@Override
public double[] distributionForInstance(Instance xy) throws Exception {
int L = xy.classIndex();
double y[] = new double[L];
double w = 0.0;
/*
* e.g. K = [3,3,5]
* we push y_[] from [0,0,0] to [2,2,4] over all necessary iterations.
*/
int K[] = getKs(xy.dataset());
if (getDebug()) System.out.println("K[] = " + Arrays.toString(K));
double y_[] = new double[L];
for (int i = 0; i < 1000000; i++) { // limit to 1m
// System.out.println(""+i+" "+Arrays.toString(y_));
double w_ = A.product(super.probabilityForInstance(xy, y_));
if (w_ > w) {
if (getDebug()) System.out.println("y' = " + Arrays.toString(y_) + ", :" + w_);
y = Arrays.copyOf(y_, y_.length);
w = w_;
}
if (push(y_, K, 0)) {
// Done !
if (getDebug()) System.out.println("Tried all " + (i + 1) + " combinations.");
break;
}
}
return y;
}
/** This is (mostly) copied from CRF4.java */
public boolean[][] labelConnectionsIn(
Alphabet outputAlphabet, InstanceList trainingSet, String start) {
int numLabels = outputAlphabet.size();
boolean[][] connections = new boolean[numLabels][numLabels];
for (int i = 0; i < trainingSet.size(); i++) {
Instance instance = trainingSet.getInstance(i);
FeatureSequence output = (FeatureSequence) instance.getTarget();
for (int j = 1; j < output.size(); j++) {
int sourceIndex = outputAlphabet.lookupIndex(output.get(j - 1));
int destIndex = outputAlphabet.lookupIndex(output.get(j));
assert (sourceIndex >= 0 && destIndex >= 0);
connections[sourceIndex][destIndex] = true;
}
}
// Handle start state
if (start != null) {
int startIndex = outputAlphabet.lookupIndex(start);
for (int j = 0; j < outputAlphabet.size(); j++) {
connections[startIndex][j] = true;
}
}
return connections;
}
public int accept(int ins_num, int income_seq, String content) throws RemoteException {
if (!work) return -1;
Instance res = instances.get(ins_num);
if (res == null) return -1;
else {
if (income_seq >= res.n_p) {
res.n_p = income_seq;
res.n_a = income_seq;
res.content = content;
res.decided = true;
INS_NUM++;
return income_seq;
}
}
return -1;
}
public static void printNeighbors(ArrayList neighbors) {
int i = 0;
for(Neighbor neighbor : neighbors) {
Instance instance = neighbor.getInstance();
System.out.println("\nNeighbor " + (i + 1) + ", distance: " + neighbor.getDistance());
i++;
for(Feature f : instance.getAttributes()) {
System.out.print(f.getName() + ": ");
if(f instanceof Category) {
System.out.println(((Category)f).getCategory().toString());
}
else if(f instanceof Distance) {
System.out.println(((Distance)f).getDistance().toString());
}
else if (f instanceof Expiration) {
System.out.println(((Expiration)f).getExpiry().toString());
}
else if (f instanceof Handset) {
System.out.print(((Handset)f).getOs().toString() + ", ");
System.out.println(((Handset)f).getDevice().toString());
}
else if (f instanceof Offer) {
System.out.println(((Offer)f).getOfferType().toString());
}
else if (f instanceof WSAction) {
System.out.println(((WSAction)f).getAction().toString());
}
}
}
}
/**
* Determines whether the AMI of the given instance matches the AMI of template and has the
* required label (if requiredLabel is non-null)
*/
private boolean checkInstance(
PrintStream logger,
Instance existingInstance,
Label requiredLabel,
EC2AbstractSlave[] returnNode) {
logProvision(logger, "checkInstance: " + existingInstance);
if (StringUtils.isNotBlank(getIamInstanceProfile())) {
if (existingInstance.getIamInstanceProfile() != null) {
if (!existingInstance.getIamInstanceProfile().getArn().equals(getIamInstanceProfile())) {
logProvision(logger, " false - IAM Instance profile does not match");
return false;
}
// Match, fall through
} else {
logProvision(logger, " false - Null IAM Instance profile");
return false;
}
}
if (existingInstance
.getState()
.getName()
.equalsIgnoreCase(InstanceStateName.Terminated.toString())
|| existingInstance
.getState()
.getName()
.equalsIgnoreCase(InstanceStateName.ShuttingDown.toString())) {
logProvision(logger, " false - Instance is terminated or shutting down");
