Merge branch 'groovy-time'

This uses Groovy to parse template values.
Much cleaner, much slicker, much more powerful.

For details, see b5d3778.

src/main/groovy/generate.groovy

@@ -54,135 +54,15 @@ def processTemplate(engine, context, templateFile, outFilename) {
 	out.close();
 }
 
-/* Parses a string to a string, list or map. */
-def parseValue(str) {
-	symbols = new Stack<Character>();
-	parsed = new Stack<Object>();
-
-	buffer = "";
-
-	for (char c : str.toCharArray()) {
-		try {
-			// top symbol determines what kind of structure we're
-			// currently working on TODO: Speedup?
-			top = symbols.peek();
-
-			if (top == '\\') { // escaped
-				symbols.pop();
-			}
-			else {
-				if (top == '{') {
-					// parse a map
-					if (c == ':') {
-						// key is complete, push the key to parsed
-						if (!buffer.isEmpty()) {
-							parsed.push(new String(buffer));
-							buffer = "";
-						} // else
-								// buffer has probably already been pushed,
-								// therefore must have been enclosed in '"'
-						continue;
-					}
-					if (c == ',' || c == '}') {
-						if (buffer.isEmpty()) {
-							value = parsed.pop();
-						}
-						else {
-							value = new String(buffer);
-							buffer = "";
-						}
-
-						key = parsed.pop();
-
-						parsed.peek().put(key.trim(), value);
-
-						if (c == '}') {
-							// finish up this map.
-							symbols.pop();
-						}
-
-						continue;
-					}
-				}
-				else if (top == '[') {
-					// parse a list
-					if (c == ',' || c == ']') {
-						if (buffer.isEmpty()) {
-							value = parsed.pop();
-						}
-						else {
-							value = new String(buffer);
-							buffer = "";
-						}
-
-						parsed.peek().add(value);
-
-						if (c == ']') {
-							// finish up this map.
-							symbols.pop();
-						}
-
-						continue;
-					}
-				}
-				else if (top == '"') {
-					if (c == '"') {
-						parsed.push(new String(buffer));
-						buffer = "";
-						symbols.pop();
-						continue;
-					}
-				}
-
-				if (c == '[') {
-					symbols.push(c);
-					parsed.push(new ArrayList<Object>());
-					continue;
-				}
-				if (c == '{') {
-					symbols.push(c);
-					parsed.push(new HashMap<Object, Object>());
-					continue;
-				}
-				if (c == '"') {
-					symbols.push(c);
-					continue;
-					// uses buffer
-				}
-			}
-
-			// no special meaning to this char.
-			if (buffer.isEmpty() && isWhitespace(c)) {
-				// skip leading whitespaces
-				continue;
-			}
-			buffer += c;
-		}
-		catch (EmptyStackException e) {
-			if (isWhitespace(c)) {
-				// skip leading whitespaces
-			}
-			else if (c == '{') {
-				symbols.push(c);
-				parsed.push(new HashMap<Object, Object>());
-			}
-			else if (c == '[') {
-				symbols.push(c);
-				parsed.push(new ArrayList<Object>());
-			}
-			else {
-				// this is a simple string value, we're done.
-				parsed.push(new String(str.trim()));
-				break;
-			}
-		}
+/* Parses a string to a scalar, list or map. */
+def parseValue(sh, translationsFile, key, expression) {
+	try {
+		return sh.evaluate(expression);
+	}
+	catch (groovy.lang.GroovyRuntimeException e) {
+		print("[WARNING] $translationsFile: " +
+			"key '$key' has unparseable value: " + e.getMessage());
 	}
-
-	return parsed.pop();
-}
-
-def isWhitespace(c) {
- return c == ' ' || c == '\t' || c == '\n';
 }
 
