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autoweka.patch
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Index: src/main/java/weka/attributeSelection/AttributeSelection.java
===================================================================
--- src/main/java/weka/attributeSelection/AttributeSelection.java (revision 9272)
+++ src/main/java/weka/attributeSelection/AttributeSelection.java (working copy)
@@ -570,11 +570,11 @@
if (m_ASEvaluator instanceof AttributeEvaluator &&
!(m_searchMethod instanceof Ranker)) {
- System.err.println("AttributeEvaluators must use a Ranker search "
- +"method. Switching to Ranker...");
- m_searchMethod = new Ranker();
- // throw new Exception("AttributeEvaluators must use the Ranker search "
- // + "method");
+ // System.err.println("AttributeEvaluators must use a Ranker search "
+ // +"method. Switching to Ranker...");
+ // m_searchMethod = new Ranker();
+ throw new Exception("AttributeEvaluators must use the Ranker search "
+ + "method");
}
if (m_searchMethod instanceof RankedOutputSearch) {
diff -uNr trunk/weka/src/main/java/weka/attributeSelection/BestFirst.java /home/chris/src/autoweka/weka/src/main/java/weka/attributeSelection/BestFirst.java
--- src/main/java/weka/attributeSelection/BestFirst.java 2013-05-14 14:00:53.843247804 -0700
+++ src/main/java/weka/attributeSelection/BestFirst.java 2013-02-08 19:08:38.000000000 -0800
@@ -871,6 +871,8 @@
if (!added) {
stale++;
}
+ if(Thread.interrupted())
+ break;
}
m_bestMerit = best_merit;
diff -uNr trunk/weka/src/main/java/weka/attributeSelection/GreedyStepwise.java /home/chris/src/autoweka/weka/src/main/java/weka/attributeSelection/GreedyStepwise.java
--- src/main/java/weka/attributeSelection/GreedyStepwise.java 2013-05-14 14:00:53.843247804 -0700
+++ src/main/java/weka/attributeSelection/GreedyStepwise.java 2013-02-08 19:12:07.000000000 -0800
@@ -712,6 +712,8 @@
m_rankedAtts[m_rankedSoFar][1] = best_merit;
m_rankedSoFar++;
}
+ if(Thread.interrupted())
+ break;
}
m_bestMerit = best_merit;
return attributeList(m_best_group);
diff -uNr trunk/weka/src/main/java/weka/classifiers/Evaluation.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/Evaluation.java
--- src/main/java/weka/classifiers/Evaluation.java 2013-05-14 14:00:52.529914394 -0700
+++ src/main/java/weka/classifiers/Evaluation.java 2013-03-13 16:24:17.000000000 -0700
@@ -1649,6 +1649,8 @@
if (classificationOutput != null)
classificationOutput.printClassification(p, data.instance(i), i);
+ if(Thread.interrupted())
+ break;
}
} else {
// Need to be able to collect predictions if appropriate (for AUC)
@@ -1659,6 +1661,8 @@
if (classificationOutput != null)
classificationOutput.printClassification(classifier,
data.instance(i), i);
+ if(Thread.interrupted())
+ break;
}
}
@@ -2514,6 +2518,7 @@
}
text.append(title + "\n");
+
try {
if (m_WithClass > 0) {
if (m_ClassIsNominal) {
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/global/GeneticSearch.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/global/GeneticSearch.java
--- src/main/java/weka/classifiers/bayes/net/search/global/GeneticSearch.java 2013-05-14 14:00:52.273247713 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/global/GeneticSearch.java 2012-11-29 17:05:28.000000000 -0800
@@ -405,6 +405,8 @@
population[i] = descendantPopulation[iSelected];
bSelected[iSelected] = true;
}
+ if(Thread.interrupted())
+ break;
}
// restore current network to best network
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/global/HillClimber.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/global/HillClimber.java
--- src/main/java/weka/classifiers/bayes/net/search/global/HillClimber.java 2013-05-14 14:00:52.273247713 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/global/HillClimber.java 2012-11-29 17:05:28.000000000 -0800
@@ -157,6 +157,8 @@
performOperation(bayesNet, instances, oOperation);
fScore = oOperation.m_fScore;