return false;
}
// See if we know about this and it has capacity
for (EC2AbstractSlave node : NodeIterator.nodes(EC2AbstractSlave.class)) {
if (node.getInstanceId().equals(existingInstance.getInstanceId())) {
logProvision(logger, "Found existing corresponding Jenkins slave: " + node.getInstanceId());
if (!node.toComputer().isPartiallyIdle()) {
logProvision(logger, " false - Node is not partially idle");
return false;
}
// REMOVEME - this was added to force provision to work, but might not allow
// stopped instances to be found - need to investigate further
else if (false && node.toComputer().isOffline()) {
logProvision(logger, " false - Node is offline");
return false;
} else if (requiredLabel != null && !requiredLabel.matches(node.getAssignedLabels())) {
logProvision(logger, " false - we need a Node having label " + requiredLabel);
return false;
} else {
logProvision(logger, " true - Node has capacity - can use it");
returnNode[0] = node;
return true;
}
}
}
logProvision(logger, " true - Instance has no node, but can be used");
return true;
}
private boolean containInstance(Instance sel, Slot slot, Instance instance) {
if (itsInstance == null) return false;
Collection instances = sel.getOwnSlotValues(slot);
Iterator i = instances.iterator();
while (i.hasNext()) {
Instance tmpInstance = (Instance) i.next();
if (tmpInstance.equals(instance)) return true;
}
return false;
}
public String toString() {
StringBuffer buf = new StringBuffer();
for (int i = 0; i < numSources(); i++) {
String src = getSource(i);
for (int j = 0; j < numInstances(src); j++) {
Instance inst = getInstance(src, j);
buf.append(inst.toString() + "\n");
}
}
return buf.toString();
}
/**
* Labels the artificially generated data.
*
* @param artData the artificially generated instances
* @exception Exception if instances cannot be labeled successfully
*/
protected void labelData(Instances artData) throws Exception {
Instance curr;
double[] probs;
for (int i = 0; i < artData.numInstances(); i++) {
curr = artData.instance(i);
// compute the class membership probs predicted by the current ensemble
probs = distributionForInstance(curr);
// select class label inversely proportional to the ensemble predictions
curr.setClassValue(inverseLabel(probs));
}
}
/**
* Computes the error in classification on the given data.
*
* @param data the instances to be classified
* @return classification error
* @exception Exception if error can not be computed successfully
*/
protected double computeError(Instances data) throws Exception {
double error = 0.0;
int numInstances = data.numInstances();
Instance curr;
for (int i = 0; i < numInstances; i++) {
curr = data.instance(i);
// Check if the instance has been misclassified
if (curr.classValue() != ((int) classifyInstance(curr))) error++;
}
return (error / numInstances);
}
public void dump() throws RemoteException {
int num_ins = instances.size();
System.out.println(getServerName() + ":");
for (int i = 1; i <= num_ins; i++) {
Instance tmp = instances.get(i);
System.out.println(i + ": " + tmp.toString());
}
return;
}
public static void main(String[] args) {
ArrayList instances = null;
ArrayList distances = null;
ArrayList neighbors = null;
WSAction.Action classification = null;
Instance classificationInstance = null;
FileReader reader = null;
int numRuns = 0, truePositives = 0, falsePositives = 0, falseNegatives = 0, trueNegatives = 0;
double precision = 0, recall = 0, fMeasure = 0;
falsePositives = 1;
reader = new FileReader(PATH_TO_DATA_FILE);
instances = reader.buildInstances();
do {
classificationInstance = extractIndividualInstance(instances);
distances = calculateDistances(instances, classificationInstance);
neighbors = getNearestNeighbors(distances);
classification = determineMajority(neighbors);
System.out.println("Gathering " + K + " nearest neighbors to:");
printClassificationInstance(classificationInstance);
printNeighbors(neighbors);
