/**
* Calculates the area under the ROC curve as the Wilcoxon-Mann-Whitney statistic.
*
* @param tcurve a previously extracted threshold curve Instances.
* @return the ROC area, or Double.NaN if you don't pass in a ThresholdCurve generated Instances.
*/
public static double getROCArea(Instances tcurve) {
final int n = tcurve.numInstances();
if (!RELATION_NAME.equals(tcurve.relationName()) || (n == 0)) {
return Double.NaN;
}
final int tpInd = tcurve.attribute(TRUE_POS_NAME).index();
final int fpInd = tcurve.attribute(FALSE_POS_NAME).index();
final double[] tpVals = tcurve.attributeToDoubleArray(tpInd);
final double[] fpVals = tcurve.attributeToDoubleArray(fpInd);
double area = 0.0, cumNeg = 0.0;
final double totalPos = tpVals[0];
final double totalNeg = fpVals[0];
for (int i = 0; i < n; i++) {
double cip, cin;
if (i < n - 1) {
cip = tpVals[i] - tpVals[i + 1];
cin = fpVals[i] - fpVals[i + 1];
} else {
cip = tpVals[n - 1];
cin = fpVals[n - 1];
}
area += cip * (cumNeg + (0.5 * cin));
cumNeg += cin;
}
area /= (totalNeg * totalPos);
return area;
}
/**
* Calculates the area under the precision-recall curve (AUPRC).
*
* @param tcurve a previously extracted threshold curve Instances.
* @return the PRC area, or Double.NaN if you don't pass in a ThresholdCurve generated Instances.
*/
public static double getPRCArea(Instances tcurve) {
final int n = tcurve.numInstances();
if (!RELATION_NAME.equals(tcurve.relationName()) || (n == 0)) {
return Double.NaN;
}
final int pInd = tcurve.attribute(PRECISION_NAME).index();
final int rInd = tcurve.attribute(RECALL_NAME).index();
final double[] pVals = tcurve.attributeToDoubleArray(pInd);
final double[] rVals = tcurve.attributeToDoubleArray(rInd);
double area = 0;
double xlast = rVals[n - 1];
// start from the first real p/r pair (not the artificial zero point)
for (int i = n - 2; i >= 0; i--) {
double recallDelta = rVals[i] - xlast;
area += (pVals[i] * recallDelta);
xlast = rVals[i];
}
if (area == 0) {
return Utils.missingValue();
}
return area;
}
/**
* Builds the model of the base learner.
*
* @param data the training data
* @throws Exception if the classifier could not be built successfully
*/
public void buildClassifier(Instances data) throws Exception {
// can classifier handle the data?
getCapabilities().testWithFail(data);
// remove instances with missing class
data = new Instances(data);
data.deleteWithMissingClass();
if (m_Classifier == null) {
throw new Exception("No base classifier has been set!");
}
if (m_MatrixSource == MATRIX_ON_DEMAND) {
String costName = data.relationName() + CostMatrix.FILE_EXTENSION;
File costFile = new File(getOnDemandDirectory(), costName);
if (!costFile.exists()) {
throw new Exception("On-demand cost file doesn't exist: " + costFile);
}
setCostMatrix(new CostMatrix(new BufferedReader(new FileReader(costFile))));
} else if (m_CostMatrix == null) {
// try loading an old format cost file
m_CostMatrix = new CostMatrix(data.numClasses());
m_CostMatrix.readOldFormat(new BufferedReader(new FileReader(m_CostFile)));
}
if (!m_MinimizeExpectedCost) {
Random random = null;
if (!(m_Classifier instanceof WeightedInstancesHandler)) {
random = new Random(m_Seed);
}
data = m_CostMatrix.applyCostMatrix(data, random);
}
m_Classifier.buildClassifier(data);
}
/**
* Determines the output format based on the input format and returns this. In case the output
* format cannot be returned immediately, i.e., immediateOutputFormat() returns false, then this
* method will be called from batchFinished().
*
* @param inputFormat the input format to base the output format on
* @return the output format
* @throws Exception in case the determination goes wrong
* @see #hasImmediateOutputFormat()
* @see #batchFinished()
*/
protected Instances determineOutputFormat(Instances inputFormat) throws Exception {
Instances data;
Instances result;
FastVector atts;
FastVector values;
HashSet hash;
int i;
int n;
boolean isDate;
Instance inst;
Vector sorted;
m_Cols.setUpper(inputFormat.numAttributes() - 1);
data = new Instances(inputFormat);
atts = new FastVector();
for (i = 0; i < data.numAttributes(); i++) {
if (!m_Cols.isInRange(i) || !data.attribute(i).isNumeric()) {
atts.addElement(data.attribute(i));
continue;
}
// date attribute?
