A B C D E F G H I J K L M N O P R S T U V W Z

A

aboutMyRoutines() - Method in class bar.gui.GuiUtils

actionPerformed(ActionEvent) - Method in class bar.plugin.Commander

actionPerformed(ActionEvent) - Method in class bar.plugin.SnippetCreator

ALIASES - Static variable in interface bar.BAR.GCD

B

bar - package bar

BAR - Class in bar

BAR() - Constructor for class bar.BAR

BAR.GCD - Interface in bar

bar.gui - package bar.gui

bar.plugin - package bar.plugin

BARService - Class in bar

BARService() - Constructor for class bar.BARService

browseMyRoutines() - Method in class bar.gui.GuiUtils

bshHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a BSH snippet (BeanShell).

BUILD_DATE - Static variable in class bar.Utils

A reference to the build date

BUILD_YEAR - Static variable in class bar.Utils

A reference to the build year

C

changedUpdate(DocumentEvent) - Method in class bar.plugin.Commander

CLEAN_EXIT - Variable in class bar.Installer

cljHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a CLJ snippet (Clojure).

Commander - Class in bar.plugin

Implements a light-weight and fast keyboard-based file browser for ImageJ (BAR>BAR Commander... command).

Commander() - Constructor for class bar.plugin.Commander

Commander(String) - Constructor for class bar.plugin.Commander

D

DATA_FLAVOR - Static variable in class bar.FileDrop.TransferableObject

The default DataFlavor for FileDrop.TransferableObject has the representation class net.iharder.dnd.TransferableObject.class and the MIME type application/x-net.iharder.dnd.TransferableObject.

DefaultGCD - Class in bar

DefaultGCD() - Constructor for class bar.DefaultGCD

dialogItemChanged(GenericDialog, AWTEvent) - Method in class bar.plugin.ShenCastan

Reads dialog parameters (during preview and upon dismissal of dialog prompt).

dialogItemChanged(GenericDialog, AWTEvent) - Method in class bar.plugin.SnippetCreator

E

ERROR - Variable in class bar.Installer

Event(File[], Object) - Constructor for class bar.FileDrop.Event

Constructs an FileDrop.Event with the array of files that were dropped and the FileDrop that initiated the event.

exportChartAsPDF(JFreeChart, Rectangle, File) - Static method in class bar.PlotUtils

Exports the specified JFreeChart to a PDF file using iText, bundled with Fiji.

exportChartAsPDF(JFreeChart, Rectangle) - Static method in class bar.PlotUtils

Exports the specified JFreeChart to a PDF file using iText, assumed to be installed as third party-library in the ImageJ jars directory (iText is bundled with Fiji).

exportChartAsSVG(JFreeChart, Rectangle, File) - Static method in class bar.PlotUtils

Exports a JFreeChart to a SVG file using the Batik SVG Toolkit, bundled with Fiji.

exportChartAsSVG(JFreeChart, Rectangle) - Static method in class bar.PlotUtils

Exports the specified JFreeChart to a SVG file using the Batik SVG Toolkit, , assumed to be installed as third party-library in the ImageJ jars directory (Batik is bundled with Fiji).

F

FileDrop - Class in bar

This class makes it easy to drag and drop files from the operating system to a Java program.

FileDrop(Component, FileDrop.Listener) - Constructor for class bar.FileDrop

Constructs a FileDrop with a default light-blue border and, if c is a Container, recursively sets all elements contained within as drop targets, though only the top level container will change borders.

FileDrop(Component, boolean, FileDrop.Listener) - Constructor for class bar.FileDrop

Constructor with a default border and the option to recursively set drop targets.

FileDrop(PrintStream, Component, FileDrop.Listener) - Constructor for class bar.FileDrop

Constructor with a default border and debugging optionally turned on.

FileDrop(PrintStream, Component, boolean, FileDrop.Listener) - Constructor for class bar.FileDrop

Constructor with a default border, debugging optionally turned on and the option to recursively set drop targets.

