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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.util.HashSet;
import java.util.Set;
/**
* Assorted legacy patches / extension points for use in the legacy mode.
*
*
* The Fiji distribution of ImageJ accumulated patches and extensions to ImageJ
* 1.x over the years.
*
*
*
* However, there was a lot of overlap with the ImageJ2 project, so it was
* decided to focus Fiji more on the life-science specific part and move all the
* parts that are of more general use into ImageJ2. That way, it is pretty
* clear-cut what goes into Fiji and what goes into ImageJ2.
*
*
*
* This class contains the extension points (such as being able to override the
* macro editor) ported from Fiji as well as the code for runtime patching
* ImageJ 1.x needed both for the extension points and for more backwards
* compatibility than ImageJ 1.x wanted to provide (e.g. when public methods or
* classes that were used by Fiji plugins were removed all of a sudden, without
* being deprecated first).
*
*
*
* The code in this class is only used in the legacy mode.
*
*
* @author Johannes Schindelin
*/
class LegacyExtensions {
/*
* Extension points
*/
/*
* Runtime patches (using CodeHacker for patching)
*/
/**
* Applies runtime patches to ImageJ 1.x for backwards-compatibility and extension points.
*
*
* These patches enable a patched ImageJ 1.x to call a different script editor or to override
* the application icon.
*
*
*
* This method is called by {@link LegacyInjector#injectHooks(ClassLoader)}.
*
*
* @param hacker the {@link CodeHacker} instance
*/
public static void injectHooks(final CodeHacker hacker, boolean headless) {
//
// Below are patches to make ImageJ 1.x more backwards-compatible
//
// add back the (deprecated) killProcessor(), and overlay methods
final String[] imagePlusMethods = {
"public void killProcessor()",
"{}",
"public void setDisplayList(java.util.Vector list)",
"getCanvas().setDisplayList(list);",
"public java.util.Vector getDisplayList()",
"return getCanvas().getDisplayList();",
"public void setDisplayList(ij.gui.Roi roi, java.awt.Color strokeColor,"
+ " int strokeWidth, java.awt.Color fillColor)",
"setOverlay(roi, strokeColor, strokeWidth, fillColor);"
};
for (int i = 0; i < imagePlusMethods.length; i++) try {
hacker.insertNewMethod("ij.ImagePlus",
imagePlusMethods[i], imagePlusMethods[++i]);
} catch (Exception e) { /* ignore */ }
// make sure that ImageJ has been initialized in batch mode
hacker.insertAtTopOfMethod("ij.IJ",
"public static java.lang.String runMacro(java.lang.String macro, java.lang.String arg)",
"if (ij==null && ij.Menus.getCommands()==null) init();");
try {
hacker.insertNewMethod("ij.CompositeImage",
"public ij.ImagePlus[] splitChannels(boolean closeAfter)",
"ij.ImagePlus[] result = ij.plugin.ChannelSplitter.split(this);"
+ "if (closeAfter) close();"
+ "return result;");
hacker.insertNewMethod("ij.plugin.filter.RGBStackSplitter",
"public static ij.ImagePlus[] splitChannelsToArray(ij.ImagePlus imp, boolean closeAfter)",
"if (!imp.isComposite()) {"
+ " ij.IJ.error(\"splitChannelsToArray was called on a non-composite image\");"
+ " return null;"
+ "}"
+ "ij.ImagePlus[] result = ij.plugin.ChannelSplitter.split(imp);"
+ "if (closeAfter)"
+ " imp.close();"
+ "return result;");
} catch (IllegalArgumentException e) {
final Throwable cause = e.getCause();
if (cause != null && !cause.getClass().getName().endsWith("DuplicateMemberException")) {
throw e;
}
}
// handle mighty mouse (at least on old Linux, Java mistakes the horizontal wheel for a popup trigger)
for (String fullClass : new String[] {
"ij.gui.ImageCanvas",
"ij.plugin.frame.RoiManager",
"ij.text.TextPanel",
"ij.gui.Toolbar"
}) {
hacker.handleMightyMousePressed(fullClass);
}
// tell IJ#runUserPlugIn to catch NoSuchMethodErrors
final String runUserPlugInSig = "static java.lang.Object runUserPlugIn(java.lang.String commandName, java.lang.String className, java.lang.String arg, boolean createNewLoader)";
hacker.addCatch("ij.IJ", runUserPlugInSig, "java.lang.NoSuchMethodError",
"if (ij.IJ._hooks.handleNoSuchMethodError($e))"
+ " throw new RuntimeException(ij.Macro.MACRO_CANCELED);"
+ "throw $e;");
// tell IJ#runUserPlugIn to be more careful about catching NoClassDefFoundError
hacker.insertPrivateStaticField("ij.IJ", String.class, "originalClassName");
hacker.insertAtTopOfMethod("ij.IJ", runUserPlugInSig, "originalClassName = $2;");
hacker.insertAtTopOfExceptionHandlers("ij.IJ", runUserPlugInSig, "java.lang.NoClassDefFoundError",
"java.lang.String realClassName = $1.getMessage();"
+ "int spaceParen = realClassName.indexOf(\" (\");"
+ "if (spaceParen > 0) realClassName = realClassName.substring(0, spaceParen);"
+ "if (!originalClassName.replace('.', '/').equals(realClassName)) {"
+ " if (realClassName.startsWith(\"javax/vecmath/\") || realClassName.startsWith(\"com/sun/j3d/\") || realClassName.startsWith(\"javax/media/j3d/\"))"
+ " ij.IJ.error(\"The class \" + originalClassName + \" did not find Java3D (\" + realClassName + \")\\nPlease call Plugins>3D Viewer to install\");"
+ " else"
+ " ij.IJ.handleException($1);"
+ " return null;"
+ "}");
// let the plugin class loader find stuff in $HOME/.plugins, too
addExtraPlugins(hacker);
// make sure that the GenericDialog is disposed in macro mode
if (hacker.hasMethod("ij.gui.GenericDialog", "public void showDialog()")) {
hacker.insertAtTopOfMethod("ij.gui.GenericDialog", "public void showDialog()", "if (macro) dispose();");
}
// make sure NonBlockingGenericDialog does not wait in macro mode
