Index (ImageJ API)

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A

ABGR - Static variable in class ij.io.FileInfo: 32-bit interleaved ABGR.
abort() - Static method in class ij.Macro: Aborts the currently running macro or any plugin using IJ.run().
abort() - Static method in class ij.macro.Interpreter: Aborts currently running macro.
abort() - Method in class ij.measure.Minimizer: Aborts minimization.
abort(Interpreter) - Static method in class ij.macro.Interpreter: Absolete, replaced by abortMacro().
abort(String) - Method in class ij.macro.Interpreter
ABORTED - Static variable in class ij.measure.Minimizer: Status returned: aborted by call to abort method.
abortMacro() - Method in class ij.macro.Interpreter: Aborts this macro.
abortModification(ImagePlus) - Method in class ij.gui.Roi: Aborts constructing or modifying the roi (called by the ImageJ class on escape)
abortPaste() - Method in class ij.gui.Roi
ABOUT_MENU - Static variable in class ij.Menus
AboutBox - Class in ij.plugin: This plugin implements the Help/About ImageJ command by opening about.jpg in ij.jar, scaling it 600% and adding text to an overlay.
AboutBox() - Constructor for class ij.plugin.AboutBox
abs() - Method in class ij.process.FloatProcessor
abs() - Method in class ij.process.ImageProcessor: If this is a 32-bit or signed 16-bit image, performs an absolute value transform, otherwise does nothing.
abs() - Method in class ij.process.ShortProcessor
ABS - Static variable in interface ij.macro.MacroConstants
accept(File, String) - Method in class ij.plugin.Compiler
ACOS - Static variable in interface ij.macro.MacroConstants
actionPerformed(ActionEvent) - Method in class ij.gui.GenericDialog
actionPerformed(ActionEvent) - Method in class ij.gui.HistogramWindow
actionPerformed(ActionEvent) - Method in class ij.gui.HTMLDialog
actionPerformed(ActionEvent) - Method in class ij.gui.MessageDialog
actionPerformed(ActionEvent) - Method in class ij.gui.NonBlockingGenericDialog
actionPerformed(ActionEvent) - Method in class ij.gui.PlotWindow: Called if user has activated a button or popup menu item
actionPerformed(ActionEvent) - Method in class ij.gui.SaveChangesDialog
actionPerformed(ActionEvent) - Method in class ij.gui.StackWindow
actionPerformed(ActionEvent) - Method in class ij.gui.Toolbar
actionPerformed(ActionEvent) - Method in class ij.gui.WaitForUserDialog
actionPerformed(ActionEvent) - Method in class ij.gui.YesNoCancelDialog
actionPerformed(ActionEvent) - Method in class ij.ImageJ: Handle menu events.
actionPerformed(ActionEvent) - Method in class ij.macro.FunctionFinder
actionPerformed(ActionEvent) - Method in class ij.measure.ResultsTableMacros
actionPerformed(ActionEvent) - Method in class ij.plugin.BatchConverter
actionPerformed(ActionEvent) - Method in class ij.plugin.BatchProcessor
actionPerformed(ActionEvent) - Method in class ij.plugin.CommandFinder
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Calibrator
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Convolver
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Channels
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ColorThresholder
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Commands
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ContrastAdjuster
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Editor
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Fitter
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Recorder
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.RoiManager
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.SyncWindows: Implementation of ActionListener interface.
