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A runtime patcher to introduce extension points into the original ImageJ (1.x). This project offers extension points for use with ImageJ2 and it also offers limited support for headless operations.
/*
* #%L
* ImageJ software for multidimensional image processing and analysis.
* %%
* Copyright (C) 2009 - 2016 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 net.imagej.patcher;
import java.awt.event.KeyEvent;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLClassLoader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.jar.Attributes.Name;
import java.util.jar.JarFile;
import java.util.jar.Manifest;
import java.util.regex.Pattern;
/**
* Extension points for ImageJ 1.x.
*
* These extension points will be patched into ImageJ 1.x by the
* {@link CodeHacker}. To override the behavior of ImageJ 1.x, a new instance of
* this class needs to be installed into ij.IJ._hooks.
*
*
* The essential functionality of the hooks is provided in the
* {@link EssentialLegacyHooks} class, which makes an excellent base class for
* project-specific implementations.
*
*
* @author Johannes Schindelin
*/
public abstract class LegacyHooks {
/**
* Determines whether the image windows should be displayed or not.
*
* @return false if ImageJ 1.x should be prevented from opening image windows.
*/
public boolean isLegacyMode() {
return true;
}
/**
* Returns the current context, if any.
*
* For ImageJ2-specific hooks, the returned object will be the current SciJava
* context, or null if the context is not yet initialized.
*
*
* @return the context, or null
*/
public Object getContext() {
return null;
}
/**
* Allows interception of ImageJ 1.x's {@link ij.ImageJ#quit()} method.
*
* @return whether ImageJ 1.x should proceed with its usual quitting routine
*/
public boolean quit() {
return true;
}
/**
* Runs when the hooks are installed into an existing legacy environment.
*/
public void installed() {
// ignore
}
/**
* Disposes of the hooks.
*
* This method is called when ImageJ 1.x is quitting or when new hooks are
* installed.
*
*/
public void dispose() {
// ignore
}
/**
* Intercepts the call to {@link ij.IJ#runPlugIn(String, String)}.
*
* @param className the class name
* @param arg the argument passed to the {@code runPlugIn} method
* @return the object to return, or null to let ImageJ 1.x handle the call
*/
public Object interceptRunPlugIn(final String className, final String arg) {
return null;
}
/**
* Updates the progress bar, where {@code 0 <= progress <= 1.0}.
*
* @param progress between 0.0 and 1.0
*/
public void showProgress(final double progress) {}
/**
* Updates the progress bar, where the length of the bar is set to
* {@code (currentValue + 1) / finalValue} of the maximum bar length. The bar
* is erased if {@code currentValue >= finalValue}.
*
* @param currentIndex the step that was just started
* @param finalIndex the final step.
*/
public void showProgress(final int currentIndex, final int finalIndex) {}
/**
* Shows a status message.
*
* @param status the message
*/
public void showStatus(final String status) {}
/**
* Logs a message.
*
* @param message the message
*/
public void log(final String message) {}
/**
* Registers an image (possibly not seen before).
*
* @param image the new image
*/
public void registerImage(final Object image) {}
/**
* Releases an image.
*
* @param image the image
*/
public void unregisterImage(final Object image) {}
/**
* Logs a debug message (to be shown only in debug mode).
*
* @param string the debug message
*/
public void debug(final String string) {
System.err.println(string);
}
/**
* Shows an exception.
*
* @param t the exception
*/
public void error(final Throwable t) {
// ignore
}
/**
* Returns the name to use in place of "ImageJ".
*
* @return the application name
*/
public String getAppName() {
return "ImageJ";
}
/**
* Returns the version to use in place of the legacy version.
*
* @return the application version, or null if we do not override
*/
public String getAppVersion() {
return null;
}
/**
* Returns the icon to use in place of the ImageJ microscope.
*
* @return the URL to the icon to use, or null
*/
public URL getIconURL() {
return null;
}
/**
* Extension point to override ImageJ 1.x' editor.
*
* @param path the path to the file to open
* @return true if the hook opened a different editor
*/
public boolean openInEditor(final String path) {
return false;
}
/**
* Extension point to override ImageJ 1.x' editor.