System.out.println("\nExpected situation result for instance: " + classification.toString());
if(classification.toString().equals(((WSAction)classificationInstance.getAttributes().get(WSACTION_INDEX)).getAction().toString())) {
truePositives++;
}
else {
falseNegatives++;
}
numRuns++;
instances.add(classificationInstance);
} while(numRuns < NUM_RUNS);
precision = ((double)(truePositives / (double)(truePositives + falsePositives)));
recall = ((double)(truePositives / (double)(truePositives + falseNegatives)));
fMeasure = ((double)(precision * recall) / (double)(precision + recall));
System.out.println("Precision: " + precision);
System.out.println("Recall: " + recall);
System.out.println("F-Measure: " + fMeasure);
System.out.println("Average distance: " + (double)(averageDistance / (double)(NUM_RUNS * K)));
}
private boolean testInstance(int testIndex, Instance instance, Slot slot) {
String value;
if (specification.getValue() == null) return false;
if (((String) specification.getValue()).length() < 1) return false;
value = instance.getBrowserText();
return testInstance(testIndex, instance, slot, value);
}
public Instance prepare(int ins_num, int income_seq) throws RemoteException {
if (!work) return null;
Instance res = instances.get(ins_num);
if (res == null) return null;
else {
if (income_seq > res.n_p) {
res.n_p = income_seq;
return res;
} else return null;
}
}
/**
* It checks if the complex covers a given example
*
* @param m The example
* @return boolean True if it covers the example. False in other case
*/
public boolean covered(Instance m) {
boolean cubierto = true;
double[] ejemplo = m.getMuest();
for (int i = 0; i < this.size() && cubierto; i++) {
Selector s = this.getSelector(i);
switch (s.getOperator()) {
case 0: // equal operator
double[] valor = s.getValues();
cubierto = false;
for (int j = 0; (j < valor.length) && (!cubierto); j++) {
cubierto = (ejemplo[s.getAttribute()] == valor[j]);
}
break;
case 1: // distinct operator
cubierto = ejemplo[s.getAttribute()] != s.getValue();
break;
case 2: // lower or equal
cubierto = ejemplo[s.getAttribute()] <= s.getValue();
break;
case 3: // higher
cubierto = ejemplo[s.getAttribute()] > s.getValue();
break;
}
}
return cubierto;
}
/** Analogous to binaryFeatureSet */
private Set<Feature> numericFeatureSet(int start, int end, Instance otherInstance) {
Set<Feature> s = new HashSet<Feature>();
for (int i = start; i < end; i++) {
addAll(s, unitInstance[i].numericFeatureIterator());
}
if (otherInstance != null) addAll(s, otherInstance.numericFeatureIterator());
return s;
}
public void updated(final Instance instance) {
if (!Player.Slides.PLAYLIST.equals(listActivity.getCurrSlide())) {
return;
}
Instance instanceToAdd =
instance.accept(
new InstanceVisitor<Instance>() {
public Instance visit(Track track) {
if (getFilter().accept(new MatchFilterVisitor<Track, Tables.Tracks>(track))) {
switch (currMode) {
case Album:
return track.GetAlbum() == AlbumDigest.NO_ALBUM ? track : track.GetAlbum();
case Artist:
return track.GetArtist() == ArtistDigest.NO_ARTIST
? track
: track.GetArtist();
case Genre:
return track.GetGenre() == GenreDigest.NO_GENRE ? track : track.GetGenre();
case Track:
return track;
case Dir:
return track;
default:
throw new RuntimeException(currMode.name() + " not expexted here");
}
}
return null;
}
public Instance visit(SongDigest track) {
throw new RuntimeException("not supported yet");
}
public Instance visit(Album album) {
throw new RuntimeException("not supported yet");
}
public Instance visit(GenreDigest genre) {
throw new RuntimeException("not supported yet");
}
public Instance visit(ArtistDigest artist) {
throw new RuntimeException("not supported yet");
}
public Instance visit(FSobject dir) {
return getDirFilter().accept(new MatchFilterVisitor<FSobject, Tables.Dirs>(dir))
&& Mode.Dir.equals(currMode)
? dir
: null;
}
});
if (instanceToAdd != null) {
listAdapter.add(instanceToAdd);
}
}
/**
* Calculates the class membership probabilities for the given test instance.