isDate = (data.attribute(i).type() == Attribute.DATE);
// determine all available attribtues in dataset
hash = new HashSet();
for (n = 0; n < data.numInstances(); n++) {
inst = data.instance(n);
if (inst.isMissing(i)) continue;
if (isDate) hash.add(inst.stringValue(i));
else hash.add(new Double(inst.value(i)));
}
// sort values
sorted = new Vector();
for (Object o : hash) sorted.add(o);
Collections.sort(sorted);
// create attribute from sorted values
values = new FastVector();
for (Object o : sorted) {
if (isDate) values.addElement(o.toString());
else values.addElement(Utils.doubleToString(((Double) o).doubleValue(), MAX_DECIMALS));
}
atts.addElement(new Attribute(data.attribute(i).name(), values));
}
result = new Instances(inputFormat.relationName(), atts, 0);
result.setClassIndex(inputFormat.classIndex());
return result;
}
/**
* Determines the output format based on the input format and returns this. In case the output
* format cannot be returned immediately, i.e., hasImmediateOutputFormat() returns false, then
* this method will called from batchFinished() after the call of preprocess(Instances), in which,
* e.g., statistics for the actual processing step can be gathered.
*
* @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;
FastVector atts;
int i;
int numAtts;
Vector<Integer> indices;
Vector<Integer> subset;
Random rand;
int index;
// determine the number of attributes
numAtts = inputFormat.numAttributes();
if (inputFormat.classIndex() > -1) numAtts--;
if (m_NumAttributes < 1) {
numAtts = (int) Math.round((double) numAtts * m_NumAttributes);
} else {
if (m_NumAttributes < numAtts) numAtts = (int) m_NumAttributes;
}
if (getDebug()) System.out.println("# of atts: " + numAtts);
// determine random indices
indices = new Vector<Integer>();
for (i = 0; i < inputFormat.numAttributes(); i++) {
if (i == inputFormat.classIndex()) continue;
indices.add(i);
}
subset = new Vector<Integer>();
rand = new Random(m_Seed);
for (i = 0; i < numAtts; i++) {
index = rand.nextInt(indices.size());
subset.add(indices.get(index));
indices.remove(index);
}
Collections.sort(subset);
if (inputFormat.classIndex() > -1) subset.add(inputFormat.classIndex());
if (getDebug()) System.out.println("indices: " + subset);
// generate output format
atts = new FastVector();
m_Indices = new int[subset.size()];
for (i = 0; i < subset.size(); i++) {
atts.addElement(inputFormat.attribute(subset.get(i)));
m_Indices[i] = subset.get(i);
}
result = new Instances(inputFormat.relationName(), atts, 0);
if (inputFormat.classIndex() > -1) result.setClassIndex(result.numAttributes() - 1);
return result;
}
/**
* Gets the index of the instance with the closest threshold value to the desired target
*
* @param tcurve a set of instances that have been generated by this class
* @param threshold the target threshold
* @return the index of the instance that has threshold closest to the target, or -1 if this could
* not be found (i.e. no data, or bad threshold target)
*/
public static int getThresholdInstance(Instances tcurve, double threshold) {
if (!RELATION_NAME.equals(tcurve.relationName())
|| (tcurve.numInstances() == 0)
|| (threshold < 0)
|| (threshold > 1.0)) {
return -1;
}
if (tcurve.numInstances() == 1) {
return 0;
}
double[] tvals = tcurve.attributeToDoubleArray(tcurve.numAttributes() - 1);
int[] sorted = Utils.sort(tvals);
return binarySearch(sorted, tvals, threshold);
}
/**
* 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;
}
/**
* Calculates the n point precision result, which is the precision averaged over n evenly spaced
* (w.r.t recall) samples of the curve.
*
* @param tcurve a previously extracted threshold curve Instances.
* @param n the number of points to average over.
* @return the n-point precision.
*/
public static double getNPointPrecision(Instances tcurve, int n) {
if (!RELATION_NAME.equals(tcurve.relationName()) || (tcurve.numInstances() == 0)) {
return Double.NaN;
}
int recallInd = tcurve.attribute(RECALL_NAME).index();
int precisInd = tcurve.attribute(PRECISION_NAME).index();
double[] recallVals = tcurve.attributeToDoubleArray(recallInd);
int[] sorted = Utils.sort(recallVals);
double isize = 1.0 / (n - 1);
double psum = 0;
for (int i = 0; i < n; i++) {
int pos = binarySearch(sorted, recallVals, i * isize);
double recall = recallVals[sorted[pos]];
double precis = tcurve.instance(sorted[pos]).value(precisInd);
/*
System.err.println("Point " + (i + 1) + ": i=" + pos
+ " r=" + (i * isize)
+ " p'=" + precis
+ " r'=" + recall);
*/
// interpolate figures for non-endpoints
while ((pos != 0) && (pos < sorted.length - 1)) {
pos++;
double recall2 = recallVals[sorted[pos]];
if (recall2 != recall) {
double precis2 = tcurve.instance(sorted[pos]).value(precisInd);
double slope = (precis2 - precis) / (recall2 - recall);
double offset = precis - recall * slope;
precis = isize * i * slope + offset;
/*
System.err.println("Point2 " + (i + 1) + ": i=" + pos
+ " r=" + (i * isize)
+ " p'=" + precis2
+ " r'=" + recall2
+ " p''=" + precis);
*/
break;
}
}
psum += precis;
}
return psum / n;
}
public boolean batchFinished() throws Exception {
Instances input = getInputFormat();
String relation = input.relationName();
Instances output = new Instances(relation);
int numAttributes = input.numAttributes();
int numInstances = input.numInstances();
for (int i = 0; i < numAttributes; i++) {
FastVector vector = new FastVector();
for (int j = 0; j < numInstances; j++) {
double value = input.instance(j).value(i);
String string = String.valueOf(value);
if (vector.indexOf(string) == -1) vector.addElement(string);
}
Attribute attribute = new Attribute(input.attribute(i).name(), vector);
output.appendAttribute(attribute);
}
setOutputFormat(output);
for (int i = 0; i < numInstances; i++) push(input.instance(i));
return super.batchFinished();
}
/**
* Sets the format of output instances. The derived class should use this method once it has
* determined the outputformat. The output queue is cleared.