hacker.replaceCallInMethod("ij.gui.NonBlockingGenericDialog", "public void showDialog()", "java.lang.Object", "wait", "if (isShowing()) wait();");
// tell the showStatus() method to show the version() instead of empty status
hacker.insertAtTopOfMethod("ij.ImageJ", "void showStatus(java.lang.String s)", "if ($1 == null || \"\".equals($1)) $1 = version();");
// make sure that the GenericDialog does not make a hidden main window visible
if (!headless) {
hacker.replaceCallInMethod("ij.gui.GenericDialog",
"public (java.lang.String title, java.awt.Frame f)",
"java.awt.Dialog", "super",
"$proceed($1 != null && $1.isVisible() ? $1 : null, $2, $3);");
}
// handle custom icon (e.g. for Fiji)
addIconHooks(hacker);
// optionally disallow batch mode from calling System.exit()
hacker.insertPrivateStaticField("ij.ImageJ", Boolean.TYPE, "batchModeMayExit");
hacker.insertAtTopOfMethod("ij.ImageJ", "public static void main(java.lang.String[] args)",
"batchModeMayExit = true;"
+ "for (int i = 0; i < $1.length; i++) {"
+ " if (\"-batch-no-exit\".equals($1[i])) {"
+ " batchModeMayExit = false;"
+ " $1[i] = \"-batch\";"
+ " }"
+ "}");
hacker.replaceCallInMethod("ij.ImageJ", "public static void main(java.lang.String[] args)", "java.lang.System", "exit",
"if (batchModeMayExit) System.exit($1);"
+ "if ($1 == 0) return;"
+ "throw new RuntimeException(\"Exit code: \" + $1);");
// do not use the current directory as IJ home on Windows
String prefsDir = System.getenv("IJ_PREFS_DIR");
if (prefsDir == null && System.getProperty("os.name").startsWith("Windows")) {
prefsDir = System.getenv("user.home");
}
if (prefsDir != null) {
hacker.overrideFieldWrite("ij.Prefs", "public static java.lang.String getPrefsDir()",
"prefsDir", "$_ = \"" + prefsDir + "\";");
}
// tool names can be prefixes of other tools, watch out for that!
hacker.replaceCallInMethod("ij.gui.Toolbar", "public int getToolId(java.lang.String name)", "java.lang.String", "startsWith",
"$_ = $0.equals($1) || $0.startsWith($1 + \"-\") || $0.startsWith($1 + \" -\");");
// make sure Rhino gets the correct class loader
final String javascript = hacker.existsClass("JavaScriptEvaluator") ?
"JavaScriptEvaluator" : "ij.plugin.JavaScriptEvaluator";
hacker.insertAtTopOfMethod(javascript, "public void run()",
"Thread.currentThread().setContextClassLoader(ij.IJ.getClassLoader());");
// make sure that the check for Bio-Formats is correct
hacker.addToClassInitializer("ij.io.Opener",
"try {"
+ " ij.IJ.getClassLoader().loadClass(\"loci.plugins.LociImporter\");"
+ " bioformats = true;"
+ "} catch (ClassNotFoundException e) {"
+ " bioformats = false;"
+ "}");
// make sure that symbolic links are *not* resolved (because then the parent info in the FileInfo would be wrong)
hacker.replaceCallInMethod("ij.plugin.DragAndDrop", "public void openFile(java.io.File f)", "java.io.File", "getCanonicalPath",
"$_ = $0.getAbsolutePath();");
// make sure no dialog is opened in headless mode
hacker.insertAtTopOfMethod("ij.macro.Interpreter", "void showError(java.lang.String title, java.lang.String msg, java.lang.String[] variables)",
"if (ij.IJ.getInstance() == null) {"
+ " java.lang.System.err.println($1 + \": \" + $2);"
+ " return;"
+ "}");
// let IJ.handleException override the macro interpreter's call()'s exception handling
hacker.insertAtTopOfExceptionHandlers("ij.macro.Functions", "java.lang.String call()", "java.lang.reflect.InvocationTargetException",
"ij.IJ.handleException($1);"
+ "return null;");
// Add back the "Convert to 8-bit Grayscale" checkbox to Import>Image Sequence
if (!hacker.hasField("ij.plugin.FolderOpener", "convertToGrayscale")) {
hacker.insertPrivateStaticField("ij.plugin.FolderOpener", Boolean.TYPE, "convertToGrayscale");
hacker.replaceCallInMethod("ij.plugin.FolderOpener", "public void run(java.lang.String arg)", "ij.io.Opener", "openImage",
"$_ = $0.openImage($1, $2);"
+ "if (convertToGrayscale) {"
+ " final String saved = ij.Macro.getOptions();"
+ " ij.IJ.run($_, \"8-bit\", \"\");"
+ " if (saved != null && !saved.equals(\"\")) ij.Macro.setOptions(saved);"
+ "}");
hacker.replaceCallInMethod("ij.plugin.FolderOpener", "boolean showDialog(ij.ImagePlus imp, java.lang.String[] list)",
"ij.plugin.FolderOpener$FolderOpenerDialog", "addCheckbox",
"$0.addCheckbox(\"Convert to 8-bit Grayscale\", convertToGrayscale);"
+ "$0.addCheckbox($1, $2);", 1);
hacker.replaceCallInMethod("ij.plugin.FolderOpener", "boolean showDialog(ij.ImagePlus imp, java.lang.String[] list)",
"ij.plugin.FolderOpener$FolderOpenerDialog", "getNextBoolean",
"convertToGrayscale = $0.getNextBoolean();"
+ "$_ = $0.getNextBoolean();"
+ "if (convertToGrayscale && $_) {"
+ " ij.IJ.error(\"Cannot convert to grayscale and RGB at the same time.\");"
+ " return false;"
+ "}", 1);
}
// handle HTTPS in addition to HTTP
hacker.handleHTTPS("ij.macro.Functions", "java.lang.String exec()");
hacker.handleHTTPS("ij.plugin.DragAndDrop", "public void drop(java.awt.dnd.DropTargetDropEvent dtde)");
hacker.handleHTTPS("ij.plugin.ListVirtualStack", "public void run(java.lang.String arg)");
hacker.handleHTTPS("ij.plugin.ListVirtualStack", "java.lang.String[] open(java.lang.String path)");
addEditorExtensionPoints(hacker);
overrideAppVersion(hacker);
insertAppNameHooks(hacker);
insertRefreshMenusHook(hacker);
overrideStartupMacrosForFiji(hacker);
handleMacAdapter(hacker);
handleMenuCallbacks(hacker, headless);
installOpenInterceptor(hacker);
handleMacroGetOptions(hacker);
interceptCloseAllWindows(hacker);
interceptImageWindowClose(hacker);
interceptDisposal(hacker);
}
// -- methods to install additional hooks into ImageJ 1.x --
/**
* Install a hook to optionally run a Runnable at the end of Help>Refresh Menus.
