A C D E F G H I J L M N O P Q R S T U W

A

accessTextFields() - Method in class net.imagej.patcher.HeadlessGenericDialog

addCheckbox(String, boolean) - Method in class net.imagej.patcher.HeadlessGenericDialog

addCheckboxGroup(int, int, String[], boolean[]) - Method in class net.imagej.patcher.HeadlessGenericDialog

addCheckboxGroup(int, int, String[], boolean[], String[]) - Method in class net.imagej.patcher.HeadlessGenericDialog

addChoice(String, String[], String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addDialogListener(DialogListener) - Method in class net.imagej.patcher.HeadlessGenericDialog

addDirectoryField(String, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addDirectoryField(String, String, int) - Method in class net.imagej.patcher.HeadlessGenericDialog

addEnumChoice(String, Enum<E>) - Method in class net.imagej.patcher.HeadlessGenericDialog

addFileField(String, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addFileField(String, String, int) - Method in class net.imagej.patcher.HeadlessGenericDialog

addHelp(String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addImage(ImagePlus) - Method in class net.imagej.patcher.HeadlessGenericDialog

addImageChoice(String, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addMenuItem(String, String) - Method in class net.imagej.patcher.LegacyHooks

Callback for ImageJ 1.x' menu parsing machinery.

addMessage(String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addMessage(String, Font) - Method in class net.imagej.patcher.HeadlessGenericDialog

addMessage(String, Font, Color) - Method in class net.imagej.patcher.HeadlessGenericDialog

addNumericField(String, double) - Method in class net.imagej.patcher.HeadlessGenericDialog

addNumericField(String, double, int) - Method in class net.imagej.patcher.HeadlessGenericDialog

addNumericField(String, double, int, int, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addPanel(Panel) - Method in class net.imagej.patcher.HeadlessGenericDialog

addPanel(Panel, int, Insets) - Method in class net.imagej.patcher.HeadlessGenericDialog

addPluginClasspath(ClassLoader) - Method in class net.imagej.patcher.LegacyEnvironment

Adds the class path of a given ClassLoader to the plugin class loader.

addPluginClasspath(File...) - Method in class net.imagej.patcher.LegacyEnvironment

Adds extra elements to the class path of ImageJ 1.x' plugin class loader.

addPluginClasspath(File) - Method in class net.imagej.patcher.LegacyHooks

addPluginDirectory(File, String[]) - Method in class net.imagej.patcher.LegacyHooks

Extension point to modify the order in which .jar files are added to the PluginClassLoader.

addPreviewCheckbox(PlugInFilterRunner) - Method in class net.imagej.patcher.HeadlessGenericDialog

addPreviewCheckbox(PlugInFilterRunner, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addRadioButtonGroup(String, String[], int, int, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

Adds a radio button group.

addSlider(String, double, double, double) - Method in class net.imagej.patcher.HeadlessGenericDialog

addSlider(String, double, double, double, double) - Method in class net.imagej.patcher.HeadlessGenericDialog

addStringField(String, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

addStringField(String, String, int) - Method in class net.imagej.patcher.HeadlessGenericDialog

addTextAreas(String, String, int, int) - Method in class net.imagej.patcher.HeadlessGenericDialog

applyPatches() - Method in class net.imagej.patcher.LegacyEnvironment

Applies the configuration patches.

autoGenerateConfigFile(File) - Method in class net.imagej.patcher.LegacyHooks

autoGenerateConfigFile(File, File, String, String, StringBuilder) - Method in class net.imagej.patcher.LegacyHooks

C

centerDialog(boolean) - Method in class net.imagej.patcher.HeadlessGenericDialog

checkboxes - Variable in class net.imagej.patcher.HeadlessGenericDialog

checkboxIndex - Variable in class net.imagej.patcher.HeadlessGenericDialog

choiceIndex - Variable in class net.imagej.patcher.HeadlessGenericDialog

choiceIndices - Variable in class net.imagej.patcher.HeadlessGenericDialog

choices - Variable in class net.imagej.patcher.HeadlessGenericDialog

compare(String, String) - Method in class net.imagej.patcher.LegacyHooks.FatJarNameComparator

createInEditor(String, String) - Method in class net.imagej.patcher.LegacyHooks

Extension point to override ImageJ 1.x' editor.