*
* @param instance the instance to be classified
* @return predicted class probability distribution
* @exception Exception if distribution can't be computed successfully
*/
public double[] distributionForInstance(Instance instance) throws Exception {
if (instance.classAttribute().isNumeric()) {
throw new UnsupportedClassTypeException("Decorate can't handle a numeric class!");
}
double[] sums = new double[instance.numClasses()], newProbs;
Classifier curr;
for (int i = 0; i < m_Committee.size(); i++) {
curr = (Classifier) m_Committee.get(i);
newProbs = curr.distributionForInstance(instance);
for (int j = 0; j < newProbs.length; j++) sums[j] += newProbs[j];
}
if (Utils.eq(Utils.sum(sums), 0)) {
return sums;
} else {
Utils.normalize(sums);
return sums;
}
}
/**
* Returns the fraction of correct instances of the instance's set for the rule 'regla'
*
* @param i Number of the rule
* @return Fraction of correct instances of the instance's set for the rule 'regla'
*/
private double getAccuracy(int i) {
Instance instancia;
double Accuracy;
num_cubiertas = 0;
num_correctas = 0;
for (int k = 0; k < instancias.getNumInstances(); k++) {
instancia = instancias.getInstance(k);
cubierta = regla.reglaCubreInstancia(instancia);
if (cubierta) {
num_cubiertas++;
clase = instancia.getOutputNominalValuesInt(0);
if (clase == i) num_correctas++;
}
}
Accuracy = (double) num_correctas / (double) num_cubiertas;
if (num_cubiertas == 0) Accuracy = 0;
return Accuracy;
}
/**
* Calculates the distance between two instances
*
* @param test the first instance
* @param train the second instance
* @return the distance between the two given instances, between 0 and 1
*/
protected double distance(Instance first, Instance second) {
double distance = 0;
int firstI, secondI;
for (int p1 = 0, p2 = 0; p1 < first.numValues() || p2 < second.numValues(); ) {
if (p1 >= first.numValues()) {
firstI = m_instances.numAttributes();
} else {
firstI = first.index(p1);
}
if (p2 >= second.numValues()) {
secondI = m_instances.numAttributes();
} else {
secondI = second.index(p2);
}
if (firstI == m_instances.classIndex()) {
p1++;
continue;
}
if (secondI == m_instances.classIndex()) {
p2++;
continue;
}
double diff;
if (firstI == secondI) {
diff = difference(firstI, first.valueSparse(p1), second.valueSparse(p2));
p1++;
p2++;
} else if (firstI > secondI) {
diff = difference(secondI, 0, second.valueSparse(p2));
p2++;
} else {
diff = difference(firstI, first.valueSparse(p1), 0);
p1++;
}
distance += diff * diff;
}
return Math.sqrt(distance / m_instances.numAttributes());
}
/**
* Input an instance for filtering. Ordinarily the instance is processed and made available for
* output immediately. Some filters require all instances be read before producing output.
*
* @param instance the input instance
* @return true if the filtered instance may now be collected with output().
* @exception IllegalStateException if no input format has been defined.
*/
public boolean input(Instance instance) {
if (getInputFormat() == null) {
throw new IllegalStateException("No input instance format defined");
}
if (m_NewBatch) {
resetQueue();
m_NewBatch = false;
}
push((Instance) instance.copy());
return true;
}
/**
* Removes from the instance's set those instances that matches with the rule
*
* @param i Numebr of the rule
*/
private void removeInstancesCovered(int i) {
for (int k = 0; k < instancias.getNumInstances(); k++) {
instancia = instancias.getInstance(k);
/*System.out.print(k+" ");
instancia.print();
System.out.println();*/
cubierta = regla.reglaCubreInstancia(instancia);
if (cubierta) {
// System.out.println("CUBIERTA");
clase = instancia.getOutputNominalValuesInt(0);
// if(clase==i){
instancias.removeInstance(k);
instancia.print();
System.out.println();
k = k - 1;
// }
}
}
}
/**
* Classifies an instance w.r.t. the partitions found. It applies a naive min-distance algorithm.