*
*
* See {@link LegacyHooks#runAfterRefreshMenus()}.
*
*
* @param hacker the {@link CodeHacker} to use for patching
*/
private static void insertRefreshMenusHook(CodeHacker hacker) {
hacker.insertAtBottomOfMethod("ij.Menus", "public static void updateImageJMenus()",
"ij.IJ._hooks.runAfterRefreshMenus();");
}
private static void addEditorExtensionPoints(final CodeHacker hacker) {
hacker.insertAtTopOfMethod("ij.io.Opener", "public void open(java.lang.String path)",
"if (isText($1) && ij.IJ._hooks.openInEditor($1)) return;");
hacker.dontReturnOnNull("ij.plugin.frame.Recorder", "void createMacro()");
hacker.replaceCallInMethod("ij.plugin.frame.Recorder", "void createMacro()",
"ij.IJ", "runPlugIn",
"$_ = null;");
hacker.replaceCallInMethod("ij.plugin.frame.Recorder", "void createMacro()",
"ij.plugin.frame.Editor", "createMacro",
"if ($1.endsWith(\".txt\")) {"
+ " $1 = $1.substring($1.length() - 3) + \"ijm\";"
+ "}"
+ "if (!ij.IJ._hooks.createInEditor($1, $2)) {"
+ " ((ij.plugin.frame.Editor)ij.IJ.runPlugIn(\"ij.plugin.frame.Editor\", \"\")).createMacro($1, $2);"
+ "}");
hacker.insertPublicStaticField("ij.plugin.frame.Recorder", String.class, "nameForEditor", null);
hacker.insertAtTopOfMethod("ij.plugin.frame.Recorder", "void createPlugin(java.lang.String text, java.lang.String name)",
"this.nameForEditor = $2;");
hacker.replaceCallInMethod("ij.plugin.frame.Recorder", "void createPlugin(java.lang.String text, java.lang.String name)",
"ij.IJ", "runPlugIn",
"$_ = null;"
+ "new ij.plugin.NewPlugin().createPlugin(this.nameForEditor, ij.plugin.NewPlugin.PLUGIN, $2);"
+ "return;");
hacker.replaceCallInMethod("ij.plugin.NewPlugin", "public void createMacro(java.lang.String name)",
"ij.plugin.frame.Editor", "",
"$_ = null;");
hacker.replaceCallInMethod("ij.plugin.NewPlugin", "public void createMacro(java.lang.String name)",
"ij.plugin.frame.Editor", "create",
"if ($1.endsWith(\".txt\")) {"
+ " $1 = $1.substring(0, $1.length() - 3) + \"ijm\";"
+ "}"
+ "if ($1.endsWith(\".ijm\") && ij.IJ._hooks.createInEditor($1, $2)) return;"
+ "int options = (monospaced ? ij.plugin.frame.Editor.MONOSPACED : 0)"
+ " | (menuBar ? ij.plugin.frame.Editor.MENU_BAR : 0);"
+ "new ij.plugin.frame.Editor(rows, columns, 0, options).create($1, $2);");
hacker.dontReturnOnNull("ij.plugin.NewPlugin", "public void createPlugin(java.lang.String name, int type, java.lang.String methods)");
hacker.replaceCallInMethod("ij.plugin.NewPlugin", "public void createPlugin(java.lang.String name, int type, java.lang.String methods)",
"ij.IJ", "runPlugIn",
"$_ = null;");
hacker.replaceCallInMethod("ij.plugin.NewPlugin", "public void createPlugin(java.lang.String name, int type, java.lang.String methods)",
"ij.plugin.frame.Editor", "create",
"if (!ij.IJ._hooks.createInEditor($1, $2)) {"
+ " ((ij.plugin.frame.Editor)ij.IJ.runPlugIn(\"ij.plugin.frame.Editor\", \"\")).create($1, $2);"
+ "}");
hacker.replaceCallInMethod("ij.plugin.Compiler",
"void edit()",
"ij.IJ", "runPlugIn",
"if (ij.IJ._hooks.openInEditor(dir + name)) $_ = null;" +
"else $_ = $proceed($$);");
// hacker.hasMethod check for private void showCode(String title, String code) then replace in there otherwise keep the existing code
String methodSig;
if (hacker.hasMethod("ij.gui.Toolbar", "private void showCode(java.lang.String title, java.lang.String code)")) {
methodSig = "private void showCode(java.lang.String title, java.lang.String code)";
} else {
methodSig = "public void itemStateChanged(java.awt.event.ItemEvent e)";
}
hacker.replaceCallInMethod("ij.gui.Toolbar",
methodSig,
"ij.plugin.frame.Editor", "create",
"if ($1.endsWith(\".txt\")) $1 = $1.substring(0, $1.length() - 4);" +
"$1 += \".ijm\";" +
"if (!ij.IJ._hooks.createInEditor($1, $2)) $_ = $proceed($$);");
hacker.replaceCallInMethod("ij.plugin.CommandFinder",
"private boolean showMacro(java.lang.String cmd)",
"ij.plugin.frame.Editor", "create",
"if ($1.endsWith(\".txt\")) $1 = $1.substring(0, $1.length() - 4);" +
"$1 += \".ijm\";" +
"if (!ij.IJ._hooks.createInEditor($1, $2)) $_ = $proceed($$);");
}
private static void overrideAppVersion(final CodeHacker hacker) {
hacker.insertAtBottomOfMethod("ij.ImageJ",
"public java.lang.String version()",
"String version = ij.IJ._hooks.getAppVersion();" +
"if (version != null) {" +
" $_ = $_.replace(VERSION, version);" +
"}");
// Of course there is not a *single* way to obtain the version.