D

debug(String) - Method in class net.imagej.patcher.LegacyHooks

Logs a debug message (to be shown only in debug mode).

debug - Static variable in class net.imagej.patcher.MemoryProfiler

debug - Static variable in class net.imagej.patcher.PerformanceProfiler

directories - Variable in class net.imagej.patcher.HeadlessGenericDialog

disableIJ1PluginDirs() - Method in class net.imagej.patcher.LegacyEnvironment

Disallows the encapsulated ImageJ 1.x from parsing the directories listed in ij1.plugin.dirs.

disableInitializer() - Method in class net.imagej.patcher.LegacyEnvironment

Disables the execution of the ij1.patcher.initializer.

dispose() - Method in class net.imagej.patcher.HeadlessGenericDialog

dispose() - Method in class net.imagej.patcher.LegacyHooks

Disposes of the hooks.

disposing() - Method in class net.imagej.patcher.LegacyHooks

Allows interception of ImageJ 1.x's disposal routine while quitting.

dontCall(int) - Static method in class net.imagej.patcher.JavaAgent

E

enableIJ1PluginDirs(boolean) - Method in class net.imagej.patcher.LegacyHooks

enableYesNoCancel() - Method in class net.imagej.patcher.HeadlessGenericDialog

enableYesNoCancel(String, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

error(Throwable) - Method in class net.imagej.patcher.EssentialLegacyHooks

error(Throwable) - Method in class net.imagej.patcher.LegacyHooks

Shows an exception.

errorMessage - Variable in class net.imagej.patcher.HeadlessGenericDialog

EssentialLegacyHooks - Class in net.imagej.patcher

The base LegacyHooks to be used in the patched ImageJ 1.x.

EssentialLegacyHooks() - Constructor for class net.imagej.patcher.EssentialLegacyHooks

F

files - Variable in class net.imagej.patcher.HeadlessGenericDialog

finalizeRecording() - Method in class net.imagej.patcher.HeadlessGenericDialog

findClass(String) - Method in class net.imagej.patcher.LegacyClassLoader

focusGained(FocusEvent) - Method in class net.imagej.patcher.HeadlessGenericDialog

focusLost(FocusEvent) - Method in class net.imagej.patcher.HeadlessGenericDialog

G

gc() - Static method in class net.imagej.patcher.MemoryProfiler

get() - Static method in class net.imagej.patcher.MemoryProfiler

getAppName() - Method in class net.imagej.patcher.LegacyHooks

Returns the name to use in place of "ImageJ".

getAppVersion() - Method in class net.imagej.patcher.LegacyHooks

Returns the version to use in place of the legacy version.

getButtons() - Method in class net.imagej.patcher.HeadlessGenericDialog

getCheckboxes() - Method in class net.imagej.patcher.HeadlessGenericDialog

getChoices() - Method in class net.imagej.patcher.HeadlessGenericDialog

getClassLoader() - Method in class net.imagej.patcher.LegacyEnvironment

Gets the class loader containing the ImageJ 1.x classes used in this legacy environment.

getClasspathElements(ClassLoader, StringBuilder, ClassLoader...) - Static method in class net.imagej.patcher.LegacyHooks

Do not use: for internal use only.

getContext() - Method in class net.imagej.patcher.LegacyHooks

Returns the current context, if any.

getErrorMessage() - Method in class net.imagej.patcher.HeadlessGenericDialog

getIconURL() - Method in class net.imagej.patcher.LegacyHooks

Returns the icon to use in place of the ImageJ microscope.

