Started working on a CSVWriter for the IOService to be used by the

Reflectivity tests. Added ReflectivityCalculator and friends.

Signed-off-by: Jay Jay Billings <billingsjj@ornl.gov>

src/org.eclipse.ice.io/src/org/eclipse/ice/io/csv/CSVReader.java

@@ -0,0 +1,71 @@
+/*******************************************************************************
+ * Copyright (c) 2013, 2014 UT-Battelle, LLC.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *   Initial API and implementation and/or initial documentation - 
+ *   Jay Jay Billings
+ *******************************************************************************/
+package org.eclipse.ice.io.csv;
+
+import java.util.ArrayList;
+
+import org.eclipse.core.resources.IFile;
+import org.eclipse.ice.datastructures.form.Entry;
+import org.eclipse.ice.datastructures.form.Form;
+import org.eclipse.ice.io.serializable.IReader;
+
+/**
+ * This class implements the IReader interface to provide a reader for CSV
+ * files. It can read any well-formed CSV file. It stores its results in a
+ * ListComponent<String []\> on the Form returned from read(). Each String [] in
+ * the ListComponent is a line of the file, split and trimmed but uncast.
+ * Clients must know the concrete type to which they want to cast.
+ * 
+ * Comments are ignored and begin with the "#" character.
+ * 
+ * @author Jay Jay Billings
+ *
+ */
+public class CSVReader implements IReader {
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see
+	 * org.eclipse.ice.io.serializable.IReader#read(org.eclipse.core.resources
+	 * .IFile)
+	 */
+	@Override
+	public Form read(IFile file) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see
+	 * org.eclipse.ice.io.serializable.IReader#findAll(org.eclipse.core.resources
+	 * .IFile, java.lang.String)
+	 */
+	@Override
+	public ArrayList<Entry> findAll(IFile file, String regex) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * 
+	 * @see org.eclipse.ice.io.serializable.IReader#getReaderType()
+	 */
+	@Override
+	public String getReaderType() {
+		return "csv";
+	}
+
+}

src/org.eclipse.ice.reflectivity/src/org/eclipse/ice/reflectivity/ReflectivityCalculator.java

@@ -0,0 +1,50 @@
+/*******************************************************************************
+ * Copyright (c) 2013, 2014 UT-Battelle, LLC.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *   Initial API and implementation and/or initial documentation - 
+ *   Jay Jay Billings
+ *******************************************************************************/
+package org.eclipse.ice.reflectivity;
+
+/**
+ * This class performs all of the operations necessary to calculate the
+ * reflectivity of a stack of materials. It follows the code originally
+ * developed by John Ankner at Oak Ridge National Laboratory.
+ * 
+ * @author Jay Jay Billings, John Ankner
+ *
+ */
+public class ReflectivityCalculator {
+
+	/**
+	 * The constructor
+	 */
+	public ReflectivityCalculator() {
+		// TODO Auto-generated constructor stub
+	}
+
+	/**
+	 * This operation returns the value of the squared modulus of the specular
+	 * reflectivity for a single wave vector Q.
+	 * 
+	 * @param waveVectorQ
+	 *            the value of the wave vector
+	 * @param wavelength
+	 *            the wavelength of the incident neutrons
+	 * @param tiles
+	 *            the list of TIles that contains the physical parameters needed
+	 *            for the calculation, including the scattering densities,
+	 *            absorption parameters and thicknesses.
+	 * @return the squared modulus of the specular reflectivity
+	 */
+	public double getSpecRefSqrdMod(double waveVectorQ, double wavelength,
+			Tile[] tiles) {
+		return 0.0;
+	}
+
+}

src/org.eclipse.ice.reflectivity/src/org/eclipse/ice/reflectivity/Tile.java

@@ -0,0 +1,46 @@
+/*******************************************************************************
+ * Copyright (c) 2013, 2014 UT-Battelle, LLC.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *   Initial API and implementation and/or initial documentation - 
+ *   Jay Jay Billings
+ *******************************************************************************/
+package org.eclipse.ice.reflectivity;
+
+/**
+ * This class represents a tile or layer of material of a particular type in the
+ * reflectivity calculator.
+ * 
+ * It has no accessors and everything is public because it is made for a
+ * calculation. It should not be used outside of its package.
+ * 
+ * @author Jay Jay Billings, John Ankner
+ *
+ */
+public class Tile {
+
+	/**
+	 * The scattering length of the reflecting tile/layer.
+	 */
+	double scatteringLength = 0.0;
+
+	/**
+	 * The true absorption length of the reflecting tile/layer.
+	 */
+	double trueAbsLength = 0.0;
+
+	/**
+	 * The incoherent absorption length of the reflecting tile/layer.
+	 */
+	double incAbsLength = 0.0;
+
+	/**
+	 * The thickness of this tile/layer.
+	 */
+	double thickness = 0.0;
+
+}

tests/org.eclipse.ice.io.test/src/org/eclipse/ice/io/csv/test/CSVReaderTester.java