// That would have been too easy, wouldn't it?
hacker.insertAtTopOfMethod("ij.IJ",
"public static String getVersion()",
"String version = ij.IJ._hooks.getAppVersion();" +
"if (version != null) return version;");
}
/**
* Inserts hooks to replace the application name.
*/
private static void insertAppNameHooks(final CodeHacker hacker) {
final String appName = "ij.IJ._hooks.getAppName()";
final String replace = ".replace(\"ImageJ\", " + appName + ")";
hacker.insertAtTopOfMethod("ij.IJ", "public void error(java.lang.String title, java.lang.String msg)",
"if ($1 == null || $1.equals(\"ImageJ\")) $1 = " + appName + ";");
hacker.insertAtBottomOfMethod("ij.ImageJ", "public java.lang.String version()", "$_ = $_" + replace + ";");
hacker.replaceAppNameInCall("ij.ImageJ", "public (java.applet.Applet applet, int mode)", "super", 1, appName);
hacker.replaceAppNameInNew("ij.ImageJ", "public void run()", "ij.gui.GenericDialog", 1, appName);
hacker.replaceAppNameInCall("ij.ImageJ", "public void run()", "addMessage", 1, appName);
if (hacker.hasMethod("ij.plugin.CommandFinder", "public void export()")) {
hacker.replaceAppNameInNew("ij.plugin.CommandFinder", "public void export()", "ij.text.TextWindow", 1, appName);
}
hacker.replaceAppNameInCall("ij.plugin.Hotkeys", "public void removeHotkey()", "addMessage", 1, appName);
hacker.replaceAppNameInCall("ij.plugin.Hotkeys", "public void removeHotkey()", "showStatus", 1, appName);
if (hacker.existsClass("ij.plugin.AppearanceOptions")) {
hacker.replaceAppNameInCall("ij.plugin.AppearanceOptions", "void showDialog()", "showMessage", 2, appName);
} else {
hacker.replaceAppNameInCall("ij.plugin.Options", "public void appearance()", "showMessage", 2, appName);
}
if (hacker.hasMethod("ij.gui.YesNoCancelDialog", "public (java.awt.Frame parent, java.lang.String title, java.lang.String msg, java.lang.String yesLabel, java.lang.String noLabel)")) {
hacker.replaceAppNameInCall("ij.gui.YesNoCancelDialog", "public (java.awt.Frame parent, java.lang.String title, java.lang.String msg, java.lang.String yesLabel, java.lang.String noLabel)", "super", 2, appName);
} else {
hacker.replaceAppNameInCall("ij.gui.YesNoCancelDialog", "public (java.awt.Frame parent, java.lang.String title, java.lang.String msg)", "super", 2, appName);
}
hacker.replaceAppNameInCall("ij.gui.Toolbar", "private void showMessage(int toolId)", "showStatus", 1, appName);
}
private static void addIconHooks(final CodeHacker hacker) {
final String icon = "ij.IJ._hooks.getIconURL()";
hacker.replaceCallInMethod("ij.ImageJ", "void setIcon()", "java.lang.Class", "getResource",
"java.net.URL _iconURL = " + icon + ";\n" +
"if (_iconURL == null) $_ = $0.getResource($1);" +
"else $_ = _iconURL;");
hacker.insertAtTopOfMethod("ij.ImageJ", "public (java.applet.Applet applet, int mode)",
"if ($2 != 2 /* ij.ImageJ.NO_SHOW */) setIcon();");
hacker.insertAtTopOfMethod("ij.WindowManager", "public void addWindow(java.awt.Frame window)",
"java.net.URL _iconURL = " + icon + ";\n"
+ "if (_iconURL != null && $1 != null) {"
+ " java.awt.Image img = $1.createImage((java.awt.image.ImageProducer)_iconURL.getContent());"
+ " if (img != null) {"
+ " $1.setIconImage(img);"
+ " }"
+ "}");
}
/**
* Makes sure that the legacy plugin class loader finds stuff in
* {@code $HOME/.plugins/}.