*
* @param fileName the name of the new file
* @param content the initial content
* @return true if the hook opened a different editor
*/
public boolean createInEditor(final String fileName, final String content) {
return false;
}
private boolean enableIJ1PluginDirs = true;
protected void enableIJ1PluginDirs(final boolean enable) {
enableIJ1PluginDirs = enable;
}
final private Collection pluginClasspath = new LinkedHashSet();
protected void addPluginClasspath(final File file) {
pluginClasspath.add(file);
}
/**
* Extension point to add to ImageJ 1.x' PluginClassLoader's class path.
*
* @return a list of class path elements to add
*/
public List handleExtraPluginJars() {
final List result = new ArrayList();
result.addAll(pluginClasspath);
if (!enableIJ1PluginDirs) return result;
final String extraPluginDirs = System.getProperty("ij1.plugin.dirs");
if (extraPluginDirs != null) {
for (final String dir : extraPluginDirs.split(File.pathSeparator)) {
final File directory = new File(dir);
if (directory.isDirectory()) {
result.add(directory);
handleExtraPluginJars(directory, result);
}
}
return result;
}
final String userHome = System.getProperty("user.home");
if (userHome != null) {
final File dir = new File(userHome, ".plugins");
if (dir.isDirectory()) {
result.add(dir);
handleExtraPluginJars(dir, result);
}
}
return result;
}
private void handleExtraPluginJars(final File directory,
final List result)
{
final File[] list = directory.listFiles();
if (list == null) return;
for (final File file : list) {
if (file.isDirectory()) handleExtraPluginJars(file, result);
else if (file.isFile() && file.getName().endsWith(".jar")) {
result.add(file);
}
}
}
/**
* Extension point to run after Help>Refresh Menus
*/
public void runAfterRefreshMenus() {
// ignore
}
/**
* Extension point to enhance ImageJ 1.x' error reporting upon
* {@link NoSuchMethodError}.
*
* @param error the exception to handle
* @return true if the error was handled by the legacy hook
*/
public boolean handleNoSuchMethodError(final NoSuchMethodError error) {
String message = error.getMessage();
int paren = message.indexOf("(");
if (paren < 0) return false;
int dot = message.lastIndexOf(".", paren);
if (dot < 0) return false;
String path = message.substring(0, dot).replace('.', '/') + ".class";
Set urls = new LinkedHashSet();
final ClassLoader loader = Thread.currentThread().getContextClassLoader();
try {
Enumeration e = loader.getResources(path);
while (e.hasMoreElements()) {
urls.add(e.nextElement().toString());
}
e = loader.getResources("/" + path);
while (e.hasMoreElements()) {
urls.add(e.nextElement().toString());
}
} catch (Throwable t) {
t.printStackTrace();
return false;
}
if (urls.size() == 0) return false;
StringBuilder buffer = new StringBuilder();
buffer.append("There was a problem with the class ");
buffer.append(message.substring(0, dot));
buffer.append(" which can be found here:\n");
for (String url : urls) {
if (url.startsWith("jar:")) url = url.substring(4);
if (url.startsWith("file:")) url = url.substring(5);
int bang = url.indexOf("!");
if (bang < 0) buffer.append(url);
else buffer.append(url.substring(0, bang));
buffer.append("\n");
}
if (urls.size() > 1) {
buffer.append("\nWARNING: multiple locations found!\n");
}
StringWriter writer = new StringWriter();
error.printStackTrace(new PrintWriter(writer));
buffer.append(writer.toString());
System.out.println(buffer.toString());
final NoSuchMethodException throwable =
new NoSuchMethodException("Could not find method " + message +
"\n" + buffer);
throwable.setStackTrace(error.getStackTrace());
error(throwable);
return true;
}
/**
* Extension point to run after a new PluginClassLoader was initialized.
*
* @param loader the PluginClassLoader instance
*/
public void newPluginClassLoader(final ClassLoader loader) {
// do nothing
}
/**
* Extension point to modify the order in which .jar files are added to the
* PluginClassLoader.
*
* There is a problem which only strikes large distributions of ImageJ such as
* Fiji: some .jar files try to be helpful and bundle classes which are
* actually not theirs, causing problems when newer versions of those .jar
* files which they shadow are present in the plugins/ or jars/
* directory but are not respected by the class loader.
*
*
* The default hook of this extension point therefore hard-codes a few file
* names of known offenders (which we politely will call fat .jar files
* normally) and just pushes them back to the end of the list.