oOperation = getOptimalOperation(bayesNet, instances);
+ if(Thread.interrupted())
+ break;
}
} // search
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/global/K2.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/global/K2.java
--- src/main/java/weka/classifiers/bayes/net/search/global/K2.java 2013-05-14 14:00:52.276581046 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/global/K2.java 2012-11-29 17:04:34.000000000 -0800
@@ -210,7 +210,11 @@
} else {
bProgress = false;
}
+ if(Thread.interrupted())
+ break;
}
+ if(Thread.interrupted())
+ break;
}
} // search
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/global/RepeatedHillClimber.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/global/RepeatedHillClimber.java
--- src/main/java/weka/classifiers/bayes/net/search/global/RepeatedHillClimber.java 2013-05-14 14:00:52.273247713 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/global/RepeatedHillClimber.java 2012-11-29 17:04:48.000000000 -0800
@@ -129,6 +129,8 @@
fBestScore = fCurrentScore;
copyParentSets(bestBayesNet, bayesNet);
}
+ if(Thread.interrupted())
+ break;
}
// restore current network to best network
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/global/SimulatedAnnealing.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/global/SimulatedAnnealing.java
--- src/main/java/weka/classifiers/bayes/net/search/global/SimulatedAnnealing.java 2013-05-14 14:00:52.273247713 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/global/SimulatedAnnealing.java 2012-11-29 17:05:07.000000000 -0800
@@ -195,11 +195,15 @@
}
}
}
+ if(Thread.interrupted())
+ break;
}
if (fCurrentScore > fBestScore) {
copyParentSets(bestBayesNet, bayesNet);
}
fTemp = fTemp * m_fDelta;
+ if(Thread.interrupted())
+ break;
}
copyParentSets(bayesNet, bestBayesNet);
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/global/TabuSearch.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/global/TabuSearch.java
--- src/main/java/weka/classifiers/bayes/net/search/global/TabuSearch.java 2013-05-14 14:00:52.273247713 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/global/TabuSearch.java 2012-11-29 17:05:20.000000000 -0800
@@ -187,6 +187,8 @@
if (bayesNet.getDebug()) {
printTabuList();
}
+ if(Thread.interrupted())
+ break;
}
// restore current network to best network
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/local/GeneticSearch.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/local/GeneticSearch.java
--- src/main/java/weka/classifiers/bayes/net/search/local/GeneticSearch.java 2013-05-14 14:00:52.356581050 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/local/GeneticSearch.java 2012-11-29 13:55:29.000000000 -0800
@@ -404,6 +404,8 @@
population[i] = descendantPopulation[iSelected];
bSelected[iSelected] = true;
}
+ if(Thread.interrupted())
+ break;
}
// restore current network to best network
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/local/HillClimber.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/local/HillClimber.java
--- src/main/java/weka/classifiers/bayes/net/search/local/HillClimber.java 2013-05-14 14:00:52.356581050 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/local/HillClimber.java 2012-11-29 13:56:23.000000000 -0800
@@ -217,6 +217,8 @@
while ((oOperation != null) && (oOperation.m_fDeltaScore > 0)) {
performOperation(bayesNet, instances, oOperation);
oOperation = getOptimalOperation(bayesNet, instances);
+ if(Thread.interrupted())
+ break;
}
// free up memory
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/local/K2.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/local/K2.java
--- src/main/java/weka/classifiers/bayes/net/search/local/K2.java 2013-05-14 14:00:52.356581050 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/local/K2.java 2012-11-29 18:16:35.000000000 -0800
@@ -192,7 +192,6 @@
for (int iOrder = 1; iOrder < instances.numAttributes(); iOrder++) {
int iAttribute = nOrder[iOrder];
