/**
* Function to read the .dat file that contains the information of the dataset.
*
* @param name The reader object where the itemsets are readed.
* @param train The flag if the file is for training
*/
public MyDataset(String name, boolean train) {
try {
// create the set of instances
IS = new InstanceSet();
// Read the itemsets.
IS.readSet(name, train);
} catch (DatasetException e) {
System.out.println("Error loading dataset instances");
e.printStackTrace();
System.exit(-1);
} catch (HeaderFormatException e) {
System.out.println("Error loading dataset instances");
e.printStackTrace();
System.exit(-1);
}
// Store Dataset file attributes
readHeader();
itemsets = new Vector(IS.getNumInstances());
// read all the itemsets
getItemsetFull();
totalCond = this.numAllConditions();
}
/**
* It reads the whole input data-set and it stores each example and its associated output value in
* local arrays to ease their use.
*
* @param datasetFile String name of the file containing the dataset
* @param train boolean It must have the value "true" if we are reading the training data-set
* @throws IOException If there ocurs any problem with the reading of the data-set
*/
public void readRegressionSet(String datasetFile, boolean train) throws IOException {
try {
// Load in memory a dataset that contains a regression problem
IS.readSet(datasetFile, train);
nData = IS.getNumInstances();
nInputs = Attributes.getInputNumAttributes();
nVars = nInputs + Attributes.getOutputNumAttributes();
// outputIntegerheck that there is only one output variable
if (Attributes.getOutputNumAttributes() > 1) {
System.out.println("This algorithm can not process MIMO datasets");
System.out.println("All outputs but the first one will be removed");
System.exit(1);
}
boolean noOutputs = false;
if (Attributes.getOutputNumAttributes() < 1) {
System.out.println("This algorithm can not process datasets without outputs");
System.out.println("Zero-valued output generated");
noOutputs = true;
System.exit(1);
}
// Initialice and fill our own tables
X = new double[nData][nInputs];
missing = new boolean[nData][nInputs];
outputInteger = new int[nData];
// Maximum and minimum of inputs
emax = new double[nInputs];
emin = new double[nInputs];
for (int i = 0; i < nInputs; i++) {
emax[i] = Attributes.getAttribute(i).getMaxAttribute();
emin[i] = Attributes.getAttribute(i).getMinAttribute();
}
// All values are casted into double/integer
nClasses = 0;
for (int i = 0; i < nData; i++) {
Instance inst = IS.getInstance(i);
for (int j = 0; j < nInputs; j++) {
X[i][j] = IS.getInputNumericValue(i, j); // inst.getInputRealValues(j);
missing[i][j] = inst.getInputMissingValues(j);
if (missing[i][j]) {
X[i][j] = emin[j] - 1;
}
}
if (noOutputs) {
outputReal[i] = outputInteger[i] = 0;
} else {
outputReal[i] = IS.getOutputNumericValue(i, 0);
outputInteger[i] = (int) outputReal[i];
}
}
} catch (Exception e) {
System.out.println("DBG: Exception in readSet");
e.printStackTrace();
}
computeStatistics();
}
static void checkDataset() {
Attribute[] outputs = Attributes.getOutputAttributes();
if (outputs.length != 1) {
LogManager.printErr("Only datasets with one output are supported");
System.exit(1);
}
if (outputs[0].getType() != Attribute.NOMINAL) {
LogManager.printErr("Output attribute should be nominal");
System.exit(1);
}
Parameters.numClasses = outputs[0].getNumNominalValues();
Parameters.numAttributes = Attributes.getInputAttributes().length;
}
private void normalizarTest() {
