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The Waikato Environment for Knowledge Analysis (WEKA), a machine
learning workbench. This is the stable version. Apart from bugfixes, this version
does not receive any other updates.
/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see File to read from
* @return a PMML model
* @throws Exception if there is a problem while reading the file
*/
public static PMMLModel getPMMLModel(File file) throws Exception {
return getPMMLModel(file, null);
}
/**
* Read and return a PMML model.
*
* @param stream the InputStream to read from
* @return a PMML model
* @throws Exception if there is a problem while reading from the stream
*/
public static PMMLModel getPMMLModel(InputStream stream) throws Exception {
return getPMMLModel(stream, null);
}
/**
* Read and return a PMML model.
*
* @param filename the name of the file to read from
* @param log the logging object to use (or null if none is to be used)
* @return a PMML model
* @throws Exception if there is a problem while reading the file
*/
public static PMMLModel getPMMLModel(String filename, Logger log)
throws Exception {
return getPMMLModel(new File(filename), log);
}
/**
* Read and return a PMML model.
*
* @param file a File to read from
* @param log the logging object to use (or null if none is to be used)
* @return a PMML model
* @throws Exception if there is a problem while reading the file
*/
public static PMMLModel getPMMLModel(File file, Logger log) throws Exception {
return getPMMLModel(new BufferedInputStream(new FileInputStream(file)), log);
}
private static boolean isPMML(Document doc) {
NodeList tempL = doc.getElementsByTagName("PMML");
if (tempL.getLength() == 0) {
return false;
}
return true;
}
/**
* Read and return a PMML model.
*
* @param stream the InputStream to read from
* @param log the logging object to use (or null if none is to be used)
* @return a PMML model
* @throws Exception if there is a problem while reading from the stream
*/
public static PMMLModel getPMMLModel(InputStream stream, Logger log)
throws Exception {
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
Document doc = db.parse(stream);
stream.close();
doc.getDocumentElement().normalize();
if (!isPMML(doc)) {
throw new IllegalArgumentException(
"[PMMLFactory] Source is not a PMML file!!");
}
// System.out.println("Root element " +
// doc.getDocumentElement().getNodeName());
Instances dataDictionary = getDataDictionaryAsInstances(doc);
TransformationDictionary transDict = getTransformationDictionary(doc,
dataDictionary);
ModelType modelType = getModelType(doc);
if (modelType == ModelType.UNKNOWN_MODEL) {
throw new Exception("Unsupported PMML model type");
}
Element model = getModelElement(doc, modelType);
// Construct mining schema and meta data
MiningSchema ms = new MiningSchema(model, dataDictionary, transDict);
// System.out.println(ms);
// System.exit(1);
// Instances miningSchema = getMiningSchemaAsInstances(model,
// dataDictionary);
PMMLModel theModel = getModelInstance(doc, modelType, model,
dataDictionary, ms);
if (log != null) {
theModel.setLog(log);
}
return theModel;
}
/**
* Get the transformation dictionary (if there is one).
