/** Computes average class values for each attribute and value */
private void computeAverageClassValues() {
double totalCounts, sum;
Instance instance;
double[] counts;
double[][] avgClassValues = new double[getInputFormat().numAttributes()][0];
m_Indices = new int[getInputFormat().numAttributes()][0];
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if (att.isNominal()) {
avgClassValues[j] = new double[att.numValues()];
counts = new double[att.numValues()];
for (int i = 0; i < getInputFormat().numInstances(); i++) {
instance = getInputFormat().instance(i);
if (!instance.classIsMissing() && (!instance.isMissing(j))) {
counts[(int) instance.value(j)] += instance.weight();
avgClassValues[j][(int) instance.value(j)] += instance.weight() * instance.classValue();
}
}
sum = Utils.sum(avgClassValues[j]);
totalCounts = Utils.sum(counts);
if (Utils.gr(totalCounts, 0)) {
for (int k = 0; k < att.numValues(); k++) {
if (Utils.gr(counts[k], 0)) {
avgClassValues[j][k] /= counts[k];
} else {
avgClassValues[j][k] = sum / totalCounts;
}
}
}
m_Indices[j] = Utils.sort(avgClassValues[j]);
}
}
}
/**
* Set the output format. Takes the current average class values and m_InputFormat and calls
* setOutputFormat(Instances) appropriately.
*/
private void setOutputFormat() {
Instances newData;
FastVector newAtts, newVals;
// Compute new attributes
newAtts = new FastVector(getInputFormat().numAttributes());
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if (!m_AttIndices.isInRange(j) || !att.isString()) {
// We don't have to copy the attribute because the
// attribute index remains unchanged.
newAtts.addElement(att);
} else {
// Compute list of attribute values
newVals = new FastVector(att.numValues());
for (int i = 0; i < att.numValues(); i++) {
newVals.addElement(att.value(i));
}
newAtts.addElement(new Attribute(att.name(), newVals));
}
}
// Construct new header
newData = new Instances(getInputFormat().relationName(), newAtts, 0);
newData.setClassIndex(getInputFormat().classIndex());
setOutputFormat(newData);
}
/**
* Adds this tree recursively to the buffer.
*
* @param id the unqiue id for the method
* @param buffer the buffer to add the source code to
* @return the last ID being used
* @throws Exception if something goes wrong
*/
protected int toSource(int id, StringBuffer buffer) throws Exception {
int result;
int i;
int newID;
StringBuffer[] subBuffers;
buffer.append("\n");
buffer.append(" protected static double node" + id + "(Object[] i) {\n");
// leaf?
if (m_Attribute == null) {
result = id;
if (Double.isNaN(m_ClassValue)) buffer.append(" return Double.NaN;");
else buffer.append(" return " + m_ClassValue + ";");
if (m_ClassAttribute != null)
buffer.append(" // " + m_ClassAttribute.value((int) m_ClassValue));
buffer.append("\n");
buffer.append(" }\n");
} else {
buffer.append(" // " + m_Attribute.name() + "\n");
// subtree calls
subBuffers = new StringBuffer[m_Attribute.numValues()];
newID = id;
for (i = 0; i < m_Attribute.numValues(); i++) {
newID++;
buffer.append(" ");
if (i > 0) buffer.append("else ");
buffer.append(
"if (((String) i["
+ m_Attribute.index()
+ "]).equals(\""
+ m_Attribute.value(i)
+ "\"))\n");
buffer.append(" return node" + newID + "(i);\n");
subBuffers[i] = new StringBuffer();
newID = m_Successors[i].toSource(newID, subBuffers[i]);
}
buffer.append(" else\n");
buffer.append(
" throw new IllegalArgumentException(\"Value '\" + i["
+ m_Attribute.index()
+ "] + \"' is not allowed!\");\n");
buffer.append(" }\n");
// output subtree code
for (i = 0; i < m_Attribute.numValues(); i++) {
buffer.append(subBuffers[i].toString());
}
subBuffers = null;
result = newID;
}
return result;
}
/**
* Convert a single instance over if the class is nominal. The converted instance is added to the
* end of the output queue.
*
* @param instance the instance to convert
*/
private void convertInstanceNominal(Instance instance) {
if (!m_needToTransform) {
push(instance);
return;
}
double[] vals = new double[outputFormatPeek().numAttributes()];
int attSoFar = 0;
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if ((!att.isNominal()) || (j == getInputFormat().classIndex())) {
vals[attSoFar] = instance.value(j);
attSoFar++;
} else {
if ((att.numValues() <= 2) && (!m_TransformAll)) {
vals[attSoFar] = instance.value(j);
attSoFar++;
} else {
if (instance.isMissing(j)) {
for (int k = 0; k < att.numValues(); k++) {
vals[attSoFar + k] = instance.value(j);
}
} else {
for (int k = 0; k < att.numValues(); k++) {
if (k == (int) instance.value(j)) {
vals[attSoFar + k] = 1;
} else {
vals[attSoFar + k] = 0;
}
}
}
attSoFar += att.numValues();
}
}
}
Instance inst = null;
if (instance instanceof SparseInstance) {
inst = new SparseInstance(instance.weight(), vals);
} else {
inst = new DenseInstance(instance.weight(), vals);
}
inst.setDataset(getOutputFormat());
copyValues(inst, false, instance.dataset(), getOutputFormat());
inst.setDataset(getOutputFormat());
push(inst);
}
/**
* Sets up the structure for the plot instances. Sets m_PlotInstances to null if instances are not
* saved for visualization.
*
* @see #getSaveForVisualization()
*/
protected void determineFormat() {
FastVector hv;
Attribute predictedClass;
Attribute classAt;
FastVector attVals;
int i;
if (!m_SaveForVisualization) {
m_PlotInstances = null;
return;
}
hv = new FastVector();
classAt = m_Instances.attribute(m_ClassIndex);
if (classAt.isNominal()) {
attVals = new FastVector();
for (i = 0; i < classAt.numValues(); i++) attVals.addElement(classAt.value(i));
predictedClass = new Attribute("predicted" + classAt.name(), attVals);
} else {
predictedClass = new Attribute("predicted" + classAt.name());
}
for (i = 0; i < m_Instances.numAttributes(); i++) {
if (i == m_Instances.classIndex()) hv.addElement(predictedClass);
hv.addElement(m_Instances.attribute(i).copy());
}
m_PlotInstances =
new Instances(m_Instances.relationName() + "_predicted", hv, m_Instances.numInstances());
m_PlotInstances.setClassIndex(m_ClassIndex + 1);
}
/**
* Splits a dataset according to the values of a nominal attribute.