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
actionPerformed(ActionEvent) - Method in class ij.plugin.LUT_Editor
actionPerformed(ActionEvent) - Method in class ij.plugin.MacroInstaller
actionPerformed(ActionEvent) - Method in class ij.plugin.Orthogonal_Views
actionPerformed(ActionEvent) - Method in class ij.text.TextPanel
actionPerformed(ActionEvent) - Method in class ij.text.TextWindow
activateImage(ImagePlus) - Static method in class ij.macro.Interpreter
add(double) - Method in class ij.process.FloatProcessor
add(double) - Method in class ij.process.ImageProcessor: Adds 'value' to each pixel in the image or ROI.
add(double) - Method in class ij.process.ShortProcessor
add(float) - Method in class ij.util.FloatArray: Appends the specified value to the end of this FloatArray.
add(float[], int) - Method in class ij.util.FloatArray: Appends the first n values from the specified array to this FloatArray.
add(int) - Method in class ij.process.FloatProcessor
add(int) - Method in class ij.process.ImageProcessor: Adds 'value' to each pixel in the image or ROI.
add(int) - Method in class ij.process.ShortProcessor
add(Roi) - Method in class ij.gui.Overlay: Adds an ROI to this Overlay.
add(Roi, int) - Method in class ij.plugin.frame.RoiManager: Adds the specified ROI to the list.
add(Roi, String) - Method in class ij.gui.Overlay: Adds an ROI to this Overlay using the specified name.
add(ImagePlus, Roi, int) - Method in class ij.plugin.frame.RoiManager: Adds the specified ROI to the list.
add(ImageProcessor, double) - Method in class ij.plugin.filter.SaltAndPepper
add(Component) - Method in class ij.gui.ImageWindow
add(String, double[]) - Method in class ij.gui.Plot: Adds a curve, set of points or error bars to this plot, where 'type' is "line", "connected circle", "filled", "bar", "separated bar", "circle", "box", "triangle", "diamond", "cross", "x", "dot", "error bars" or "xerror bars".
add(String, double[], double[]) - Method in class ij.gui.Plot: Adds a curve or set of points to this plot, where 'type' is "line", "connected circle", "filled", "bar", "separated bar", "circle", "box", "triangle", "diamond", "cross", "x" or "dot".
add(String, String) - Static method in class ij.Menus: Adds a command to the ImageJ menu bar.
ADD - Static variable in interface ij.process.Blitter: dst=dst+src
ADD_FIT - Static variable in class ij.gui.PlotContentsDialog: Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_FROM_ARRAYS - Static variable in class ij.gui.PlotContentsDialog: Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_FROM_PLOT - Static variable in class ij.gui.PlotContentsDialog: Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_FROM_TABLE - Static variable in class ij.gui.PlotContentsDialog: Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
ADD_TO_MANAGER - Static variable in class ij.plugin.filter.ParticleAnalyzer: Add particles to ROI Manager.
ADD_TO_OVERLAY - Static variable in interface ij.measure.Measurements
addAdjustmentListener(AdjustmentListener) - Method in class ij.gui.ScrollbarWithLabel
addBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
addButton(String, ActionListener) - Method in class ij.gui.GenericDialog: Add button to the dialog
addChar(char) - Method in class ij.gui.TextRoi: This method is used by the text tool to add typed characters to displayed text selections.
addCheckbox(String, boolean) - Method in class ij.gui.GenericDialog: Adds a checkbox.
addCheckboxGroup(int, int, String[], boolean[]) - Method in class ij.gui.GenericDialog: Adds a group of checkboxs using a grid layout.
addCheckboxGroup(int, int, String[], boolean[], String[]) - Method in class ij.gui.GenericDialog: Adds a group of checkboxs using a grid layout.
addChoice(String, String[], String) - Method in class ij.gui.GenericDialog: Adds a popup menu.
addColumns() - Method in class ij.measure.ResultsTable: Obsolete; the addValue() method automatically adds columns as needed.
addCommandListener(CommandListener) - Static method in class ij.Executer: Adds the specified command listener.
addDialogListener(DialogListener) - Method in class ij.gui.GenericDialog: Add an Object implementing the DialogListener interface.
addDirectoryField(String, String) - Method in class ij.gui.GenericDialog: Adds a directory text field and "Browse" button, where the field width is determined by the length of 'defaultPath', with a minimum of 25 columns.
addDirectoryField(String, String, int) - Method in class ij.gui.GenericDialog
addElement(Roi) - Method in class ij.gui.Overlay: Adds an ROI to this Overlay.