 /*
@@ -202,6 +82,9 @@ def translate(templateSubdirectory, templateFile, translationsFile) {
 	// initialize the Velocity engine
 	engine = new org.apache.velocity.app.VelocityEngine();
 	p = new java.util.Properties();
+	// fail if template uses an invalid expression; e.g., an undefined variable
+	p.setProperty("runtime.references.strict", "true");
+	// tell Velocity where the templates are located
 	p.setProperty("file.resource.loader.path", "$templateSubdirectory");
 	// tell Velocity to log to stderr rather than to a velocity.log file
 	p.setProperty(org.apache.velocity.runtime.RuntimeConstants.RUNTIME_LOG_LOGSYSTEM_CLASS,
@@ -217,6 +100,7 @@ def translate(templateSubdirectory, templateFile, translationsFile) {
 		timestamp(templateSubdirectory, translationsFile),
 		timestamp(templateSubdirectory, templateFile));
 
+	sh = new groovy.lang.GroovyShell();
 	for (;;) {
 		// read the line
 		line = reader.readLine();
@@ -240,7 +124,11 @@ def translate(templateSubdirectory, templateFile, translationsFile) {
 		}
 
 		// ignore blank lines
-		if (line.trim().isEmpty()) continue;
+		trimmedLine = line.trim();
+		if (trimmedLine.isEmpty()) continue;
+
+		// ignore comments
+		if (trimmedLine.startsWith("#")) continue;
 
 		// parse key/value pair lines separate by equals
 		if (!line.contains('=')) {
@@ -273,7 +161,7 @@ def translate(templateSubdirectory, templateFile, translationsFile) {
 
 		//For debugging: System.out.println("<" + key + ">: " + parseValue(value).toString());
 
-		context.put(key, parseValue(value));
+		context.put(key, parseValue(sh, translationsFile, key, value));
 	}
 	reader.close();
 

src/main/java/net/imagej/ops/OpRef.java

@@ -1,9 +1,9 @@
 /*
  * #%L
- * ImageJ OPS: a framework for reusable algorithms.
+ * ImageJ software for multidimensional image processing and analysis.
  * %%
  * Copyright (C) 2014 - 2015 Board of Regents of the University of
- * Wisconsin-Madison and University of Konstanz.
+ * Wisconsin-Madison, University of Konstanz and Brian Northan.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

src/main/java/net/imagej/ops/arithmetic/real/RealAbs.java

@@ -0,0 +1,58 @@
+
+/*
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2015 Board of Regents of the University of
+ * Wisconsin-Madison, University of Konstanz and Brian Northan.
+ * %%
+ * 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 net.imagej.ops.arithmetic.real;
+
+import net.imagej.ops.AbstractStrictFunction;
+import net.imagej.ops.MathOps;
+import net.imagej.ops.Op;
+import net.imglib2.type.numeric.RealType;
+
+import org.scijava.plugin.Plugin;
+
+/**
+ * Sets the real component of an output real number to the absolute value of the
+ * real component of an input real number.
+ * 
+ * @author Barry DeZonia
+ * @author Jonathan Hale
+ */
+@Plugin(type = Op.class, name = MathOps.Abs.NAME)
+public class RealAbs<I extends RealType<I>, O extends RealType<O>> extends
+	AbstractStrictFunction<I, O> implements MathOps.Abs
+{
+
+	@Override
+	public O compute(final I input, final O output) {
+		output.setReal(Math.abs(input.getRealDouble()));
+		return output;
+	}
+}

src/main/java/net/imagej/ops/arithmetic/real/RealAdd.java

@@ -0,0 +1,62 @@
+
+/*
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2015 Board of Regents of the University of
+ * Wisconsin-Madison, University of Konstanz and Brian Northan.
+ * %%
+ * 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 net.imagej.ops.arithmetic.real;
+
+import net.imagej.ops.AbstractStrictFunction;
+import net.imagej.ops.MathOps;
+import net.imagej.ops.Op;
+import net.imglib2.type.numeric.RealType;
+
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+/**
+ * Sets the real component of an output real number to the addition of the real
+ * component of an input real number with a constant value.
+ * 
+ * @author Barry DeZonia
+ * @author Jonathan Hale
+ */
+@Plugin(type = Op.class, name = MathOps.Add.NAME)
+public class RealAdd<I extends RealType<I>, O extends RealType<O>> extends
+	AbstractStrictFunction<I, O> implements MathOps.Add
+{
+
+	@Parameter
+	private double constant;
+
+	@Override
+	public O compute(final I input, final O output) {
+		output.setReal(input.getRealDouble() + constant);
+		return output;
+	}
+}