Merge branch 'matlab-commands'

Adds extensible command plugins to expose static utility-like methods in
MATLAB.

Author: hinerm

src/main/java/org/scijava/plugins/scripting/matlab/DefaultMATLABService.java

@@ -31,29 +31,89 @@
 
 package org.scijava.plugins.scripting.matlab;
 
+import javax.script.ScriptEngine;
+
 import matlabcontrol.extensions.MatlabNumericArray;
 
+import org.scijava.log.LogService;
+import org.scijava.plugin.AbstractSingletonService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.script.ScriptService;
-import org.scijava.service.AbstractService;
 import org.scijava.service.Service;
 
 /**
+ * Default {@link MATLABService} implementation.
+ *
  * @author Mark Hiner
  */
 @Plugin(type = Service.class)
-public class DefaultMATLABService extends AbstractService implements
-	MATLABService
+public class DefaultMATLABService extends
+	AbstractSingletonService<MATLABCommands> implements MATLABService
 {
 
 	@Parameter
 	private ScriptService scriptService;
 
+	@Parameter
+	private LogService logService;
+
+	private boolean initializedCommands = false;
+
+	@Override
+	public String commandHelp() {
+		String helpMessage = "--- MATLAB Command Plugins ---\n\n";
+
+		for (final MATLABCommands command : getInstances()) {
+			helpMessage += command.usage();
+		}
+
+		helpMessage += "\n";
+
+		return helpMessage;
+	}
+
+	@Override
+	public void initializeCommands() {
+		if (!initializedCommands) createCommandVariables();
+	}
+
+	@Override
+	public void makeMATLABVariable(final String name, final Object value) {
+		final ScriptEngine engine =
+				scriptService.getLanguageByName("MATLAB").getScriptEngine();
+		engine.put(name, value);
+	}
+
 	// -- Service methods --
 
 	@Override
 	public void initialize() {
+		// Register known data type aliases for use in script @parameters
 		scriptService.addAlias("matrix", MatlabNumericArray.class);
 	}
+
+	// -- Typed methods --
+
+	@Override
+	public Class<MATLABCommands> getPluginType() {
+		return MATLABCommands.class;
+	}
+
+	// -- Helper methods --
+
+	/**
+	 * Helper method to create variables for each {@link MATLABCommands} within
+	 * MATLAB.
+	 */
+	private synchronized void createCommandVariables() {
+		if (!initializedCommands) {
+			for (final MATLABCommands command : getInstances()) {
+				final String name = command.getInfo().getName();
+
+				makeMATLABVariable(name, command);
+			}
+			initializedCommands = true;
+		}
+	}
 }

src/main/java/org/scijava/plugins/scripting/matlab/MATLABBindings.java

@@ -41,16 +41,23 @@
 import javax.script.Bindings;
 
 import matlabcontrol.MatlabInvocationException;
+import matlabcontrol.MatlabProxy;
 import matlabcontrol.extensions.MatlabNumericArray;
 import matlabcontrol.extensions.MatlabTypeConverter;
 
+import org.scijava.options.OptionsService;
+import org.scijava.plugin.Parameter;
+
 /**
  * A {@link Bindings} wrapper around MATLAB's local variables.
  *
  * @author Mark Hiner
  */
 public class MATLABBindings implements Bindings {
 
+	@Parameter
+	private OptionsService optionsService;
+
 	@Override
 	public int size() {
 		return getVars().length;
@@ -69,7 +76,7 @@ public boolean containsValue(final Object value) {
 	@Override
 	public void clear() {
 		try {
-			MATLABControlUtils.proxy().eval("clear");
+			MATLABControlUtils.proxy(opts()).eval("clear");
 		}
 		catch (final MatlabInvocationException e) {}
 	}
@@ -101,26 +108,31 @@ public Set<java.util.Map.Entry<String, Object>> entrySet() {
 
