Major refactoring

* Added ScriptInfoWidget to allow ScriptInfo parameters with a style attribute defining the input type
* Added ModuleBatchProcessor that takes a ModuleInfo input
* Added MenuScriptBatchProcessor and FileScriptBatchProcessor that both call ModuleBatchProcessor

Closes #1, closes #2.

Author: imagejan

pom.xml

@@ -100,5 +100,14 @@
 			<groupId>net.imagej</groupId>
 			<artifactId>imagej</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.scijava</groupId>
+			<artifactId>scijava-ui-swing</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>commons-io</groupId>
+			<artifactId>commons-io</artifactId>
+			<version>2.4</version>
+		</dependency>
 	</dependencies>
 </project>

src/main/java/org/scijava/batch/BatchProcessor.java

@@ -0,0 +1,145 @@
+package org.scijava.batch;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.regex.PatternSyntaxException;
+
+import org.apache.commons.io.filefilter.DirectoryFileFilter;
+import org.apache.commons.io.filefilter.RegexFileFilter;
+import org.apache.commons.io.filefilter.WildcardFileFilter;
+import org.scijava.ItemVisibility;
+import org.scijava.command.Command;
+import org.scijava.command.CommandService;
+import org.scijava.command.DynamicCommand;
+import org.scijava.convert.ConvertService;
+import org.scijava.module.ModuleInfo;
+import org.scijava.module.ModuleItem;
+import org.scijava.module.ModuleService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.script.ScriptService;
+import org.scijava.widget.ChoiceWidget;
+import org.scijava.widget.FileWidget;
+
+@Plugin(type = Command.class, label = "Process Folder", menuPath = "Process>Batch>Run Script from File")
+public class FileScriptBatchProcessor extends DynamicCommand {
+
+	private final String WILDCARD = "Wildcard";
+	private final String REGEX = "Regex";
+
+	@Parameter
+	private ModuleService modules;
+
+	@Parameter
+	private ScriptService scripts;
+
+	@Parameter
+	private CommandService commands;
+	
+	@Parameter
+	private ConvertService convert;
+
+	@Parameter(label = "Script file to run", callback = "scriptFileCallback")
+	private File scriptFile;
+	
+	@Parameter(visibility=ItemVisibility.MESSAGE, persist = false)
+	private String scriptMessage = "";
+
+	@Parameter(style = FileWidget.DIRECTORY_STYLE, callback = "directoryCallback")
+	private File inputFolder;
+
+	@Parameter(label = "Recursive (with subfolders)", callback = "directoryCallback")
+	private boolean recursive;
+
+	@Parameter(label = "File selection method", choices = { WILDCARD, REGEX }, style = ChoiceWidget.RADIO_BUTTON_HORIZONTAL_STYLE, callback = "directoryCallback")
+	private String filterChoice = WILDCARD;
+
+	@Parameter(label = "File name pattern", callback = "directoryCallback")
+	private String pattern = "*.tif";
+
+	@Parameter(visibility = ItemVisibility.MESSAGE, persist = false)
+	private String message = " "; // Placeholder message
+
+	@Parameter(label = "Output directory", style = FileWidget.DIRECTORY_STYLE, required = false)
+	private File outputFolder;
+
+	private FilenameFilter inputFilter;
+	private List<File> fileList;
+	private ModuleInfo moduleInfo;
+
+	@Override
+	public void run() {
+		// Get list of files from input folder
+		if (fileList == null) {
+			directoryCallback();
+		}
+		
+		if (moduleInfo == null) {
+			scriptFileCallback();
+		}
+
+		HashMap<String, Object> inputMap = new HashMap<>();
+		inputMap.put("moduleInfo", moduleInfo);
+		File[] fileArray = fileList.toArray(new File[fileList.size()]);
+		inputMap.put("inputFileList", fileArray);
+		inputMap.put("outputFolder", outputFolder);
+		commands.run(ModuleBatchProcessor.class, true, inputMap);
+	}
+
+	// -- Helper methods --
+
+	private List<File> populateFileList(File folder, FilenameFilter filter, boolean rec) {
+		List<File> list = new ArrayList<>();
+		if (rec) {
+			for (File file : folder.listFiles((FilenameFilter) DirectoryFileFilter.DIRECTORY)) {
+				list.addAll(populateFileList(file, filter, rec));
+			}
+		}
+		for (File file : folder.listFiles(filter)) {
+			list.add(file);
+		}
+		return list;
+	}
+	
+	// -- Callback methods --
+	
+	/**
+	 * Count all applicable files and display them in the dialog message
+	 */
+	protected void directoryCallback() {
+		// get list of all applicable files
+		try {
+			switch (filterChoice) {
+			case WILDCARD:
+				inputFilter = new WildcardFileFilter(pattern);
+				break;
+			case REGEX:
+			default:
+				inputFilter = new RegexFileFilter(pattern);
+			}
+			fileList = populateFileList(inputFolder, inputFilter, recursive);
+		} catch (PatternSyntaxException e) {
+			fileList = null;
+			message = "Syntax error in regex.";
+		}
+		if (fileList != null) {
+			message = "Found " + fileList.size() + " files.";
+		}
+	}
+
+	protected void scriptFileCallback() {
+		if (scriptFile != null) {
+			moduleInfo = scripts.getScript(scriptFile);
+			int nCompatibleInputs = 0;
+			for (ModuleItem<?> input : moduleInfo.inputs()) {
+				if (convert.supports(new File(""), input.getType())) {
+					nCompatibleInputs++;
+				}
+			}
+			scriptMessage = "This script contains " + nCompatibleInputs + " compatible inputs.";
+		}
+	}
+}