*
* @param data the data which is to be split
* @param att the attribute to be used for splitting
* @return the sets of instances produced by the split
*/
private Instances[] splitData(Instances data, Attribute att) {
Instances[] splitData = new Instances[att.numValues()];
for (int j = 0; j < att.numValues(); j++) {
splitData[j] = new Instances(data, data.numInstances());
}
Enumeration instEnum = data.enumerateInstances();
while (instEnum.hasMoreElements()) {
Instance inst = (Instance) instEnum.nextElement();
splitData[(int) inst.value(att)].add(inst);
}
for (int i = 0; i < splitData.length; i++) {
splitData[i].compactify();
}
return splitData;
}
/**
* Cálculo da precisão de Laplace
*
* @return Precisão de Laplace
*/
public double getLaplace() {
double temp = matrizContigencia.getB();
int numClasses = classe.numValues();
if (temp != 0) laplace = (matrizContigencia.getH_B() + 1) / (temp + numClasses);
else laplace = 0;
return laplace;
}
/**
* Determines the output format based on the input format and returns this.
*
* @param inputFormat the input format to base the output format on
* @return the output format
* @throws Exception in case the determination goes wrong
*/
protected Instances determineOutputFormat(Instances inputFormat) throws Exception {
Instances result;
Attribute att;
Attribute attSorted;
FastVector atts;
FastVector values;
Vector<String> sorted;
int i;
int n;
m_AttributeIndices.setUpper(inputFormat.numAttributes() - 1);
// determine sorted indices
atts = new FastVector();
m_NewOrder = new int[inputFormat.numAttributes()][];
for (i = 0; i < inputFormat.numAttributes(); i++) {
att = inputFormat.attribute(i);
if (!att.isNominal() || !m_AttributeIndices.isInRange(i)) {
m_NewOrder[i] = new int[0];
atts.addElement(inputFormat.attribute(i).copy());
continue;
}
// sort labels
sorted = new Vector<String>();
for (n = 0; n < att.numValues(); n++) sorted.add(att.value(n));
Collections.sort(sorted, m_Comparator);
// determine new indices
m_NewOrder[i] = new int[att.numValues()];
values = new FastVector();
for (n = 0; n < att.numValues(); n++) {
m_NewOrder[i][n] = sorted.indexOf(att.value(n));
values.addElement(sorted.get(n));
}
attSorted = new Attribute(att.name(), values);
attSorted.setWeight(att.weight());
atts.addElement(attSorted);
}
// generate new header
result = new Instances(inputFormat.relationName(), atts, 0);
result.setClassIndex(inputFormat.classIndex());
return result;
}
/**
* Returns a description of the classifier.
*
* @return a description of the classifier as a string.
*/
@Override
public String toString() {
if (m_Instances == null) {
return "Naive Bayes (simple): No model built yet.";
}
try {
StringBuffer text = new StringBuffer("Naive Bayes (simple)");
int attIndex;
for (int i = 0; i < m_Instances.numClasses(); i++) {
text.append(
"\n\nClass "
+ m_Instances.classAttribute().value(i)
+ ": P(C) = "
+ Utils.doubleToString(m_Priors[i], 10, 8)
+ "\n\n");
Enumeration<Attribute> enumAtts = m_Instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
text.append("Attribute " + attribute.name() + "\n");
if (attribute.isNominal()) {
for (int j = 0; j < attribute.numValues(); j++) {
text.append(attribute.value(j) + "\t");
}
text.append("\n");
for (int j = 0; j < attribute.numValues(); j++) {
text.append(Utils.doubleToString(m_Counts[i][attIndex][j], 10, 8) + "\t");
}
} else {
text.append("Mean: " + Utils.doubleToString(m_Means[i][attIndex], 10, 8) + "\t");
text.append("Standard Deviation: " + Utils.doubleToString(m_Devs[i][attIndex], 10, 8));
}
text.append("\n\n");
attIndex++;
}
}
return text.toString();
} catch (Exception e) {
return "Can't print Naive Bayes classifier!";
}
}
/**
* Compute the number of all possible conditions that could appear in a rule of a given data. For
* nominal attributes, it's the number of values that could appear; for numeric attributes, it's
* the number of values * 2, i.e. <= and >= are counted as different possible conditions.
*
* @param data the given data
* @return number of all conditions of the data
*/
public static double numAllConditions(Instances data) {
double total = 0;
Enumeration attEnum = data.enumerateAttributes();
while (attEnum.hasMoreElements()) {
Attribute att = (Attribute) attEnum.nextElement();
if (att.isNominal()) total += (double) att.numValues();
else total += 2.0 * (double) data.numDistinctValues(att);
}
return total;
}
/**
* Gives a string representation of the test in Prolog notation, starting from the comparison
* symbol.
*
* @return a string representing the test in Prolog notation
*/
private String testPrologComparisonString() {
Attribute att = m_Dataset.attribute(m_AttIndex);
if (att.isNumeric()) {
return ((m_Not ? ">= " : "< ") + Utils.doubleToString(m_Split, 3));
} else {
if (att.numValues() != 2) return ((m_Not ? "!= " : "= ") + att.value((int) m_Split));
else
return ("= " + (m_Not ? att.value((int) m_Split == 0 ? 1 : 0) : att.value((int) m_Split)));
}
}
/**
* Method for building an Id3 tree.
*
* @param data the training data
* @exception Exception if decision tree can't be built successfully
*/
private void makeTree(Instances data) throws Exception {
// Check if no instances have reached this node.
if (data.numInstances() == 0) {
m_Attribute = null;
m_ClassValue = Utils.missingValue();
m_Distribution = new double[data.numClasses()];
return;
}
// Compute attribute with maximum information gain.
double[] infoGains = new double[data.numAttributes()];
Enumeration attEnum = data.enumerateAttributes();
while (attEnum.hasMoreElements()) {
Attribute att = (Attribute) attEnum.nextElement();
infoGains[att.index()] = computeInfoGain(data, att);
}
m_Attribute = data.attribute(Utils.maxIndex(infoGains));
// Make leaf if information gain is zero.
// Otherwise create successors.
if (Utils.eq(infoGains[m_Attribute.index()], 0)) {
m_Attribute = null;
m_Distribution = new double[data.numClasses()];
Enumeration instEnum = data.enumerateInstances();
while (instEnum.hasMoreElements()) {
Instance inst = (Instance) instEnum.nextElement();
m_Distribution[(int) inst.classValue()]++;
}
Utils.normalize(m_Distribution);
m_ClassValue = Utils.maxIndex(m_Distribution);
m_ClassAttribute = data.classAttribute();
} else {
Instances[] splitData = splitData(data, m_Attribute);
m_Successors = new Id3[m_Attribute.numValues()];
for (int j = 0; j < m_Attribute.numValues(); j++) {
m_Successors[j] = new Id3();
m_Successors[j].makeTree(splitData[j]);
}
}
}
/**
* Set the output format. Swapss the desired nominal attribute values in the header and calls
* setOutputFormat(Instances) appropriately.