*/
private static void addExtraPlugins(final CodeHacker hacker) {
for (final String methodName : new String[] { "addJAR", "addJar" }) {
if (hacker.hasMethod("ij.io.PluginClassLoader", "private void "
+ methodName + "(java.io.File file)")) {
hacker.insertAtTopOfMethod("ij.io.PluginClassLoader",
"void init(java.lang.String path)",
extraPluginJarsHandler("if (file.isDirectory()) addDirectory(file);" +
"else " + methodName + "(file);"));
}
}
// avoid parsing ij.jar for plugins
hacker.replaceCallInMethod("ij.Menus",
"InputStream autoGenerateConfigFile(java.lang.String jar)",
"java.util.zip.ZipEntry", "getName",
"$_ = $proceed($$);" +
"if (\"IJ_Props.txt\".equals($_)) return null;");
// make sure that extra directories added to the plugin class path work, too
hacker.insertAtTopOfMethod("ij.Menus",
"InputStream getConfigurationFile(java.lang.String jar)",
"java.io.File isDir = new java.io.File($1);" +
"if (!isDir.exists()) return null;" +
"if (isDir.isDirectory()) {" +
" java.io.File config = new java.io.File(isDir, \"plugins.config\");" +
" if (config.exists()) return new java.io.FileInputStream(config);" +
" return ij.IJ._hooks.autoGenerateConfigFile(isDir);" +
"}");
// fix overzealous assumption that all plugins are in plugins.dir
hacker.insertPrivateStaticField("ij.Menus", Set.class, "_extraJars");
hacker.insertAtTopOfMethod("ij.Menus",
"java.lang.String getSubmenuName(java.lang.String jarPath)",
"if (_extraJars.contains($1)) return null;");
// make sure that .jar files are iterated in alphabetical order
hacker.replaceCallInMethod("ij.Menus",
"public static synchronized java.lang.String[] getPlugins()",
"java.io.File", "list",
"$_ = $proceed($$);"
+ "if ($_ != null) java.util.Arrays.sort($_);");
// add the extra .jar files to the list of plugin .jar files to be processed.
hacker.insertAtBottomOfMethod("ij.Menus",
"public static synchronized java.lang.String[] getPlugins()",
"if (_extraJars == null) _extraJars = new java.util.HashSet();" +
extraPluginJarsHandler("if (jarFiles == null) jarFiles = new java.util.Vector();" +
"jarFiles.addElement(file.getAbsolutePath());" +
"_extraJars.add(file.getAbsolutePath());"));
// exclude -sources.jar entries generated by Maven.
hacker.insertAtBottomOfMethod("ij.Menus",
"public static synchronized java.lang.String[] getPlugins()",
"if (jarFiles != null) {" +
" for (int i = jarFiles.size() - 1; i >= 0; i--) {" +
" String entry = (String) jarFiles.elementAt(i);" +
" if (entry.endsWith(\"-sources.jar\")) {" +
" jarFiles.remove(i);" +
" }" +
" }" +
"}");
// force IJ.getClassLoader() to instantiate a PluginClassLoader
hacker.replaceCallInMethod(
"ij.IJ",
"public static ClassLoader getClassLoader()",
"java.lang.System",
"getProperty",
"$_ = System.getProperty($1);\n"
+ "if ($_ == null && $1.equals(\"plugins.dir\")) $_ = \"/non-existant/\";");
}
private static String extraPluginJarsHandler(final String code) {
return "for (java.util.Iterator iter = ij.IJ._hooks.handleExtraPluginJars().iterator();\n" +
"iter.hasNext(); ) {\n" +
"\tjava.io.File file = (java.io.File)iter.next();\n" +
code + "\n" +
"}\n";
}
private static void overrideStartupMacrosForFiji(CodeHacker hacker) {
hacker.replaceCallInMethod("ij.Menus", "void installStartupMacroSet()", "java.io.File", "",
"if ($1.endsWith(\"StartupMacros.txt\")) {" +
" java.lang.String fijiPath = $1.substring(0, $1.length() - 3) + \"fiji.ijm\";" +
" java.io.File fijiFile = new java.io.File(fijiPath);" +
" $_ = fijiFile.exists() ? fijiFile : new java.io.File($1);" +
"} else $_ = new java.io.File($1);");
if (hacker.hasMethod("ij.plugin.MacroInstaller", "public void installStartupMacros(java.lang.String path)")) {
hacker.replaceCallInMethod("ij.plugin.MacroInstaller", "public void installStartupMacros(java.lang.String path)", "ij.plugin.MacroInstaller", "installFile",
"if ($1.endsWith(\"StartupMacros.txt\")) {" +
" java.lang.String fijiPath = $1.substring(0, $1.length() - 3) + \"fiji.ijm\";" +
" java.io.File fijiFile = new java.io.File(fijiPath);" +
" $0.installFile(fijiFile.exists() ? fijiFile.getPath() : $1);" +
"} else $0.installFile($1);");
} else {
hacker.replaceCallInMethod("ij.Menus", "void installStartupMacroSet()", "ij.plugin.MacroInstaller", "installFile",
"if ($1.endsWith(\"StartupMacros.txt\")) {" +
" java.lang.String fijiPath = $1.substring(0, $1.length() - 3) + \"fiji.ijm\";" +
" java.io.File fijiFile = new java.io.File(fijiPath);" +
" $0.installFile(fijiFile.exists() ? fijiFile.getPath() : $1);" +
"} else $0.installFile($1);");
}
}
private static void handleMacAdapter(final CodeHacker hacker) {
// Without the ApplicationListener, MacAdapter cannot load, and hence CodeHacker would fail
// to load it if we patched the class.
