# HG changeset patch
# User stevenh
# Date 1357669132 0
# Node ID eb086fc2680372c49bb9a581dfd4ef1dc70cf3b0
# Parent  5a3a1c7fa3a827d85d14cc122889e21d09c2e779
new

diff -r 5a3a1c7fa3a8 -r eb086fc26803 src/org/qmul/eecs/c4dm/sia/SiaTecMain.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/org/qmul/eecs/c4dm/sia/SiaTecMain.java	Tue Jan 08 18:18:52 2013 +0000
@@ -0,0 +1,363 @@
+package org.qmul.eecs.c4dm.sia;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.mindswap.pellet.jena.PelletReasonerFactory;
+import org.qmul.eecs.c4dm.sia.exceptions.DimensionException;
+import org.qmul.eecs.c4dm.sia.model.Datapoint;
+import org.qmul.eecs.c4dm.sia.model.NDimensionalObject;
+import org.qmul.eecs.c4dm.sia.model.SiatecX;
+import org.qmul.eecs.c4dm.sia.model.VectorTable;
+import org.qmul.eecs.c4dm.sia.model.VectorTableElement;
+import org.qmul.eecs.c4dm.sia.rdf.Namespaces;
+import org.qmul.eecs.c4dm.sia.utilities.Display;
+import org.qmul.eecs.c4dm.sparql.utilities.SparqlWrapperMethods;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
+/**
+ * <p>
+ * Title: SiaTecMain
+ * </p>
+ * <p>
+ * Description: An RDF/OWL/Java implementation of the SIATEC pattern discovery algorithm.
+ * See "Algorithms for discovering repeated patterns in multidimensional representations of polyphonic music"
+ * by Meredith, D. and Lemstr&ouml;m, K. and Wiggins, G.A.
+ * </p>
+ * 
+ * @author Steve Hargreaves, C4DM, Queen Mary University of London
+ */
+public class SiaTecMain {
+
+	// The ontology loaded as dataset
+	private static final String ontology = "file:src/rdf/siaDatapointOntology.n3";
+
+	// The final output file
+	private static final String finalModelFileName = "src/rdf/finalSiaTecModel";
+
+	// SPARQL queries
+	private static final String[] selectQueries = new String[] {
+		// A SPARQL-DL query
+		"file:src/sparql/select_all.sparql"
+		};
+
+	// CONSTRUCT queries
+	private static final String[] constructQueries = new String[] {
+		// SPARQL-DL CONSTRUCT queries
+		"file:src/sparql/construct_siatec_vector_table_bnodes.sparql",
+		"file:src/sparql/construct_vector_table_details.sparql" };
+
+	// ASK queries
+	private static final String[] askQueries = new String[] {
+		// A SPARQL-DL ASK query
+		};
+	
+	public void run() {
+
+		// First create a Jena ontology model backed by the Pellet reasoner
+		// (note, the Pellet reasoner is required)
+		OntModel ontModel = ModelFactory
+				.createOntologyModel(PelletReasonerFactory.THE_SPEC);
+
+		// Then read the data from the file into the ontology model
+		ontModel.read(ontology, "N3");
+		
+		// Set the value of SIA_NS_URI as the namespace for 'sia' found in
+		// the ontology
+		Namespaces.SIA_NS_URI = ontModel.getNsPrefixURI("sia");
+
+		// Create custom sia Datapoint objects
+		List<Datapoint> datapoints = SiaDatapointFactory.create(ontModel);
+		
+		// STEP 1 - Order the datapoints
+		Collections.sort(datapoints);
+
+		// Add datapoint order info to model
+		SiaDatapointFactory.assertOrder(ontModel, datapoints);
+		
+		// STEP 2 - Compute the vector table W, and sort
+		// Run all the CONSTRUCT queries
+		for (int i = 0; i < constructQueries.length; i++) {
+			String constructQuery = constructQueries[i];
+
+			Model newModel = SparqlWrapperMethods.executeConstructQuery(constructQuery, ontModel);
+
+			// Add new triples to the current model
+			ontModel.add(newModel);
+		}
+		VectorTable vectorTableW = SiaVectorTableElementFactory.createW(ontModel, datapoints);
+
+		// STEP 3 - Create custom SIATEC VectorTableElement objects (V)