addEnumChoice(String, Enum<E>) - Method in class ij.gui.GenericDialog: Adds a group of choices to the dialog with menu items taken from the enum class of the specified default item (enum constant).
addErrorBars(double[]) - Method in class ij.gui.Plot: Adds vertical error bars to the last data passed to the plot (via the constructor or addPoints).
addErrorBars(float[]) - Method in class ij.gui.Plot: Adds vertical error bars to the last data passed to the plot (via the constructor or addPoints).
addErrorBars(float[]) - Method in class ij.gui.PlotWindow: Deprecated.
use the corresponding method of the Plot class
addErrorBars(String, float[]) - Method in class ij.gui.Plot
addEventListener(IJEventListener) - Static method in class ij.IJ
addFileField(String, String) - Method in class ij.gui.GenericDialog: Adds a file text field and "Browse" button, where the field width is determined by the length of 'defaultPath', with a minimum of 25 columns.
addFileField(String, String, int) - Method in class ij.gui.GenericDialog
addHelp(String) - Method in class ij.gui.GenericDialog: Adds a "Help" button that opens the specified URL in the default browser.
addHistogram(double[]) - Method in class ij.gui.Plot: Plots a histogram from an array using auto-binning.
addHistogram(double[], double) - Method in class ij.gui.Plot: Plots a histogram from an array using the specified bin width.
addHistogram(double[], double, double) - Method in class ij.gui.Plot: Plots a histogram of the value distribution (bin counts) from an array
addHorizontalErrorBars(double[]) - Method in class ij.gui.Plot: Adds horizontal error bars to the last data passed to the plot (via the constructor or addPoints).
addHorizontalErrorBars(float[]) - Method in class ij.gui.Plot: Adds horizontal error bars to the last data passed to the plot (via the constructor or addPoints).
addImage(ImagePlus) - Method in class ij.gui.GenericDialog: Adds an image to the dialog.
addImage(FileInfo) - Method in class ij.plugin.FileInfoVirtualStack: Adds an image to this stack.
addImageChoice(String, String) - Method in class ij.gui.GenericDialog: Adds a popup menu that lists the currently open images.
addImageListener(ImageListener) - Static method in class ij.ImagePlus
addKeyListener(KeyListener) - Method in class ij.gui.ScrollbarWithLabel
addKeyListener(KeyListener) - Method in class ij.text.TextPanel: Unused keyPressed and keyTyped events will be passed to 'listener'.
addLabel(double, double, String) - Method in class ij.gui.Plot: Draws text at the specified location, where (0,0) is the upper left corner of the the plot frame and (1,1) is the lower right corner.
addLabel(double, double, String) - Method in class ij.gui.PlotWindow: Deprecated.
use the corresponding method of the Plot class
addLabel(String) - Method in class ij.measure.ResultsTable: Adds a label to the beginning of the current row.
addLabel(String, String) - Method in class ij.measure.ResultsTable: Deprecated.
Replaced by setValue(String,int,String)
addLayoutComponent(String, Component) - Method in class ij.gui.ImageLayout: Not used by this class.
addLegend(String) - Method in class ij.gui.Plot: Adds an automatically positioned legend, where 'labels' can be a tab-delimited or newline-delimited list of curve or point labels in the sequence these data were added.
addLegend(String, String) - Method in class ij.gui.Plot: Adds a legend at the position given in 'options', where 'labels' can be tab-delimited or newline-delimited list of curve or point labels in the sequence these data were added.
addMacroTool(String, MacroInstaller) - Method in class ij.gui.Toolbar: Used by the MacroInstaller class to add a macro tool to the toolbar.
addMacroTool(String, MacroInstaller, int) - Method in class ij.gui.Toolbar: Used by the MacroInstaller class to install a set of macro tools.
addMessage(String) - Method in class ij.gui.GenericDialog: Adds a message consisting of one or more lines of text.
addMessage(String, Font) - Method in class ij.gui.GenericDialog: Adds a message consisting of one or more lines of text, which will be displayed using the specified font.