getImageJ1Version(CodeHacker) - Static method in class net.imagej.patcher.LegacyInjector

Determines the ImageJ version without loading the ImageJ classes.

getInsets() - Method in class net.imagej.patcher.HeadlessGenericDialog

getMenuStructure() - Method in class net.imagej.patcher.LegacyEnvironment

Gets the ImageJ 1.x menu structure as a map

getMenuStructure() - Method in class net.imagej.patcher.LegacyHooks

Returns ImageJ 1.x' menu structure as a map.

getMessage() - Method in class net.imagej.patcher.HeadlessGenericDialog

getNanos() - Static method in class net.imagej.patcher.PerformanceProfiler

Gets nanoseconds per thread for relative time measurements

getNanosQnD() - Static method in class net.imagej.patcher.PerformanceProfiler

A much faster, but less accurate version of PerformanceProfiler.getNanos() The problem with this is that it does not measure the current Thread's CPU cycles.

getNextBoolean() - Method in class net.imagej.patcher.HeadlessGenericDialog

getNextChoice() - Method in class net.imagej.patcher.HeadlessGenericDialog

getNextChoiceIndex() - Method in class net.imagej.patcher.HeadlessGenericDialog

getNextEnumChoice(Class<E>) - Method in class net.imagej.patcher.HeadlessGenericDialog

getNextImage() - Method in class net.imagej.patcher.HeadlessGenericDialog

getNextNumber() - Method in class net.imagej.patcher.HeadlessGenericDialog

getNextRadioButton() - Method in class net.imagej.patcher.HeadlessGenericDialog

Returns the selected item in the next radio button group.

getNextString() - Method in class net.imagej.patcher.HeadlessGenericDialog

Returns the contents of the next text field.

getNextText() - Method in class net.imagej.patcher.HeadlessGenericDialog

getNumericFields() - Method in class net.imagej.patcher.HeadlessGenericDialog

getPatchedImageJ1() - Static method in class net.imagej.patcher.LegacyEnvironment

Launches a fully-patched, self-contained ImageJ.

getPreviewCheckbox() - Method in class net.imagej.patcher.HeadlessGenericDialog

getRadioButtonGroups() - Method in class net.imagej.patcher.HeadlessGenericDialog

getResource(String) - Method in class net.imagej.patcher.LegacyClassLoader

getSliders() - Method in class net.imagej.patcher.HeadlessGenericDialog

getStringFields() - Method in class net.imagej.patcher.HeadlessGenericDialog

getTextArea1() - Method in class net.imagej.patcher.HeadlessGenericDialog

getTextArea2() - Method in class net.imagej.patcher.HeadlessGenericDialog

getThreadAncestors() - Method in class net.imagej.patcher.LegacyHooks

Iterates through the current thread's ancestors.

H

handle(CtBehavior) - Method in class net.imagej.patcher.MemoryProfiler

handleExtraPluginJars() - Method in class net.imagej.patcher.LegacyHooks

Extension point to add to ImageJ 1.x' PluginClassLoader's class path.

handleNoSuchMethodError(NoSuchMethodError) - Method in class net.imagej.patcher.LegacyHooks

Extension point to enhance ImageJ 1.x' error reporting upon NoSuchMethodError.

HeadlessGenericDialog - Class in net.imagej.patcher

Rump implementation of a pseudo dialog intended to stand in for the GenericDialog in headless mode.

