relationalPredictor ? getNumRelational() : 0,
multiInstance);
if (missingLevel > 0)
addMissing(train, missingLevel, predictorMissing, classMissing);
clusterers = AbstractClusterer.makeCopies(getClusterer(), 2);
evaluationB = new ClusterEvaluation();
evaluationI = new ClusterEvaluation();
clusterers[0].buildClusterer(train);
evaluationB.setClusterer(clusterers[0]);
} catch (Exception ex) {
throw new Error("Error setting up for tests: " + ex.getMessage());
}
try {
clusterers[1].buildClusterer(new Instances(train, 0));
for (int i = 0; i < train.numInstances(); i++) {
((UpdateableClusterer)clusterers[1]).updateClusterer(
train.instance(i));
}
built = true;
evaluationI.setClusterer(clusterers[1]);
if (!evaluationB.equals(evaluationI)) {
println("no");
result[0] = false;
if (m_Debug) {
println("\n=== Full Report ===");
println("Results differ between batch and "
+ "incrementally built models.\n"
+ "Depending on the classifier, this may be OK");
println("Here are the results:\n");
println("\nbatch built results\n" + evaluationB.clusterResultsToString());
println("\nincrementally built results\n" + evaluationI.clusterResultsToString());
println("Here are the datasets:\n");
println("=== Train Dataset ===\n"
+ train.toString() + "\n");
}
}
else {
println("yes");
result[0] = true;
}
} catch (Exception ex) {
result[0] = false;
print("Problem during");
if (built)
print(" testing");
else
print(" training");
println(": " + ex.getMessage() + "\n");
}
return result;
}
/**
* Runs a text on the datasets with the given characteristics.
*
* @param nominalPredictor if true use nominal predictor attributes
* @param numericPredictor if true use numeric predictor attributes
* @param stringPredictor if true use string predictor attributes
* @param datePredictor if true use date predictor attributes
* @param relationalPredictor if true use relational predictor attributes
* @param multiInstance whether multi-instance is needed
* @param missingLevel the percentage of missing values
* @param predictorMissing true if the missing values may be in
* the predictors
* @param numTrain the number of instances in the training set
* @param accepts the acceptable string in an exception
* @return index 0 is true if the test was passed, index 1 is true if test
* was acceptable
*/
protected boolean[] runBasicTest(boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance,
int missingLevel,
boolean predictorMissing,
int numTrain,
FastVector accepts) {
boolean[] result = new boolean[2];
Instances train = null;
Clusterer clusterer = null;
try {
train = makeTestDataset(42, numTrain,
nominalPredictor ? getNumNominal() : 0,
numericPredictor ? getNumNumeric() : 0,
stringPredictor ? getNumString() : 0,
datePredictor ? getNumDate() : 0,
relationalPredictor ? getNumRelational() : 0,
multiInstance);
if (nominalPredictor && !multiInstance)
train.deleteAttributeAt(0);
if (missingLevel > 0)
addMissing(train, missingLevel, predictorMissing);
clusterer = AbstractClusterer.makeCopies(getClusterer(), 1)[0];
} catch (Exception ex) {
ex.printStackTrace();
throw new Error("Error setting up for tests: " + ex.getMessage());
}
try {
clusterer.buildClusterer(train);
println("yes");
result[0] = true;
}
catch (Exception ex) {
boolean acceptable = false;
String msg = ex.getMessage().toLowerCase();
for (int i = 0; i < accepts.size(); i++) {
if (msg.indexOf((String)accepts.elementAt(i)) >= 0) {
acceptable = true;
}
}
println("no" + (acceptable ? " (OK error message)" : ""));
result[1] = acceptable;
if (m_Debug) {
println("\n=== Full Report ===");
print("Problem during training");
println(": " + ex.getMessage() + "\n");
if (!acceptable) {
if (accepts.size() > 0) {
print("Error message doesn't mention ");
for (int i = 0; i < accepts.size(); i++) {
if (i != 0) {
print(" or ");
}
print('"' + (String)accepts.elementAt(i) + '"');
}
}
println("here is the dataset:\n");
println("=== Train Dataset ===\n"
+ train.toString() + "\n");
}
}
}
return result;
}
/**
* Add missing values to a dataset.
*
* @param data the instances to add missing values to
* @param level the level of missing values to add (if positive, this
* is the probability that a value will be set to missing, if negative
* all but one value will be set to missing (not yet implemented))
* @param predictorMissing if true, predictor attributes will be modified
*/
protected void addMissing(Instances data, int level, boolean predictorMissing) {
Random random = new Random(1);
for (int i = 0; i < data.numInstances(); i++) {
Instance current = data.instance(i);
for (int j = 0; j < data.numAttributes(); j++) {
if (predictorMissing) {
if (Math.abs(random.nextInt()) % 100 < level)
current.setMissing(j);
}
}
}
}
/**
* Make a simple set of instances with variable position of the class
* attribute, which can later be modified for use in specific tests.
*
* @param seed the random number seed
* @param numInstances the number of instances to generate
* @param numNominal the number of nominal attributes
* @param numNumeric the number of numeric attributes
* @param numString the number of string attributes
* @param numDate the number of date attributes
* @param numRelational the number of relational attributes
* @param multiInstance whether the dataset should a multi-instance dataset
* @return the test dataset
* @throws Exception if the dataset couldn't be generated
* @see TestInstances#CLASS_IS_LAST
*/
protected Instances makeTestDataset(int seed, int numInstances,
int numNominal, int numNumeric,
int numString, int numDate,
int numRelational,
boolean multiInstance)
throws Exception {
TestInstances dataset = new TestInstances();
dataset.setSeed(seed);
dataset.setNumInstances(numInstances);
dataset.setNumNominal(numNominal);
dataset.setNumNumeric(numNumeric);
dataset.setNumString(numString);
dataset.setNumDate(numDate);
dataset.setNumRelational(numRelational);
dataset.setClassIndex(TestInstances.NO_CLASS);
dataset.setMultiInstance(multiInstance);
return dataset.generate();
}
/**
* Print out a short summary string for the dataset characteristics
*
* @param nominalPredictor true if nominal predictor attributes are present
* @param numericPredictor true if numeric predictor attributes are present
* @param stringPredictor true if string predictor attributes are present
* @param datePredictor true if date predictor attributes are present
* @param relationalPredictor true if relational predictor attributes are present
* @param multiInstance whether multi-instance is needed
*/
protected void printAttributeSummary(boolean nominalPredictor,
boolean numericPredictor,
boolean stringPredictor,
boolean datePredictor,
boolean relationalPredictor,
boolean multiInstance) {
String str = "";
if (numericPredictor)
str += "numeric";
if (nominalPredictor) {
if (str.length() > 0)
str += " & ";
str += "nominal";
}
if (stringPredictor) {
if (str.length() > 0)
str += " & ";
str += "string";
}
if (datePredictor) {
if (str.length() > 0)
str += " & ";
str += "date";
}
if (relationalPredictor) {
if (str.length() > 0)
str += " & ";
str += "relational";
}
str = " (" + str + " predictors)";
print(str);
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.11 $");
}
/**
* Test method for this class
*
* @param args the commandline options
*/
public static void main(String [] args) {
runCheck(new CheckClusterer(), args);
}
}
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