*
* @param doc the Document containing the PMML model
* @param dataDictionary the data dictionary as an Instances object
* @return the transformation dictionary or null if there is none defined in
* the Document
* @throws Exception if there is a problem getting the transformation
* dictionary
*/
protected static TransformationDictionary getTransformationDictionary(
Document doc, Instances dataDictionary) throws Exception {
TransformationDictionary transDict = null;
NodeList transL = doc.getElementsByTagName("TransformationDictionary");
// should be of size 0 or 1
if (transL.getLength() > 0) {
Node transNode = transL.item(0);
if (transNode.getNodeType() == Node.ELEMENT_NODE) {
transDict = new TransformationDictionary((Element) transNode,
dataDictionary);
}
}
return transDict;
}
/**
* Serialize a PMMLModel object that encapsulates a PMML model
*
* @param model the PMMLModel to serialize
* @param filename the name of the file to save to
* @throws Exception if something goes wrong during serialization
*/
public static void serializePMMLModel(PMMLModel model, String filename)
throws Exception {
serializePMMLModel(model, new File(filename));
}
/**
* Serialize a PMMLModel object that encapsulates a PMML model
*
* @param model the PMMLModel to serialize
* @param file the File to save to
* @throws Exception if something goes wrong during serialization
*/
public static void serializePMMLModel(PMMLModel model, File file)
throws Exception {
serializePMMLModel(model, new BufferedOutputStream(new FileOutputStream(
file)));
}
/**
* Serialize a PMMLModel object that encapsulates a PMML model
*
* @param model the PMMLModel to serialize
* @param stream the OutputStream to serialize to
* @throws Exception if something goes wrong during serialization
*/
public static void serializePMMLModel(PMMLModel model, OutputStream stream)
throws Exception {
ObjectOutputStream oo = new ObjectOutputStream(stream);
Instances header = model.getMiningSchema().getFieldsAsInstances();
oo.writeObject(header);
oo.writeObject(model);
oo.flush();
oo.close();
}
/**
* Get an instance of a PMMLModel from the supplied Document
*
* @param doc the Document holding the pmml
* @param modelType the type of model
* @param model the Element encapsulating the model part of the Document
* @param dataDictionary the data dictionary as an Instances object
* @param miningSchema the mining schema
* @return a PMMLModel object
* @throws Exception if there is a problem constructing the model or if the
* model type is not supported
*/
protected static PMMLModel getModelInstance(Document doc,
ModelType modelType, Element model, Instances dataDictionary,
MiningSchema miningSchema) throws Exception {
PMMLModel pmmlM = null;
switch (modelType) {
case REGRESSION_MODEL:
pmmlM = new Regression(model, dataDictionary, miningSchema);
// System.out.println(pmmlM);
break;
case GENERAL_REGRESSION_MODEL:
pmmlM = new GeneralRegression(model, dataDictionary, miningSchema);
// System.out.println(pmmlM);
break;
case NEURAL_NETWORK_MODEL:
pmmlM = new NeuralNetwork(model, dataDictionary, miningSchema);
break;
case TREE_MODEL:
pmmlM = new TreeModel(model, dataDictionary, miningSchema);
break;
case RULESET_MODEL:
pmmlM = new RuleSetModel(model, dataDictionary, miningSchema);
break;
case SVM_MODEL:
pmmlM = new SupportVectorMachineModel(model, dataDictionary, miningSchema);
break;
default:
throw new Exception("[PMMLFactory] Unknown model type!!");
}
pmmlM.setPMMLVersion(doc);
pmmlM.setCreatorApplication(doc);
return pmmlM;
}
/**
* Get the type of model
*
* @param doc the Document encapsulating the pmml
* @return the type of model
*/
protected static ModelType getModelType(Document doc) {
NodeList temp = doc.getElementsByTagName("RegressionModel");
if (temp.getLength() > 0) {
return ModelType.REGRESSION_MODEL;
}
temp = doc.getElementsByTagName("GeneralRegressionModel");
if (temp.getLength() > 0) {
return ModelType.GENERAL_REGRESSION_MODEL;
}
temp = doc.getElementsByTagName("NeuralNetwork");
if (temp.getLength() > 0) {
return ModelType.NEURAL_NETWORK_MODEL;
}
temp = doc.getElementsByTagName("TreeModel");
if (temp.getLength() > 0) {