HeadlessGenericDialog() - Constructor for class net.imagej.patcher.HeadlessGenericDialog

hideCancelButton() - Method in class net.imagej.patcher.HeadlessGenericDialog

I

initialized() - Method in class net.imagej.patcher.EssentialLegacyHooks

initialized() - Method in class net.imagej.patcher.LegacyHooks

First extension point to run just after ImageJ 1.x spun up.

injectHooks(ClassLoader) - Method in class net.imagej.patcher.LegacyInjector

Overrides class behavior of ImageJ classes by injecting method hooks.

injectHooks(ClassLoader, boolean) - Method in class net.imagej.patcher.LegacyInjector

Overrides class behavior of ImageJ1 classes by injecting method hooks.

installed() - Method in class net.imagej.patcher.LegacyHooks

Runs when the hooks are installed into an existing legacy environment.

installHooks(ClassLoader, LegacyHooks) - Static method in class net.imagej.patcher.LegacyInjector

interceptCloseAllWindows() - Method in class net.imagej.patcher.LegacyHooks

Allows closing additional windows at the end of WindowManager.closeAllWindows().

interceptDragAndDropFile(File) - Method in class net.imagej.patcher.LegacyHooks

Optionally override opening drag-and-dropped files via legacy hooks.

interceptFileOpen(String) - Method in class net.imagej.patcher.LegacyHooks

Optionally override opening resources via legacy hooks.

interceptImageWindowClose(Object) - Method in class net.imagej.patcher.LegacyHooks

Hook to ensure ImageWindows are fully cleaned up when they are closed.

interceptKeyPressed(KeyEvent) - Method in class net.imagej.patcher.LegacyHooks

Intercepts keyboard events sent to ImageJ 1.x.

interceptOpen(String, int, boolean) - Method in class net.imagej.patcher.LegacyHooks

Deprecated.

this will be removed before ij1-patcher 1.0.0

interceptOpenImage(String, int) - Method in class net.imagej.patcher.LegacyHooks

Optionally override opening images via legacy hooks.

interceptOpenRecent(String) - Method in class net.imagej.patcher.LegacyHooks

Optionally override opening recent images via legacy hooks.

interceptRunPlugIn(String, String) - Method in class net.imagej.patcher.EssentialLegacyHooks

Intercepts LegacyInitializer's Context creation.

interceptRunPlugIn(String, String) - Method in class net.imagej.patcher.LegacyHooks

Intercepts the call to IJ.runPlugIn(String, String).

invalidNumber - Variable in class net.imagej.patcher.HeadlessGenericDialog

invalidNumber() - Method in class net.imagej.patcher.HeadlessGenericDialog

isActive() - Static method in class net.imagej.patcher.PerformanceProfiler

Reports whether profiling is in progress

isImageJ1Initialized(ClassLoader) - Static method in class net.imagej.patcher.LegacyEnvironment

Determines whether there is already an original ImageJ instance.

isImageJ1VersionAtLeast(CodeHacker, String) - Static method in class net.imagej.patcher.LegacyInjector

isLegacyMode() - Method in class net.imagej.patcher.LegacyHooks

Determines whether the image windows should be displayed or not.

isPreviewActive() - Method in class net.imagej.patcher.HeadlessGenericDialog

J

JavaAgent - Class in net.imagej.patcher

A Java agent to help with legacy issues.

JavaAgent() - Constructor for class net.imagej.patcher.JavaAgent

L

LegacyClassLoader - Class in net.imagej.patcher

A special purpose class loader to encapsulate ImageJ 1.x "instances" from each other.

LegacyClassLoader(boolean) - Constructor for class net.imagej.patcher.LegacyClassLoader

LegacyClassLoader() - Constructor for class net.imagej.patcher.LegacyClassLoader

LegacyEnvironment - Class in net.imagej.patcher

Encapsulates an ImageJ 1.x "instance".

LegacyEnvironment(ClassLoader, boolean) - Constructor for class net.imagej.patcher.LegacyEnvironment

Constructs a new legacy environment.

LegacyHooks - Class in net.imagej.patcher

Extension points for ImageJ 1.x.

LegacyHooks() - Constructor for class net.imagej.patcher.LegacyHooks

LegacyHooks.FatJarNameComparator - Class in net.imagej.patcher

Comparator to ensure that problematic fat JARs are sorted last.

LegacyInjector - Class in net.imagej.patcher

Overrides class behavior of ImageJ classes using bytecode manipulation.