FileDrop(Component, Border, FileDrop.Listener) - Constructor for class bar.FileDrop

Constructor with a specified border

FileDrop(Component, Border, boolean, FileDrop.Listener) - Constructor for class bar.FileDrop

Constructor with a specified border and the option to recursively set drop targets.

FileDrop(PrintStream, Component, Border, FileDrop.Listener) - Constructor for class bar.FileDrop

Constructor with a specified border and debugging optionally turned on.

FileDrop(PrintStream, Component, Border, boolean, FileDrop.Listener) - Constructor for class bar.FileDrop

Full constructor with a specified border and debugging optionally turned on.

FileDrop.Event - Class in bar

This is the event that is passed to the filesDropped(...) method in your FileDrop.Listener when files are dropped onto a registered drop target.

FileDrop.Listener - Interface in bar

Implement this inner interface to listen for when files are dropped.

FileDrop.TransferableObject - Class in bar

At last an easy way to encapsulate your custom objects for dragging and dropping in your Java programs! When you need to create a Transferable object, use this class to wrap your object.

FileDrop.TransferableObject.Fetcher - Interface in bar

Instead of passing your data directly to the FileDrop.TransferableObject constructor, you may want to know exactly when your data was received in case you need to remove it from its source (or do anyting else to it).

fileExists(File) - Static method in class bar.Utils

Tests whether a file or directory exists.

fileExists(String) - Static method in class bar.Utils

Tests whether a file or directory exists at the specified path.

filesDropped(File[]) - Method in interface bar.FileDrop.Listener

This method is called when files have been successfully dropped.

findEdges(ImageProcessor, double) - Method in class bar.plugin.ShenCastan

Method implementing Shen-Castan edge detection.

G

gcd(Object...) - Method in class bar.BAR

gcd(double, double) - Method in class bar.BAR

generateGaussianData() - Static method in class bar.Utils

Returns a ResultsTable containing Gaussian ("normally") distributed values without displaying it.

getBARDir() - Static method in class bar.Utils

Returns the path to the root directory of BAR.

getBARresource(String) - Static method in class bar.Utils

getClipboardText() - Static method in class bar.Utils

Retrieves text from the system clipboard.

getCustomDataFlavor() - Method in class bar.FileDrop.TransferableObject

Returns the custom DataFlavor associated with the encapsulated object or null if the FileDrop.TransferableObject.Fetcher constructor was used without passing a Class.

getDocURL() - Static method in class bar.Utils

Returns the URL of BAR's documentation page.

getFileCount(String) - Method in class bar.gui.GuiUtils

getFiles() - Method in class bar.FileDrop.Event

Returns an array of files that were dropped on a registered drop target.

getJavadocURL() - Static method in class bar.Utils

Returns the URL of BAR's API.

getLastLoadedResource() - Method in class bar.Runner

getLibDir() - Static method in class bar.Utils

Returns the path to BAR/lib/.

getMyRoutinesCount() - Method in class bar.gui.GuiUtils

getMyRoutinesDir() - Static method in class bar.Utils

Returns the path to BAR/My_Routines/, creating it .

getName() - Method in class bar.BAR

getObject() - Method in interface bar.FileDrop.TransferableObject.Fetcher

Return the object being encapsulated in the FileDrop.TransferableObject.

getPluginsBasedBARDir() - Static method in class bar.Utils

The absolute path to the legacy /BAR directory on the "plugins" folder.

getResultsTable() - Static method in class bar.Utils

Returns a reference to the default IJ Results table.

getSnippetsDir() - Static method in class bar.Utils

Deprecated.

getSourceURL() - Static method in class bar.Utils

Returns the URL of BAR's Git repository.

getStatus() - Method in class bar.Runner

getTable() - Static method in class bar.Utils

Variant of Utils.getTable(boolean, WindowListener) that ignores WindowListeners.