*/
private void setOutputFormat() {
Instances newData;
ArrayList<Attribute> newAtts;
ArrayList<String> newVals;
// Compute new attributes
newAtts = new ArrayList<Attribute>(getInputFormat().numAttributes());
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if (j != m_AttIndex.getIndex()) {
newAtts.add((Attribute) att.copy());
} else {
// Compute list of attribute values
newVals = new ArrayList<String>(att.numValues());
for (int i = 0; i < att.numValues(); i++) {
if (i == m_FirstIndex.getIndex()) {
newVals.add(att.value(m_SecondIndex.getIndex()));
} else if (i == m_SecondIndex.getIndex()) {
newVals.add(att.value(m_FirstIndex.getIndex()));
} else {
newVals.add(att.value(i));
}
}
Attribute newAtt = new Attribute(att.name(), newVals);
newAtt.setWeight(att.weight());
newAtts.add(newAtt);
}
}
// Construct new header
newData = new Instances(getInputFormat().relationName(), newAtts, 0);
newData.setClassIndex(getInputFormat().classIndex());
setOutputFormat(newData);
}
/**
* Computes information gain for an attribute.
*
* @param data the data for which info gain is to be computed
* @param att the attribute
* @return the information gain for the given attribute and data
* @throws Exception if computation fails
*/
private double computeInfoGain(Instances data, Attribute att) throws Exception {
double infoGain = computeEntropy(data);
Instances[] splitData = splitData(data, att);
for (int j = 0; j < att.numValues(); j++) {
if (splitData[j].numInstances() > 0) {
infoGain -=
((double) splitData[j].numInstances() / (double) data.numInstances())
* computeEntropy(splitData[j]);
}
}
return infoGain;
}
/**
* Outputs a tree at a certain level.
*
* @param level the level at which the tree is to be printed
* @return the tree as string at the given level
*/
private String toString(int level) {
StringBuffer text = new StringBuffer();
if (m_Attribute == null) {
if (Utils.isMissingValue(m_ClassValue)) {
text.append(": null");
} else {
text.append(": " + m_ClassAttribute.value((int) m_ClassValue));
}
} else {
for (int j = 0; j < m_Attribute.numValues(); j++) {
text.append("\n");
for (int i = 0; i < level; i++) {
text.append("| ");
}
text.append(m_Attribute.name() + " = " + m_Attribute.value(j));
text.append(m_Successors[j].toString(level + 1));
}
}
return text.toString();
}
/**
* use for training data
*
* @param instancesWithMeta
* @param labelInstances
* @return
* @throws Exception
*/
public static Instances addNominalLabelsForClassificationToTrainingData(
Instances instances, AttributeFilterMeta instancesWithMeta, Instances labelInstances)
throws Exception {
Instances finalCleaned = Instances.mergeInstances(instances, labelInstances);
finalCleaned.setClassIndex(finalCleaned.numAttributes() - 1);
Attribute classAt = finalCleaned.classAttribute();
int numOfAttValues = classAt.numValues();
String attValues = "";
for (int nai = 0; nai < numOfAttValues; nai++) {
if (nai != 0) {
attValues += ",";
}
attValues += classAt.value(nai);
}
instancesWithMeta.setClassAtrributeValues(attValues);
instancesWithMeta.setInstances(finalCleaned);
return finalCleaned;
}
public void setDatasetKeyFromDialog() {
ListSelectorDialog jd = new ListSelectorDialog(null, m_DatasetKeyList);
// Open the dialog
int result = jd.showDialog();
// =============== BEGIN EDIT melville ===============
// Check if learning curves should be generated
boolean noise = false;
boolean learning = false;
boolean fraction = false;
int learning_key = -1;
// If accepted, update the ttester
if (result == ListSelectorDialog.APPROVE_OPTION) {
int[] selected = m_DatasetKeyList.getSelectedIndices();
String selectedList = "";
Object[] selected_string = m_DatasetKeyList.getSelectedValues();
for (int i = 0; i < selected.length; i++) {
if (((String) selected_string[i]).toLowerCase().equals("key_noise_levels")) {
learning_key = i;
learning = true;
// fraction = true;
noise = true;
} else if (((String) selected_string[i]).toLowerCase().equals("key_fraction_instances")) {
learning_key = i;
learning = true;
fraction = true;
} else if (((String) selected_string[i]).toLowerCase().equals("key_total_instances")
&& !learning) {
learning = true;
learning_key = i;
} else selectedList += "," + (selected[i] + 1);
}
m_TTester.setLearningCurve(learning);
m_TTester.setFraction(fraction);
if (learning) { // get points on the learning curve
selectedList += "," + (selected[learning_key] + 1);
Attribute attr;
if (noise) { // override fraction
attr = m_Instances.attribute("Key_Noise_levels");
} else if (fraction) {
attr = m_Instances.attribute("Key_Fraction_instances");
} else {
attr = m_Instances.attribute("Key_Total_instances");
}
double[] pts = new double[attr.numValues()];
for (int k = 0; k < attr.numValues(); k++) {
pts[k] = Double.parseDouble(attr.value(k));
}
Arrays.sort(pts);
m_TTester.setPoints(pts);
}
// ================ END EDIT melville ================
Range generatorRange = new Range();
if (selectedList.length() != 0) {
try {
generatorRange.setRanges(selectedList);
} catch (Exception ex) {
ex.printStackTrace();
System.err.println(ex.getMessage());
}
}
m_TTester.setDatasetKeyColumns(generatorRange);
setTTester();
}
}
/**
* The procedure implementing the SMOTE algorithm. The output instances are pushed onto the output
* queue for collection.
