com.github.TKnudsen.ComplexDataObject.model.tools.WekaConversion Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of complex-data-object Show documentation
Show all versions of complex-data-object Show documentation
A library that models real-world objects in Java, referred to as ComplexDataObjects. Other features: IO and preprocessing of ComplexDataObjects.
package com.github.TKnudsen.ComplexDataObject.model.tools;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import com.github.TKnudsen.ComplexDataObject.data.complexDataObject.ComplexDataContainer;
import com.github.TKnudsen.ComplexDataObject.data.complexDataObject.ComplexDataObject;
import com.github.TKnudsen.ComplexDataObject.data.features.AbstractFeatureVector;
import com.github.TKnudsen.ComplexDataObject.data.features.Feature;
import com.github.TKnudsen.ComplexDataObject.data.features.FeatureContainer;
import com.github.TKnudsen.ComplexDataObject.data.features.FeatureType;
import com.github.TKnudsen.ComplexDataObject.data.features.mixedData.MixedDataFeatureVector;
import com.github.TKnudsen.ComplexDataObject.data.features.numericalData.NumericalFeatureVector;
import weka.core.Attribute;
import weka.core.DenseInstance;
import weka.core.Instance;
import weka.core.Instances;
/**
*
* Title: WekaConversion
*
*
*
* Description: helper tools that ease the use of WEKA data structures, i.e.,
* Instances and Instance objects.
*
*
*
* Copyright: Copyright (c) 2016
*
*
* @author Juergen Bernard
* @version 1.04
*/
public class WekaConversion {
public static Instances getInstances(ComplexDataContainer container) {
if (container == null)
return null;
List attrs = new ArrayList();
Map attributeMap = new HashMap<>();
int dims = container.getAttributeNames().size();
if (!container.getAttributeNames().contains("Name")) {
dims++;
Attribute a = new Attribute("Name", (List) null);
attrs.add(a);
attributeMap.put("Name", a);
}
if (!container.getAttributeNames().contains("Description")) {
dims++;
Attribute a = new Attribute("Description", (List) null);
attrs.add(a);
attributeMap.put("Description", a);
}
for (Iterator iterator = container.getAttributeNames().iterator(); iterator.hasNext();) {
String string = iterator.next();
Attribute a = null;
if (container.isNumeric(string))
a = new Attribute(string);
else if (container.isBoolean(string))
a = new Attribute(string);
else
a = new Attribute(string, (List) null);
attrs.add(a);
attributeMap.put(string, a);
}
Instances instances = new Instances("ComplexDataContainer " + container.toString(), (ArrayList) attrs, container.size());
// create instance objects
for (ComplexDataObject cdo : container) {
Instance instance = new DenseInstance(dims);
Iterator attNames = cdo.iterator();
while (attNames.hasNext()) {
String attName = attNames.next();
Attribute attribute = attributeMap.get(attName);
Object value = cdo.getAttribute(attName);
if (container.isNumeric(attName)) {
if (value != null)
instance.setValue(attribute, ((Number) value).doubleValue());
} else if (container.isBoolean(attName)) {
if (value != null) {
Integer i = ((Boolean) value).booleanValue() ? 1 : 0;
instance.setValue(attribute, ((Number) i).doubleValue());
}
} else if (value != null)
instance.setValue(attribute, value.toString());
}
Attribute nameAttribute = attributeMap.get("Name");
instance.setValue(nameAttribute, cdo.getName());
Attribute descripptionAttribute = attributeMap.get("Description");
instance.setValue(descripptionAttribute, cdo.getDescription());
instances.add(instance);
}
return instances;
}
/**
*
* @param fvs
* @return
* @deprecated use
*/
public static >> Instances getInstances(List fvs) {
int length = fvs.get(0).getDimensions();
List attrs = new ArrayList(length);
for (int i = 0; i < length; i++) {
Attribute a = null;
if (fvs.get(0).getFeature(i).getFeatureType().equals(FeatureType.DOUBLE))
a = new Attribute(i + 1 + "");
else
a = new Attribute(i + 1 + "", (List) null);
attrs.add(a);
}