if (!hacker.existsClass("com.apple.eawt.ApplicationListener")) return;
hacker.insertAtTopOfMethod("MacAdapter", "public void run(java.lang.String arg)",
"return;");
}
private static void handleMenuCallbacks(final CodeHacker hacker, boolean headless) {
hacker.insertAtTopOfMethod("ij.Menus",
"java.lang.String addMenuBar()",
"ij.IJ._hooks.addMenuItem(null, null);");
hacker.insertPrivateStaticField("ij.Menus", String.class, "_currentMenuPath");
// so that addSubMenu() has the correct menu path -- even in headless mode
hacker.insertAtTopOfMethod("ij.Menus",
"private static java.awt.Menu getMenu(java.lang.String menuName, boolean readFromProps)",
"_currentMenuPath = $1;");
// so that addPlugInItem() has the correct menu path -- even in headless mode
hacker.insertAtBottomOfMethod("ij.Menus",
"private static java.awt.Menu getMenu(java.lang.String menuName, boolean readFromProps)",
"_currentMenuPath = $1;");
hacker.insertAtTopOfMethod("ij.Menus",
"static java.awt.Menu addSubMenu(java.awt.Menu menu, java.lang.String name)",
"_currentMenuPath += \">\" + $2.replace('_', ' ');");
hacker.replaceCallInMethod("ij.Menus",
"void addPluginsMenu()",
"ij.Menus",
"addPluginItem",
"_currentMenuPath = \"Plugins\";" +
"$_ = $proceed($$);");
hacker.replaceCallInMethod("ij.Menus",
"void addPluginsMenu()",
"ij.Menus",
"addSubMenu",
"_currentMenuPath = \"Plugins\";" +
"$_ = $proceed($$);");
hacker.replaceCallInMethod("ij.Menus",
"java.lang.String addMenuBar()",
"ij.Menus",
"addPlugInItem",
"if (\"Quit\".equals($2) || \"Open...\".equals($2) || \"Close\".equals($2) || \"Revert\".equals($2))" +
" _currentMenuPath = \"File\";" +
"else if(\"Show Info...\".equals($2) || \"Crop\".equals($2))" +
" _currentMenuPath = \"Image\";" +
"else if (\"Image Calculator...\".equals($2))" +
" _currentMenuPath = \"Process\";" +
"else if (\"About ImageJ...\".equals($2) || \"Update ImageJ...\".equals($2))" +
" _currentMenuPath = \"Help\";" +
"else if (\"Open as Panel\".equals($2))" +
" _currentMenuPath = \"Help>Examples\";" +
"else if ($3.startsWith(\"ij.plugin.SimpleCommands(\\\"showdir\"))" +
" _currentMenuPath = \"File>Show Folder\";" +
"$_ = $proceed($$);");
// Wow. There are so many different ways ImageJ 1.x adds menu entries. See e.g. "Repeat Command".
hacker.replaceCallInMethod("ij.Menus",
"java.lang.String addMenuBar()",
"ij.Menus",
"addItem",
"ij.IJ._hooks.addMenuItem(_currentMenuPath + \">\" + $2, null);" +
"$_ = $proceed($$);");
hacker.insertPrivateStaticField("ij.Menus",
HashSet.class, "_separators");
hacker.insertAtTopOfMethod("ij.Menus",
"void installJarPlugin(java.lang.String jar, java.lang.String s)",
" if (_separators == null) _separators = new java.util.HashSet();" +
"_currentMenuPath = \"Plugins\";");
hacker.replaceCallInMethod("ij.Menus",
"void installJarPlugin(java.lang.String jar, java.lang.String s)",
"java.lang.String", "substring",
"$_ = $proceed($$);" +
"ij.IJ._hooks.addMenuItem(_currentMenuPath, $_);",
4);
hacker.insertAtTopOfMethod("ij.Menus",
"void addPlugInItem(java.awt.Menu menu, java.lang.String label, java.lang.String className, int shortcut, boolean shift)",
"ij.IJ._hooks.addMenuItem(_currentMenuPath + \">\" + $2, $3);");
hacker.insertAtTopOfMethod("ij.Menus",
"static void addPluginItem(java.awt.Menu submenu, java.lang.String s)",
"int comma = $2.lastIndexOf(',');" +
"if (comma > 0) {" +
" java.lang.String label = $2.substring(1, comma - 1);" +
" if (label.endsWith(\"]\")) {" +
" int open = label.indexOf(\"[\");" +
" if (open > 0 && label.substring(open + 1, comma - 3).matches(\"[A-Za-z0-9]\"))" +
" label = label.substring(0, open);" +
" }" +
" while (comma + 2 < $2.length() && $2.charAt(comma + 1) == ' ')" +
" comma++;" +
" if (mbar == null && _separators != null) {" +
" if (!_separators.contains(_currentMenuPath)) {" +
" _separators.add(_currentMenuPath);" +
" ij.IJ._hooks.addMenuItem(_currentMenuPath + \">-\", null);" +
" }" +
" }" +
" ij.IJ._hooks.addMenuItem(_currentMenuPath + \">\" + label," +
" $2.substring(comma + 1));" +
"}");
hacker.insertAtTopOfMethod("ij.Menus",
"java.awt.CheckboxMenuItem addCheckboxItem(java.awt.Menu menu, java.lang.String label, java.lang.String className)",
"ij.IJ._hooks.addMenuItem(_currentMenuPath + \">\" + $2, $3);");
// handle separators (we cannot simply look for java.awt.Menu#addSeparator
// because we might be running in headless mode)
hacker.replaceCallInMethod("ij.Menus",
"java.lang.String addMenuBar()",
"ij.Menus",
"addPlugInItem",
"if (\"Cache Sample Images \".equals($2))" +
" ij.IJ._hooks.addMenuItem(\"File>Open Samples>-\", null);" +
"else if (\"Close\".equals($2) || \"Page Setup...\".equals($2) || \"Cut\".equals($2) ||" +
" \"Clear\".equals($2) || \"Crop\".equals($2) || \"Set Scale...\".equals($2) ||" +
" \"Dev. Resources...\".equals($2) || \"Update ImageJ...\".equals($2) ||" +
" \"Quit\".equals($2)) {" +
" int separator = _currentMenuPath.indexOf('>');" +
" if (separator < 0) separator = _currentMenuPath.length();" +