*
* @throws Exception if provided options cannot be executed on input instances
*/
protected void doSMOTE() throws Exception {
int minIndex = 0;
int min = Integer.MAX_VALUE;
if (m_DetectMinorityClass) {
// find minority class
int[] classCounts =
getInputFormat().attributeStats(getInputFormat().classIndex()).nominalCounts;
for (int i = 0; i < classCounts.length; i++) {
if (classCounts[i] != 0 && classCounts[i] < min) {
min = classCounts[i];
minIndex = i;
}
}
} else {
String classVal = getClassValue();
if (classVal.equalsIgnoreCase("first")) {
minIndex = 1;
} else if (classVal.equalsIgnoreCase("last")) {
minIndex = getInputFormat().numClasses();
} else {
minIndex = Integer.parseInt(classVal);
}
if (minIndex > getInputFormat().numClasses()) {
throw new Exception("value index must be <= the number of classes");
}
minIndex--; // make it an index
}
int nearestNeighbors;
if (min <= getNearestNeighbors()) {
nearestNeighbors = min - 1;
} else {
nearestNeighbors = getNearestNeighbors();
}
if (nearestNeighbors < 1) throw new Exception("Cannot use 0 neighbors!");
// compose minority class dataset
// also push all dataset instances
Instances sample = getInputFormat().stringFreeStructure();
Enumeration instanceEnum = getInputFormat().enumerateInstances();
while (instanceEnum.hasMoreElements()) {
Instance instance = (Instance) instanceEnum.nextElement();
push((Instance) instance.copy());
if ((int) instance.classValue() == minIndex) {
sample.add(instance);
}
}
// compute Value Distance Metric matrices for nominal features
Map vdmMap = new HashMap();
Enumeration attrEnum = getInputFormat().enumerateAttributes();
while (attrEnum.hasMoreElements()) {
Attribute attr = (Attribute) attrEnum.nextElement();
if (!attr.equals(getInputFormat().classAttribute())) {
if (attr.isNominal() || attr.isString()) {
double[][] vdm = new double[attr.numValues()][attr.numValues()];
vdmMap.put(attr, vdm);
int[] featureValueCounts = new int[attr.numValues()];
int[][] featureValueCountsByClass =
new int[getInputFormat().classAttribute().numValues()][attr.numValues()];
instanceEnum = getInputFormat().enumerateInstances();
while (instanceEnum.hasMoreElements()) {
Instance instance = (Instance) instanceEnum.nextElement();
int value = (int) instance.value(attr);
int classValue = (int) instance.classValue();
featureValueCounts[value]++;
featureValueCountsByClass[classValue][value]++;
}
for (int valueIndex1 = 0; valueIndex1 < attr.numValues(); valueIndex1++) {
for (int valueIndex2 = 0; valueIndex2 < attr.numValues(); valueIndex2++) {
double sum = 0;
for (int classValueIndex = 0;
classValueIndex < getInputFormat().numClasses();
classValueIndex++) {
double c1i = featureValueCountsByClass[classValueIndex][valueIndex1];
double c2i = featureValueCountsByClass[classValueIndex][valueIndex2];
double c1 = featureValueCounts[valueIndex1];
double c2 = featureValueCounts[valueIndex2];
double term1 = c1i / c1;
double term2 = c2i / c2;
sum += Math.abs(term1 - term2);
}
vdm[valueIndex1][valueIndex2] = sum;
}
}
}
}
}
// use this random source for all required randomness
Random rand = new Random(getRandomSeed());
// find the set of extra indices to use if the percentage is not evenly
// divisible by 100
List extraIndices = new LinkedList();
double percentageRemainder = (getPercentage() / 100) - Math.floor(getPercentage() / 100.0);
int extraIndicesCount = (int) (percentageRemainder * sample.numInstances());
if (extraIndicesCount >= 1) {
for (int i = 0; i < sample.numInstances(); i++) {
extraIndices.add(i);
}
}
Collections.shuffle(extraIndices, rand);
extraIndices = extraIndices.subList(0, extraIndicesCount);
Set extraIndexSet = new HashSet(extraIndices);
// the main loop to handle computing nearest neighbors and generating SMOTE
// examples from each instance in the original minority class data
Instance[] nnArray = new Instance[nearestNeighbors];
for (int i = 0; i < sample.numInstances(); i++) {
Instance instanceI = sample.instance(i);
// find k nearest neighbors for each instance
List distanceToInstance = new LinkedList();
for (int j = 0; j < sample.numInstances(); j++) {
Instance instanceJ = sample.instance(j);
if (i != j) {
double distance = 0;
attrEnum = getInputFormat().enumerateAttributes();
while (attrEnum.hasMoreElements()) {
Attribute attr = (Attribute) attrEnum.nextElement();
if (!attr.equals(getInputFormat().classAttribute())) {
double iVal = instanceI.value(attr);
double jVal = instanceJ.value(attr);
if (attr.isNumeric()) {
distance += Math.pow(iVal - jVal, 2);
} else {
distance += ((double[][]) vdmMap.get(attr))[(int) iVal][(int) jVal];
}
}
}
distance = Math.pow(distance, .5);
distanceToInstance.add(new Object[] {distance, instanceJ});
}
}
// sort the neighbors according to distance
Collections.sort(
distanceToInstance,
new Comparator() {
public int compare(Object o1, Object o2) {
double distance1 = (Double) ((Object[]) o1)[0];
double distance2 = (Double) ((Object[]) o2)[0];
return Double.compare(distance1, distance2);
}
});
// populate the actual nearest neighbor instance array
Iterator entryIterator = distanceToInstance.iterator();
int j = 0;
while (entryIterator.hasNext() && j < nearestNeighbors) {
nnArray[j] = (Instance) ((Object[]) entryIterator.next())[1];
j++;
}
// create synthetic examples
int n = (int) Math.floor(getPercentage() / 100);
while (n > 0 || extraIndexSet.remove(i)) {
double[] values = new double[sample.numAttributes()];
int nn = rand.nextInt(nearestNeighbors);
attrEnum = getInputFormat().enumerateAttributes();
while (attrEnum.hasMoreElements()) {
Attribute attr = (Attribute) attrEnum.nextElement();
if (!attr.equals(getInputFormat().classAttribute())) {
if (attr.isNumeric()) {
double dif = nnArray[nn].value(attr) - instanceI.value(attr);
double gap = rand.nextDouble();
values[attr.index()] = (instanceI.value(attr) + gap * dif);
} else if (attr.isDate()) {
double dif = nnArray[nn].value(attr) - instanceI.value(attr);
double gap = rand.nextDouble();
values[attr.index()] = (long) (instanceI.value(attr) + gap * dif);
} else {
int[] valueCounts = new int[attr.numValues()];
int iVal = (int) instanceI.value(attr);
valueCounts[iVal]++;
for (int nnEx = 0; nnEx < nearestNeighbors; nnEx++) {
int val = (int) nnArray[nnEx].value(attr);
valueCounts[val]++;
}
int maxIndex = 0;
int max = Integer.MIN_VALUE;
for (int index = 0; index < attr.numValues(); index++) {
if (valueCounts[index] > max) {
max = valueCounts[index];
maxIndex = index;
}
}
values[attr.index()] = maxIndex;
}
}
}
values[sample.classIndex()] = minIndex;
Instance synthetic = new Instance(1.0, values);
push(synthetic);
n--;
}
}
}
/** Set the output format if the class is numeric. */
private void setOutputFormatNumeric() {
if (m_Indices == null) {
setOutputFormat(null);
return;
}
ArrayList<Attribute> newAtts;
int newClassIndex;
StringBuffer attributeName;
Instances outputFormat;
ArrayList<String> vals;
// Compute new attributes
m_needToTransform = false;
for (int i = 0; i < getInputFormat().numAttributes(); i++) {
Attribute att = getInputFormat().attribute(i);
if (att.isNominal() && (att.numValues() > 2 || m_Numeric || m_TransformAll)) {
m_needToTransform = true;
break;
}
}
if (!m_needToTransform) {
setOutputFormat(getInputFormat());
return;
}
newClassIndex = getInputFormat().classIndex();
newAtts = new ArrayList<Attribute>();
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if ((!att.isNominal()) || (j == getInputFormat().classIndex())) {
newAtts.add((Attribute) att.copy());
} else {
if (j < getInputFormat().classIndex()) {
newClassIndex += att.numValues() - 2;
}
// Compute values for new attributes
for (int k = 1; k < att.numValues(); k++) {
attributeName = new StringBuffer(att.name() + "=");
for (int l = k; l < att.numValues(); l++) {
if (l > k) {
attributeName.append(',');
}
attributeName.append(att.value(m_Indices[j][l]));
}
if (m_Numeric) {
newAtts.add(new Attribute(attributeName.toString()));
} else {
vals = new ArrayList<String>(2);
vals.add("f");
vals.add("t");
newAtts.add(new Attribute(attributeName.toString(), vals));
}
}
}
}
outputFormat = new Instances(getInputFormat().relationName(), newAtts, 0);
outputFormat.setClassIndex(newClassIndex);
setOutputFormat(outputFormat);
}
/**
* Generates the classifier.