Instances data = new Instances(fvs.get(0).getClass().getName(), (ArrayList) attrs, fvs.size());
addInstances(fvs, data);
return data;
}
/**
*
* @param fvs
* @return
* @deprecated use
*/
public static , FV extends AbstractFeatureVector> Instances getInstances(FeatureContainer featureContainer) {
// FeatureContainer featureContainer = new
// FeatureContainer<>(fvs);
List attrs = new ArrayList(featureContainer.getFeatureNames().size());
for (String featureName : featureContainer.getFeatureNames()) {
Attribute a = null;
if (featureContainer.isNumeric(featureName))
a = new Attribute(featureName);
else
a = new Attribute(featureName, (List) null);
attrs.add(a);
}
Instances instances = new Instances("asdf", (ArrayList) attrs, featureContainer.size());
addInstances(featureContainer, instances);
return instances;
}
/**
*
* @param fvs
* @param stringToNominal
* decides whether string values are represented as nominal
* values (with a concrete alphabet of observations)
* @return
*/
public static >> Instances getInstances(List fvs, boolean stringToNominal) {
// TODO
System.out.println("WekaConversion.getInstances: unimplemented method. there is a difference between strings and nominals in WEKA which has to be considered in future");
System.exit(-1);
int length = fvs.get(0).getDimensions();
List attrs = new ArrayList(length);
for (int i = 0; i < length; i++) {
Attribute a = null;
if (fvs.get(0).getFeature(i).getFeatureType().equals(FeatureType.DOUBLE))
a = new Attribute(i + 1 + "");
else
a = new Attribute(i + 1 + "", (List) null);
attrs.add(a);
}
Instances data = new Instances(fvs.get(0).getClass().getName(), (ArrayList) attrs, fvs.size());
addInstances(fvs, data);
return data;
}
public static >> void addInstances(List fvs, Instances data) {
if (fvs == null || fvs.size() == 0)
return;
int dim = fvs.get(0).getVectorRepresentation().size();
for (FV fv : fvs) {
int length = fv.getVectorRepresentation().size();
if (dim != length)
throw new IllegalArgumentException("List of input FV has different features.");
data.add(new DenseInstance(length));
Instance ins = data.get(data.size() - 1);
List> vectorRepresentation = fv.getVectorRepresentation();
for (int i = 0; i < length; i++) {
if (vectorRepresentation.get(i).getFeatureType() == FeatureType.DOUBLE)
ins.setValue(i, (Double) vectorRepresentation.get(i).getFeatureValue());
else if (vectorRepresentation.get(i).getFeatureType() == FeatureType.STRING) {
String str = vectorRepresentation.get(i).getFeatureValue().toString();
try {
ins.setValue(i, str.toString());
} catch (Exception e) {
ins.setValue(i, "");
}
} else if (vectorRepresentation.get(i).getFeatureType() == FeatureType.BOOLEAN) {
Boolean b = (Boolean) vectorRepresentation.get(i).getFeatureValue();
ins.setValue(i, b.toString());
} else {
System.out.println("");
}
// TODO check whether WEKA automatically maps string to nominal.
}
}
}
public static >> void addInstances(FeatureContainer featureContainer, Instances instances) {
if (featureContainer == null || featureContainer.size() == 0)
return;
for (FV fv : featureContainer) {
instances.add(new DenseInstance(fv.getDimensions()));
Instance ins = instances.get(instances.size() - 1);
for (String featureName : featureContainer.getFeatureNames()) {
Feature feature = fv.getFeature(featureName);
Attribute attribute = instances.attribute(featureName);
if (feature.getFeatureType() == FeatureType.DOUBLE) {
Number n = (Number) feature.getFeatureValue();
ins.setValue(attribute, n.doubleValue());
} else if (feature.getFeatureType() == FeatureType.STRING) {
String string = feature.getFeatureValue().toString();
try {
ins.setValue(attribute, string);
} catch (Exception e) {
ins.setValue(attribute, "");
}
} else if (feature.getFeatureType() == FeatureType.BOOLEAN) {
Boolean b = (Boolean) feature.getFeatureValue();
ins.setValue(attribute, b.toString());
} else {
System.out.println("");
}
// TODO check whether WEKA automatically maps string to nominal.