*
* @param instance the instance to classify
* @return the cluster that contains the nearest point to the instance
*/
public int clusterInstance(Instance instance) throws java.lang.Exception {
DoubleMatrix1D u = DoubleFactory1D.dense.make(instance.toDoubleArray());
double min_dist = Double.POSITIVE_INFINITY;
int c = -1;
for (int i = 0; i < v.rows(); i++) {
double dist = distnorm2(u, v.viewRow(i));
if (dist < min_dist) {
c = cluster[i];
min_dist = dist;
}
}
return c;
}
public void decide(int income_seq, Operation op) throws RemoteException {
// set corresponding Op decided, assume no collision happens
if (!work) return;
if (op == null) return;
Instance ins = instances.get(op.op_num);
if (!ins.decided) {
ins.decided = true;
INS_NUM++;
ins.n_a = income_seq;
ins.content = op.content;
}
return;
}
/* The main tree traversal function; if node is a leaf,
* return classification; otherwise, determine whether
* instance is higher or lower than this attribute-value
* pair and returns testInstance of proper child
*/
public boolean testInstance(Instance in) {
if (majority) {
return majClass;
}
if (leaf) {
return classification;
} else {
if (in.get((int) attribute) <= value) {
return leftChild.testInstance(in);
} else {
return rightChild.testInstance(in);
}
}
}
protected EC2OndemandSlave newOndemandSlave(Instance inst) throws FormException, IOException {
return new EC2OndemandSlave(
inst.getInstanceId(),
description,
remoteFS,
getNumExecutors(),
labels,
mode,
initScript,
tmpDir,
remoteAdmin,
jvmopts,
stopOnTerminate,
idleTerminationMinutes,
inst.getPublicDnsName(),
inst.getPrivateDnsName(),
EC2Tag.fromAmazonTags(inst.getTags()),
parent.name,
usePrivateDnsName,
useDedicatedTenancy,
getLaunchTimeout(),
amiType);
}
/**
* @param selection
* @return null if no track was selected, track if trak was selected
*/
public Track choose(Instance selection) {
return selection.accept(
new InstanceVisitor<Track>() {
public Track visit(Track track) {
return track;
}
public Track visit(SongDigest track) {
Filter<Tables.SongsReadable> trackFilter =
new FieldFilter<Tables.SongsReadable, Track, String>(
Tables.SongsReadable.TITLE, Operator.EQ, track.getSongName());
return database
.getTracks(new FilterSet<Tables.Tracks>(getFilter(), trackFilter))
.iterator()
.next();
}
public Track visit(Album album) {
Filter<Tables.AlbumsReadable> filter =
new FieldFilter<Tables.AlbumsReadable, Track, String>(
Tables.AlbumsReadable.ALBUM, Operator.EQ, album.getAlbumId());
change(Mode.Track, filter, false);
return null;
}
public Track visit(GenreDigest genre) {
Filter<Tables.GenresReadable> filter =
new FieldFilter<Tables.GenresReadable, Track, String>(
Tables.GenresReadable.GENRE, Operator.EQ, genre.getGenreId());
change(Mode.Artist, filter, false);
return null;
}
public Track visit(ArtistDigest artist) {
Filter<Tables.ArtistsReadable> filter =
new FieldFilter<Tables.ArtistsReadable, Track, String>(
Tables.ArtistsReadable.ARTIST, Operator.EQ, artist.getArtistId());
change(Mode.Album, filter, false);
return null;
}
public Track visit(FSobject FSobject) {
Filter<Tables.FsObjects> filter =
new DirFilter(Operator.LIKE, FSobject.getFullPath() + "/%");
change(Mode.Dir, filter, true);
return null;
}
});
}
@Test
public void testSplittable() throws SchedulerException {
List<VM> vms = Arrays.asList(vm1, vm2, vm3);
Collection<Collection<Node>> parts = new ArrayList<>();
parts.add(Arrays.asList(n1, n2));
parts.add(Arrays.asList(n3));
parts.add(Arrays.asList(n4));
Among single = new Among(vms, parts);
/*
N1 v1 v2
N2 v3
---
N3 v4
--
N4 v5
*/
FixedNodeSetsPartitioning partitionner = new FixedNodeSetsPartitioning(parts);
partitionner.setPartitions(parts);
List<Instance> instances =
partitionner.split(
new DefaultParameters(),