*
* @param instances set of instances serving as training data
* @exception Exception if the classifier has not been generated successfully
*/
@Override
public void buildClassifier(Instances instances) throws Exception {
int attIndex = 0;
double sum;
// can classifier handle the data?
getCapabilities().testWithFail(instances);
// remove instances with missing class
instances = new Instances(instances);
instances.deleteWithMissingClass();
m_Instances = new Instances(instances, 0);
// Reserve space
m_Counts = new double[instances.numClasses()][instances.numAttributes() - 1][0];
m_Means = new double[instances.numClasses()][instances.numAttributes() - 1];
m_Devs = new double[instances.numClasses()][instances.numAttributes() - 1];
m_Priors = new double[instances.numClasses()];
Enumeration<Attribute> enu = instances.enumerateAttributes();
while (enu.hasMoreElements()) {
Attribute attribute = enu.nextElement();
if (attribute.isNominal()) {
for (int j = 0; j < instances.numClasses(); j++) {
m_Counts[j][attIndex] = new double[attribute.numValues()];
}
} else {
for (int j = 0; j < instances.numClasses(); j++) {
m_Counts[j][attIndex] = new double[1];
}
}
attIndex++;
}
// Compute counts and sums
Enumeration<Instance> enumInsts = instances.enumerateInstances();
while (enumInsts.hasMoreElements()) {
Instance instance = enumInsts.nextElement();
if (!instance.classIsMissing()) {
Enumeration<Attribute> enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (!instance.isMissing(attribute)) {
if (attribute.isNominal()) {
m_Counts[(int) instance.classValue()][attIndex][(int) instance.value(attribute)]++;
} else {
m_Means[(int) instance.classValue()][attIndex] += instance.value(attribute);
m_Counts[(int) instance.classValue()][attIndex][0]++;
}
}
attIndex++;
}
m_Priors[(int) instance.classValue()]++;
}
}
// Compute means
Enumeration<Attribute> enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (attribute.isNumeric()) {
for (int j = 0; j < instances.numClasses(); j++) {
if (m_Counts[j][attIndex][0] < 2) {
throw new Exception(
"attribute "
+ attribute.name()
+ ": less than two values for class "
+ instances.classAttribute().value(j));
}
m_Means[j][attIndex] /= m_Counts[j][attIndex][0];
}
}
attIndex++;
}
// Compute standard deviations
enumInsts = instances.enumerateInstances();
while (enumInsts.hasMoreElements()) {
Instance instance = enumInsts.nextElement();
if (!instance.classIsMissing()) {
enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (!instance.isMissing(attribute)) {
if (attribute.isNumeric()) {
m_Devs[(int) instance.classValue()][attIndex] +=
(m_Means[(int) instance.classValue()][attIndex] - instance.value(attribute))
* (m_Means[(int) instance.classValue()][attIndex]
- instance.value(attribute));
}
}
attIndex++;
}
}
}
enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (attribute.isNumeric()) {
for (int j = 0; j < instances.numClasses(); j++) {
if (m_Devs[j][attIndex] <= 0) {
throw new Exception(
"attribute "
+ attribute.name()
+ ": standard deviation is 0 for class "
+ instances.classAttribute().value(j));
} else {
m_Devs[j][attIndex] /= m_Counts[j][attIndex][0] - 1;
m_Devs[j][attIndex] = Math.sqrt(m_Devs[j][attIndex]);
}
}
}
attIndex++;
}
// Normalize counts
enumAtts = instances.enumerateAttributes();
attIndex = 0;
while (enumAtts.hasMoreElements()) {
Attribute attribute = enumAtts.nextElement();
if (attribute.isNominal()) {
for (int j = 0; j < instances.numClasses(); j++) {
sum = Utils.sum(m_Counts[j][attIndex]);
for (int i = 0; i < attribute.numValues(); i++) {
m_Counts[j][attIndex][i] =
(m_Counts[j][attIndex][i] + 1) / (sum + attribute.numValues());
}
}
}
attIndex++;
}
// Normalize priors
sum = Utils.sum(m_Priors);
for (int j = 0; j < instances.numClasses(); j++) {
m_Priors[j] = (m_Priors[j] + 1) / (sum + instances.numClasses());
}
}
public MappingInfo(Instances dataSet, MiningSchema miningSchema, Logger log) throws Exception {
m_log = log;
// miningSchema.convertStringAttsToNominal();
Instances fieldsI = miningSchema.getMiningSchemaAsInstances();
m_fieldsMap = new int[fieldsI.numAttributes()];
m_nominalValueMaps = new int[fieldsI.numAttributes()][];
for (int i = 0; i < fieldsI.numAttributes(); i++) {
String schemaAttName = fieldsI.attribute(i).name();
boolean found = false;
for (int j = 0; j < dataSet.numAttributes(); j++) {
if (dataSet.attribute(j).name().equals(schemaAttName)) {
Attribute miningSchemaAtt = fieldsI.attribute(i);
Attribute incomingAtt = dataSet.attribute(j);
// check type match
if (miningSchemaAtt.type() != incomingAtt.type()) {
throw new Exception(
"[MappingInfo] type mismatch for field "
+ schemaAttName
+ ". Mining schema type "
+ miningSchemaAtt.toString()
+ ". Incoming type "
+ incomingAtt.toString()
+ ".");
}
// check nominal values (number, names...)