double fBestScore = fBaseScores[iAttribute];
-
boolean bProgress = (bayesNet.getParentSet(iAttribute).getNrOfParents() < getMaxNrOfParents());
while (bProgress) {
int nBestAttribute = -1;
@@ -211,7 +210,11 @@
} else {
bProgress = false;
}
+ if(Thread.interrupted())
+ break;
}
+ if(Thread.interrupted())
+ break;
}
} // buildStructure
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/local/LAGDHillClimber.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/local/LAGDHillClimber.java
--- src/main/java/weka/classifiers/bayes/net/search/local/LAGDHillClimber.java 2013-05-14 14:00:52.356581050 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/local/LAGDHillClimber.java 2012-11-29 16:05:54.000000000 -0800
@@ -139,9 +139,15 @@
}
System.out.println("DeltaScore: "+sequenceDeltaScore);
+ if(Thread.interrupted())
+ break;
}
+ if(Thread.interrupted())
+ break;
}
--nrOfLookAheadSteps;
+ if(Thread.interrupted())
+ break;
}
/** last steps with greedy HC **/
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/local/RepeatedHillClimber.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/local/RepeatedHillClimber.java
--- src/main/java/weka/classifiers/bayes/net/search/local/RepeatedHillClimber.java 2013-05-14 14:00:52.353247717 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/local/RepeatedHillClimber.java 2012-11-29 16:11:04.000000000 -0800
@@ -130,7 +130,9 @@
if (fCurrentScore > fBestScore) {
fBestScore = fCurrentScore;
copyParentSets(bestBayesNet, bayesNet);
- }
+ }
+ if(Thread.interrupted())
+ break;
}
// restore current network to best network
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/local/SimulatedAnnealing.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/local/SimulatedAnnealing.java
--- src/main/java/weka/classifiers/bayes/net/search/local/SimulatedAnnealing.java 2013-05-14 14:00:52.356581050 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/local/SimulatedAnnealing.java 2012-11-29 16:12:14.000000000 -0800
@@ -198,11 +198,15 @@
}
}
}
+ if(Thread.interrupted())
+ break;
}
if (fCurrentScore > fBestScore) {
copyParentSets(bestBayesNet, bayesNet);
}
fTemp = fTemp * m_fDelta;
+ if(Thread.interrupted())
+ break;
}
copyParentSets(bayesNet, bestBayesNet);
diff -uNr trunk/weka/src/main/java/weka/classifiers/bayes/net/search/local/TabuSearch.java /home/chris/src/autoweka/weka/src/main/java/weka/classifiers/bayes/net/search/local/TabuSearch.java
--- src/main/java/weka/classifiers/bayes/net/search/local/TabuSearch.java 2013-05-14 14:00:52.353247717 -0700
+++ src/main/java/weka/classifiers/bayes/net/search/local/TabuSearch.java 2012-11-29 16:13:06.000000000 -0800
@@ -187,6 +187,8 @@
if (bayesNet.getDebug()) {
printTabuList();
}
+ if(Thread.interrupted())
+ break;
}
// restore current network to best network
Index: src/main/java/weka/classifiers/functions/Logistic.java
===================================================================
--- src/main/java/weka/classifiers/functions/Logistic.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/Logistic.java (working copy)
@@ -747,6 +747,8 @@
if (m_Debug)
System.out.println("First set of iterations finished, not enough!");
x = opt.findArgmin(x, b);
+ if(Thread.interrupted())
+ break;
}
if (m_Debug)
System.out.println(" -------------<Converged>--------------");
Index: src/main/java/weka/classifiers/functions/MultilayerPerceptron.java
===================================================================
--- src/main/java/weka/classifiers/functions/MultilayerPerceptron.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/MultilayerPerceptron.java (working copy)
@@ -2069,6 +2069,8 @@
m_instances = new Instances(m_instances, 0);
return;
}
+ if(Thread.interrupted())
+ return;
}
if (m_gui) {
m_win.dispose();
Index: src/main/java/weka/classifiers/functions/SGD.java
===================================================================