addMessage(String, Font, Color) - Method in class ij.gui.GenericDialog: Adds a message consisting of one or more lines of text, which will be displayed using the specified font and color.
addMouseListener(MouseListener) - Method in class ij.text.TextPanel
addNotify() - Method in class ij.gui.MultiLineLabel
addNumericField(String, double) - Method in class ij.gui.GenericDialog: Adds a numeric field.
addNumericField(String, double, int) - Method in class ij.gui.GenericDialog: Adds a numeric field.
addNumericField(String, double, int, int, String) - Method in class ij.gui.GenericDialog: Adds a numeric field.
addObjectFromPlot(Plot, int) - Method in class ij.gui.Plot: Add the i-th PlotObject (in the sequence how they were added, including hidden ones) from another plot to this one.
addOffset() - Method in class ij.gui.PolygonRoi
addOpenRecentItem(String) - Static method in class ij.Menus: Adds a file path to the beginning of the File/Open Recent submenu.
addPanel(Panel) - Method in class ij.gui.GenericDialog: Adds a Panel to the dialog.
addPanel(Panel, int, Insets) - Method in class ij.gui.GenericDialog: Adds a Panel to the dialog with custom contraint and insets.
addPlot(Plot) - Method in class ij.gui.PlotVirtualStack: Adds a plot to the end of the stack.
addPlugInTool(PlugInTool) - Static method in class ij.gui.Toolbar: Adds a plugin tool to the first available toolbar slot, or to the last slot if the toolbar is full.
addPoint(double, double) - Method in class ij.gui.PointRoi: Adds a point to this PointRoi.
addPoint(double, double) - Method in class ij.process.FloatPolygon
addPoint(double, double, int) - Method in class ij.gui.PointRoi: Adds a point at the specified stack position.
addPoint(float, float) - Method in class ij.process.FloatPolygon
addPoint(ImagePlus, double, double) - Method in class ij.gui.PointRoi: Adds a point to this PointRoi.
addPoints(double[], double[], double[], int) - Method in class ij.gui.Plot: Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(double[], double[], int) - Method in class ij.gui.Plot: Adds a set of points to the plot using double arrays.
addPoints(double[], double[], int) - Method in class ij.gui.PlotWindow: Deprecated.
use the corresponding method of the Plot class
addPoints(float[], float[], float[], int, String) - Method in class ij.gui.Plot: Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(float[], float[], int) - Method in class ij.gui.Plot: Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(float[], float[], int) - Method in class ij.gui.PlotWindow: Deprecated.
use the corresponding method of the Plot class
addPoints(String, float[], float[], int) - Method in class ij.gui.Plot
addPoints(ArrayList, ArrayList, int) - Method in class ij.gui.Plot: Adds a set of points to the plot using double ArrayLists.
addPoints(ArrayList, ArrayList, ArrayList, int) - Method in class ij.gui.Plot: Adds a set of points to the plot using double ArrayLists.
addPreviewCheckbox(PlugInFilterRunner) - Method in class ij.gui.GenericDialog: Adds a checkbox labelled "Preview" for "automatic" preview.
addPreviewCheckbox(PlugInFilterRunner, String) - Method in class ij.gui.GenericDialog: Add the preview checkbox with user-defined label; for details see the addPreviewCheckbox method with standard "Preview" label.
addRadioButtonGroup(String, String[], int, int, String) - Method in class ij.gui.GenericDialog: Adds a radio button group.
addResults() - Method in class ij.measure.ResultsTable: Adds the last row in this table to the Results window without updating it.
addRoi(Roi) - Method in class ij.plugin.frame.RoiManager: Adds the specified ROI.
addRoiListener(RoiListener) - Static method in class ij.gui.Roi
addRow() - Method in class ij.measure.ResultsTable: Adds a row to the table.
addSeparator(String) - Static method in class ij.IJ
addSlice(ImageProcessor) - Method in class ij.ImageStack: Adds the image in 'ip' to the end of the stack.