if (miningSchemaAtt.numValues() != incomingAtt.numValues()) {
String warningString =
"[MappingInfo] WARNING: incoming nominal attribute "
+ incomingAtt.name()
+ " does not have the same "
+ "number of values as the corresponding mining "
+ "schema attribute.";
if (m_log != null) {
m_log.logMessage(warningString);
} else {
System.err.println(warningString);
}
}
if (miningSchemaAtt.isNominal() || miningSchemaAtt.isString()) {
int[] valuesMap = new int[incomingAtt.numValues()];
for (int k = 0; k < incomingAtt.numValues(); k++) {
String incomingNomVal = incomingAtt.value(k);
int indexInSchema = miningSchemaAtt.indexOfValue(incomingNomVal);
if (indexInSchema < 0) {
String warningString =
"[MappingInfo] WARNING: incoming nominal attribute "
+ incomingAtt.name()
+ " has value "
+ incomingNomVal
+ " that doesn't occur in the mining schema.";
if (m_log != null) {
m_log.logMessage(warningString);
} else {
System.err.println(warningString);
}
valuesMap[k] = UNKNOWN_NOMINAL_VALUE;
} else {
valuesMap[k] = indexInSchema;
}
}
m_nominalValueMaps[i] = valuesMap;
}
/*if (miningSchemaAtt.isNominal()) {
for (int k = 0; k < miningSchemaAtt.numValues(); k++) {
if (!miningSchemaAtt.value(k).equals(incomingAtt.value(k))) {
throw new Exception("[PMMLUtils] value " + k + " (" +
miningSchemaAtt.value(k) + ") does not match " +
"incoming value (" + incomingAtt.value(k) +
") for attribute " + miningSchemaAtt.name() +
".");
}
}
}*/
found = true;
m_fieldsMap[i] = j;
}
}
if (!found) {
throw new Exception(
"[MappingInfo] Unable to find a match for mining schema "
+ "attribute "
+ schemaAttName
+ " in the "
+ "incoming instances!");
}
}
// check class attribute (if set)
if (fieldsI.classIndex() >= 0) {
if (dataSet.classIndex() < 0) {
// first see if we can find a matching class
String className = fieldsI.classAttribute().name();
Attribute classMatch = dataSet.attribute(className);
if (classMatch == null) {
throw new Exception(
"[MappingInfo] Can't find match for target field "
+ className
+ "in incoming instances!");
}
dataSet.setClass(classMatch);
} else if (!fieldsI.classAttribute().name().equals(dataSet.classAttribute().name())) {
throw new Exception(
"[MappingInfo] class attribute in mining schema does not match "
+ "class attribute in incoming instances!");
}
}
// Set up the textual description of the mapping
fieldsMappingString(fieldsI, dataSet);
}
/**
* Writes a Batch of instances
*
* @throws IOException throws IOException if saving in batch mode is not possible
*/
public void writeBatch() throws IOException {
Instances instances = getInstances();
if (instances == null) throw new IOException("No instances to save");
if (instances.classIndex() == -1) {
instances.setClassIndex(instances.numAttributes() - 1);
System.err.println("No class specified. Last attribute is used as class attribute.");
}
if (instances.attribute(instances.classIndex()).isNumeric())
throw new IOException("To save in C4.5 format the class attribute cannot be numeric.");
if (getRetrieval() == INCREMENTAL)
throw new IOException("Batch and incremental saving cannot be mixed.");
setRetrieval(BATCH);
if (retrieveFile() == null || getWriter() == null) {
throw new IOException(
"C4.5 format requires two files. Therefore no output to standard out can be generated.\nPlease specifiy output files using the -o option.");
}
setWriteMode(WRITE);
// print names file
setFileExtension(".names");
PrintWriter outW = new PrintWriter(getWriter());
for (int i = 0; i < instances.attribute(instances.classIndex()).numValues(); i++) {
outW.write(instances.attribute(instances.classIndex()).value(i));
if (i < instances.attribute(instances.classIndex()).numValues() - 1) {
outW.write(",");
} else {
outW.write(".\n");
}
}
for (int i = 0; i < instances.numAttributes(); i++) {
if (i != instances.classIndex()) {
outW.write(instances.attribute(i).name() + ": ");
if (instances.attribute(i).isNumeric() || instances.attribute(i).isDate()) {
outW.write("continuous.\n");
} else {
Attribute temp = instances.attribute(i);
for (int j = 0; j < temp.numValues(); j++) {
outW.write(temp.value(j));
if (j < temp.numValues() - 1) {
outW.write(",");
} else {
outW.write(".\n");
}
}
}
}
}
outW.flush();
outW.close();
// print data file
String out = retrieveFile().getAbsolutePath();
setFileExtension(".data");
out = out.substring(0, out.lastIndexOf('.')) + getFileExtension();
File namesFile = new File(out);
try {
setFile(namesFile);
} catch (Exception ex) {
throw new IOException(
"Cannot create data file, only names file created (Reason: " + ex.toString() + ").");
}
if (retrieveFile() == null || getWriter() == null) {
throw new IOException("Cannot create data file, only names file created.");
}
outW = new PrintWriter(getWriter());
// print data file
for (int i = 0; i < instances.numInstances(); i++) {
Instance temp = instances.instance(i);
for (int j = 0; j < temp.numAttributes(); j++) {
if (j != instances.classIndex()) {
if (temp.isMissing(j)) {
outW.write("?,");
} else if (instances.attribute(j).isNominal() || instances.attribute(j).isString()) {
outW.write(instances.attribute(j).value((int) temp.value(j)) + ",");
} else {
outW.write("" + temp.value(j) + ",");
}
}
}
// write the class value
if (temp.isMissing(instances.classIndex())) {
outW.write("?");
} else {
outW.write(
instances
.attribute(instances.classIndex())
.value((int) temp.value(instances.classIndex())));
}
outW.write("\n");
}
outW.flush();
outW.close();
setFileExtension(".names");
setWriteMode(WAIT);
outW = null;
resetWriter();
setWriteMode(CANCEL);
}
/**
* Saves an instances incrementally. Structure has to be set by using the setStructure() method or
* setInstances() method.
*
* @param inst the instance to save
* @throws IOException throws IOEXception if an instance cannot be saved incrementally.