int i, j, cont = 0, k;
Instance temp;
boolean hecho;
double caja[];
StringTokenizer tokens;
boolean nulls[];
/* Check if dataset corresponding with a classification problem */
if (Attributes.getOutputNumAttributes() < 1) {
System.err.println(
"This dataset haven´t outputs, so it not corresponding to a classification problem.");
System.exit(-1);
} else if (Attributes.getOutputNumAttributes() > 1) {
System.err.println("This dataset have more of one output.");
System.exit(-1);
}
if (Attributes.getOutputAttribute(0).getType() == Attribute.REAL) {
System.err.println(
"This dataset have an input attribute with floating values, so it not corresponding to a classification problem.");
System.exit(-1);
}
datosTest = new double[test.getNumInstances()][Attributes.getInputNumAttributes()];
clasesTest = new int[test.getNumInstances()];
caja = new double[1];
for (i = 0; i < test.getNumInstances(); i++) {
temp = test.getInstance(i);
nulls = temp.getInputMissingValues();
datosTest[i] = test.getInstance(i).getAllInputValues();
for (j = 0; j < nulls.length; j++) if (nulls[j]) datosTest[i][j] = 0.0;
caja = test.getInstance(i).getAllOutputValues();
clasesTest[i] = (int) caja[0];
for (k = 0; k < datosTest[i].length; k++) {
if (Attributes.getInputAttribute(k).getType() == Attribute.NOMINAL) {
datosTest[i][k] /= Attributes.getInputAttribute(k).getNominalValuesList().size() - 1;
} else {
datosTest[i][k] -= Attributes.getInputAttribute(k).getMinAttribute();
datosTest[i][k] /=
Attributes.getInputAttribute(k).getMaxAttribute()
- Attributes.getInputAttribute(k).getMinAttribute();
}
}
}
}
// Read the patron file, and parse data into strings
private void config_read(String fileParam) {
File inputFile = new File(fileParam);
if (inputFile == null || !inputFile.exists()) {
System.out.println("parameter " + fileParam + " file doesn't exists!");
System.exit(-1);
}
// begin the configuration read from file
try {
FileReader file_reader = new FileReader(inputFile);
BufferedReader buf_reader = new BufferedReader(file_reader);
// FileWriter file_write = new FileWriter(outputFile);
String line;
do {
line = buf_reader.readLine();
} while (line.length() == 0); // avoid empty lines for processing -> produce exec failure
String out[] = line.split("algorithm = ");
// alg_name = new String(out[1]); //catch the algorithm name
// input & output filenames
do {
line = buf_reader.readLine();
} while (line.length() == 0);
out = line.split("inputData = ");
out = out[1].split("\\s\"");
input_train_name = new String(out[0].substring(1, out[0].length() - 1));
input_test_name = new String(out[1].substring(0, out[1].length() - 1));
if (input_test_name.charAt(input_test_name.length() - 1) == '"')
input_test_name = input_test_name.substring(0, input_test_name.length() - 1);
do {
line = buf_reader.readLine();
} while (line.length() == 0);
out = line.split("outputData = ");
out = out[1].split("\\s\"");
output_train_name = new String(out[0].substring(1, out[0].length() - 1));
output_test_name = new String(out[1].substring(0, out[1].length() - 1));
if (output_test_name.charAt(output_test_name.length() - 1) == '"')
output_test_name = output_test_name.substring(0, output_test_name.length() - 1);
file_reader.close();
} catch (IOException e) {
System.out.println("IO exception = " + e);
e.printStackTrace();
System.exit(-1);
}
}
/**
* Main method for ABB, that explores the search space by pruning nodes and checking their
* inconsistency ratio.