*
* @param outputFormat the new output format
*/
protected void setOutputFormat(Instances outputFormat) {
if (outputFormat != null) {
m_OutputFormat = outputFormat.stringFreeStructure();
initOutputLocators(m_OutputFormat, null);
// Rename the relation
String relationName = outputFormat.relationName() + "-" + this.getClass().getName();
if (this instanceof OptionHandler) {
String[] options = ((OptionHandler) this).getOptions();
for (int i = 0; i < options.length; i++) {
relationName += options[i].trim();
}
}
m_OutputFormat.setRelationName(relationName);
} else {
m_OutputFormat = null;
}
m_OutputQueue = new Queue();
}
@Override
protected void manipulateAttributes(Instances data) throws TaskException {
String[] attribs = this.getParameterVal(ATTRIBS).split("\\s+");
for (int i = 0; i < attribs.length; ++i) {
if (data.attribute(attribs[i]) == null) {
Logger.getInstance()
.message(
"Attribute " + attribs[i] + " not found in data set " + data.relationName(),
Logger.V_WARNING);
continue;
}
Enumeration<Instance> insts = data.enumerateInstances();
int attrIndex = data.attribute(attribs[i]).index();
while (insts.hasMoreElements()) {
Instance inst = insts.nextElement();
inst.setMissing(attrIndex);
}
}
}
public void fillWekaInstances(weka.core.Instances winsts) {
// set name
setName(winsts.relationName());
// set attributes
List onto_attrs = new ArrayList();
for (int i = 0; i < winsts.numAttributes(); i++) {
Attribute a = new Attribute();
a.fillWekaAttribute(winsts.attribute(i));
onto_attrs.add(a);
}
setAttributes(onto_attrs);
// set instances
List onto_insts = new ArrayList();
for (int i = 0; i < winsts.numInstances(); i++) {
Instance inst = new Instance();
weka.core.Instance winst = winsts.instance(i);
List instvalues = new ArrayList();
List instmis = new ArrayList();
for (int j = 0; j < winst.numValues(); j++) {
if (winst.isMissing(j)) {
instvalues.add(new Double(0.0));
instmis.add(new Boolean(true));
} else {
instvalues.add(new Double(winst.value(j)));
instmis.add(new Boolean(false));
}
}
inst.setValues(instvalues);
inst.setMissing(instmis);
onto_insts.add(inst);
}
setInstances(onto_insts);
setClass_index(winsts.classIndex());
}
/**
* Determines the output format based on the input format and returns this. In case the output
* format cannot be returned immediately, i.e., hasImmediateOutputFormat() returns false, then
* this method will called from batchFinished() after the call of preprocess(Instances), in which,
* e.g., statistics for the actual processing step can be gathered.
*
* @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;
ArrayList<Attribute> atts;
int i;
m_AttributeIndices.setUpper(inputFormat.numAttributes() - 1);
// generate new header
atts = new ArrayList<Attribute>();
for (i = 0; i < inputFormat.numAttributes(); i++) {
att = inputFormat.attribute(i);
if (m_AttributeIndices.isInRange(i)) {
if (m_ReplaceAll) atts.add(att.copy(att.name().replaceAll(m_Find, m_Replace)));
else atts.add(att.copy(att.name().replaceFirst(m_Find, m_Replace)));
} else {
atts.add((Attribute) att.copy());
}
}
result = new Instances(inputFormat.relationName(), atts, 0);
result.setClassIndex(inputFormat.classIndex());
return result;
}
/**
* Sets the format of the input instances.
*
* @param instanceInfo an Instances object containing the input instance structure (any instances
* contained in the object are ignored - only the structure is required).