@@ -0,0 +1,129 @@
+/*******************************************************************************
+ * Copyright (c) 2013, 2014 UT-Battelle, LLC.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *   Initial API and implementation and/or initial documentation - 
+ *   Jay Jay Billings
+ *******************************************************************************/
+package org.eclipse.ice.io.csv.test;
+
+import static org.junit.Assert.*;
+
+import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IProjectDescription;
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.IWorkspaceRoot;
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.core.runtime.NullProgressMonitor;
+import org.eclipse.core.runtime.Path;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URI;
+
+/**
+ * Test class for {@link org.eclipse.ice.io.csv.CSVReader}.
+ * 
+ * @author Jay Jay Billings
+ *
+ */
+public class CSVReaderTester {
+
+	private static IFile testFile;
+
+	/**
+	 * @throws java.lang.Exception
+	 */
+	@BeforeClass
+	public static void setUpBeforeClass() throws Exception {
+		// Get the file separator used on this system, which is different across
+		// OSes.
+		String separator = System.getProperty("file.separator");
+		// Create the path for the reflectivity file in the ICE tests directory
+		String userHome = System.getProperty("user.home");
+		IWorkspaceRoot workspaceRoot = ResourcesPlugin.getWorkspace().getRoot();
+		URI defaultProjectLocation = null;
+		IProject project = null;
+		String projectName = "CSVLoaderTesterWorkspace";
+		String filename = "getSpecRefSqrdMod_q841.csv";
+		String fullFilename = userHome + separator + "ICETests" + separator
+				+ projectName + separator + filename;
+		IPath projectPath = new Path(userHome + separator + "ICETests"
+				+ separator + projectName + separator + ".project");
+
+		// Setup the project
+		try {
+			// Create the project description
+			IProjectDescription desc = ResourcesPlugin.getWorkspace()
+					.loadProjectDescription(projectPath);
+			// Get the project handle and create it
+			project = workspaceRoot.getProject(desc.getName());
+			project.create(desc, new NullProgressMonitor());
+			// Open the project if it is not already open
+			if (project.exists() && !project.isOpen()) {
+				project.open(new NullProgressMonitor());
+			}
+			// Refresh the workspace
+			project.refreshLocal(IResource.DEPTH_INFINITE,
+					new NullProgressMonitor());
+			// Create the IFile handle for the csv file
+			testFile = project.getFile(filename);
+		} catch (CoreException e) {
+			// Catch exception for creating the project
+			e.printStackTrace();
+			fail();
+		}
+
+		return;
+	}
+
+	/**
+	 * Test method for
+	 * {@link org.eclipse.ice.io.csv.CSVReader#read(org.eclipse.core.resources.IFile)}
+	 * .
+	 * 
+	 * @throws CoreException
+	 * @throws IOException
+	 */
+	@Test
+	public void testRead() throws CoreException, IOException {
+		System.out.println(testFile.getLocation().toOSString());
+		BufferedReader reader = new BufferedReader(new InputStreamReader(
+				testFile.getContents()));
+		System.out.println(reader.readLine());
+		System.out.println(reader.readLine());
+		fail("Not yet implemented");
+		reader.close();
+	}
+
+	/**
+	 * Test method for
+	 * {@link org.eclipse.ice.io.csv.CSVReader#findAll(org.eclipse.core.resources.IFile, java.lang.String)}
+	 * .
+	 */
+	@Test
+	public void testFindAll() {
+		fail("Not yet implemented");
+	}
+
+	/**
+	 * Test method for {@link org.eclipse.ice.io.csv.CSVReader#getReaderType()}.
+	 */
+	@Test
+	public void testGetReaderType() {
+		fail("Not yet implemented");
+	}
+
+}

tests/org.eclipse.ice.reflectivity.test/src/org/eclipse/ice/reflectivity/test/ReflectivityCalculatorTester.java

@@ -0,0 +1,44 @@
+/*******************************************************************************
+ * Copyright (c) 2013, 2014 UT-Battelle, LLC.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *   Initial API and implementation and/or initial documentation - 
+ *   Jay Jay Billings, John Ankner
+ *******************************************************************************/
+package org.eclipse.ice.reflectivity.test;
+
+import static org.junit.Assert.*;
+
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+/**
+ * This class tests {@link org.eclipse.ice.reflectivity.ReflectivityCalculator}.
+ * 
+ * @author Jay Jay Billings, John Ankner
+ *
+ */
+public class ReflectivityCalculatorTester {
+
+	/**
+	 * This class loads the files for the test.
+	 * 
+	 * @throws java.lang.Exception
+	 */
+	@BeforeClass
+	public static void setUpBeforeClass() throws Exception {
+	}
+
+	/**
+	 * This class tests {@link ReflectivityCalculator#getSpectRefSqrdMod}.
+	 */
+	@Test
+	public void testGetSpecRefSqrdMod() {
+		fail("Not yet implemented");
+	}
+
+}