" ij.IJ._hooks.addMenuItem(_currentMenuPath.substring(0, separator) + \">-\", null);" +
"}" +
"$_ = $proceed($$);" +
"if (\"Tile\".equals($2))" +
" ij.IJ._hooks.addMenuItem(\"Window>-\", null);");
hacker.replaceCallInMethod("ij.Menus",
"java.lang.String addMenuBar()",
"ij.Menus",
"addCheckboxItem",
"if (\"RGB Stack\".equals($2))" +
" ij.IJ._hooks.addMenuItem(_currentMenuPath + \">-\", null);" +
"$_ = $proceed($$);");
hacker.replaceCallInMethod("ij.Menus",
"java.lang.String addMenuBar()",
"ij.Menus",
"getMenu",
"if (\"Edit>Selection\".equals($1) || \"Image>Adjust\".equals($1) || \"Image>Lookup Tables\".equals($1) ||" +
" \"Process>Batch\".equals($1) || \"Help>About Plugins\".equals($1)) {" +
" int separator = $1.indexOf('>');" +
" ij.IJ._hooks.addMenuItem($1.substring(0, separator) + \">-\", null);" +
"}" +
"$_ = $proceed($$);");
hacker.replaceCallInMethod("ij.Menus",
"static java.awt.Menu addSubMenu(java.awt.Menu menu, java.lang.String name)",
"java.lang.String",
"equals",
"$_ = $proceed($$);" +
"if ($_ && \"-\".equals($1))" +
" ij.IJ._hooks.addMenuItem(_currentMenuPath + \">-\", null);");
hacker.replaceCallInMethod("ij.Menus",
"static void addLuts(java.awt.Menu submenu)",
"ij.IJ",
"isLinux",
"ij.IJ._hooks.addMenuItem(_currentMenuPath + \">-\", null);" +
"$_ = $proceed($$);");
hacker.replaceCallInMethod("ij.Menus",
"void addPluginsMenu()",
"ij.Prefs",
"getString",
"$_ = $proceed($$);" +
"if ($_ != null && $_.startsWith(\"-\"))" +
" ij.IJ._hooks.addMenuItem(\"Plugins>-\", null);");
hacker.insertAtTopOfMethod("ij.Menus",
"static void addSeparator(java.awt.Menu menu)",
"ij.IJ._hooks.addMenuItem(_currentMenuPath + \">-\", null);");
hacker.replaceCallInMethod("ij.Menus", "void installPlugins()",
"ij.Prefs", "getString",
"$_ = $proceed($$);" +
"if ($_ != null && $_.length() > 0) {" +
" String className = $_.substring($_.lastIndexOf(',') + 1);" +
" if (!className.startsWith(\"ij.\")) _currentMenuPath = null;" +
" else {" +
" char c = $_.charAt(0);" +
" if (c == IMPORT_MENU) _currentMenuPath = \"File>Import\";" +
" else if (c == SAVE_AS_MENU) _currentMenuPath = \"File>Save As\";" +
" else if (c == SHORTCUTS_MENU) _currentMenuPath = \"Plugins>Shortcuts\";" +
" else if (c == ABOUT_MENU) _currentMenuPath = \"Help>About Plugins\";" +
" else if (c == FILTERS_MENU) _currentMenuPath = \"Process>Filters\";" +
" else if (c == TOOLS_MENU) _currentMenuPath = \"Analyze>Tools\";" +
" else if (c == UTILITIES_MENU) _currentMenuPath = \"Plugins>Utilities\";" +
" else _currentMenuPath = \"Plugins\";" +
" }" +
"}");
if (headless) {
hacker.replaceCallInMethod("ij.Menus", "void installPlugins()",
"java.lang.String", "substring",
"$_ = $proceed($$);" +
"if (_currentMenuPath != null) addPluginItem((java.awt.Menu) null, $_);", 2);
}
}
private static void installOpenInterceptor(CodeHacker hacker) {
// Intercept ij.IJ open methods
// If the open method is intercepted, the hooks.interceptOpen method needs
// to perform any necessary display operations
hacker.insertAtTopOfMethod("ij.IJ",
"public static void open(java.lang.String path)",
"Object result = ij.IJ._hooks.interceptFileOpen($1);" +
"if (result != null) {" +
"if (result instanceof java.lang.String) path = (java.lang.String)result;" +
"else return;" +
"}");
// If openImage is intercepted, we return the opened ImagePlus without displaying it
hacker.insertAtTopOfMethod("ij.IJ",
"public static ij.ImagePlus openImage(java.lang.String path)",
"Object result = ij.IJ._hooks.interceptOpenImage($1, -1);" +
"if (result != null) {" +
"if (result instanceof ij.ImagePlus) return (ij.ImagePlus)result;" +
"else if (result instanceof java.lang.String) path = (java.lang.String)result;" +
"else return null; " +
"}");
hacker.insertAtTopOfMethod("ij.IJ",
"public static ij.ImagePlus openImage(java.lang.String path, int sliceIndex)",
"Object result = ij.IJ._hooks.interceptOpenImage($1, $2);" +
"if (result != null) {" +
"if (result instanceof ij.ImagePlus) return (ij.ImagePlus)result;" +
"else if (result instanceof java.lang.String) path = (java.lang.String)result;" +
"else return null; " +
"}");
hacker.replaceCallInMethod("ij.plugin.FolderOpener", "public void run(java.lang.String arg)", "ij.io.Opener", "openImage",
"Object result = ij.IJ._hooks.interceptOpenImage($1 + $2, -1);" +
"if (result != null && result instanceof ij.ImagePlus) {" +
" $_ = (ij.ImagePlus)result;" +
"} else {" +
" $_ = $proceed($$);" +
"}");
// Intercept File > Open Recent
hacker.replaceCallInMethod("ij.RecentOpener", "public void run()",
"ij.io.Opener", "open",
"Object result = ij.IJ._hooks.interceptOpenRecent(path);" +
"if (result == null) o.open(path);" +
"else if (! (result instanceof ij.ImagePlus)) return;");
// Intercept DragAndDrop openings
hacker.insertAtTopOfMethod("ij.plugin.DragAndDrop",
"public void openFile(java.io.File f)",
"Object result = ij.IJ._hooks.interceptDragAndDropFile($1);" +
"if (result != null && !(result instanceof java.lang.String)) {" +