* @return true if the outputFormat may be collected immediately
* @throws Exception if the format couldn't be set successfully
*/
@Override
public boolean setInputFormat(Instances instanceInfo) throws Exception {
super.setInputFormat(instanceInfo);
int classIndex = instanceInfo.classIndex();
// setup the map
if (m_renameVals != null && m_renameVals.length() > 0) {
String[] vals = m_renameVals.split(",");
for (String val : vals) {
String[] parts = val.split(":");
if (parts.length != 2) {
throw new WekaException("Invalid replacement string: " + val);
}
if (parts[0].length() == 0 || parts[1].length() == 0) {
throw new WekaException("Invalid replacement string: " + val);
}
m_renameMap.put(
m_ignoreCase ? parts[0].toLowerCase().trim() : parts[0].trim(), parts[1].trim());
}
}
// try selected atts as a numeric range first
Range tempRange = new Range();
tempRange.setInvert(m_invert);
if (m_selectedColsString == null) {
m_selectedColsString = "";
}
try {
tempRange.setRanges(m_selectedColsString);
tempRange.setUpper(instanceInfo.numAttributes() - 1);
m_selectedAttributes = tempRange.getSelection();
m_selectedCols = tempRange;
} catch (Exception r) {
// OK, now try as named attributes
StringBuffer indexes = new StringBuffer();
String[] attNames = m_selectedColsString.split(",");
boolean first = true;
for (String n : attNames) {
n = n.trim();
Attribute found = instanceInfo.attribute(n);
if (found == null) {
throw new WekaException(
"Unable to find attribute '" + n + "' in the incoming instances'");
}
if (first) {
indexes.append("" + (found.index() + 1));
first = false;
} else {
indexes.append("," + (found.index() + 1));
}
}
tempRange = new Range();
tempRange.setRanges(indexes.toString());
tempRange.setUpper(instanceInfo.numAttributes() - 1);
m_selectedAttributes = tempRange.getSelection();
m_selectedCols = tempRange;
}
ArrayList<Attribute> attributes = new ArrayList<Attribute>();
for (int i = 0; i < instanceInfo.numAttributes(); i++) {
if (m_selectedCols.isInRange(i)) {
if (instanceInfo.attribute(i).isNominal()) {
List<String> valsForAtt = new ArrayList<String>();
for (int j = 0; j < instanceInfo.attribute(i).numValues(); j++) {
String origV = instanceInfo.attribute(i).value(j);
String replace =
m_ignoreCase ? m_renameMap.get(origV.toLowerCase()) : m_renameMap.get(origV);
if (replace != null && !valsForAtt.contains(replace)) {
valsForAtt.add(replace);
} else {
valsForAtt.add(origV);
}
}
Attribute newAtt = new Attribute(instanceInfo.attribute(i).name(), valsForAtt);
attributes.add(newAtt);
} else {
// ignore any selected attributes that are not nominal
Attribute att = (Attribute) instanceInfo.attribute(i).copy();
attributes.add(att);
}
} else {
Attribute att = (Attribute) instanceInfo.attribute(i).copy();
attributes.add(att);
}
}
Instances outputFormat = new Instances(instanceInfo.relationName(), attributes, 0);
outputFormat.setClassIndex(classIndex);
setOutputFormat(outputFormat);
return true;
}
@Override
protected Instances determineOutputFormat(Instances inputFormat) throws Exception {
if (m_excludeNominalAttributes && m_excludeNumericAttributes) {
throw new Exception(
"No transformation will be done if both nominal and "
+ "numeric attributes are excluded!");
}
if (m_remove == null) {
List<Integer> attsToExclude = new ArrayList<Integer>();
if (m_excludeNumericAttributes) {
for (int i = 0; i < inputFormat.numAttributes(); i++) {
if (inputFormat.attribute(i).isNumeric() && i != inputFormat.classIndex()) {
attsToExclude.add(i);
}
}
}
if (m_excludeNominalAttributes || m_nominalConversionThreshold > 1) {
for (int i = 0; i < inputFormat.numAttributes(); i++) {
if (inputFormat.attribute(i).isNominal() && i != inputFormat.classIndex()) {
if (m_excludeNominalAttributes
|| inputFormat.attribute(i).numValues() < m_nominalConversionThreshold) {
attsToExclude.add(i);
}
}
}
}
if (attsToExclude.size() > 0) {
int[] r = new int[attsToExclude.size()];
for (int i = 0; i < attsToExclude.size(); i++) {
r[i] = attsToExclude.get(i);
}
m_remove = new Remove();
m_remove.setAttributeIndicesArray(r);
m_remove.setInputFormat(inputFormat);
Remove forRetaining = new Remove();
forRetaining.setAttributeIndicesArray(r);
forRetaining.setInvertSelection(true);
forRetaining.setInputFormat(inputFormat);
m_unchanged = Filter.useFilter(inputFormat, forRetaining);
}
}
ArrayList<Attribute> atts = new ArrayList<Attribute>();
for (int i = 0; i < inputFormat.numAttributes(); i++) {
if (i != inputFormat.classIndex()) {
if (m_unchanged != null && m_unchanged.attribute(inputFormat.attribute(i).name()) != null) {
atts.add((Attribute) m_unchanged.attribute(inputFormat.attribute(i).name()).copy());
continue;
}
for (int j = 0; j < inputFormat.classAttribute().numValues(); j++) {
String name =
"pr_" + inputFormat.attribute(i).name() + "|" + inputFormat.classAttribute().value(j);
atts.add(new Attribute(name));
}
}
}
atts.add((Attribute) inputFormat.classAttribute().copy());
Instances data = new Instances(inputFormat.relationName(), atts, 0);
data.setClassIndex(data.numAttributes() - 1);