*
*
* @param directory the directory which ImageJ 1.x looked at
* @param names the list of file names in the order ImageJ 1.x discovered them
* @return the ordered, filtered and/or augmented list
*/
public String[]
addPluginDirectory(final File directory, final String[] names)
{
if (names != null) {
/*
Note that this code is replicated in imagej-launcher's ClassLoaderPlus
class. Improvements to this Pattern string should also be mirrored there.
*/
final Pattern pattern =
Pattern.compile("(batik|jython|jython-standalone|jruby)(-[0-9].*)?\\.jar");
Arrays.sort(names, new FatJarNameComparator(pattern));
}
return names;
}
/**
* Comparator to ensure that problematic fat JARs are sorted last.
* It is intended to be used with a {@link Pattern} that filters things this
* way.
*/
public final static class FatJarNameComparator implements Comparator {
private final Pattern pattern;
private FatJarNameComparator(Pattern pattern) {
this.pattern = pattern;
}
@Override
public int compare(final String a, final String b) {
return (pattern.matcher(a).matches() ? 1 : 0) -
(pattern.matcher(b).matches() ? 1 : 0);
}
}
/**
* First extension point to run just after ImageJ 1.x spun up.
*/
public void initialized() {
// do nothing by default
}
public InputStream autoGenerateConfigFile(final File directory) {
// skip unpacked ImageJ 1.x
if (new File(directory, "IJ_Props.txt").exists()) return null;
return new ByteArrayInputStream(autoGenerateConfigFile(directory,
directory, "Plugins", "", new StringBuilder()).toString().getBytes());
}
protected StringBuilder autoGenerateConfigFile(final File topLevelDirectory,
final File directory, final String menuPath, final String packageName,
final StringBuilder builder)
{
final File[] list = directory.listFiles();
if (list == null) return builder;
// make order consistent
Arrays.sort(list);
for (final File file : list) {
String name = file.getName();
if (name.startsWith("_")) continue;
if (file.isDirectory()) {
autoGenerateConfigFile(topLevelDirectory, file, menuPath + ">" +
name.replace('_', ' '), packageName + name + ".", builder);
}
else if (name.endsWith(".class") && name.contains("_") &&
!name.contains("$"))
{
if (topLevelDirectory == directory &&
Character.isLowerCase(name.charAt(0))) continue;
final String className = packageName + name.substring(0, name.length() - 6);
name = name.substring(0, name.length() - 6).replace('_', ' ');
builder.append(menuPath + ", \"" + name + "\", " + className + "\n");
}
}
return builder;
}
private Map menuStructure = new LinkedHashMap();
/**
* Callback for ImageJ 1.x' menu parsing machinery.
*
* This method is called whenever ImageJ 1.x adds a command to the menu structure.
*
*
* @param menuPath the menu path of the menu item, or null when reinitializing
* @param command the command associated with the menu item, or null when reinitializing
*/
public void addMenuItem(final String menuPath, final String command) {
if (menuPath == null) {
menuStructure.clear();
}
else if (menuPath.startsWith("Help>Examples>")) {
// NB: Skip the Help>Examples menu. We do not need it in headless mode.
return;
}
else if (menuPath.endsWith(">-")) {
int i = 1;
while (menuStructure.containsKey(menuPath + i)) {
i++;
}
menuStructure.put(menuPath + i, command);
}
else {
menuStructure.put(menuPath, command);
}
}
/**
* Returns ImageJ 1.x' menu structure as a map.
*
* @return the menu structure
*/
public Map getMenuStructure() {
return Collections.unmodifiableMap(menuStructure);
}
/**
* Optionally override opening resources via legacy hooks.
*
* This is intended as a "HandleExtraFileTypesPlus".
*
*
* @param path the path to the resource to open, or {@code null} if a dialog
* needs to be shown
* @param planeIndex
* If applicable - the index of plane to open or -1 for all planes
* @param display
* if true, the opened object should be displayed before returning
* @return The opened object, or {@code null} to let ImageJ 1.x open the path.
* @deprecated this will be removed before ij1-patcher 1.0.0
*/
@Deprecated
public Object interceptOpen(final String path, final int planeIndex,
final boolean display) {
return null;
}
/**
* Optionally override opening resources via legacy hooks.
*
* This is intended as a "HandleExtraFileTypesPlus".
*
*
* @param path the path to the resource to open, or {@code null} if a dialog
* needs to be shown
* @return The opened object, or {@code null} to let ImageJ 1.x open the resource.