+		VectorTable vectorTableV = SiaVectorTableElementFactory.createV(ontModel, datapoints);
+		List<VectorTableElement> vteListV = vectorTableV.getVteList();
+
+		// STEP 4 - Sort V
+		Collections.sort(vteListV);
+
+		// Add vector table element order info to model
+		SiaVectorTableElementFactory.assertOrder(ontModel, vteListV);
+		
+		// STEP 5 - "Vectorize" the MTPs
+		int m = vteListV.size();
+		int i = 0;
+		ArrayList<SiatecX> x = new ArrayList<SiatecX>();
+		
+		while (i < m)
+		{
+			ArrayList<NDimensionalObject> q = new ArrayList<NDimensionalObject>();
+			int j = i + 1;
+			while (j < m && (vteListV.get(i).compareToIgnoreDatapoints(vteListV.get(j)) == 0))
+			{
+				NDimensionalObject vector = vteListV.get(j).getFromDatapoint().subtract(vteListV.get(j - 1).getFromDatapoint());
+				q.add(vector);
+				j++;
+			}
+			
+			SiatecX iq = new SiatecX();
+			iq.setI(i+1);
+			iq.setQ(q);
+			x.add(iq);
+			i = j;
+		}
+		
+		System.out.println("X");
+		printX(x);
+
+		// Sort the elements of x
+		Collections.sort(x);
+		
+		// Rename as y to match algorithm description in paper
+		ArrayList<SiatecX> y = (ArrayList<SiatecX>) x.clone();
+		
+		System.out.println("\nY = Sorted X");
+		printX(y);
+		
+		// Display results using algorithm figures 23, 24 and 25 of the research paper
+		int r = y.size();
+		m = vteListV.size();
+		i = 0; // *** check indexing
+		System.out.println();
+		System.out.print("{");
+		if (r > 0) // *** check indexing
+		{
+			do
+			{
+				int j = y.get(i).getI() - 1; // *** check indexing
+				List<Integer> iList = new ArrayList<Integer>();
+				while (j < m && (vteListV.get(j).getVector().compareTo(vteListV.get(y.get(i).getI() - 1).getVector()) == 0)) // *** check indexing
+				{
+//					// debug start
+//					for (int hundip = 0; hundip < vteList.size(); hundip++)
+//					{
+//						System.out.println("v[" + hundip + ",2] = " + vteList.get(hundip).getFromDatapoint().getOrderedIndex());
+//					}
+//					// debug start					
+
+					iList.add(vteListV.get(j).getFromDatapoint().getOrderedIndex());					
+					j++;
+				}
+				System.out.print("<");
+				Display.printPattern(iList, datapoints);
+				System.out.print(",");
+				printSetOfTranslators(iList, datapoints, vectorTableW);
+				System.out.print(">");
+				do
+				{
+					i++;
+				} while (i < r && (y.get(i).compareToIgnoreI(y.get(i - 1)) == 0)); // *** check indexing
+				
+				if (i < r) // *** check indexing
+				{
+					System.out.print(",");
+					System.out.println();
+				}
+			} while (i < r); // *** check indexing
+		}
+		System.out.println("}");
+
+		// Run all the SELECT queries
+		for (i = 0; i < selectQueries.length; i++) {
+
+			String selectQuery = selectQueries[i];
+			SparqlWrapperMethods.queryTheModel(selectQuery, ontModel);
+
+		}
+
+		// Run all the ASK queries
+		for (i = 0; i < askQueries.length; i++) {
+
+			String askQuery = askQueries[i];
+			SparqlWrapperMethods.askTheModel(askQuery, ontModel);
+
+		}
+
+		// Write the model to a file
+		File outFileRdf = new File(finalModelFileName + ".rdf");
+		File outFileN3 = new File(finalModelFileName + ".n3");
+		FileOutputStream outFileOutputStreamRdf;
+		FileOutputStream outFileOutputStreamN3;
+
+		// RDF/XML version
+		try {
+			outFileOutputStreamRdf = new FileOutputStream(outFileRdf);
+			ontModel.writeAll(outFileOutputStreamRdf, "RDF/XML", null);
+		} catch (FileNotFoundException e) {
+			System.out.println("Unable to write to file: "
+					+ outFileRdf.getAbsolutePath());
+			e.printStackTrace();
+			System.exit(1);
+		}
+
+		// N3 version
+		try {
+			outFileOutputStreamN3 = new FileOutputStream(outFileN3);