LegacyInjector() - Constructor for class net.imagej.patcher.LegacyInjector

listener - Variable in class net.imagej.patcher.HeadlessGenericDialog

log(String) - Method in class net.imagej.patcher.LegacyHooks

Logs a message.

M

main(String...) - Static method in class net.imagej.patcher.JavaAgent

Writes out a minimal java agent .jar file.

main(String...) - Method in class net.imagej.patcher.LegacyEnvironment

Runs ImageJ.main(args) in the legacy environment.

main(String[]) - Static method in class net.imagej.patcher.MemoryProfiler

main(String...) - Static method in class net.imagej.patcher.PerformanceProfiler

The main method.

MemoryProfiler - Class in net.imagej.patcher

A very simple memory profiler.

MemoryProfiler() - Constructor for class net.imagej.patcher.MemoryProfiler

MemoryProfiler(String) - Constructor for class net.imagej.patcher.MemoryProfiler

MemoryProfiler(Collection<String>) - Constructor for class net.imagej.patcher.MemoryProfiler

missingSubdirs(ClassLoader, boolean) - Static method in class net.imagej.patcher.EssentialLegacyHooks

Intended for sole use with patches in IJ.

N

net.imagej.patcher - package net.imagej.patcher

newImageJ1(boolean) - Method in class net.imagej.patcher.LegacyEnvironment

Initializes a new instance of ij.ImageJ.

newPluginClassLoader(ClassLoader) - Method in class net.imagej.patcher.LegacyHooks

Extension point to run after a new PluginClassLoader was initialized.

noPluginClassLoader() - Method in class net.imagej.patcher.LegacyEnvironment

Forces ImageJ 1.x to use the same ClassLoader for plugins as for ImageJ 1.x itself.

numberfieldIndex - Variable in class net.imagej.patcher.HeadlessGenericDialog

numbers - Variable in class net.imagej.patcher.HeadlessGenericDialog

O

onLoad(ClassPool, String) - Method in class net.imagej.patcher.MemoryProfiler

onLoad(ClassPool, String) - Method in class net.imagej.patcher.PerformanceProfiler

only - Variable in class net.imagej.patcher.MemoryProfiler

openInEditor(String) - Method in class net.imagej.patcher.LegacyHooks

Extension point to override ImageJ 1.x' editor.

P

PerformanceProfiler - Class in net.imagej.patcher

A Javassist-backed performance profiler.

PerformanceProfiler() - Constructor for class net.imagej.patcher.PerformanceProfiler

The constructor.

preinit() - Static method in class net.imagej.patcher.LegacyInjector

preinit(ClassLoader) - Static method in class net.imagej.patcher.LegacyInjector

premain(String, Instrumentation) - Static method in class net.imagej.patcher.JavaAgent

The premain method started at JVM startup.

previewRunning(boolean) - Method in class net.imagej.patcher.HeadlessGenericDialog

Q

quit() - Method in class net.imagej.patcher.LegacyHooks

Allows interception of ImageJ 1.x's ImageJ.quit() method.

R

radioButtonIndex - Variable in class net.imagej.patcher.HeadlessGenericDialog

radioButtons - Variable in class net.imagej.patcher.HeadlessGenericDialog

realReport - Static variable in class net.imagej.patcher.PerformanceProfiler

registerImage(Object) - Method in class net.imagej.patcher.LegacyHooks

Registers an image (possibly not seen before).

report(long) - Static method in class net.imagej.patcher.MemoryProfiler

report(File, int) - Static method in class net.imagej.patcher.PerformanceProfiler

Writes a profile report to a file.

report(PrintStream) - Static method in class net.imagej.patcher.PerformanceProfiler

Writes a report.

report(PrintStream, int) - Static method in class net.imagej.patcher.PerformanceProfiler

Writes a report.

reportCaller(PrintStream, int) - Static method in class net.imagej.patcher.PerformanceProfiler

Reports a caller.