*/
public Object interceptFileOpen(final String path) {
return null;
}
/**
* Optionally override opening images via legacy hooks.
*
* This is intended as a "HandleExtraFileTypesPlus".
*
*
* @param path the path to the image to open, or {@code null} if a dialog
* needs to be shown
* @param planeIndex
* If applicable - the index of plane to open or -1 for all planes
* @return The opened image, or {@code null} to let ImageJ 1.x open the image.
*/
public Object interceptOpenImage(final String path, final int planeIndex) {
return null;
}
/**
* Optionally override opening recent images via legacy hooks.
*
* @param path the path to the recent image to open
* @return The opened object, or {@code null} to let ImageJ 1.x open the image.
*/
public Object interceptOpenRecent(final String path) {
return null;
}
/**
* Optionally override opening drag-and-dropped files via legacy hooks.
*
* @param f the file that was dragged onto the IJ UI
* @return The opened object, or {@code null} to let ImageJ 1.x open the file
* as normal.
*/
public Object interceptDragAndDropFile(final File f) {
return null;
}
/**
* Do not use: for internal use only.
*/
public static Collection getClasspathElements(
final ClassLoader fromClassLoader, final StringBuilder errors,
final ClassLoader... excludeClassLoaders)
{
final Set exclude =
new HashSet(Arrays.asList(excludeClassLoaders));
final List result = new ArrayList();
for (ClassLoader loader = fromClassLoader; loader != null; loader =
loader.getParent()) {
if (exclude.contains(loader)) break;
if (!(loader instanceof URLClassLoader)) {
errors.append("Cannot add class path from ClassLoader of type ")
.append(fromClassLoader.getClass().getName()).append("\n");
continue;
}
for (final URL url : ((URLClassLoader) loader).getURLs()) {
if (!"file".equals(url.getProtocol())) {
errors.append("Not a file URL! ").append(url).append("\n");
continue;
}
result.add(new File(url.getPath()));
final String path = url.getPath();
if (path.matches(".*/target/surefire/surefirebooter[0-9]*\\.jar")) try {
final JarFile jar = new JarFile(path);
final Manifest manifest = jar.getManifest();
if (manifest != null) {
final String classPath =
manifest.getMainAttributes().getValue(Name.CLASS_PATH);
if (classPath != null) {
for (final String element : classPath.split(" +"))
try {
final URL url2 = new URL(element);
if (!"file".equals(url2.getProtocol())) {
errors.append("Not a file URL! ").append(url2).append("\n");
continue;
}
result.add(new File(url2.getPath()));
}
catch (final MalformedURLException e) {
e.printStackTrace();
}
}
}
}
catch (final IOException e) {
System.err
.println("Warning: could not add plugin class path due to ");
e.printStackTrace();
}
}
}
return result;
}
/**
* Intercepts keyboard events sent to ImageJ 1.x.
*
* @param e the keyboard event
* @return whether the event was intercepted
*/
public boolean interceptKeyPressed(final KeyEvent e) {
return false;
}
/**
* Iterates through the current thread's ancestors.
*
* ImageJ 1.x' macro options are thread-local. Unfortunately, this does not
* take into account thread relationships e.g. when threads are spawned in
* parallel.
*
*
* By overriding this method, legacy hooks can force ImageJ 1.x to look harder
* for macro options.
*
*
* @return the ancestor(s) of the current thread, or null
*/
public Iterable getThreadAncestors() {
return null;
}
/**
* Allows closing additional windows at the end of
* {@link ij.WindowManager#closeAllWindows()}.
*
* When returning {@code false}, ImageJ 1.x will be disallowed from quitting.
*
*
* @return whether it is okay to quit
*/
public boolean interceptCloseAllWindows() {
return true;
}
/**
* Hook to ensure {@link ij.gui.ImageWindow}s are fully cleaned up when
* they are closed.
*/
public void interceptImageWindowClose(final Object window) {
// nothing to do
}
/**
* Allows interception of ImageJ 1.x's disposal routine while quitting.
*
* This method is called after it has been confirmed that quitting should
* proceed. That is, the user OKed all the windows being closed, etc.
* This method provides one final chance to cancel the quit operation by
* returning false; otherwise, it performs any needed disposal and cleanup.
*
*
* @return whether ImageJ 1.x should proceed in quitting
* @see ij.ImageJ#run() which is where ImageJ 1.x actually quits
*/
public boolean disposing() {
return true;
}
}