return data;
}
/**
* generates source code from the filter
*
* @param filter the filter to output as source
* @param className the name of the generated class
* @param input the input data the header is generated for
* @param output the output data the header is generated for
* @return the generated source code
* @throws Exception if source code cannot be generated
*/
public static String wekaStaticWrapper(
Sourcable filter, String className, Instances input, Instances output) throws Exception {
StringBuffer result;
int i;
int n;
result = new StringBuffer();
result.append("// Generated with Weka " + Version.VERSION + "\n");
result.append("//\n");
result.append("// This code is public domain and comes with no warranty.\n");
result.append("//\n");
result.append("// Timestamp: " + new Date() + "\n");
result.append("// Relation: " + input.relationName() + "\n");
result.append("\n");
result.append("package weka.filters;\n");
result.append("\n");
result.append("import weka.core.Attribute;\n");
result.append("import weka.core.Capabilities;\n");
result.append("import weka.core.Capabilities.Capability;\n");
result.append("import weka.core.FastVector;\n");
result.append("import weka.core.Instance;\n");
result.append("import weka.core.Instances;\n");
result.append("import weka.filters.Filter;\n");
result.append("\n");
result.append("public class WekaWrapper\n");
result.append(" extends Filter {\n");
// globalInfo
result.append("\n");
result.append(" /**\n");
result.append(" * Returns only the toString() method.\n");
result.append(" *\n");
result.append(" * @return a string describing the filter\n");
result.append(" */\n");
result.append(" public String globalInfo() {\n");
result.append(" return toString();\n");
result.append(" }\n");
// getCapabilities
result.append("\n");
result.append(" /**\n");
result.append(" * Returns the capabilities of this filter.\n");
result.append(" *\n");
result.append(" * @return the capabilities\n");
result.append(" */\n");
result.append(" public Capabilities getCapabilities() {\n");
result.append(((Filter) filter).getCapabilities().toSource("result", 4));
result.append(" return result;\n");
result.append(" }\n");
// objectsToInstance
result.append("\n");
result.append(" /**\n");
result.append(" * turns array of Objects into an Instance object\n");
result.append(" *\n");
result.append(" * @param obj the Object array to turn into an Instance\n");
result.append(" * @param format the data format to use\n");
result.append(" * @return the generated Instance object\n");
result.append(" */\n");
result.append(" protected Instance objectsToInstance(Object[] obj, Instances format) {\n");
result.append(" Instance result;\n");
result.append(" double[] values;\n");
result.append(" int i;\n");
result.append("\n");
result.append(" values = new double[obj.length];\n");
result.append("\n");
result.append(" for (i = 0 ; i < obj.length; i++) {\n");
result.append(" if (obj[i] == null)\n");
result.append(" values[i] = Instance.missingValue();\n");
result.append(" else if (format.attribute(i).isNumeric())\n");
result.append(" values[i] = (Double) obj[i];\n");
result.append(" else if (format.attribute(i).isNominal())\n");
result.append(" values[i] = format.attribute(i).indexOfValue((String) obj[i]);\n");
result.append(" }\n");
result.append("\n");
result.append(" // create new instance\n");
result.append(" result = new Instance(1.0, values);\n");
result.append(" result.setDataset(format);\n");
result.append("\n");
result.append(" return result;\n");
result.append(" }\n");
// instanceToObjects
result.append("\n");
result.append(" /**\n");
result.append(" * turns the Instance object into an array of Objects\n");
result.append(" *\n");
result.append(" * @param inst the instance to turn into an array\n");
result.append(" * @return the Object array representing the instance\n");
result.append(" */\n");
result.append(" protected Object[] instanceToObjects(Instance inst) {\n");
result.append(" Object[] result;\n");
result.append(" int i;\n");
result.append("\n");
result.append(" result = new Object[inst.numAttributes()];\n");
result.append("\n");
result.append(" for (i = 0 ; i < inst.numAttributes(); i++) {\n");
result.append(" if (inst.isMissing(i))\n");
result.append(" result[i] = null;\n");
result.append(" else if (inst.attribute(i).isNumeric())\n");
result.append(" result[i] = inst.value(i);\n");
result.append(" else\n");
result.append(" result[i] = inst.stringValue(i);\n");
result.append(" }\n");
result.append("\n");
result.append(" return result;\n");
result.append(" }\n");
// instancesToObjects
result.append("\n");
result.append(" /**\n");
result.append(" * turns the Instances object into an array of Objects\n");
result.append(" *\n");
result.append(" * @param data the instances to turn into an array\n");
result.append(" * @return the Object array representing the instances\n");
result.append(" */\n");
result.append(" protected Object[][] instancesToObjects(Instances data) {\n");
result.append(" Object[][] result;\n");