getTable(String) - Static method in class bar.Utils

Returns the ResultsTable associated with the specified TextWindow.

getTable(boolean, WindowListener) - Static method in class bar.Utils

Prompts the user for tabular data, retrieved from several sources including 1) Importing a new text/csv file; 2) Trying to import data from the system clipboard; 3) Importing a demo dataset populated by random (Gaussian) values; 4) the ResultsTable of any TextWindow or a PlotWindow currently being displayed in ImageJ.

getTable(Component, boolean, boolean, WindowListener) - Static method in class bar.Utils

getTransferData(DataFlavor) - Method in class bar.FileDrop.TransferableObject

Returns the data encapsulated in this FileDrop.TransferableObject.

getTransferDataFlavors() - Method in class bar.FileDrop.TransferableObject

Returns a two- or three-element array containing first the custom data flavor, if one was created in the constructors, second the default FileDrop.TransferableObject.DATA_FLAVOR associated with FileDrop.TransferableObject, and third the DataFlavor.stringFlavor.

getX() - Method in class bar.plugin.ShenCastan

Returns the horizontal component of the computed gradient.

getY() - Method in class bar.plugin.ShenCastan

Returns the vertical component of the computed gradient.

grvHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a GRV snippet (Groovy).

GuiUtils - Class in bar.gui

GuiUtils(UIService) - Constructor for class bar.gui.GuiUtils

GuiUtils() - Constructor for class bar.gui.GuiUtils

IJ1 constructor

H

Help - Class in bar.plugin

Implements the About BAR... command

Help() - Constructor for class bar.plugin.Help

I

ijmHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a IJM snippet (IJ1 macro).

initialize() - Method in class bar.BARService

insertUpdate(DocumentEvent) - Method in class bar.plugin.Commander

Installer - Class in bar

Installs lib files in the user's local installation

Installer() - Constructor for class bar.Installer

installIJ1Macro(String) - Method in class bar.Runner

installIJ1Macro(String, boolean) - Method in class bar.Runner

installLib() - Method in class bar.Installer

installLib(boolean) - Method in class bar.Installer

InteractivePlotter - Class in bar.plugin

Interactively creates a multi-series plot (XY with or without error bars, and vector fields) from existing ImageJ tables and plots, the system clipboard or imported spreadsheet data.

InteractivePlotter() - Constructor for class bar.plugin.InteractivePlotter

isDataFlavorSupported(DataFlavor) - Method in class bar.FileDrop.TransferableObject

Returns true if flavor is one of the supported flavors.

isEmptyMyRoutines() - Method in class bar.gui.GuiUtils

isSilent() - Method in class bar.Runner

return true if the LogService is not logging errors.

J

jsHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a JS snippet (JavaScript).

K

keyPressed(KeyEvent) - Method in class bar.plugin.Commander

keyReleased(KeyEvent) - Method in class bar.plugin.Commander

keyTyped(KeyEvent) - Method in class bar.plugin.Commander

L

listDirectory(String, int, int) - Static method in class bar.Utils

Prints the contents of a directory to a dedicated TextWindow displayed at the specified location.

listDirectory(String) - Static method in class bar.Utils

Prints the contents of a directory to a dedicated TextWindow displayed on the center of the screen.

listDirectory(String, boolean) - Static method in class bar.Utils

Prints the contents of a directory to a dedicated TextWindow allowed to be displayed with a slight offset from frontmost window.

listMyRoutines() - Method in class bar.gui.GuiUtils

M

main(String...) - Static method in class bar.gui.GuiUtils

main(String...) - Static method in class bar.Installer

main(String...) - Static method in class bar.plugin.Commander

main(String...) - Static method in class bar.plugin.Help

main(String[]) - Static method in class bar.plugin.InteractivePlotter

main(String...) - Static method in class bar.plugin.MDReader

main(String[]) - Static method in class bar.plugin.ShenCastan

Calls fiji.Debug.runFilter() so that the plugin can be debugged from an IDE

main(String...) - Static method in class bar.plugin.Tutorials

main(String...) - Static method in class bar.Runner

Debug method

MDReader - Class in bar.plugin

Renders GitHub README.md files as HTML files that once JARified are used as offline documentation of BAR)