*/
public void writeIncremental(Instance inst) throws IOException {
int writeMode = getWriteMode();
Instances structure = getInstances();
PrintWriter outW = null;
if (structure != null) {
if (structure.classIndex() == -1) {
structure.setClassIndex(structure.numAttributes() - 1);
System.err.println("No class specified. Last attribute is used as class attribute.");
}
if (structure.attribute(structure.classIndex()).isNumeric())
throw new IOException("To save in C4.5 format the class attribute cannot be numeric.");
}
if (getRetrieval() == BATCH || getRetrieval() == NONE)
throw new IOException("Batch and incremental saving cannot be mixed.");
if (retrieveFile() == null || getWriter() == null) {
throw new IOException(
"C4.5 format requires two files. Therefore no output to standard out can be generated.\nPlease specifiy output files using the -o option.");
}
outW = new PrintWriter(getWriter());
if (writeMode == WAIT) {
if (structure == null) {
setWriteMode(CANCEL);
if (inst != null)
System.err.println("Structure(Header Information) has to be set in advance");
} else setWriteMode(STRUCTURE_READY);
writeMode = getWriteMode();
}
if (writeMode == CANCEL) {
if (outW != null) outW.close();
cancel();
}
if (writeMode == STRUCTURE_READY) {
setWriteMode(WRITE);
// write header: here names file
for (int i = 0; i < structure.attribute(structure.classIndex()).numValues(); i++) {
outW.write(structure.attribute(structure.classIndex()).value(i));
if (i < structure.attribute(structure.classIndex()).numValues() - 1) {
outW.write(",");
} else {
outW.write(".\n");
}
}
for (int i = 0; i < structure.numAttributes(); i++) {
if (i != structure.classIndex()) {
outW.write(structure.attribute(i).name() + ": ");
if (structure.attribute(i).isNumeric() || structure.attribute(i).isDate()) {
outW.write("continuous.\n");
} else {
Attribute temp = structure.attribute(i);
for (int j = 0; j < temp.numValues(); j++) {
outW.write(temp.value(j));
if (j < temp.numValues() - 1) {
outW.write(",");
} else {
outW.write(".\n");
}
}
}
}
}
outW.flush();
outW.close();
writeMode = getWriteMode();
String out = retrieveFile().getAbsolutePath();
setFileExtension(".data");
out = out.substring(0, out.lastIndexOf('.')) + getFileExtension();
File namesFile = new File(out);
try {
setFile(namesFile);
} catch (Exception ex) {
throw new IOException("Cannot create data file, only names file created.");
}
if (retrieveFile() == null || getWriter() == null) {
throw new IOException("Cannot create data file, only names file created.");
}
outW = new PrintWriter(getWriter());
}
if (writeMode == WRITE) {
if (structure == null) throw new IOException("No instances information available.");
if (inst != null) {
// write instance: here data file
for (int j = 0; j < inst.numAttributes(); j++) {
if (j != structure.classIndex()) {
if (inst.isMissing(j)) {
outW.write("?,");
} else if (structure.attribute(j).isNominal() || structure.attribute(j).isString()) {
outW.write(structure.attribute(j).value((int) inst.value(j)) + ",");
} else {
outW.write("" + inst.value(j) + ",");
}
}
}
// write the class value
if (inst.isMissing(structure.classIndex())) {
outW.write("?");
} else {
outW.write(
structure
.attribute(structure.classIndex())
.value((int) inst.value(structure.classIndex())));
}
outW.write("\n");
// flushes every 100 instances
m_incrementalCounter++;
if (m_incrementalCounter > 100) {
m_incrementalCounter = 0;
outW.flush();
}
} else {
// close
if (outW != null) {
outW.flush();
outW.close();
}
setFileExtension(".names");
m_incrementalCounter = 0;
resetStructure();
outW = null;
resetWriter();
}
}
}
/**
* Set the output format. Takes the current average class values and m_InputFormat and calls
* setOutputFormat(Instances) appropriately.
*/
private void setOutputFormat() {
Instances newData;
FastVector newAtts, newVals;
boolean firstEndsWithPrime = false, secondEndsWithPrime = false;
StringBuffer text = new StringBuffer();
// Compute new attributes
newAtts = new FastVector(getInputFormat().numAttributes());
for (int j = 0; j < getInputFormat().numAttributes(); j++) {
Attribute att = getInputFormat().attribute(j);
if (j != m_AttIndex.getIndex()) {
newAtts.addElement(att.copy());
} else {
// Compute new value
if (att.value(m_FirstIndex.getIndex()).endsWith("'")) {
firstEndsWithPrime = true;
}
if (att.value(m_SecondIndex.getIndex()).endsWith("'")) {
secondEndsWithPrime = true;
}
if (firstEndsWithPrime || secondEndsWithPrime) {
text.append("'");
}
if (firstEndsWithPrime) {
text.append(
((String) att.value(m_FirstIndex.getIndex()))
.substring(1, ((String) att.value(m_FirstIndex.getIndex())).length() - 1));
} else {
text.append((String) att.value(m_FirstIndex.getIndex()));
}
text.append('_');
if (secondEndsWithPrime) {
text.append(
((String) att.value(m_SecondIndex.getIndex()))
.substring(1, ((String) att.value(m_SecondIndex.getIndex())).length() - 1));
} else {
text.append((String) att.value(m_SecondIndex.getIndex()));
}
if (firstEndsWithPrime || secondEndsWithPrime) {
text.append("'");
}
// Compute list of attribute values
newVals = new FastVector(att.numValues() - 1);
for (int i = 0; i < att.numValues(); i++) {
if (i == m_FirstIndex.getIndex()) {
newVals.addElement(text.toString());
} else if (i != m_SecondIndex.getIndex()) {
newVals.addElement(att.value(i));
}
}
Attribute newAtt = new Attribute(att.name(), newVals);
newAtt.setWeight(getInputFormat().attribute(j).weight());
newAtts.addElement(newAtt);
}
}
// Construct new header
newData = new Instances(getInputFormat().relationName(), newAtts, 0);
newData.setClassIndex(getInputFormat().classIndex());
setOutputFormat(newData);
}
/**
* Sets up the panel with a new set of instances, attempting to guess the correct settings for
* various columns.
*
* @param newInstances the new set of results.