result.append(" int i;\n");
result.append("\n");
result.append(" result = new Object[data.numInstances()][];\n");
result.append("\n");
result.append(" for (i = 0; i < data.numInstances(); i++)\n");
result.append(" result[i] = instanceToObjects(data.instance(i));\n");
result.append("\n");
result.append(" return result;\n");
result.append(" }\n");
// setInputFormat
result.append("\n");
result.append(" /**\n");
result.append(" * Only tests the input data.\n");
result.append(" *\n");
result.append(" * @param instanceInfo the format of the data to convert\n");
result.append(" * @return always true, to indicate that the output format can \n");
result.append(" * be collected immediately.\n");
result.append(" */\n");
result.append(" public boolean setInputFormat(Instances instanceInfo) throws Exception {\n");
result.append(" super.setInputFormat(instanceInfo);\n");
result.append(" \n");
result.append(" // generate output format\n");
result.append(" FastVector atts = new FastVector();\n");
result.append(" FastVector attValues;\n");
for (i = 0; i < output.numAttributes(); i++) {
result.append(" // " + output.attribute(i).name() + "\n");
if (output.attribute(i).isNumeric()) {
result.append(
" atts.addElement(new Attribute(\"" + output.attribute(i).name() + "\"));\n");
} else if (output.attribute(i).isNominal()) {
result.append(" attValues = new FastVector();\n");
for (n = 0; n < output.attribute(i).numValues(); n++) {
result.append(" attValues.addElement(\"" + output.attribute(i).value(n) + "\");\n");
}
result.append(
" atts.addElement(new Attribute(\""
+ output.attribute(i).name()
+ "\", attValues));\n");
} else {
throw new UnsupportedAttributeTypeException(
"Attribute type '"
+ output.attribute(i).type()
+ "' (position "
+ (i + 1)
+ ") is not supported!");
}
}
result.append(" \n");
result.append(
" Instances format = new Instances(\"" + output.relationName() + "\", atts, 0);\n");
result.append(" format.setClassIndex(" + output.classIndex() + ");\n");
result.append(" setOutputFormat(format);\n");
result.append(" \n");
result.append(" return true;\n");
result.append(" }\n");
// input
result.append("\n");
result.append(" /**\n");
result.append(" * Directly filters the instance.\n");
result.append(" *\n");
result.append(" * @param instance the instance to convert\n");
result.append(" * @return always true, to indicate that the output can \n");
result.append(" * be collected immediately.\n");
result.append(" */\n");
result.append(" public boolean input(Instance instance) throws Exception {\n");
result.append(
" Object[] filtered = " + className + ".filter(instanceToObjects(instance));\n");
result.append(" push(objectsToInstance(filtered, getOutputFormat()));\n");
result.append(" return true;\n");
result.append(" }\n");
// batchFinished
result.append("\n");
result.append(" /**\n");
result.append(" * Performs a batch filtering of the buffered data, if any available.\n");
result.append(" *\n");
result.append(" * @return true if instances were filtered otherwise false\n");
result.append(" */\n");
result.append(" public boolean batchFinished() throws Exception {\n");
result.append(" if (getInputFormat() == null)\n");
result.append(" throw new NullPointerException(\"No input instance format defined\");;\n");
result.append("\n");
result.append(" Instances inst = getInputFormat();\n");
result.append(" if (inst.numInstances() > 0) {\n");
result.append(
" Object[][] filtered = " + className + ".filter(instancesToObjects(inst));\n");
result.append(" for (int i = 0; i < filtered.length; i++) {\n");
result.append(" push(objectsToInstance(filtered[i], getOutputFormat()));\n");
result.append(" }\n");
result.append(" }\n");
result.append("\n");
result.append(" flushInput();\n");
result.append(" m_NewBatch = true;\n");
result.append(" m_FirstBatchDone = true;\n");
result.append("\n");
result.append(" return (inst.numInstances() > 0);\n");
result.append(" }\n");
// toString
result.append("\n");
result.append(" /**\n");
result.append(" * Returns only the classnames and what filter it is based on.\n");
result.append(" *\n");
result.append(" * @return a short description\n");
result.append(" */\n");
result.append(" public String toString() {\n");
result.append(
" return \"Auto-generated filter wrapper, based on "
+ filter.getClass().getName()
+ " (generated with Weka "
+ Version.VERSION
+ ").\\n"
+ "\" + this.getClass().getName() + \"/"
+ className
+ "\";\n");
result.append(" }\n");
// main
result.append("\n");
result.append(" /**\n");
result.append(" * Runs the filter from commandline.\n");
result.append(" *\n");
result.append(" * @param args the commandline arguments\n");
result.append(" */\n");
result.append(" public static void main(String args[]) {\n");
result.append(" runFilter(new WekaWrapper(), args);\n");
result.append(" }\n");
result.append("}\n");
// actual filter code
result.append("\n");
result.append(filter.toSource(className, input));
return result.toString();
}
/**
* Takes an evaluation object from a task and aggregates it with the overall one.