return ModelType.TREE_MODEL;
}
temp = doc.getElementsByTagName("RuleSetModel");
if (temp.getLength() > 0) {
return ModelType.RULESET_MODEL;
}
temp = doc.getElementsByTagName("SupportVectorMachineModel");
if (temp.getLength() > 0) {
return ModelType.SVM_MODEL;
}
return ModelType.UNKNOWN_MODEL;
}
/**
* Get the Element that contains the pmml model
*
* @param doc the Document encapsulating the pmml
* @param modelType the type of model
* @throws Exception if the model type is unsupported/unknown
*/
protected static Element getModelElement(Document doc, ModelType modelType)
throws Exception {
NodeList temp = null;
Element model = null;
switch (modelType) {
case REGRESSION_MODEL:
temp = doc.getElementsByTagName("RegressionModel");
break;
case GENERAL_REGRESSION_MODEL:
temp = doc.getElementsByTagName("GeneralRegressionModel");
break;
case NEURAL_NETWORK_MODEL:
temp = doc.getElementsByTagName("NeuralNetwork");
break;
case TREE_MODEL:
temp = doc.getElementsByTagName("TreeModel");
break;
case RULESET_MODEL:
temp = doc.getElementsByTagName("RuleSetModel");
break;
case SVM_MODEL:
temp = doc.getElementsByTagName("SupportVectorMachineModel");
break;
default:
throw new Exception("[PMMLFactory] unknown/unsupported model type.");
}
if (temp != null && temp.getLength() > 0) {
Node modelNode = temp.item(0);
if (modelNode.getNodeType() == Node.ELEMENT_NODE) {
model = (Element) modelNode;
}
}
return model;
}
/**
* Get the mining schema as an Instances object
*
* @param model the Element containing the pmml model
* @param dataDictionary the data dictionary as an Instances object
* @return the mining schema as an Instances object
* @throws Exception if something goes wrong during reading the mining schema
* @deprecated Use the MiningSchema class instead
*/
@Deprecated
protected static Instances getMiningSchemaAsInstances(Element model,
Instances dataDictionary) throws Exception {
ArrayList attInfo = new ArrayList();
NodeList fieldList = model.getElementsByTagName("MiningField");
int classIndex = -1;
int addedCount = 0;
for (int i = 0; i < fieldList.getLength(); i++) {
Node miningField = fieldList.item(i);
if (miningField.getNodeType() == Node.ELEMENT_NODE) {
Element miningFieldEl = (Element) miningField;
String name = miningFieldEl.getAttribute("name");
String usage = miningFieldEl.getAttribute("usageType");
// TO-DO: also missing value replacement etc.
// find this attribute in the dataDictionary
Attribute miningAtt = dataDictionary.attribute(name);
if (miningAtt != null) {
if (usage.length() == 0 || usage.equals("active")
|| usage.equals("predicted")) {
attInfo.add(miningAtt);
addedCount++;
}
if (usage.equals("predicted")) {
classIndex = addedCount - 1;
}
} else {
throw new Exception("Can't find mining field: " + name
+ " in the data dictionary.");
}
}
}
Instances insts = new Instances("miningSchema", attInfo, 0);
// System.out.println(insts);
if (classIndex != -1) {
insts.setClassIndex(classIndex);
}
return insts;
}
/**
* Get the data dictionary as an Instances object
*
* @param doc the Document encapsulating the pmml
* @return the data dictionary as an Instances object
* @throws Exception if there are fields that are not continuous, ordinal or
* categorical in the data dictionary
*/
protected static Instances getDataDictionaryAsInstances(Document doc)
throws Exception {
// TO-DO: definition of missing values (see below)
ArrayList attInfo = new ArrayList();
NodeList dataDictionary = doc.getElementsByTagName("DataField");
for (int i = 0; i < dataDictionary.getLength(); i++) {
Node dataField = dataDictionary.item(i);
if (dataField.getNodeType() == Node.ELEMENT_NODE) {
Element dataFieldEl = (Element) dataField;
String name = dataFieldEl.getAttribute("name");
String type = dataFieldEl.getAttribute("optype");
Attribute tempAtt = null;
if (name != null && type != null) {
if (type.equals("continuous")) {
tempAtt = new Attribute(name);
} else if (type.equals("categorical") || type.equals("ordinal")) {
NodeList valueList = dataFieldEl.getElementsByTagName("Value");
if (valueList == null || valueList.getLength() == 0) {
// assume that categorical values will be revealed in the actual
// model.