*/
private void runABB() {
boolean[] root = startSolution();
System.arraycopy(root, 0, features, 0, root.length);
abb(root);
/* checks if a subset satisfies the condition (more than 0 selected features) */
if (features == null) {
System.err.println("ERROR: It couldn't be possible to find any solution.");
System.exit(0);
}
}
public LVQ(String ficheroScript) {
super(ficheroScript);
try {
referencia = new InstanceSet();
referencia.readSet(ficheroReferencia, false);
/*Normalize the data*/
normalizarReferencia();
} catch (Exception e) {
System.err.println(e);
System.exit(1);
}
}
/**
* Constructor of the Class Parametros
*
* @param nombreFileParametros is the pathname of input parameter file
*/
Parametros(String nombreFileParametros) {
try {
int i;
String fichero, linea, tok;
StringTokenizer lineasFile, tokens;
/* read the parameter file using Files class */
fichero = Files.readFile(nombreFileParametros);
fichero += "\n";
/* remove all \r characters. it is neccesary for a correst use in Windows and UNIX */
fichero = fichero.replace('\r', ' ');
/* extracts the differents tokens of the file */
lineasFile = new StringTokenizer(fichero, "\n");
i = 0;
while (lineasFile.hasMoreTokens()) {
linea = lineasFile.nextToken();
i++;
tokens = new StringTokenizer(linea, " ,\t");
if (tokens.hasMoreTokens()) {
tok = tokens.nextToken();
if (tok.equalsIgnoreCase("algorithm")) nameAlgorithm = getParamString(tokens);
else if (tok.equalsIgnoreCase("inputdata")) getInputFiles(tokens);
else if (tok.equalsIgnoreCase("outputdata")) getOutputFiles(tokens);
else if (tok.equalsIgnoreCase("seed")) seed = getParamLong(tokens);
else throw new java.io.IOException("Syntax error on line " + i + ": [" + tok + "]\n");
}
}
} catch (java.io.FileNotFoundException e) {
System.err.println(e + "Parameter file");
} catch (java.io.IOException e) {
System.err.println(e + "Aborting program");
System.exit(-1);
}
/** show the read parameter in the standard output */
String contents = "-- Parameters echo --- \n";
contents += "Algorithm name: " + nameAlgorithm + "\n";
contents += "Input Train File: " + trainFileNameInput + "\n";
contents += "Input Test File: " + testFileNameInput + "\n";
contents += "Output Train File: " + trainFileNameOutput + "\n";
contents += "Output Test File: " + testFileNameOutput + "\n";
System.out.println(contents);
}
/** @param args the command line arguments */
public static void main(String[] args) {
ParserParameters.doParse(args[0]);
LogManager.initLogManager();
InstanceSet is = new InstanceSet();
try {
is.readSet(Parameters.trainInputFile, true);
} catch (Exception e) {
LogManager.printErr(e.toString());
System.exit(1);
}
checkDataset();
Discretizer dis;
String name = Parameters.algorithmName;
dis = new FayyadDiscretizer();
dis.buildCutPoints(is);
dis.applyDiscretization(Parameters.trainInputFile, Parameters.trainOutputFile);
dis.applyDiscretization(Parameters.testInputFile, Parameters.testOutputFile);
LogManager.closeLog();
}
// Write data matrix X to disk, in KEEL format
private void write_results(String output) {
// File OutputFile = new File(output_train_name.substring(1, output_train_name.length()-1));
try {
FileWriter file_write = new FileWriter(output);
file_write.write(IS.getHeader());
// now, print the normalized data
file_write.write("@data\n");
for (int i = 0; i < ndatos; i++) {
file_write.write(X[i][0]);
for (int j = 1; j < nvariables; j++) {
file_write.write("," + X[i][j]);
}
file_write.write("\n");
}
file_write.close();
} catch (IOException e) {
System.out.println("IO exception = " + e);
System.exit(-1);
}
}
/** Process the training and test files provided in the parameters file to the constructor. */
public void process() {
double[] outputs;
double[] outputs2;
Instance neighbor;
double dist, mean;
int actual;
int[] N = new int[nneigh];
double[] Ndist = new double[nneigh];
boolean allNull;
svm_problem SVMp = null;
svm_parameter SVMparam = new svm_parameter();
svm_model svr = null;
svm_node SVMn[];
double[] outputsCandidate = null;
boolean same = true;
Vector instancesSelected = new Vector();
Vector instancesSelected2 = new Vector();
// SVM PARAMETERS
SVMparam.C = C;
SVMparam.cache_size = 10; // 10MB of cache
SVMparam.degree = degree;
SVMparam.eps = eps;
SVMparam.gamma = gamma;
SVMparam.nr_weight = 0;