*
* @param eval the evaluation object to aggregate
* @param classifier the classifier used by the task
* @param testData the testData from the task
* @param plotInstances the ClassifierErrorsPlotInstances object from the task
* @param setNum the set number processed by the task
* @param maxSetNum the maximum number of sets in this batch
*/
protected synchronized void aggregateEvalTask(
Evaluation eval,
Classifier classifier,
Instances testData,
ClassifierErrorsPlotInstances plotInstances,
int setNum,
int maxSetNum) {
m_eval.aggregate(eval);
if (m_aggregatedPlotInstances == null) {
m_aggregatedPlotInstances = new Instances(plotInstances.getPlotInstances());
m_aggregatedPlotShapes = plotInstances.getPlotShapes();
m_aggregatedPlotSizes = plotInstances.getPlotSizes();
} else {
Instances temp = plotInstances.getPlotInstances();
for (int i = 0; i < temp.numInstances(); i++) {
m_aggregatedPlotInstances.add(temp.get(i));
m_aggregatedPlotShapes.addElement(plotInstances.getPlotShapes().get(i));
m_aggregatedPlotSizes.addElement(plotInstances.getPlotSizes().get(i));
}
}
m_setsComplete++;
// if (ce.getSetNumber() == ce.getMaxSetNumber()) {
if (m_setsComplete == maxSetNum) {
try {
String textTitle = classifier.getClass().getName();
String textOptions = "";
if (classifier instanceof OptionHandler) {
textOptions = Utils.joinOptions(((OptionHandler) classifier).getOptions());
}
textTitle = textTitle.substring(textTitle.lastIndexOf('.') + 1, textTitle.length());
String resultT =
"=== Evaluation result ===\n\n"
+ "Scheme: "
+ textTitle
+ "\n"
+ ((textOptions.length() > 0) ? "Options: " + textOptions + "\n" : "")
+ "Relation: "
+ testData.relationName()
+ "\n\n"
+ m_eval.toSummaryString();
if (testData.classAttribute().isNominal()) {
resultT += "\n" + m_eval.toClassDetailsString() + "\n" + m_eval.toMatrixString();
}
TextEvent te = new TextEvent(ClassifierPerformanceEvaluator.this, resultT, textTitle);
notifyTextListeners(te);
// set up visualizable errors
if (m_visualizableErrorListeners.size() > 0) {
PlotData2D errorD = new PlotData2D(m_aggregatedPlotInstances);
errorD.setShapeSize(m_aggregatedPlotSizes);
errorD.setShapeType(m_aggregatedPlotShapes);
errorD.setPlotName(textTitle + " " + textOptions);
/* PlotData2D errorD = m_PlotInstances.getPlotData(
textTitle + " " + textOptions); */
VisualizableErrorEvent vel =
new VisualizableErrorEvent(ClassifierPerformanceEvaluator.this, errorD);
notifyVisualizableErrorListeners(vel);
m_PlotInstances.cleanUp();
}
if (testData.classAttribute().isNominal() && m_thresholdListeners.size() > 0) {
ThresholdCurve tc = new ThresholdCurve();
Instances result = tc.getCurve(m_eval.predictions(), 0);
result.setRelationName(testData.relationName());
PlotData2D pd = new PlotData2D(result);
String htmlTitle = "<html><font size=-2>" + textTitle;
String newOptions = "";
if (classifier instanceof OptionHandler) {
String[] options = ((OptionHandler) classifier).getOptions();
if (options.length > 0) {
for (int ii = 0; ii < options.length; ii++) {
if (options[ii].length() == 0) {
continue;
}
if (options[ii].charAt(0) == '-'
&& !(options[ii].charAt(1) >= '0' && options[ii].charAt(1) <= '9')) {
newOptions += "<br>";
}
newOptions += options[ii];
}
}
}
htmlTitle +=
" "
+ newOptions
+ "<br>"
+ " (class: "
+ testData.classAttribute().value(0)
+ ")"
+ "</font></html>";
pd.setPlotName(textTitle + " (class: " + testData.classAttribute().value(0) + ")");
pd.setPlotNameHTML(htmlTitle);
boolean[] connectPoints = new boolean[result.numInstances()];
for (int jj = 1; jj < connectPoints.length; jj++) {
connectPoints[jj] = true;
}
pd.setConnectPoints(connectPoints);
ThresholdDataEvent rde =
new ThresholdDataEvent(
ClassifierPerformanceEvaluator.this, pd, testData.classAttribute());
notifyThresholdListeners(rde);
}
if (m_logger != null) {
m_logger.statusMessage(statusMessagePrefix() + "Finished.");
}
} catch (Exception ex) {
if (m_logger != null) {
m_logger.logMessage(
"[ClassifierPerformanceEvaluator] "
+ statusMessagePrefix()
+ " problem constructing evaluation results. "
+ ex.getMessage());
}
ex.printStackTrace();
} finally {
m_visual.setStatic();
// save memory
m_PlotInstances = null;
m_setsComplete = 0;
m_tasks = null;
m_aggregatedPlotInstances = null;
}
}
}
/**
* Determines the output format based on the input format and returns this. In case the output
* format cannot be returned immediately, i.e., hasImmediateOutputFormat() returns false, then
* this method will called from batchFinished() after the call of preprocess(Instances), in which,
* e.g., statistics for the actual processing step can be gathered.