// Create a string attribute for now
ArrayList nullV = null;
tempAtt = new Attribute(name, nullV);
} else {
// add the values (if defined as "valid")
ArrayList valueVector = new ArrayList();
for (int j = 0; j < valueList.getLength(); j++) {
Node val = valueList.item(j);
if (val.getNodeType() == Node.ELEMENT_NODE) {
// property is optional (default value is "valid")
String property = ((Element) val).getAttribute("property");
if (property == null || property.length() == 0
|| property.equals("valid")) {
String value = ((Element) val).getAttribute("value");
valueVector.add(value);
} else {
// Just ignore invalid or missing value definitions for
// now...
// TO-DO: implement Value meta data with missing/invalid
// value defs.
}
}
}
tempAtt = new Attribute(name, valueVector);
}
} else {
throw new Exception("[PMMLFactory] can't handle " + type
+ "attributes.");
}
attInfo.add(tempAtt);
}
}
}
// TO-DO: check whether certain values are declared to represent
// missing or invalid values (applies to both categorical and continuous
// attributes
// create the Instances structure
Instances insts = new Instances("dataDictionary", attInfo, 0);
// System.out.println(insts);
return insts;
}
public static String applyClassifier(PMMLModel model, Instances test)
throws Exception {
StringBuffer buff = new StringBuffer();
if (!(model instanceof PMMLClassifier)) {
throw new Exception("PMML model is not a classifier!");
}
double[] preds = null;
PMMLClassifier classifier = (PMMLClassifier) model;
for (int i = 0; i < test.numInstances(); i++) {
buff.append("Actual: ");
Instance temp = test.instance(i);
if (temp.classAttribute().isNumeric()) {
buff.append(temp.value(temp.classIndex()) + " ");
} else {
buff.append(temp.classAttribute().value(
(int) temp.value(temp.classIndex()))
+ " ");
}
preds = classifier.distributionForInstance(temp);
buff.append(" Predicted: ");
for (double pred : preds) {
buff.append("" + pred + " ");
}
buff.append("\n");
}
return buff.toString();
}
private static class PMMLClassifierRunner extends AbstractClassifier {
/** ID added to avoid warning */
private static final long serialVersionUID = -3742334356788083347L;
@Override
public double[] distributionForInstance(Instance test) throws Exception {
throw new Exception("Don't call this method!!");
}
@Override
public void buildClassifier(Instances instances) throws Exception {
throw new Exception("Don't call this method!!");
}
@Override
public String getRevision() {
return weka.core.RevisionUtils.extract("$Revision: 10203 $");
}
public void evaluatePMMLClassifier(String[] options) {
runClassifier(this, options);
}
}
public static void main(String[] args) {
try {
String[] optionsTmp = new String[args.length];
for (int i = 0; i < args.length; i++) {
optionsTmp[i] = args[i];
}
String pmmlFile = Utils.getOption('l', optionsTmp);
if (pmmlFile.length() == 0) {
throw new Exception(
"[PMMLFactory] must specify a PMML file using the -l option.");
}
// see if it is supported before going any further
getPMMLModel(pmmlFile, null);
PMMLClassifierRunner pcr = new PMMLClassifierRunner();
pcr.evaluatePMMLClassifier(args);
/*
* PMMLModel model = getPMMLModel(args[0], null);
* System.out.println(model); if (args.length == 2) { // load an arff file
* Instances testData = new Instances(new java.io.BufferedReader(new
* java.io.FileReader(args[1]))); Instances miningSchemaI =
* model.getMiningSchema().getFieldsAsInstances(); if
* (miningSchemaI.classIndex() >= 0) { String className =
* miningSchemaI.classAttribute().name(); for (int i = 0; i <
* testData.numAttributes(); i++) { if
* (testData.attribute(i).name().equals(className)) {
* testData.setClassIndex(i); System.out.println("Found class " +
* className + " in test data."); break; } } }
* System.out.println(applyClassifier(model, testData)); }
*/
} catch (Exception ex) {
ex.printStackTrace();
}
}
}