addSlice(String) - Method in class ij.VirtualStack: Adds an image to the end of a virtual stack created using the VirtualStack(w,h,cm,path) constructor.
addSlice(String, ImageProcessor) - Method in class ij.ImageStack: Adds the image in 'ip' to the end of the stack, setting the string 'sliceLabel' as the slice metadata.
addSlice(String, ImageProcessor) - Method in class ij.VirtualStack: Does nothing..
addSlice(String, ImageProcessor, int) - Method in class ij.ImageStack: Adds the image in 'ip' to the stack following slice 'n'.
addSlice(String, ImageProcessor, int) - Method in class ij.VirtualStack: Does noting.
addSlice(String, Object) - Method in class ij.ImageStack: Adds an image in the form of a pixel array to the end of the stack.
addSlice(String, Object) - Method in class ij.VirtualStack: Does nothing.
addSlider(String, double, double, double) - Method in class ij.gui.GenericDialog: Adds a slider (scroll bar) to the dialog box.
addSlider(String, double, double, double, double) - Method in class ij.gui.GenericDialog: This vesion of addSlider() adds a 'stepSize' argument.
Example: http://wsr.imagej.net/macros/SliderDemo.txt
addStringField(String, String) - Method in class ij.gui.GenericDialog: Adds an 8 column text field.
addStringField(String, String, int) - Method in class ij.gui.GenericDialog: Adds a text field.
addText(String, double, double) - Method in class ij.gui.Plot
addTextAreas(String, String, int, int) - Method in class ij.gui.GenericDialog: Adds one or two (side by side) text areas.
addToArray(float[], float) - Static method in class ij.util.Tools: Adds a number to all array elements
addToManager - Variable in class ij.plugin.filter.ParticleAnalyzer
addTool(String) - Method in class ij.gui.Toolbar: Adds a tool to the toolbar.
addToOverlay() - Method in class ij.gui.PointRoi
addToOverlay() - Static method in class ij.plugin.filter.Analyzer
addToSameRow() - Method in class ij.gui.GenericDialog: Makes the next item appear in the same row as the previous.
addToStack() - Method in class ij.gui.Plot: Appends the current plot to a virtual stack and resets allPlotObjects for next slice N.
addUnsignedShortSlice(String, Object) - Method in class ij.ImageStack: Deprecated.
Short images are always unsigned.
addUserPoint(ImagePlus, double, double) - Method in class ij.gui.PointRoi
addValue(int, double) - Method in class ij.measure.ResultsTable: Adds a numeric value to the specified column, on the last table row.
addValue(String, double) - Method in class ij.measure.ResultsTable: Adds a numeric value to the specified column, on the last table row.
addValue(String, String) - Method in class ij.measure.ResultsTable: Adds a string value to the specified column, on the last table row.
addWindow(Frame) - Static method in class ij.WindowManager: Adds the specified Frame to the Window menu.
addWindow(Window) - Static method in class ij.WindowManager: Adds the specified window to the Window menu.
adjustCalibration(Calibration) - Method in class ij.gui.Plot: Adjusts a Calibration object to fit the current axes.
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.ColorChooser
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.GenericDialog
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.ScrollbarWithLabel
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.StackWindow
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ColorThresholder
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ContrastAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.Orthogonal_Views
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.text.TextPanel
ALL_KEYS - Static variable in class ij.IJ
ALL_STATS - Static variable in interface ij.measure.Measurements: All measurement options
allowRecording(boolean) - Method in class ij.plugin.frame.RoiManager
allPoints() - Static method in class ij.gui.Wand: Returns 'true' if output contains intermediate points for straight lines longer than one pixel.
altKeyDown() - Static method in class ij.IJ: Returns true if the alt key is down.
alwaysOnTop - Static variable in class ij.Prefs: "ImageJ" window is always on top.
analyze(ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer: Uses extracts a set of coordinate pairs from a digitized line graph.
analyze(ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer: Performs particle analysis on the specified image.
analyze(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer: Performs particle analysis on the specified ImagePlus and ImageProcessor.
analyzer - Variable in class ij.plugin.filter.ParticleAnalyzer
Analyzer - Class in ij.plugin.filter: This plugin implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.