+			ontModel.writeAll(outFileOutputStreamN3, "N3", null);
+		} catch (FileNotFoundException e) {
+			System.out.println("Unable to write to file: "
+					+ outFileN3.getAbsolutePath());
+			e.printStackTrace();
+			System.exit(1);
+		}
+
+		System.out.println("Model written to files: "
+				+ outFileRdf.getAbsolutePath() + " and " + outFileN3.getAbsolutePath());
+	}
+
+	private void printSetOfTranslators(List<Integer> iList, List<Datapoint> datapoints, VectorTable vectorTableW) {
+		int p = iList.size();
+		int n = datapoints.size();
+
+		if (p == 1)
+		{
+//			// debug start
+//			for (int f = 0; f < vectorTableW.size(); f++)
+//			{
+//				try {
+//					System.out.println("W[" + f + "] = <<" + vectorTableW.getVteList().get(f).getDimensionValue(1) + "," + vectorTableW.getVteList().get(f).getDimensionValue(2) + ">," + vectorTableW.getVteList().get(f).getFromDatapoint().getOrderedIndex() + ">");
+//				} catch (DimensionException e) {
+//					// TODO Auto-generated catch block
+//					e.printStackTrace();
+//				}
+//			}
+//			// debug end
+			System.out.print("{");
+			Display.printVector(vectorTableW.getVector(iList.get(0), 1));
+			for (int k = 2; k <= n; k++)
+			{
+				System.out.print(",");
+				Display.printVector(vectorTableW.getVector(iList.get(0), k));
+			}
+			System.out.print("}");
+		}
+		else
+		{
+			System.out.print("{");
+			List<Integer> jList = new ArrayList<Integer>();
+			for (int k = 0; k < p; k++)
+			{
+				jList.add(1);
+			}
+			boolean finished = false;
+			boolean first_vector = true;
+			int k = 1;
+
+			while (!finished)
+			{
+				if (jList.get(k) <= jList.get(k - 1))
+				{
+					jList.set(k, jList.get(k - 1) + 1);
+				}
+				
+				while (jList.get(k) <= (n - p + k + 1)
+						&& (vectorTableW.getVector(iList.get(k), jList.get(k)).compareTo(vectorTableW.getVector(iList.get(k - 1), jList.get(k - 1))) < 0))
+				{
+					jList.set(k, jList.get(k) + 1);
+				}
+				
+				if (jList.get(k) > n - p + k + 1)
+				{
+					finished = true;
+				}
+				else if (vectorTableW.getVector(iList.get(k), jList.get(k)).compareTo(vectorTableW.getVector(iList.get(k - 1), jList.get(k - 1))) > 0)
+				{
+					k = 1;
+					jList.set(0, jList.get(0) + 1);
+					if (jList.get(0) > n - p + 1)
+					{
+						finished = true;
+					}
+				}
+				else if (k + 1 == p)
+				{
+					if (!first_vector)
+					{
+						System.out.print(",");
+					}
+					else
+					{
+						first_vector = false;
+					}
+					
+					Display.printVector(vectorTableW.getVector(iList.get(k), jList.get(k)));
+					k = 0;
+					
+					while (k < p)
+					{
+						jList.set(k, jList.get(k) + 1);
+						if (jList.get(k) > n - p + k +1)
+						{
+							finished = true;
+							k = p -1;
+						}
+						k++;
+					}
+					k = 1;
+				}
+				else
+				{
+					k++;
+				}
+			}
+			System.out.print("}");
+		}
+	}
+
+	private void printX(ArrayList<SiatecX> x) {
+		for (SiatecX iq : x)
+		{
+			System.out.print(iq.getI() + ",");
+			for (NDimensionalObject q : iq.getQ())
+			{
+				System.out.print("<");
+				int dimensions = q.getDimensionValues().size();
+				for (int dim = 1; dim <= dimensions; dim++)
+				{
+					try {
+						System.out.print(q.getDimensionValue(dim) + (dim == dimensions ? "" : ","));
+					} catch (DimensionException e) {
+						e.printStackTrace();
+						System.exit(1);
+					}
+				}
+				System.out.println(">");
+			}
+			System.out.println();
+		}
+	}
+
+	/**
+	 * @param args
+	 */
+	public static void main(String[] args) {
+		SiaTecMain app = new SiaTecMain();
+		app.run();
+	}
+
+}