*/
public void setInstances(Instances newInstances) {
m_Instances = newInstances;
m_TTester.setInstances(m_Instances);
m_FromLab.setText("Got " + m_Instances.numInstances() + " results");
// Temporarily remove the configuration listener
m_RunCombo.removeActionListener(m_ConfigureListener);
// Do other stuff
m_DatasetKeyModel.removeAllElements();
m_RunModel.removeAllElements();
m_ResultKeyModel.removeAllElements();
m_CompareModel.removeAllElements();
int datasetCol = -1;
int runCol = -1;
String selectedList = "";
String selectedListDataset = "";
// =============== BEGIN EDIT melville ===============
boolean noise = false; // keep track of whether noise levels eval is required
boolean learning = false; // keep track of whether learning curve eval is required
boolean fraction =
false; // keep track of whether fractions of datasets are provided for learning
// the key on which to base the learning curves (either total instances or fraction)
int learning_key = -1;
boolean classificationTask =
false; // used to determine if regression measures should be selected
// =============== END EDIT melville ===============
for (int i = 0; i < m_Instances.numAttributes(); i++) {
String name = m_Instances.attribute(i).name();
m_DatasetKeyModel.addElement(name);
m_RunModel.addElement(name);
m_ResultKeyModel.addElement(name);
m_CompareModel.addElement(name);
// =============== BEGIN EDIT melville ===============
// If learning curves were generated then treat each
// dataset + pt combination as a different dataset
if (name.toLowerCase().equals("key_noise_levels")) {
// noise overrides learning curves - but treat noise levels
// like pts on learning curve
learning_key = i;
learning = true;
noise = true;
// fraction = true;
} else if (name.toLowerCase().equals("key_fraction_instances") && !noise) {
// fraction overrides total_instances
learning_key = i;
learning = true;
fraction = true;
} else if (name.toLowerCase().equals("key_total_instances") && !learning) {
learning_key = i;
learning = true;
} else
// =============== END EDIT melville ===============
if (name.toLowerCase().equals("key_dataset")) {
m_DatasetKeyList.addSelectionInterval(i, i);
selectedListDataset += "," + (i + 1);
} else if ((runCol == -1) && (name.toLowerCase().equals("key_run"))) {
m_RunCombo.setSelectedIndex(i);
runCol = i;
} else if (name.toLowerCase().equals("key_scheme")
|| name.toLowerCase().equals("key_scheme_options")
|| name.toLowerCase().equals("key_scheme_version_id")) {
m_ResultKeyList.addSelectionInterval(i, i);
selectedList += "," + (i + 1);
// =============== BEGIN EDIT mbilenko ===============
// automatic selection of the correct measure for clustering experiments
} else if (name.toLowerCase().indexOf("pairwise_f_measure") != -1) {
m_CompareCombo.setSelectedIndex(i);
m_ErrorCompareCol = i;
}
// automatic selection of the correct measure for deduping experiments
else if (name.toLowerCase().equals("precision")) {
m_CompareCombo.setSelectedIndex(i);
// =============== END EDIT mbilenko ===============
} else if (name.toLowerCase().indexOf("percent_correct") != -1) {
m_CompareCombo.setSelectedIndex(i);
classificationTask = true;
} else if (!classificationTask
&& (name.toLowerCase().indexOf("root_mean_squared_error") != -1)) {
// automatic selection of the correct measure for regression experiments
m_CompareCombo.setSelectedIndex(i);
} else if (name.toLowerCase().indexOf("percent_incorrect") != -1) {
m_ErrorCompareCol = i;
// remember index of error for computing error reductions
}
}
// =============== BEGIN EDIT melville ===============
if (learning) {
m_DatasetKeyList.addSelectionInterval(learning_key, learning_key);
selectedListDataset += "," + (learning_key + 1);
m_CompareModel.addElement("%Error_reduction");
m_CompareModel.addElement("Top_20%_%Error_reduction");
}
// =============== END EDIT melville ===============
if (runCol == -1) {
runCol = 0;
}
m_DatasetKeyBut.setEnabled(true);
m_RunCombo.setEnabled(true);
m_ResultKeyBut.setEnabled(true);
m_CompareCombo.setEnabled(true);
// Reconnect the configuration listener
m_RunCombo.addActionListener(m_ConfigureListener);
// Set up the TTester with the new data
m_TTester.setRunColumn(runCol);
Range generatorRange = new Range();
if (selectedList.length() != 0) {
try {
generatorRange.setRanges(selectedList);
} catch (Exception ex) {
ex.printStackTrace();
System.err.println(ex.getMessage());
}
}
m_TTester.setResultsetKeyColumns(generatorRange);
generatorRange = new Range();
if (selectedListDataset.length() != 0) {
try {
generatorRange.setRanges(selectedListDataset);
} catch (Exception ex) {
ex.printStackTrace();
System.err.println(ex.getMessage());
}
}
m_TTester.setDatasetKeyColumns(generatorRange);
// =============== BEGIN EDIT melville ===============
m_TTester.setLearningCurve(learning);
m_TTester.setFraction(fraction);
if (learning) { // get points on the learning curve
Attribute attr;
if (noise) { // override fraction
attr = m_Instances.attribute("Key_Noise_levels");
} else if (fraction) {
attr = m_Instances.attribute("Key_Fraction_instances");
} else {
attr = m_Instances.attribute("Key_Total_instances");
}
double[] pts = new double[attr.numValues()];
for (int k = 0; k < attr.numValues(); k++) {
pts[k] = Double.parseDouble(attr.value(k));
}
// sort points
Arrays.sort(pts);
m_TTester.setPoints(pts);
}
// =============== END EDIT melville ===============
m_SigTex.setEnabled(true);
m_PrecTex.setEnabled(true);
setTTester();
}
/**
* TextDirectoryLoader is unable to process a data set incrementally.
*
* @param structure ignored
* @return never returns without throwing an exception
* @throws IOException always. TextDirectoryLoader is unable to process a data set incrementally.
*/
public Instance getNextInstance(Instances structure) throws IOException {
// throw new IOException("TextDirectoryLoader can't read data sets incrementally.");
String directoryPath = getDirectory().getAbsolutePath();
Attribute classAtt = structure.classAttribute();
if (m_filesByClass == null) {
m_filesByClass = new ArrayList<LinkedList<String>>();
for (int i = 0; i < classAtt.numValues(); i++) {
File classDir = new File(directoryPath + File.separator + classAtt.value(i));
String[] files = classDir.list();
LinkedList<String> classDocs = new LinkedList<String>();
for (String cd : files) {
File txt =
new File(directoryPath + File.separator + classAtt.value(i) + File.separator + cd);
if (txt.isFile()) {
classDocs.add(cd);
}
}
m_filesByClass.add(classDocs);
}
}
// cycle through the classes
int count = 0;
LinkedList<String> classContents = m_filesByClass.get(m_lastClassDir);
boolean found = (classContents.size() > 0);
while (classContents.size() == 0) {
m_lastClassDir++;
count++;
if (m_lastClassDir == structure.classAttribute().numValues()) {
m_lastClassDir = 0;
}
classContents = m_filesByClass.get(m_lastClassDir);
if (classContents.size() > 0) {
found = true; // we have an instance we can create
break;
}
if (count == structure.classAttribute().numValues()) {
break; // must be finished
}
}
if (found) {
String nextDoc = classContents.poll();
File txt =
new File(
directoryPath
+ File.separator
+ classAtt.value(m_lastClassDir)
+ File.separator
+ nextDoc);
BufferedReader is;
if (m_charSet == null || m_charSet.length() == 0) {
is = new BufferedReader(new InputStreamReader(new FileInputStream(txt)));
} else {
is = new BufferedReader(new InputStreamReader(new FileInputStream(txt), m_charSet));
}
StringBuffer txtStr = new StringBuffer();
int c;
while ((c = is.read()) != -1) {
txtStr.append((char) c);
}
double[] newInst = null;
if (m_OutputFilename) newInst = new double[3];
else newInst = new double[2];
if (getRetainStringValues()) {
newInst[0] = (double) structure.attribute(0).addStringValue(txtStr.toString());
} else {
newInst[0] = 0;
structure.attribute(0).setStringValue(txtStr.toString());
}
if (m_OutputFilename) {
if (getRetainStringValues()) {
newInst[1] = (double) structure.attribute(1).addStringValue(txt.getAbsolutePath());
} else {
newInst[1] = 0;
structure.attribute(1).setStringValue(txt.getAbsolutePath());
}
}
newInst[structure.classIndex()] = (double) m_lastClassDir;
Instance inst = new DenseInstance(1.0, newInst);
inst.setDataset(structure);
is.close();
m_lastClassDir++;
if (m_lastClassDir == structure.classAttribute().numValues()) {
m_lastClassDir = 0;
}
return inst;
} else {
return null; // done!
}
}