MDReader() - Constructor for class bar.plugin.MDReader

MIME_TYPE - Static variable in class bar.FileDrop.TransferableObject

The MIME type for FileDrop.TransferableObject.DATA_FLAVOR is application/x-net.iharder.dnd.TransferableObject.

mouseClicked(MouseEvent) - Method in class bar.plugin.Commander

mouseEntered(MouseEvent) - Method in class bar.plugin.Commander

mouseExited(MouseEvent) - Method in class bar.plugin.Commander

mousePressed(MouseEvent) - Method in class bar.plugin.Commander

mouseReleased(MouseEvent) - Method in class bar.plugin.Commander

N

NAME - Static variable in interface bar.BAR.GCD

nnHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a snippet of unknown language

O

openAndDisplayTable(String, String, WindowListener, boolean) - Static method in class bar.Utils

Opens a tab or comma delimited text file.

openAndDisplayTable(String, String, WindowListener) - Static method in class bar.Utils

Opens a tab or comma delimited text file.

openIJ1Script(String, String) - Static method in class bar.Utils

Opens the specified file in the ImageJ1 built-in editor.

openIJ2Script(File) - Static method in class bar.Utils

Opens the specified file in the ImageJ2 Script Editor.

openLastLoadedResource() - Method in class bar.Runner

openLib(String) - Static method in class bar.Utils

Opens the specified file in the "lib" directory of BAR.

openREADME(String) - Method in class bar.plugin.MDReader

openScript(String, String) - Static method in class bar.Utils

Alias for Utils.openIJ2Script(File)

openSnippet(String) - Static method in class bar.Utils

Opens the specified file in the "My Routines" directory of BAR.

optionsMenu - Variable in class bar.plugin.InteractivePlotter

P

PlotUtils - Class in bar

Provides utility methods that improve ImageJ's plotting capabilities.

PlotUtils() - Constructor for class bar.PlotUtils

pyHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a PY snippet (Python).

R

rbHeader() - Static method in class bar.plugin.SnippetCreator

Returns the header for a RB snippet (Ruby).

readContents(String) - Method in class bar.Runner

readContents(URL, boolean) - Method in class bar.Runner

remove(Component) - Static method in class bar.FileDrop

Removes the drag-and-drop hooks from the component and optionally from the all children.

remove(PrintStream, Component, boolean) - Static method in class bar.FileDrop

Removes the drag-and-drop hooks from the component and optionally from the all children.

removeUpdate(DocumentEvent) - Method in class bar.plugin.Commander

revealFile(String) - Static method in class bar.Utils

"Reveals" the file associated with the specified file path in the operating system.

revealFile(File) - Static method in class bar.Utils

"Reveals" the specified file path in the operating system.

revealMyRoutines() - Method in class bar.gui.GuiUtils

run() - Method in class bar.DefaultGCD

run() - Method in class bar.Installer

run() - Method in class bar.plugin.Commander

run() - Method in class bar.plugin.Help

run(String) - Method in class bar.plugin.InteractivePlotter

run() - Method in class bar.plugin.MDReader

run(ImageProcessor) - Method in class bar.plugin.ShenCastan

run(String) - Method in class bar.plugin.SnippetCreator

This method is called when the plugin is loaded.

run() - Method in class bar.plugin.Tutorials

run(String) - Method in class bar.Utils

runBARMacro(String, String) - Method in class bar.Runner

Legacy method that supports IJ1 macros that do not use script parameters.

runIJ1Macro(String, String) - Method in class bar.Runner

Legacy method that supports IJ1 macros that do not use script parameters.