SVMparam.nu = nu;
SVMparam.p = p;
SVMparam.shrinking = shrinking;
SVMparam.probability = 0;
if (kernelType.compareTo("LINEAR") == 0) {
SVMparam.kernel_type = svm_parameter.LINEAR;
} else if (kernelType.compareTo("POLY") == 0) {
SVMparam.kernel_type = svm_parameter.POLY;
} else if (kernelType.compareTo("RBF") == 0) {
SVMparam.kernel_type = svm_parameter.RBF;
} else if (kernelType.compareTo("SIGMOID") == 0) {
SVMparam.kernel_type = svm_parameter.SIGMOID;
}
SVMparam.svm_type = svm_parameter.EPSILON_SVR;
try {
// Load in memory a dataset that contains a classification problem
IS.readSet(input_train_name, true);
int in = 0;
int out = 0;
ndatos = IS.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
X = new String[ndatos][2]; // matrix with transformed data
mostCommon = new String[nvariables];
SVMp = new svm_problem();
SVMp.l = ndatos;
SVMp.y = new double[SVMp.l];
SVMp.x = new svm_node[SVMp.l][nentradas + 1];
for (int l = 0; l < SVMp.l; l++) {
for (int n = 0; n < Attributes.getInputNumAttributes() + 1; n++) {
SVMp.x[l][n] = new svm_node();
}
}
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
SVMp.y[i] = inst.getAllOutputValues()[0];
for (int n = 0; n < Attributes.getInputNumAttributes(); n++) {
SVMp.x[i][n].index = n;
SVMp.x[i][n].value = inst.getAllInputValues()[n];
SVMp.y[i] = inst.getAllOutputValues()[0];
}
// end of instance
SVMp.x[i][nentradas].index = -1;
}
if (svm.svm_check_parameter(SVMp, SVMparam) != null) {
System.out.println("SVM parameter error in training:");
System.out.println(svm.svm_check_parameter(SVMp, SVMparam));
System.exit(-1);
}
// train the SVM
if (ndatos > 0) {
svr = svm.svm_train(SVMp, SVMparam);
}
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
X[i][0] = new String(String.valueOf(inst.getAllOutputValues()[0]));
// the values used for regression
SVMn = new svm_node[Attributes.getInputNumAttributes() + 1];
for (int n = 0; n < Attributes.getInputNumAttributes(); n++) {
SVMn[n] = new svm_node();
SVMn[n].index = n;
SVMn[n].value = inst.getAllInputValues()[n];
}
SVMn[nentradas] = new svm_node();
SVMn[nentradas].index = -1;
// pedict the class
X[i][1] = new String(String.valueOf((svm.svm_predict(svr, SVMn))));
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
write_results(output_train_name);
/** ************************************************************************************ */
try {
// Load in memory a dataset that contains a classification
// problem
IS.readSet(input_test_name, false);
int in = 0;
int out = 0;
ndatos = IS.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
X = new String[ndatos][2]; // matrix with transformed data
// data
mostCommon = new String[nvariables];
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
X[i][0] = new String(String.valueOf(inst.getAllOutputValues()[0]));
SVMn = new svm_node[Attributes.getInputNumAttributes() + 1];
for (int n = 0; n < Attributes.getInputNumAttributes(); n++) {
SVMn[n] = new svm_node();
SVMn[n].index = n;
SVMn[n].value = inst.getAllInputValues()[n];
}
SVMn[nentradas] = new svm_node();
SVMn[nentradas].index = -1;
// pedict the class
X[i][1] = new String(String.valueOf(svm.svm_predict(svr, SVMn)));
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
System.out.println("escribiendo test");
write_results(output_test_name);
}
/** Process the training and test files provided in the parameters file to the constructor. */
public void process() {
// declarations
double[] outputs;
double[] outputs2;
Instance neighbor;
double dist, mean;
int actual;
Randomize rnd = new Randomize();
Instance ex;
gCenter kmeans = null;
int iterations = 0;
double E;
double prevE;
int totalMissing = 0;
boolean allMissing = true;
rnd.setSeed(semilla);
// PROCESS
try {
// Load in memory a dataset that contains a classification problem
IS.readSet(input_train_name, true);
int in = 0;
int out = 0;
ndatos = IS.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
X = new String[ndatos][nvariables]; // matrix with transformed data
kmeans = new gCenter(K, ndatos, nvariables);
timesSeen = new FreqList[nvariables];
mostCommon = new String[nvariables];
// first, we choose k 'means' randomly from all
// instances
totalMissing = 0;
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
if (inst.existsAnyMissingValue()) totalMissing++;