--- src/main/java/weka/classifiers/functions/SGD.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/SGD.java (working copy)
@@ -587,6 +587,8 @@
for (int i = 0; i < data.numInstances(); i++) {
updateClassifier(data.instance(i), false);
}
+ if(Thread.interrupted())
+ return;
}
}
Index: src/main/java/weka/classifiers/functions/SGDText.java
===================================================================
--- src/main/java/weka/classifiers/functions/SGDText.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/SGDText.java (working copy)
@@ -1153,6 +1153,8 @@
updateClassifier(data.instance(i), false);
}
}
+ if(Thread.interrupted())
+ return;
}
}
Index: src/main/java/weka/classifiers/functions/SMO.java
===================================================================
--- src/main/java/weka/classifiers/functions/SMO.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/SMO.java (working copy)
@@ -570,6 +570,8 @@
} else if (numChanged == 0) {
examineAll = true;
}
+ if(Thread.interrupted())
+ break;
}
// Set threshold
Index: src/main/java/weka/classifiers/functions/VotedPerceptron.java
===================================================================
--- src/main/java/weka/classifiers/functions/VotedPerceptron.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/VotedPerceptron.java (working copy)
@@ -349,6 +349,8 @@
}
}
}
+ if(Thread.interrupted())
+ break;
}
}
Index: src/main/java/weka/classifiers/functions/supportVector/RegSMO.java
===================================================================
--- src/main/java/weka/classifiers/functions/supportVector/RegSMO.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/supportVector/RegSMO.java (working copy)
@@ -850,6 +850,8 @@
if (loopCounter == 2500) {
break;
}
+ if(Thread.interrupted())
+ break;
}
// endmain
}
Index: src/main/java/weka/classifiers/functions/supportVector/RegSMOImproved.java
===================================================================
--- src/main/java/weka/classifiers/functions/supportVector/RegSMOImproved.java (revision 9272)
+++ src/main/java/weka/classifiers/functions/supportVector/RegSMOImproved.java (working copy)
@@ -856,6 +856,8 @@
} else if (nNumChanged == 0) {
bExamineAll = true;
}
+ if(Thread.interrupted())
+ break;
}
}
@@ -922,6 +924,8 @@
} else if (nNumChanged == 0) {
bExamineAll = true;
}
+ if(Thread.interrupted())
+ break;
}
}
Index: src/main/java/weka/classifiers/lazy/kstar/KStarNominalAttribute.java
===================================================================
--- src/main/java/weka/classifiers/lazy/kstar/KStarNominalAttribute.java (revision 9272)
+++ src/main/java/weka/classifiers/lazy/kstar/KStarNominalAttribute.java (working copy)
@@ -198,8 +198,7 @@
private double stopProbUsingEntropy() {
String debug = "(KStarNominalAttribute.stopProbUsingEntropy)";
if ( m_ClassType != Attribute.NOMINAL ) {
- System.err.println("Error: "+debug+" attribute class must be nominal!");
- System.exit(1);
+ throw new RuntimeException("Error: "+debug+" attribute class must be nominal!");
}
int itcount = 0;
double stopProb;
Index: src/main/java/weka/classifiers/lazy/kstar/KStarNumericAttribute.java
===================================================================
--- src/main/java/weka/classifiers/lazy/kstar/KStarNumericAttribute.java (revision 9272)
+++ src/main/java/weka/classifiers/lazy/kstar/KStarNumericAttribute.java (working copy)
@@ -365,8 +365,7 @@
private double scaleFactorUsingEntropy() {
String debug = "(KStarNumericAttribute.scaleFactorUsingEntropy)";
if ( m_ClassType != Attribute.NOMINAL ) {
- System.err.println("Error: "+debug+" attribute class must be nominal!");
- System.exit(1);
+ throw new RuntimeException("Error: "+debug+" attribute class must be nominal!");
}
int i,j, lowestcount = 0, count, itcount;
double lowest = -1.0, nextlowest = -1.0;
Index: src/main/java/weka/classifiers/trees/j48/NBTreeSplit.java
===================================================================