Analyzer() - Constructor for class ij.plugin.filter.Analyzer
Analyzer(ImagePlus) - Constructor for class ij.plugin.filter.Analyzer: Constructs a new Analyzer using the specified ImagePlus object and the current measurement options and default results table.
Analyzer(ImagePlus, int, ResultsTable) - Constructor for class ij.plugin.filter.Analyzer: Construct a new Analyzer using an ImagePlus object and private measurement options and a ResultsTable.
Analyzer(ImagePlus, ResultsTable) - Constructor for class ij.plugin.filter.Analyzer: Construct a new Analyzer using an ImagePlus object and a ResultsTable.
and(int) - Method in class ij.process.FloatProcessor
and(int) - Method in class ij.process.ImageProcessor: Binary AND of each pixel in the image or ROI with 'value'.
and(int) - Method in class ij.process.ShortProcessor
and(ShapeRoi) - Method in class ij.gui.ShapeRoi: Unary intersection operator.
AND - Static variable in interface ij.process.Blitter: dst=dst AND src
angle - Variable in class ij.process.EllipseFitter: Angle in degrees
angle - Variable in class ij.process.ImageStatistics: Angle in degrees of fitted ellipse
ANGLE - Static variable in class ij.gui.Roi
ANGLE - Static variable in class ij.gui.Toolbar
ANGLE - Static variable in class ij.measure.ResultsTable
angstromSymbol - Static variable in class ij.IJ
animationSelector - Variable in class ij.gui.StackWindow
Animator - Class in ij.plugin: This plugin animates stacks.
Animator() - Constructor for class ij.plugin.Animator
antialiasedText - Static variable in class ij.Prefs: No longer used
antialiasedText - Variable in class ij.process.ImageProcessor
antialiasedTools - Static variable in class ij.Prefs: Draw tool icons using antialiasing (always true).
AppearanceOptions - Class in ij.plugin: This plugin implements the Edit/Options/Appearance command.
AppearanceOptions() - Constructor for class ij.plugin.AppearanceOptions
append(String) - Method in class ij.plugin.frame.Editor
append(String) - Method in class ij.text.TextPanel: Adds one or more lines to the end of this TextPanel.
append(String) - Method in class ij.text.TextWindow: Adds one or more lines of text to the window.
append(String, String) - Static method in class ij.IJ: Appends a string to the end of a file.
append(ArrayList) - Method in class ij.text.TextPanel: Adds strings contained in an ArrayList to the end of this TextPanel.
appendLine(String) - Method in class ij.text.TextPanel: Adds a single line to the end of this TextPanel.
appendToStack() - Method in class ij.gui.Plot
appendWithoutUpdate(String) - Method in class ij.text.TextPanel: Adds a single line to the end of this TextPanel without updating the display.
applyLut() - Method in class ij.process.ByteProcessor
applyMacro(ImageProcessor, String, boolean) - Static method in class ij.plugin.filter.ImageMath
applyMacro(String) - Method in class ij.measure.ResultsTable: Applies a macro to each row of the table; the columns are assigned variable names as given by getHeadingsAsVaribleNames().
applyMacro(String) - Method in class ij.process.ImageProcessor: Uses the Process/Math/Macro command to apply macro code to this image.
applyTable(int[]) - Method in class ij.process.ByteProcessor
applyTable(int[]) - Method in class ij.process.ColorProcessor
applyTable(int[]) - Method in class ij.process.FloatProcessor
applyTable(int[]) - Method in class ij.process.ImageProcessor: Transforms the image or ROI using a lookup table.
applyTable(int[]) - Method in class ij.process.ShortProcessor: Transforms the pixel data using a 65536 entry lookup table.