" return;" +
"}");
// Make sure that .lut files are not intercepted
hacker.replaceCallInMethod("ij.Executer",
"public static boolean loadLut(java.lang.String name)",
"ij.IJ", "open",
"ij.ImagePlus imp = (ij.ImagePlus) ij.IJ.runPlugIn(\"ij.plugin.LutLoader\", $1);" +
"if (imp != null && imp.getWidth() > 0) {" +
" imp.show();" +
"}");
}
private static void handleMacroGetOptions(CodeHacker hacker) {
// remove that pesky, pesky Run$_ restriction
hacker.replaceCallInMethod("ij.Macro", "public static java.lang.String getOptions()",
"java.lang.String", "startsWith",
"$_ = \"Run$_\".equals($1) ? true : $proceed($$);");
// look at more threads than just the current one, if the legacy hooks have some for us
hacker.replaceCallInMethod("ij.Macro", "public static java.lang.String getOptions()",
"java.util.Hashtable", "get",
"$_ = $proceed($$);" +
"if ($_ == null) {" +
" java.lang.Iterable ancestors = ij.IJ._hooks.getThreadAncestors();" +
" if (ancestors != null) {" +
" for (java.util.Iterator iter = ancestors.iterator(); $_ == null && iter.hasNext(); ) {" +
" $_ = $proceed(iter.next());" +
" }" +
" }" +
"}");
}
private static void interceptCloseAllWindows(final CodeHacker hacker) {
hacker.insertAtBottomOfMethod("ij.WindowManager",
"public synchronized static boolean closeAllWindows()",
"if ($_ == true) {" +
" $_ = ij.IJ._hooks.interceptCloseAllWindows();" +
"}");
}
private static void interceptImageWindowClose(final CodeHacker hacker) {
// Ensure that even if an ImageWindow is closed during quitting, it is
// still disposed.
hacker.replaceCallInMethod("ij.gui.ImageWindow",
"public boolean close()",
"ij.WindowManager",
"removeWindow",
"ij.IJ._hooks.interceptImageWindowClose(this);" +
"ij.WindowManager.removeWindow((java.awt.Frame)this);");
}
private static void interceptDisposal(final CodeHacker hacker) {
hacker.replaceCallInMethod("ij.ImageJ", "public void run()", "ij.IJ",
"cleanup",
"if (!ij.IJ._hooks.disposing()) {" +
" quitting = false;" +
" return;" +
"}" +
"$_ = $proceed($$);");
}
// -- methods to configure LegacyEnvironment instances --
static void noPluginClassLoader(final CodeHacker hacker) {
hacker.insertPrivateStaticField("ij.IJ", ClassLoader.class, "_classLoader");
final String initClassLoader =
"_classLoader = Thread.currentThread().getContextClassLoader();";
hacker.insertAtTopOfMethod("ij.IJ",
"static void init()",
initClassLoader);
hacker.insertAtTopOfMethod("ij.IJ",
"static void init(ij.ImageJ imagej, java.applet.Applet theApplet)",
initClassLoader);
// Make sure that bare .class files in plugins/ and subdirectories are seen by ImageJ 1.x.
// This needs to be done *after* Menus made sure that IJ.getDirectory("plugins") returns non-null
final String supportBarePlugins =
"java.lang.ClassLoader loader = " + LegacyInjector.ESSENTIAL_LEGACY_HOOKS_CLASS +
" .missingSubdirs(_classLoader, true);" +
"if (loader != null) {" +
" Thread.currentThread().setContextClassLoader(loader);" +
" _classLoader = loader;" +
"}";
hacker.insertAtBottomOfMethod("ij.IJ",
"static void init()",
supportBarePlugins);
hacker.insertAtBottomOfMethod("ij.IJ",
"static void init(ij.ImageJ imagej, java.applet.Applet theApplet)",
supportBarePlugins);
hacker.insertAtTopOfMethod("ij.IJ",
"public static ClassLoader getClassLoader()",
"if (_classLoader == null) {" +
initClassLoader +
supportBarePlugins +
"}" +
"return _classLoader;");
disableRefreshMenus(hacker);
// make sure that IJ#runUserPlugIn can execute package-less plugins in subdirectories of $IJ/plugin/
final String runUserPlugInSig = "static java.lang.Object runUserPlugIn(java.lang.String commandName, java.lang.String className, java.lang.String arg, boolean createNewLoader)";
hacker.insertAtTopOfExceptionHandlers("ij.IJ", runUserPlugInSig, "java.lang.NoClassDefFoundError",
"java.lang.ClassLoader loader = " + LegacyInjector.ESSENTIAL_LEGACY_HOOKS_CLASS +
" .missingSubdirs(getClassLoader(), false);" +
"if (loader != null) _classLoader = loader;");
hacker.replaceCallInMethod("ij.IJ", runUserPlugInSig,
"java.lang.ClassLoader", "loadClass",
"try {" +
" $_ = $proceed($$);" +
"} catch (java.lang.ClassNotFoundException e) {" +
" java.lang.ClassLoader loader = " + LegacyInjector.ESSENTIAL_LEGACY_HOOKS_CLASS +
" .missingSubdirs(getClassLoader(), true);" +
" if (loader == null) {" +
" throw e;" +
" } else {" +
" _classLoader = loader;" +
" $_ = loader.loadClass($1);" +
" }" +
"}");
}
static void disableRefreshMenus(final CodeHacker hacker) {
hacker.insertAtTopOfMethod("ij.IJ",
"static void setClassLoader(java.lang.ClassLoader loader)",
"ij.IJ.showMessage(\"NOTICE: Please restart ImageJ to complete plugin or macro installation, add " +
"new commands to the menus, etc...\");" +
"return;");
}
static void suppressIJ1ScriptDiscovery(CodeHacker hacker) {
hacker.insertAtTopOfMethod("ij.Menus",
"private static boolean validMacroName(java.lang.String name, boolean hasUnderscore)",
"return false;");
}
}