/**
* sdf The test main
*
* @param args ignored
*/
public static void main(String[] args) {
// Instance[] instances = new Instance[100];
// for (int i = 0; i < instances.length; i++) {
// double[] data = new double[2];
// data[0] = Math.sin(i/2.0);
// data[1] = (Math.random() - .5)*2;
// instances[i] = new Instance(data);
// }
DataSet set = new DataSet(trainInstances);
System.out.println("Before randomizing");
System.out.println(set);
// Matrix projection = new RectangularMatrix(new double[][]{ {.6, .6}, {.4, .6}});
Matrix projection = new RectangularMatrix(new double[][] {{.1, .1}, {.1, .1}});
for (int i = 0; i < set.size(); i++) {
Instance instance = set.get(i);
instance.setData(projection.times(instance.getData()));
}
System.out.println("Before ICA");
System.out.println(set);
IndependentComponentAnalysis filter = new IndependentComponentAnalysis(set, 1);
filter.filter(set);
System.out.println("After ICA");
System.out.println(set);
}
private static Instance[] initializeInstances(String dataFile, String labelFile) {
// DataSetReader dsr = new CSVDataSetReader(new File("").getAbsolutePath() + "/src/opt/test/" +
// dataFile);
// DataSetReader lsr = new CSVDataSetReader(new File("").getAbsolutePath() + "/src/opt/test/" +
// labelFile);
URL d_path = IndepenentComponentAnalysisMyDataTest.class.getResource(dataFile);
File df = new File(d_path.getFile());
URL l_path = IndepenentComponentAnalysisMyDataTest.class.getResource(dataFile);
File lf = new File(l_path.getFile());
DataSetReader dsr = new CSVDataSetReader(df.toString());
DataSetReader lsr = new CSVDataSetReader(lf.toString());
DataSet ds;
DataSet labs;
try {
ds = dsr.read();
labs = lsr.read();
Instance[] instances = ds.getInstances();
Instance[] labels = labs.getInstances();
// for(int i = 0; i < instances.length; i++) {
// instances[i].setLabel(new Instance(labels[i].getData().get(0)));
// //instances[i].setLabel(new Instance(labels[i].getData()));
// }
return instances;
} catch (Exception e) {
System.out.println("Failed to read input file");
return null;
}
}
private static DataSet run(RandomizedProjectionFilter rca, DataSet original) {
System.out.println("The projection matrix");
System.out.println(rca.getProjection());
DataSet transformed = original.copy();
rca.filter(transformed);
return transformed;
}
private static void writeArffHeader(DataSet dataSet, String outputFile) {
MLAssignmentUtils.writeToFile(outputFile, "@Relation RCATransformed\n", false);
Vector vector = dataSet.get(0).getData();
for (int i = 0; i < vector.size(); i++) {
MLAssignmentUtils.writeToFile(outputFile, "@attribute attr" + (i + 1) + " numeric\n", true);
}
MLAssignmentUtils.writeToFile(outputFile, "@data\n", true);
}
private static void computeReconstructionError(DataSet original, DataSet reconstructed) {
EuclideanDistance distanceFunction = new EuclideanDistance();
double totalDataSetsDistance = distanceFunction.value(original, reconstructed);
double averageInstanceDistane = totalDataSetsDistance / original.size();
System.out.println(
"Total reconstruction error as Euclidean distance between data sets: "
+ totalDataSetsDistance);
System.out.println("Average Instance reconstruction error: " + averageInstanceDistane);
}
private static void saveAsArff(DataSet dataSet, String outputFile, List<String> labels) {
writeArffHeader(dataSet, outputFile);
Instance[] instances = dataSet.getInstances();
for (Instance instance : instances) {
Vector vector = instance.getData();
for (int i = 0; i < vector.size(); i++) {
MLAssignmentUtils.writeToFile(outputFile, String.valueOf(vector.get(i)) + ",", true);
}
MLAssignmentUtils.writeToFile(outputFile, getLabel(instance.getLabel(), labels) + "\n", true);
}
}
public void filter(DataSet data) {
int foldSize = data.size() / foldCount;
Random rand = new Random();
for (int currentFold = 0; currentFold < foldCount; currentFold++) {
DataSet currentSet = new DataSet(new Instance[foldSize], data.getDescription());
int i = 0;
while (i < foldSize) {
int position = rand.nextInt(data.size());
Instance instance = data.get(position);
if (instance != null && instance.getData() != null) {
currentSet.set(i, instance);
data.set(position, null);
i++;
}
}
this.folds.add(currentSet);
}
}
public void run(int iterations) throws Exception {
// 1) Construct data instances for training. These will also be run
// through the network at the bottom to verify the output
CSVDataSetReader reader = new CSVDataSetReader("data/letter_training_new.data");
DataSet set = reader.read();
LabelSplitFilter flt = new LabelSplitFilter();
flt.filter(set);
DataSetLabelBinarySeperator.seperateLabels(set);
DataSetDescription desc = set.getDescription();
DataSetDescription labelDesc = desc.getLabelDescription();
// 2) Instantiate a network using the FeedForwardNeuralNetworkFactory. This network
// will be our classifier.
FeedForwardNeuralNetworkFactory factory = new FeedForwardNeuralNetworkFactory();
// 2a) These numbers correspond to the number of nodes in each layer.
// This network has 4 input nodes, 3 hidden nodes in 1 layer, and 1 output node in the
// output layer.
FeedForwardNetwork network =
factory.createClassificationNetwork(
new int[] {
desc.getAttributeCount(),
factory.getOptimalHiddenLayerNodes(desc, labelDesc),
labelDesc.getDiscreteRange()
});
// 3) Instantiate a measure, which is used to evaluate each possible set of weights.
ErrorMeasure measure = new SumOfSquaresError();
// 4) Instantiate a DataSet, which adapts a set of instances to the optimization problem.
// DataSet set = new DataSet(patterns);
// 5) Instantiate an optimization problem, which is used to specify the dataset, evaluation
// function, mutator and crossover function (for Genetic Algorithms), and any other
// parameters used in optimization.
NeuralNetworkOptimizationProblem nno =
new NeuralNetworkOptimizationProblem(set, network, measure);
// 6) Instantiate a specific OptimizationAlgorithm, which defines how we pick our next potential
// hypothesis.
OptimizationAlgorithm o = new RandomizedHillClimbing(nno);
// 7) Instantiate a trainer. The FixtIterationTrainer takes another trainer (in this case,
// an OptimizationAlgorithm) and executes it a specified number of times.
FixedIterationTrainer fit = new FixedIterationTrainer(o, iterations);
// 8) Run the trainer. This may take a little while to run, depending on the
// OptimizationAlgorithm,
// size of the data, and number of iterations.
fit.train();
// 9) Once training is done, get the optimal solution from the OptimizationAlgorithm. These are
// the
// optimal weights found for this network.
Instance opt = o.getOptimal();
network.setWeights(opt.getData());
// 10) Run the training data through the network with the weights discovered through
// optimization, and
// print out the expected label and result of the classifier for each instance.
int[] labels = {0, 1};
TestMetric acc = new AccuracyTestMetric();
TestMetric cm = new ConfusionMatrixTestMetric(labels);
Tester t = new NeuralNetworkTester(network, acc, cm);
t.test(set.getInstances());
acc.printResults();
}
private static DataSet reconstruct(RandomizedProjectionFilter rca, DataSet transformed) {
DataSet reconstructed = transformed.copy();
rca.reverse(reconstructed);
return reconstructed;
}