run(String, String) - Method in class net.imagej.patcher.LegacyEnvironment

Runs IJ.run(command, options) in the legacy environment.

runAfterRefreshMenus() - Method in class net.imagej.patcher.LegacyHooks

Extension point to run after Help>Refresh Menus

runMacro(String, String) - Method in class net.imagej.patcher.LegacyEnvironment

Runs IJ.runMacro(macro, arg) in the legacy environment.

runPlugIn(String, String) - Method in class net.imagej.patcher.LegacyEnvironment

Runs IJ.runPlugIn(className, arg) in the legacy environment.

runtime - Static variable in class net.imagej.patcher.MemoryProfiler

S

setActive(boolean) - Static method in class net.imagej.patcher.PerformanceProfiler

Start or stop profiling This method initializes the profiling class loader if necessary.

setDefaultString(int, String) - Method in class net.imagej.patcher.HeadlessGenericDialog

setEchoChar(char) - Method in class net.imagej.patcher.HeadlessGenericDialog

setHelpLabel(String) - Method in class net.imagej.patcher.HeadlessGenericDialog

setInsets(int, int, int) - Method in class net.imagej.patcher.HeadlessGenericDialog

setLocation(int, int) - Method in class net.imagej.patcher.HeadlessGenericDialog

setMacroOptions(String) - Method in class net.imagej.patcher.LegacyEnvironment

Sets the macro options.

setOKLabel(String) - Method in class net.imagej.patcher.HeadlessGenericDialog

setSmartRecording(boolean) - Method in class net.imagej.patcher.HeadlessGenericDialog

setup() - Method in class net.imagej.patcher.HeadlessGenericDialog

show() - Method in class net.imagej.patcher.HeadlessGenericDialog

showDialog() - Method in class net.imagej.patcher.HeadlessGenericDialog

showHelp() - Method in class net.imagej.patcher.HeadlessGenericDialog

showProgress(double) - Method in class net.imagej.patcher.LegacyHooks

Updates the progress bar, where 0 <= progress <= 1.0.

showProgress(int, int) - Method in class net.imagej.patcher.LegacyHooks

Updates the progress bar, where the length of the bar is set to (currentValue + 1) / finalValue of the maximum bar length.

showStatus(String) - Method in class net.imagej.patcher.LegacyHooks

Shows a status message.

start(ClassPool) - Method in class net.imagej.patcher.MemoryProfiler

start(ClassPool) - Method in class net.imagej.patcher.PerformanceProfiler

startProfiling(String, String...) - Static method in class net.imagej.patcher.PerformanceProfiler

Convenience method to call in your main(String[]) method.

stop() - Static method in class net.imagej.patcher.JavaAgent

stringfieldIndex - Variable in class net.imagej.patcher.HeadlessGenericDialog

strings - Variable in class net.imagej.patcher.HeadlessGenericDialog

suppressIJ1ScriptDiscovery() - Method in class net.imagej.patcher.LegacyEnvironment

Disallows ImageJ 1.x from discovering macros and scripts to put into the menu structure.

T

textArea1 - Variable in class net.imagej.patcher.HeadlessGenericDialog

textArea2 - Variable in class net.imagej.patcher.HeadlessGenericDialog

textAreaIndex - Variable in class net.imagej.patcher.HeadlessGenericDialog

transform(ClassLoader, String, Class<?>, ProtectionDomain, byte[]) - Method in class net.imagej.patcher.JavaAgent

U

unregisterImage(Object) - Method in class net.imagej.patcher.LegacyHooks

Releases an image.

W

wasCanceled() - Method in class net.imagej.patcher.HeadlessGenericDialog

wasOKed() - Method in class net.imagej.patcher.HeadlessGenericDialog

writeJar(File, boolean, boolean) - Static method in class net.imagej.patcher.LegacyInjector

Writes a .jar file with the patched classes.

A C D E F G H I J L M N O P Q R S T U W