 	@Override
 	public Object put(final String name, final Object value) {
+		final MatlabProxy proxy = MATLABControlUtils.proxy(opts());
+
+		// Try special MATLAB data types
+		if (MatlabNumericArray.class.isAssignableFrom(value.getClass())) {
+			// Convert the dataset to a MATLAB array and set it as a local variable
+			// within MATLAB.
+			final MatlabTypeConverter converter =
+					new MatlabTypeConverter(proxy);
+			try {
+				converter.setNumericArray(sanitize(name), (MatlabNumericArray) value);
+				return value;
+			}
+			catch (final MatlabInvocationException e) {
+				System.err.println(e.getStackTrace());
+			}
+		}
+
 		try {
-			MATLABControlUtils.proxy().setVariable(sanitize(name), value);
+			proxy.setVariable(sanitize(name), value);
 			return value;
 		}
 		catch (final MatlabInvocationException e) {
-
-			// Try special MATLAB data types
-			if (MatlabNumericArray.class.isAssignableFrom(value.getClass())) {
-				// Convert the dataset to a MATLAB array and set it as a local variable
-				// within MATLAB.
-				final MatlabTypeConverter converter =
-					new MatlabTypeConverter(MATLABControlUtils.proxy());
-				try {
-					converter.setNumericArray(name, (MatlabNumericArray) value);
-				}
-				catch (final MatlabInvocationException e1) {
-					throw new IllegalArgumentException(e);
-				}
-			}
+				System.err.println(e.getStackTrace());
 		}
+
 		return null;
 	}
 
@@ -160,24 +172,27 @@ private Object retrieveValue(final Object key, final boolean remove) {
 		if (key instanceof String) k = (String) key;
 		else return null;
 		Object v = null;
+		final MatlabProxy proxy = MATLABControlUtils.proxy(opts());
 
+		// Attempt to retrieve special MATLAB types
 		try {
-			v = MATLABControlUtils.proxy().getVariable(k);
-			if (remove) MATLABControlUtils.proxy().eval("clear " + k);
+			// try recovering key as a MatlabNumericArray
+			final MatlabTypeConverter converter =
+					new MatlabTypeConverter(proxy);
+			v = converter.getNumericArray(k);
 		}
 		catch (final MatlabInvocationException e) {
+			System.err.println(e.getStackTrace());
+		}
 
-			// Attempt to retrieve special MATLAB types
-			try {
-				// try recovering key as a MatlabNumericArray
-				final MatlabTypeConverter converter =
-					new MatlabTypeConverter(MATLABControlUtils.proxy());
-				v = converter.getNumericArray(k);
-			}
-			catch (final MatlabInvocationException e1) {
-				System.err.println(e.getStackTrace());
-			}
+		try {
+			v = proxy.getVariable(k);
+			if (remove) proxy.eval("clear " + k);
+		}
+		catch (final MatlabInvocationException e) {
+			System.err.println(e.getStackTrace());
 		}
+
 		return v;
 	}
 
@@ -187,7 +202,7 @@ private Object retrieveValue(final Object key, final boolean remove) {
 	private String[] getVars() {
 		try {
 			final String[] vars =
-				(String[]) MATLABControlUtils.proxy().returningEval("who", 1)[0];
+				(String[]) MATLABControlUtils.proxy(opts()).returningEval("who", 1)[0];
 			return vars;
 		}
 		catch (final MatlabInvocationException e) {}
@@ -203,4 +218,13 @@ private String[] getVars() {
 	private String sanitize(final String name) {
 		return name.replaceAll("[^\\w]", "_");
 	}
+
+	/**
+	 * Convenience method for access to the {@link MATLABOptions}
+	 *
+	 * @return Active {@code MATLABOptions}
+	 */
+	private MATLABOptions opts() {
+		return optionsService.getOptions(MATLABOptions.class);
+	}
 }

src/main/java/org/scijava/plugins/scripting/matlab/MATLABCommands.java

@@ -0,0 +1,53 @@
+/*
+ * #%L
+ * MATLAB scripting language plugin.
+ * %%
+ * Copyright (C) 2014 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.scijava.plugins.scripting.matlab;
+
+import org.scijava.plugin.Plugin;
+import org.scijava.plugin.RichPlugin;
+import org.scijava.plugin.SingletonPlugin;
+
+
+/**
+ * A suite of commands for use in MATLAB. The {@link MATLABService} will create
+ * variables for each {@link MATLABCommands} using their annotated
+ * {@link Plugin#name()}, allowing convenient access to any of their methods.
+ *
+ * @see MATLABService
+ *
+ * @author Mark Hiner
+ */
+public interface MATLABCommands extends SingletonPlugin, RichPlugin {
+
+	/**
+	 * @return A string describing any commands that should be publicized.
+	 */
+	String usage();
+}