}
if (totalMissing == ndatos) allMissing = true;
else allMissing = false;
for (int numMeans = 0; numMeans < K; numMeans++) {
do {
actual = (int) (ndatos * rnd.Rand());
ex = IS.getInstance(actual);
} while (ex.existsAnyMissingValue() && !allMissing);
kmeans.copyCenter(ex, numMeans);
}
// now, iterate adjusting clusters' centers and
// instances to them
prevE = 0;
iterations = 0;
do {
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
kmeans.setClusterOf(inst, i);
}
// set new centers
kmeans.recalculateCenters(IS);
// compute RMSE
E = 0;
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
E += kmeans.distance(inst, kmeans.getClusterOf(i));
}
iterations++;
// System.out.println(iterations+"\t"+E);
if (Math.abs(prevE - E) == 0) iterations = maxIter;
else prevE = E;
} while (E > minError && iterations < maxIter);
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
in = 0;
out = 0;
for (int j = 0; j < nvariables; j++) {
Attribute a = Attributes.getAttribute(j);
direccion = a.getDirectionAttribute();
tipo = a.getType();
if (direccion == Attribute.INPUT) {
if (tipo != Attribute.NOMINAL && !inst.getInputMissingValues(in)) {
X[i][j] = new String(String.valueOf(inst.getInputRealValues(in)));
} else {
if (!inst.getInputMissingValues(in)) X[i][j] = inst.getInputNominalValues(in);
else {
actual = kmeans.getClusterOf(i);
X[i][j] = new String(kmeans.valueAt(actual, j));
}
}
in++;
} else {
if (direccion == Attribute.OUTPUT) {
if (tipo != Attribute.NOMINAL && !inst.getOutputMissingValues(out)) {
X[i][j] = new String(String.valueOf(inst.getOutputRealValues(out)));
} else {
if (!inst.getOutputMissingValues(out)) X[i][j] = inst.getOutputNominalValues(out);
else {
actual = kmeans.getClusterOf(i);
X[i][j] = new String(kmeans.valueAt(actual, j));
}
}
out++;
}
}
}
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
write_results(output_train_name);
/** ************************************************************************************ */
// does a test file associated exist?
if (input_train_name.compareTo(input_test_name) != 0) {
try {
// Load in memory a dataset that contains a classification problem
IStest.readSet(input_test_name, false);
int in = 0;
int out = 0;
ndatos = IStest.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
for (int i = 0; i < ndatos; i++) {
Instance inst = IStest.getInstance(i);
in = 0;
out = 0;
for (int j = 0; j < nvariables; j++) {
Attribute a = Attributes.getAttribute(j);
direccion = a.getDirectionAttribute();
tipo = a.getType();
if (direccion == Attribute.INPUT) {
if (tipo != Attribute.NOMINAL && !inst.getInputMissingValues(in)) {
X[i][j] = new String(String.valueOf(inst.getInputRealValues(in)));
} else {
if (!inst.getInputMissingValues(in)) X[i][j] = inst.getInputNominalValues(in);
else {
actual = kmeans.getClusterOf(i);
X[i][j] = new String(kmeans.valueAt(actual, j));
}
}
in++;
} else {
if (direccion == Attribute.OUTPUT) {
if (tipo != Attribute.NOMINAL && !inst.getOutputMissingValues(out)) {
X[i][j] = new String(String.valueOf(inst.getOutputRealValues(out)));
} else {
if (!inst.getOutputMissingValues(out)) X[i][j] = inst.getOutputNominalValues(out);
else {
actual = kmeans.getClusterOf(i);
X[i][j] = new String(kmeans.valueAt(actual, j));
}
}
out++;
}
}
}
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
write_results(output_test_name);
}
}
/** Process the training and test files provided in the parameters file to the constructor. */
public void process() {
try {
// Load in memory a dataset that contains a classification problem
IS.readSet(input_train_name, true);
int in = 0;
int out = 0;
ndatos = IS.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
X = new String[ndatos][nvariables]; // matrix with transformed data
boolean[] isMissed =
new boolean[ndatos]; // vector which points out instances with missed data
try {
FileWriter file_write = new FileWriter(output_train_name);
file_write.write(IS.getHeader());
// now, print the normalized data
file_write.write("@data\n");
// file_write.close();
PrintWriter pw = new PrintWriter(file_write);
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
if (!inst.existsAnyMissingValue()) {
inst.printAsOriginal(pw);
// file_write.write(inst.toString()); // DOES NOT WRITE BACK NON-DEF DIRECTION
// ATTRIBUTES!!!!