Runner - Class in bar

Runs a JARified script

Runner(Context) - Constructor for class bar.Runner

Default constructor-based dependency injection

Runner(boolean) - Constructor for class bar.Runner

Constructor relying on IJ1.

runScript(InputStream, String) - Method in class bar.Runner

Runs a script from an InputStream.

runScript(String) - Method in class bar.Runner

Runs a (JARified) BAR script.

runScript(String, Map<String, Object>) - Method in class bar.Runner

Runs a (JARified) BAR script.

runScript(String, String, Map<String, Object>) - Method in class bar.Runner

Runs a (JARified) BAR script.

runScript(String, String) - Method in class bar.Runner

Runs a (JARified) BAR script.

runScript(InputStream, String, Map<String, Object>) - Method in class bar.Runner

Runs a script from a jar file.

S

scriptLoaded() - Method in class bar.Runner

Assesses if last script was loaded successfully

setNPasses(int) - Method in class bar.plugin.ShenCastan

setSilent(Boolean) - Method in class bar.Runner

Should LogService display errors?

setup(String, ImagePlus) - Method in class bar.plugin.ShenCastan

Returns the flags declaring the type of supported images.

ShenCastan - Class in bar.plugin

Performs gradient computation using the method proposed by Shen and Castan, an alternative to Canny-Deriche filtering.

ShenCastan() - Constructor for class bar.plugin.ShenCastan

shiftClickWarning() - Static method in class bar.Utils

Displays a status-bar warning on "open by Shift-click" being disabled for pre-compiled plugins.

showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class bar.plugin.ShenCastan

Displays the dialog prompt.

SnippetCreator - Class in bar.plugin

Generates templates for new IJ scripts, implementing the BAR> Utilities> New Routine... command.

SnippetCreator() - Constructor for class bar.plugin.SnippetCreator

T

TransferableObject(Object) - Constructor for class bar.FileDrop.TransferableObject

Creates a new FileDrop.TransferableObject that wraps data.

TransferableObject(FileDrop.TransferableObject.Fetcher) - Constructor for class bar.FileDrop.TransferableObject

Creates a new FileDrop.TransferableObject that will return the object that is returned by fetcher.

TransferableObject(Class<?>, FileDrop.TransferableObject.Fetcher) - Constructor for class bar.FileDrop.TransferableObject

Creates a new FileDrop.TransferableObject that will return the object that is returned by fetcher.

Tutorials - Class in bar.plugin

Loads a new instance of the Script editor with jarified tutorial files

Tutorials() - Constructor for class bar.plugin.Tutorials

U

UNINITIALIZED - Variable in class bar.Installer

Utils - Class in bar

A collection of utilities to interact with BAR, including scripting aids for ImageJ.

Utils() - Constructor for class bar.Utils

V

valueChanged(ListSelectionEvent) - Method in class bar.plugin.Commander

VERSION - Static variable in class bar.Utils

The BAR version

W

windowActivated(WindowEvent) - Method in class bar.plugin.Commander

windowClosed(WindowEvent) - Method in class bar.plugin.Commander

windowClosing(WindowEvent) - Method in class bar.plugin.Commander

windowDeactivated(WindowEvent) - Method in class bar.plugin.Commander

windowDeiconified(WindowEvent) - Method in class bar.plugin.Commander

windowIconified(WindowEvent) - Method in class bar.plugin.Commander

windowOpened(WindowEvent) - Method in class bar.plugin.Commander

Z

zapCompiledFiles(File) - Static method in class bar.Utils

Removes $py.class, .class, .pyc and .pyo files from the specified directory.

zapCompiledLibs() - Static method in class bar.Utils

Removes $py.class, .class, .pyc and .pyo files from the "lib" directory of BAR.

A B C D E F G H I J K L M N O P R S T U V W Z