*
* @param inputFormat the input format to base the output format on
* @return the output format
* @throws Exception in case the determination goes wrong
* @see #hasImmediateOutputFormat()
* @see #batchFinished()
*/
protected Instances determineOutputFormat(Instances inputFormat) throws Exception {
FastVector atts;
FastVector values;
Instances result;
int i;
// attributes must be numeric
m_Attributes.setUpper(inputFormat.numAttributes() - 1);
m_AttributeIndices = m_Attributes.getSelection();
for (i = 0; i < m_AttributeIndices.length; i++) {
// ignore class
if (m_AttributeIndices[i] == inputFormat.classIndex()) {
m_AttributeIndices[i] = NON_NUMERIC;
continue;
}
// not numeric -> ignore it
if (!inputFormat.attribute(m_AttributeIndices[i]).isNumeric())
m_AttributeIndices[i] = NON_NUMERIC;
}
// get old attributes
atts = new FastVector();
for (i = 0; i < inputFormat.numAttributes(); i++) atts.addElement(inputFormat.attribute(i));
if (!getDetectionPerAttribute()) {
m_OutlierAttributePosition = new int[1];
m_OutlierAttributePosition[0] = atts.size();
// add 2 new attributes
values = new FastVector();
values.addElement("no");
values.addElement("yes");
atts.addElement(new Attribute("Outlier", values));
values = new FastVector();
values.addElement("no");
values.addElement("yes");
atts.addElement(new Attribute("ExtremeValue", values));
} else {
m_OutlierAttributePosition = new int[m_AttributeIndices.length];
for (i = 0; i < m_AttributeIndices.length; i++) {
if (m_AttributeIndices[i] == NON_NUMERIC) continue;
m_OutlierAttributePosition[i] = atts.size();
// add new attributes
values = new FastVector();
values.addElement("no");
values.addElement("yes");
atts.addElement(
new Attribute(
inputFormat.attribute(m_AttributeIndices[i]).name() + "_Outlier", values));
values = new FastVector();
values.addElement("no");
values.addElement("yes");
atts.addElement(
new Attribute(
inputFormat.attribute(m_AttributeIndices[i]).name() + "_ExtremeValue", values));
if (getOutputOffsetMultiplier())
atts.addElement(
new Attribute(inputFormat.attribute(m_AttributeIndices[i]).name() + "_Offset"));
}
}
// generate header
result = new Instances(inputFormat.relationName(), atts, 0);
result.setClassIndex(inputFormat.classIndex());
return result;
}
/**
* pads the data to conform to the necessary number of attributes
*
* @param data the data to pad
* @return the padded data
*/
protected Instances pad(Instances data) {
Instances result;
int i;
int n;
String prefix;
int numAtts;
boolean isLast;
int index;
Vector<Integer> padded;
int[] indices;
FastVector atts;
// determine number of padding attributes
switch (m_Padding) {
case PADDING_ZERO:
if (data.classIndex() > -1)
numAtts = (nextPowerOf2(data.numAttributes() - 1) + 1) - data.numAttributes();
else numAtts = nextPowerOf2(data.numAttributes()) - data.numAttributes();
break;
default:
throw new IllegalStateException(
"Padding " + new SelectedTag(m_Algorithm, TAGS_PADDING) + " not implemented!");
}
result = new Instances(data);
prefix = getAlgorithm().getSelectedTag().getReadable();
// any padding necessary?
if (numAtts > 0) {
// add padding attributes
isLast = (data.classIndex() == data.numAttributes() - 1);
padded = new Vector<Integer>();
for (i = 0; i < numAtts; i++) {
if (isLast) index = result.numAttributes() - 1;
else index = result.numAttributes();
result.insertAttributeAt(new Attribute(prefix + "_padding_" + (i + 1)), index);
// record index
padded.add(new Integer(index));
}
// get padded indices
indices = new int[padded.size()];
for (i = 0; i < padded.size(); i++) indices[i] = padded.get(i);
// determine number of padding attributes
switch (m_Padding) {
case PADDING_ZERO:
for (i = 0; i < result.numInstances(); i++) {
for (n = 0; n < indices.length; n++) result.instance(i).setValue(indices[n], 0);
}
break;
}
}
// rename all attributes apart from class
data = result;
atts = new FastVector();
n = 0;
for (i = 0; i < data.numAttributes(); i++) {
n++;
if (i == data.classIndex()) atts.addElement((Attribute) data.attribute(i).copy());
else atts.addElement(new Attribute(prefix + "_" + n));
}
// create new dataset
result = new Instances(data.relationName(), atts, data.numInstances());
result.setClassIndex(data.classIndex());
for (i = 0; i < data.numInstances(); i++)
result.add(new DenseInstance(1.0, data.instance(i).toDoubleArray()));
return result;
}