file_write.write("\n");
}
}
pw.close();
file_write.close();
} catch (IOException e) {
System.out.println("IO exception = " + e);
System.exit(-1);
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
// does a test file associated exist?
if (input_train_name.compareTo(input_test_name) != 0) {
try {
// Load in memory a dataset that contains a classification problem
IS.readSet(input_test_name, false);
int in = 0;
int out = 0;
ndatos = IS.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
X = new String[ndatos][nvariables]; // matrix with transformed data
boolean[] isMissed =
new boolean[ndatos]; // vector which points out instances with missed data
try {
FileWriter file_write = new FileWriter(output_test_name);
file_write.write(IS.getHeader());
// now, print the normalized data
file_write.write("@data\n");
PrintWriter pw = new PrintWriter(file_write);
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
if (!inst.existsAnyMissingValue()) {
inst.printAsOriginal(pw);
file_write.write("\n");
}
}
pw.close();
file_write.close();
} catch (IOException e) {
System.out.println("IO exception = " + e);
System.exit(-1);
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
}
// write_results(); / since there ins't any data transformation, is not needed
}
/** Process the training and test files provided in the parameters file to the constructor. */
public void process() {
double[] outputs;
double[] outputs2;
try {
FileWriter file_write = new FileWriter(output_train_name);
try {
// Load in memory a dataset that contains a classification problem
IS.readSet(input_train_name, true);
int in = 0;
int out = 0;
int in2 = 0;
int out2 = 0;
int lastMissing = -1;
boolean fin = false;
boolean stepNext = false;
ndatos = IS.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
String[] row = null;
X = new Vector[ndatos]; // matrix with transformed data
for (int i = 0; i < ndatos; i++) X[i] = new Vector();
timesSeen = new FreqList[nvariables];
mostCommon = new String[nvariables];
file_write.write(IS.getHeader());
// now, print the normalized data
file_write.write("@data\n");
// now, search for missed data, and replace them with
// the most common value
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
in = 0;
out = 0;
row = new String[nvariables];
for (int j = 0; j < nvariables; j++) {
Attribute a = Attributes.getAttribute(j);
direccion = a.getDirectionAttribute();
tipo = a.getType();
if (direccion == Attribute.INPUT) {
if (tipo != Attribute.NOMINAL && !inst.existsAnyMissingValue()) {
row[j] = new String(String.valueOf(inst.getInputRealValues(in)));
} else {
if (!inst.existsAnyMissingValue()) row[j] = inst.getInputNominalValues(in);
else {
// missing data
outputs = inst.getAllOutputValues();
in2 = 0;
out2 = 0;
for (int attr = 0; attr < nvariables; attr++) {
Attribute b = Attributes.getAttribute(attr);
direccion = b.getDirectionAttribute();
tipo = b.getType();
if (direccion == Attribute.INPUT) {
if (tipo != Attribute.NOMINAL && !inst.getInputMissingValues(in2)) {
row[attr] = new String(String.valueOf(inst.getInputRealValues(in2)));
} else {
if (!inst.getInputMissingValues(in2))
row[attr] = inst.getInputNominalValues(in2);
}
in2++;
} else {
if (direccion == Attribute.OUTPUT) {
if (tipo != Attribute.NOMINAL && !inst.getOutputMissingValues(out2)) {
row[attr] = new String(String.valueOf(inst.getOutputRealValues(out2)));
} else {
if (!inst.getOutputMissingValues(out2))
row[attr] = inst.getOutputNominalValues(out2);
}
out2++;
}
}
}
// make frecuencies for each attribute
for (int attr = 0; attr < nvariables; attr++) {
Attribute b = Attributes.getAttribute(attr);
direccion = b.getDirectionAttribute();
tipo = b.getType();
if (direccion == Attribute.INPUT && inst.getInputMissingValues(attr)) {
lastMissing = attr;
timesSeen[attr] = new FreqList();
for (int m = 0; m < ndatos; m++) {
Instance inst2 = IS.getInstance(m);
outputs2 = inst2.getAllOutputValues();
boolean sameClass = true;
// are they same concept instances??
