Make PrimitiveBlocks work with BufferAccess

bin/generate.groovy

@@ -0,0 +1,238 @@
+#!/usr/bin/env groovy
+
+/*
+ * #%L
+ * SciJava Operations: a framework for reusable algorithms.
+ * %%
+ * Copyright (C) 2018 SciJava developers.
+ * %%
+ * 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%
+ */
+
+debug = System.getenv('DEBUG')
+def debug(msg) {
+	if (debug) System.err.println("[DEBUG] $msg")
+}
+
+@Grab('org.apache.velocity:velocity:1.7')
+import org.apache.velocity.app.VelocityEngine
+
+// TODO: Get path to Groovy script and make these dirs relative to that.
+templateDirectory = 'templates'
+outputDirectory = 'src'
+
+knownFiles = new java.util.HashSet();
+
+/* Gets the last modified timestamp for the given file. */
+def timestamp(dir, file) {
+	if (file == null) return Long.MAX_VALUE;
+	file = new java.io.File(dir, file);
+	knownFiles.add(file);
+	return file.lastModified();
+}
+
+/* Processes a template using Apache Velocity. */
+def processTemplate(engine, context, templateFile, outFilename) {
+	debug("processTemplate('$engine', '$context', '$templateFile', '$outFilename')")
+
+	if (outFilename == null) return; // nothing to do
+
+	// create output directory if it does not already exist
+	outFile = new java.io.File(outputDirectory, outFilename);
+	knownFiles.add(outFile);
+	if (outFile.getParentFile() != null) outFile.getParentFile().mkdirs();
+
+	// apply the template and write out the result
+	t = engine.getTemplate(templateFile);
+	writer = new StringWriter();
+	t.merge(context, writer);
+	out = new PrintWriter(outFile, "UTF-8");
+	out.print(writer.toString());
+	out.close();
+}
+
+/* Evaluates a string using Groovy. */
+def parseValue(sh, translationsFile, key, expression) {
+	try {
+		result = sh.evaluate(expression)
+		sh.setVariable(key, result)
+		return result
+	}
+	catch (groovy.lang.GroovyRuntimeException e) {
+		print("[WARNING] $translationsFile: " +
+			"key '$key' has unparseable value: " + e.getMessage());
+	}
+}
+
+/* Reads a translations File */
+def readTranslation(engine, globalContext, reader, templateSubdirectory, templateFile, translationsFile, isInclude){
+	sh = new groovy.lang.GroovyShell();
+	for (;;) {
+		// read the line
+		line = reader.readLine();
+
+		if (line == null) break;
+		// check if the line starts a new section
+		if (line.startsWith("[") && line.endsWith("]")) {
+			// if we are parsing a .include file, return when we hit any sections
+			if(isInclude){
+				println("[WARNING] $translationsFile: Section definition in .include file. Ending processing of $translationsFile");
+				return context; 
+			}
+			// write out the previous file
+			processTemplate(engine, context, templateFile, outputFilename);
+
+			// start a new file
+			outputFilename = line.substring(1, line.length() - 1);
+			if (!templateDirectory.equals(templateSubdirectory)) {
+				subPath = templateSubdirectory.substring(templateDirectory.length() + 1);
+				outputFilename = "$subPath/$outputFilename";
+			}
+			context = new org.apache.velocity.VelocityContext(globalContext);
+			continue;
+		}
+
+		// ignore blank lines
+		trimmedLine = line.trim();
+		if (trimmedLine.isEmpty()) continue;
+
+		// ignore comments
+		if (trimmedLine.startsWith("#")) continue;
+
+		// include any global files
+		if (trimmedLine.startsWith(".include")){
+			includeFile = line.substring(9);
+			if(includeFile.startsWith("templates")){
+				includeSubdirectory = includeFile.substring(0, includeFile.lastIndexOf("/"))
+				includeFile = includeFile.substring(includeFile.lastIndexOf("/"))
+			}
+			else{
+			includeSubdirectory = templateSubdirectory
+			}
+			globalReader = new java.io.BufferedReader(new java.io.FileReader("$includeSubdirectory/$includeFile"));
+			encapsulatedContext = new org.apache.velocity.VelocityContext(context)
+			context = readTranslation(engine, encapsulatedContext, globalReader, templateSubdirectory, templateFile, includeFile, true) 
+			continue;
+		}
+
+		if (!line.contains('=')) {
+			print("[WARNING] $translationsFile: Ignoring spurious line: $line");
+			continue;
+		}
+
+		int idx = line.indexOf('=');
+		key = line.substring(0, idx).trim();
+		value = line.substring(idx + 1);
+
+		if (value.trim().equals('```')) {
+			// multi-line value
+			builder = new StringBuilder();
+			for (;;) {
+				line = reader.readLine();
+				if (line == null) {
+					throw new RuntimeException("Unfinished value: " + builder.toString());
+				}
+				if (line.equals('```')) {
+					break;
+				}
+				if (builder.length() > 0) {
+					builder.append("\n");
+				}
+				builder.append(line);
+			}
+			value = builder.toString();
+		}
+
+		context.put(key, parseValue(sh, translationsFile, key, value));
+	}
+
+	return context;
+}
+
+/*
+ * Translates a template into many files in the outputDirectory,
+ * given a translations file in INI style; e.g.:
+ *
+ * [filename1]
+ * variable1 = value1
+ * variable2 = value2
+ * ...
+ * [filename2]
+ * variable1 = value3
+ * variable2 = value4
+ * ...
+ */
+def translate(templateSubdirectory, templateFile, translationsFile) {
+	debug("translate('$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", "$templateSubdirectory");
+	// tell Velocity to log to stderr rather than to a velocity.log file
+	p.setProperty(org.apache.velocity.runtime.RuntimeConstants.RUNTIME_LOG_LOGSYSTEM_CLASS,
+			"org.apache.velocity.runtime.log.SystemLogChute");
+	engine.init(p);
+
+	// read translation lines
+	outputFilename = null;
+	context = globalContext = new org.apache.velocity.VelocityContext();
+	reader = new java.io.BufferedReader(new java.io.FileReader("$templateSubdirectory/$translationsFile"));
+
+	readTranslation(engine, context, reader, templateSubdirectory, templateFile, translationsFile, false);
+
+	reader.close();
+
+	// process the template
+	processTemplate(engine, context, templateFile, outputFilename);
+}
+
+/* Recursively translates all templates in the given directory. */
+def translateDirectory(templateSubdirectory) {
+	debug("translateDirectory('$templateSubdirectory')")
+
+	for (file in new java.io.File(templateSubdirectory).listFiles()) {
+		if (file.isDirectory()) {
+			// process subdirectories recursively
+			translateDirectory(file.getPath());
+		}
+		else {
+			// process Velocity template files only
+			name = file.getName();
+			if (!name.endsWith('.vm')) continue;
+			prefix = name.substring(0, name.lastIndexOf('.'));
+			translate(templateSubdirectory, name, prefix + '.list');
+		}
+	}
+}
+
+try {
+	translateDirectory(templateDirectory);
+}
+catch (Throwable t) {
+	t.printStackTrace(System.err);
+	throw t;
+}