new Instance(mo, Collections.<SatConstraint>emptyList(), new MinMTTR()));
TIntIntHashMap vmIndex = Instances.makeVMIndex(instances);
TIntIntHashMap nodeIndex = Instances.makeNodeIndex(instances);
splitter.split(single, new Instance(mo, new MinMTTR()), instances, vmIndex, nodeIndex);
Among a = (Among) instances.get(0).getSatConstraints().iterator().next();
Assert.assertEquals(a.getGroupsOfNodes().size(), 1);
Assert.assertEquals(a.getInvolvedNodes(), Arrays.asList(n1, n2));
for (Instance i : instances) {
System.out.println(i.getSatConstraints());
}
}
public void buildClusterer(ArrayList<String> seqDB, double[][] sm) {
seqList = seqDB;
this.setSimMatrix(sm);
Attribute seqString = new Attribute("sequence", (FastVector) null);
FastVector attrInfo = new FastVector();
attrInfo.addElement(seqString);
Instances data = new Instances("data", attrInfo, 0);
for (int i = 0; i < seqList.size(); i++) {
Instance currentInst = new Instance(1);
currentInst.setDataset(data);
currentInst.setValue(0, seqList.get(i));
data.add(currentInst);
}
try {
buildClusterer(data);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/**
* Calculates the class membership probabilities for the given test instance.
*
* @param instance the instance to be classified
* @return predicted class probability distribution
* @throws Exception if distribution can't be computed
*/
public double[] distributionForInstance(Instance instance) throws Exception {
DecisionTableHashKey thekey;
double[] tempDist;
double[] normDist;
m_disTransform.input(instance);
m_disTransform.batchFinished();
instance = m_disTransform.output();
m_delTransform.input(instance);
m_delTransform.batchFinished();
instance = m_delTransform.output();
thekey = new DecisionTableHashKey(instance, instance.numAttributes(), false);
// if this one is not in the table
if ((tempDist = (double[]) m_entries.get(thekey)) == null) {
if (m_useIBk) {
tempDist = m_ibk.distributionForInstance(instance);
} else {
if (!m_classIsNominal) {
tempDist = new double[1];
tempDist[0] = m_majority;
} else {
tempDist = m_classPriors.clone();
/*tempDist = new double [m_theInstances.classAttribute().numValues()];
tempDist[(int)m_majority] = 1.0; */
}
}
} else {
if (!m_classIsNominal) {
normDist = new double[1];
normDist[0] = (tempDist[0] / tempDist[1]);
tempDist = normDist;
} else {
// normalise distribution
normDist = new double[tempDist.length];
System.arraycopy(tempDist, 0, normDist, 0, tempDist.length);
Utils.normalize(normDist);
tempDist = normDist;
}
}
return tempDist;
}
/**
* Gets the subset of instances that apply to a particluar branch of the split. If the branch
* index is -1, the subset will consist of those instances that don't apply to any branch.
*
* @param branch the index of the branch
* @param sourceInstances the instances from which to find the subset
* @return the set of instances that apply
*/
public ReferenceInstances instancesDownBranch(int branch, Instances instances) {
ReferenceInstances filteredInstances = new ReferenceInstances(instances, 1);
if (branch == -1) {
for (Enumeration e = instances.enumerateInstances(); e.hasMoreElements(); ) {
Instance inst = (Instance) e.nextElement();
if (inst.isMissing(attIndex)) filteredInstances.addReference(inst);
}
} else if (branch == 0) {
for (Enumeration e = instances.enumerateInstances(); e.hasMoreElements(); ) {
Instance inst = (Instance) e.nextElement();
if (!inst.isMissing(attIndex) && inst.value(attIndex) < splitPoint)
filteredInstances.addReference(inst);
}
} else {
for (Enumeration e = instances.enumerateInstances(); e.hasMoreElements(); ) {
Instance inst = (Instance) e.nextElement();
if (!inst.isMissing(attIndex) && inst.value(attIndex) >= splitPoint)
filteredInstances.addReference(inst);
}
}
return filteredInstances;
}