for (int k = 0; k < nsalidas && sameClass; k++)
if (outputs[k] != outputs2[k]) sameClass = false;
if (sameClass) {
if (tipo != Attribute.NOMINAL && !inst2.getInputMissingValues(attr)) {
timesSeen[attr].AddElement(
new String(String.valueOf(inst2.getInputRealValues(attr))));
} else {
if (!inst2.getInputMissingValues(attr)) {
timesSeen[attr].AddElement(inst2.getInputNominalValues(attr));
}
}
}
}
}
}
for (int attr = 0; attr < nvariables; attr++) {
if (direccion == Attribute.INPUT && inst.getInputMissingValues(attr)) {
timesSeen[attr].reset();
}
}
fin = false;
stepNext = false;
while (!fin) {
in2 = 0;
for (int attr = 0; attr < nvariables && !fin; attr++) {
Attribute b = Attributes.getAttribute(attr);
direccion = b.getDirectionAttribute();
tipo = b.getType();
if (direccion == Attribute.INPUT && inst.getInputMissingValues(in2)) {
if (stepNext) {
timesSeen[attr].iterate();
stepNext = false;
}
if (timesSeen[attr].outOfBounds()) {
stepNext = true;
if (attr == lastMissing) fin = true;
timesSeen[attr].reset();
}
if (!fin)
row[attr] =
((ValueFreq) timesSeen[attr].getCurrent())
.getValue(); // replace missing data
}
in2++;
}
if (!fin) {
stepNext = true;
file_write.write(row[0]);
for (int y = 1; y < nvariables; y++) {
file_write.write("," + row[y]);
}
file_write.write("\n");
// X[i].addElement(row);
// row = (String[])row.clone();
}
}
}
}
in++;
} else {
if (direccion == Attribute.OUTPUT) {
if (tipo != Attribute.NOMINAL && !inst.getOutputMissingValues(out)) {
row[j] = new String(String.valueOf(inst.getOutputRealValues(out)));
} else {
if (!inst.getOutputMissingValues(out)) row[j] = inst.getOutputNominalValues(out);
else row[j] = new String("?");
}
out++;
}
}
}
if (!inst.existsAnyMissingValue()) {
file_write.write(row[0]);
for (int y = 1; y < nvariables; y++) {
file_write.write("," + row[y]);
}
file_write.write("\n");
}
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
file_write.close();
} catch (IOException e) {
System.out.println("IO exception = " + e);
e.printStackTrace();
System.exit(-1);
}
/** ************************************************************************************ */
// does a test file associated exist?
if (input_train_name.compareTo(input_test_name) != 0) {
try {
FileWriter file_write = new FileWriter(output_test_name);
try {
// Load in memory a dataset that contains a classification problem
IS.readSet(input_test_name, false);
int in = 0;
int out = 0;
int in2 = 0;
int out2 = 0;
int lastMissing = -1;
boolean fin = false;
boolean stepNext = false;
ndatos = IS.getNumInstances();
nvariables = Attributes.getNumAttributes();
nentradas = Attributes.getInputNumAttributes();
nsalidas = Attributes.getOutputNumAttributes();
String[] row = null;
X = new Vector[ndatos]; // matrix with transformed data
for (int i = 0; i < ndatos; i++) X[i] = new Vector();
timesSeen = new FreqList[nvariables];
mostCommon = new String[nvariables];
file_write.write(IS.getHeader());
// now, print the normalized data
file_write.write("@data\n");
// now, search for missed data, and replace them with
// the most common value
for (int i = 0; i < ndatos; i++) {
Instance inst = IS.getInstance(i);
in = 0;
out = 0;
row = new String[nvariables];
for (int j = 0; j < nvariables; j++) {
Attribute a = Attributes.getAttribute(j);
direccion = a.getDirectionAttribute();
tipo = a.getType();
if (direccion == Attribute.INPUT) {
if (tipo != Attribute.NOMINAL && !inst.existsAnyMissingValue()) {
row[j] = new String(String.valueOf(inst.getInputRealValues(in)));