src/main/java/net/imglib2/blocks/ArrayImgRangeCopier.java

@@ -11,13 +11,13 @@
  * %%
  * 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
@@ -44,13 +44,13 @@
  *
  * @param <T> a primitive array type, e.g., {@code byte[]}.
  */
-class ArrayImgRangeCopier< T > implements RangeCopier< T >
+class ArrayImgRangeCopier< S, T > implements RangeCopier< T >
 {
 	private final int n;
 	private final int[] srcDims;
 	private final Ranges findRanges;
-	private final MemCopy< T > memCopy;
-	private final T oob;
+	private final MemCopy< S, T > memCopy;
+	private final S oob;
 
 	private final List< Ranges.Range >[] rangesPerDimension;
 	private final Ranges.Range[] ranges;
@@ -60,13 +60,13 @@ class ArrayImgRangeCopier< T > implements RangeCopier< T >
 	private final int[] csteps;
 	private final int[] lengths;
 
-	private final T src;
+	private final S src;
 
 	public ArrayImgRangeCopier(
 			final ArrayImg< ?, ? > arrayImg,
 			final Ranges findRanges,
-			final MemCopy< T > memCopy,
-			final T oob )
+			final MemCopy< S, T > memCopy,
+			final S oob )
 	{
 		n = arrayImg.numDimensions();
 
@@ -86,11 +86,11 @@ public ArrayImgRangeCopier(
 		csteps = new int[ n ];
 		lengths = new int[ n ];
 
-		src = ( T ) ( ( ( ArrayDataAccess< ? > ) arrayImg.update( null ) ).getCurrentStorageArray() );
+		src = ( S ) ( ( ArrayDataAccess< ? > ) arrayImg.update( null ) ).getCurrentStorageArray();
 	}
 
 	// creates an independent copy of {@code other}
-	private ArrayImgRangeCopier( ArrayImgRangeCopier< T > copier )
+	private ArrayImgRangeCopier( ArrayImgRangeCopier< S, T > copier )
 	{
 		n = copier.n;
 		srcDims = copier.srcDims.clone();
@@ -108,7 +108,7 @@ private ArrayImgRangeCopier( ArrayImgRangeCopier< T > copier )
 	}
 
 	@Override
-	public ArrayImgRangeCopier< T > newInstance()
+	public ArrayImgRangeCopier< S, T > newInstance()
 	{
 		return new ArrayImgRangeCopier<>( this );
 	}
@@ -220,7 +220,7 @@ private void copyRanges( final T dest )
 		}
 	}
 
-	private void copyRangesRecursively( final T src, final int srcPos, final T dest, final int destPos, final int d )
+	private void copyRangesRecursively( final S src, final int srcPos, final T dest, final int destPos, final int d )
 	{
 		final int length = lengths[ d ];
 		final int cstep = csteps[ d ];