}
}
}
public static void addMixedInstances(List mfvs, Instances data) {
for (MixedDataFeatureVector mfv : mfvs) {
int length = mfv.getVectorRepresentation().size();
data.add(new DenseInstance(length));
Instance ins = data.get(data.size() - 1);
for (int i = 0; i < length; i++) {
if (mfv.getVectorRepresentation().get(i).getFeatureType() == FeatureType.DOUBLE)
ins.setValue(i, (Double) mfv.getVectorRepresentation().get(i).getFeatureValue());
else if (mfv.getVectorRepresentation().get(i).getFeatureType() == FeatureType.STRING) {
String str = (String) mfv.getVectorRepresentation().get(i).getFeatureValue();
ins.setValue(i, str);
}
}
}
}
public static Instances getLabeledInstancesNumerical(List fvs, String classAttribute) {
List labels = new ArrayList<>();
for (int i = 0; i < fvs.size(); i++)
if (fvs.get(i).getAttribute(classAttribute) instanceof String)
labels.add((String) fvs.get(i).getAttribute(classAttribute));
else
labels.add(fvs.get(i).getAttribute(classAttribute).toString());
Instances insances = getInstances(fvs);
return addLabelsToInstances(insances, labels);
}
/**
*
* @param fvs
* @param classAttribute
* @return
*/
public static >> Instances getLabeledInstances(List fvs, String classAttribute) {
return getLabeledInstances(fvs, null, classAttribute);
}
/**
* creates instances with weights for a given List of FVs.
*
* @param fvs
* @param weights
* @param classAttribute
* @return
*/
public static >> Instances getLabeledInstances(List fvs, List weights, String classAttribute) {
List labels = new ArrayList<>();
for (int i = 0; i < fvs.size(); i++)
if (fvs.get(i).getAttribute(classAttribute) instanceof String)
labels.add((String) fvs.get(i).getAttribute(classAttribute));
else
labels.add(fvs.get(i).getAttribute(classAttribute).toString());
Instances insances = getInstances(fvs);
if (weights != null && weights.size() == insances.size())
addWeightsToInstances(insances, weights);
return addLabelsToInstances(insances, labels);
}
/**
* Uses WEKAs ability to assign weights to Instances.
*
* @param instances
* @param weights
* @return
*/
private static Instances addWeightsToInstances(Instances instances, List weights) {
if (instances == null || weights == null)
return instances;
if (instances.size() != weights.size())
throw new IllegalArgumentException();
for (int i = 0; i < weights.size(); i++) {
double w = weights.get(i);
if (Double.isNaN(w))
w = 0;
instances.instance(i).setWeight(w);
}
return instances;
}
public static Instances getLabeledInstances(List fvs, List labels) {
Instances insances = getInstances(fvs);
return addLabelsToInstances(insances, labels);
}
public static Instances getNumericLabeledMixInstances(List mfvs, List numLabels) {
Instances insances = getInstances(mfvs);
return addNumericLabelsToInstances(insances, numLabels);
}
private static Instances addNumericLabelsToInstances(Instances insances, List numLabels) {
Attribute classAtt = new Attribute("num");
insances.insertAttributeAt(classAtt, insances.numAttributes());
insances.setClassIndex(insances.numAttributes() - 1);
for (int i = 0; i < numLabels.size(); i++)
insances.instance(i).setValue(insances.numAttributes() - 1, numLabels.get(i));
return insances;
}
public static Instances addLabelAttributeToInstance(Instances instances, List labels) {
List distinctLabels = distinctListCreator(labels);
Attribute classAtt = new Attribute("class", distinctLabels);
instances.insertAttributeAt(classAtt, instances.numAttributes());
instances.setClass(classAtt);
instances.setClassIndex(instances.numAttributes() - 1);
return instances;
}
public static Instances addNumericLabelAttributeToInstance(Instances insances) {
Attribute classAtt = new Attribute("num");
insances.insertAttributeAt(classAtt, insances.numAttributes());
insances.setClass(classAtt);
insances.setClassIndex(insances.numAttributes() - 1);
return insances;
}
private static Instances addLabelsToInstances(Instances instances, List labels) {
Instances inst2 = addLabelAttributeToInstance(instances, labels);
for (int i = 0; i < labels.size(); i++)
inst2.instance(i).setClassValue(labels.get(i));
return inst2;
}
/**
* Improve this piece of code!
*
* @param list
* @return
*/
public static List distinctListCreator(List list) {
List distinctList = new ArrayList();
if (list == null)
return distinctList;
for (String str : list)
if (!distinctList.contains(str))
distinctList.add(str);
return distinctList;
}
}