} else {
if (!inst.existsAnyMissingValue()) row[j] = inst.getInputNominalValues(in);
else {
// missing data
outputs = inst.getAllOutputValues();
in2 = 0;
out2 = 0;
for (int attr = 0; attr < nvariables; attr++) {
Attribute b = Attributes.getAttribute(attr);
direccion = b.getDirectionAttribute();
tipo = b.getType();
if (direccion == Attribute.INPUT) {
if (tipo != Attribute.NOMINAL && !inst.getInputMissingValues(in2)) {
row[attr] = new String(String.valueOf(inst.getInputRealValues(in2)));
} else {
if (!inst.getInputMissingValues(in2))
row[attr] = inst.getInputNominalValues(in2);
}
in2++;
} else {
if (direccion == Attribute.OUTPUT) {
if (tipo != Attribute.NOMINAL && !inst.getOutputMissingValues(out2)) {
row[attr] = new String(String.valueOf(inst.getOutputRealValues(out2)));
} else {
if (!inst.getOutputMissingValues(out2))
row[attr] = inst.getOutputNominalValues(out2);
}
out2++;
}
}
}
// make frecuencies for each attribute
for (int attr = 0; attr < nvariables; attr++) {
Attribute b = Attributes.getAttribute(attr);
direccion = b.getDirectionAttribute();
tipo = b.getType();
if (direccion == Attribute.INPUT && inst.getInputMissingValues(attr)) {
lastMissing = attr;
timesSeen[attr] = new FreqList();
for (int m = 0; m < ndatos; m++) {
Instance inst2 = IS.getInstance(m);
outputs2 = inst2.getAllOutputValues();
boolean sameClass = true;
// are they same concept instances??
for (int k = 0; k < nsalidas && sameClass; k++)
if (outputs[k] != outputs2[k]) sameClass = false;
if (sameClass) {
if (tipo != Attribute.NOMINAL && !inst2.getInputMissingValues(attr)) {
timesSeen[attr].AddElement(
new String(String.valueOf(inst2.getInputRealValues(attr))));
} else {
if (!inst2.getInputMissingValues(attr)) {
timesSeen[attr].AddElement(inst2.getInputNominalValues(attr));
}
}
}
}
}
}
for (int attr = 0; attr < nvariables; attr++) {
if (direccion == Attribute.INPUT && inst.getInputMissingValues(attr)) {
timesSeen[attr].reset();
}
}
fin = false;
stepNext = false;
while (!fin) {
in2 = 0;
for (int attr = 0; attr < nvariables && !fin; attr++) {
Attribute b = Attributes.getAttribute(attr);
direccion = b.getDirectionAttribute();
tipo = b.getType();
if (direccion == Attribute.INPUT && inst.getInputMissingValues(in2)) {
if (stepNext) {
timesSeen[attr].iterate();
stepNext = false;
}
if (timesSeen[attr].outOfBounds()) {
stepNext = true;
if (attr == lastMissing) fin = true;
timesSeen[attr].reset();
}
if (!fin)
row[attr] =
((ValueFreq) timesSeen[attr].getCurrent())
.getValue(); // replace missing data
}
in2++;
}
if (!fin) {
stepNext = true;
file_write.write(row[0]);
for (int y = 1; y < nvariables; y++) {
file_write.write("," + row[y]);
}
file_write.write("\n");
// X[i].addElement(row);
// row = (String[])row.clone();
}
}
}
}
in++;
} else {
if (direccion == Attribute.OUTPUT) {
if (tipo != Attribute.NOMINAL && !inst.getOutputMissingValues(out)) {
row[j] = new String(String.valueOf(inst.getOutputRealValues(out)));
} else {
if (!inst.getOutputMissingValues(out))
row[j] = inst.getOutputNominalValues(out);
else row[j] = new String("?");
}
out++;
}
}
}
if (!inst.existsAnyMissingValue()) {
file_write.write(row[0]);
for (int y = 1; y < nvariables; y++) {
file_write.write("," + row[y]);
}
file_write.write("\n");
}
}
} catch (Exception e) {
System.out.println("Dataset exception = " + e);
e.printStackTrace();
System.exit(-1);
}
file_write.close();
} catch (IOException e) {
System.out.println("IO exception = " + e);
e.printStackTrace();
System.exit(-1);
}
}
}