--- src/main/java/weka/classifiers/trees/j48/NBTreeSplit.java (revision 9272)
+++ src/main/java/weka/classifiers/trees/j48/NBTreeSplit.java (working copy)
@@ -162,7 +162,7 @@
ex.printStackTrace();
System.err.println("*** "+m_complexityIndex);
System.err.println(weights.length);
- System.exit(1);
+ throw new RuntimeException(ex);
}
}
}
Index: src/main/java/weka/classifiers/trees/lmt/LMTNode.java
===================================================================
--- src/main/java/weka/classifiers/trees/lmt/LMTNode.java (revision 9272)
+++ src/main/java/weka/classifiers/trees/lmt/LMTNode.java (working copy)
@@ -312,7 +312,7 @@
grow = false;
}
- if (grow) {
+ if (grow && !Thread.interrupted()) {
//create and build children of node
m_isLeaf = false;
Instances[] localInstances = m_localModel.split(m_train);
Index: src/main/java/weka/core/ConjugateGradientOptimization.java
===================================================================
--- src/main/java/weka/core/ConjugateGradientOptimization.java (revision 9272)
+++ src/main/java/weka/core/ConjugateGradientOptimization.java (working copy)
@@ -204,6 +204,10 @@
for (int i = 0; i < direct.length; i++) {
direct[i] = -grad[i] + Math.max(0, Math.min(betaHS, betaDY)) * direct[i];
}
+ if (Thread.interrupted()) {
+ finished = true;
+ break;
+ }
}
if (finished) {
Index: src/main/java/weka/core/Optimization.java
===================================================================
--- src/main/java/weka/core/Optimization.java (revision 9272)
+++ src/main/java/weka/core/Optimization.java (working copy)
@@ -1000,6 +1000,9 @@
if((hessian==null) && (toFree != null) && toFree.equal(oldToFree))
finish = true;
}
+
+ if(Thread.interrupted())
+ finish = true;
if(finish){// Min. found
if (m_Debug)
Index: src/main/java/weka/core/WekaPackageManager.java
===================================================================
--- src/main/java/weka/core/WekaPackageManager.java (revision 9272)
+++ src/main/java/weka/core/WekaPackageManager.java (working copy)
@@ -72,7 +72,7 @@
*/
public class WekaPackageManager {
- private static String WEKAFILES_DIR_NAME = "wekafiles";
+ private static String WEKAFILES_DIR_NAME = ".wekafiles";
public static File WEKA_HOME = new File(System.getProperty("user.home")
+ File.separator + WEKAFILES_DIR_NAME);
public static File PACKAGES_DIR = new File(System.getProperty("user.home")
Index: src/main/java/weka/filters/supervised/instance/Resample.java
===================================================================
--- src/main/java/weka/filters/supervised/instance/Resample.java (revision 9272)
+++ src/main/java/weka/filters/supervised/instance/Resample.java (working copy)
@@ -542,42 +542,55 @@
indices[i].add(n);
}
+ int s = 0;
+ for(int i = 0; i < classIndices.length - 1; i++)
+ s += indices[i].size();
+
// draw X samples
int currentSize = origSize;
+ int lastSize = -1;
for (int i = 0; i < sampleSize; i++) {
int index = 0;
if (random.nextDouble() < m_BiasToUniformClass) {
// Pick a random class (of those classes that actually appear)
int cIndex = random.nextInt(actualClasses);
+ boolean picked = false;
for (int j = 0, k = 0; j < classIndices.length - 1; j++) {
if ((classIndices[j] != classIndices[j + 1]) && (k++ >= cIndex)) {
// no more indices for this class left, try again
if (indices[j].size() == 0) {
- i--;
break;
}
// Pick a random instance of the designated class
index = random.nextInt(indices[j].size());
indicesNew[j].add(indices[j].get(index));
indices[j].remove(index);
+ picked = true;
break;
}
}
+ if(!picked)
+ i--;
}
else {
index = random.nextInt(currentSize);
- for (int n = 0; n < actualClasses; n++) {
+ boolean picked = false;
+ for (int n = 0; n < classIndices.length; n++) {
if (index < indices[n].size()) {
indicesNew[n].add(indices[n].get(index));
indices[n].remove(index);
+ picked = true;
+ currentSize--;
break;
}
else {
index -= indices[n].size();
}
}
- currentSize--;
+ if (!picked)
+ i--;
}
+ lastSize = currentSize;
}