applyTable(int[]) - Method in class ij.process.StackProcessor
applyTable(int[], int) - Method in class ij.process.ColorProcessor
area - Variable in class ij.process.ImageStatistics
AREA - Static variable in interface ij.measure.Measurements
AREA - Static variable in class ij.measure.ResultsTable
AREA_FRACTION - Static variable in interface ij.measure.Measurements
AREA_FRACTION - Static variable in class ij.measure.ResultsTable
areaFraction - Variable in class ij.process.ImageStatistics
ARG_ARRAY - Static variable in interface ij.macro.MacroExtension
ARG_NUMBER - Static variable in interface ij.macro.MacroExtension
ARG_OPTIONAL - Static variable in interface ij.macro.MacroExtension
ARG_OUTPUT - Static variable in interface ij.macro.MacroExtension
ARG_STRING - Static variable in interface ij.macro.MacroExtension
ARGB - Static variable in class ij.io.FileInfo: 32-bit interleaved ARGB.
argTypes - Variable in class ij.macro.ExtensionDescriptor
ARRAY - Static variable in interface ij.macro.MacroConstants
ARRAY_FUNC - Static variable in interface ij.macro.MacroConstants
ARRAY_FUNCTION - Static variable in interface ij.macro.MacroConstants
arrayFunctionIDs - Static variable in interface ij.macro.MacroConstants
arrayFunctions - Static variable in interface ij.macro.MacroConstants
ArrayUtil - Class in ij.util
ArrayUtil(float[]) - Constructor for class ij.util.ArrayUtil: constructeur
ArrayUtil(int) - Constructor for class ij.util.ArrayUtil: constructeur
Arrow - Class in ij.gui: This is an Roi subclass for creating and displaying arrows.
Arrow(double, double, double, double) - Constructor for class ij.gui.Arrow
Arrow(int, int, ImagePlus) - Constructor for class ij.gui.Arrow
ARROW - Static variable in class ij.io.RoiDecoder
ARROW_HEAD_SIZE - Static variable in class ij.io.RoiDecoder
ARROW_STYLE - Static variable in class ij.io.RoiDecoder
ArrowTool - Class in ij.plugin.tool
ArrowTool() - Constructor for class ij.plugin.tool.ArrowTool
ArrowToolOptions - Class in ij.plugin: This plugin implements the Edit/Options/Arrow Tool command.
ArrowToolOptions() - Constructor for class ij.plugin.ArrowToolOptions
ARTIST - Static variable in class ij.io.TiffDecoder
ASIN - Static variable in interface ij.macro.MacroConstants
asp_bk - Variable in class ij.gui.Roi
aspect - Variable in class ij.gui.Roi
ASPECT_RATIO - Static variable in class ij.measure.ResultsTable
ATAN - Static variable in interface ij.macro.MacroConstants
ATAN2 - Static variable in interface ij.macro.MacroConstants
AUTO_FORMAT - Static variable in class ij.measure.ResultsTable
AUTO_POSITION - Static variable in class ij.gui.Plot: Legend positions
AUTO_UPDATE - Static variable in interface ij.macro.MacroConstants
autoClose - Static variable in class ij.gui.PlotWindow: Automatically close window after saving values.
autoContrast - Static variable in class ij.Prefs: Adjust contrast when scrolling stacks
autoLivePlots - Static variable in class ij.Prefs: Turn live display on plots automatically
autoOutline(int, int) - Method in class ij.gui.Wand: Traces the boundary of an area of uniform color, where 'startX' and 'startY' are somewhere inside the area.
autoOutline(int, int, double, double) - Method in class ij.gui.Wand: Traces an object defined by lower and upper threshold values or an interior hole; whatever is found first ('legacy mode').
autoOutline(int, int, double, double, int) - Method in class ij.gui.Wand: Traces an object defined by lower and upper threshold values.
autoOutline(int, int, double, int) - Method in class ij.gui.Wand: Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel at the starting location.
autoOutline(int, int, int, int) - Method in class ij.gui.Wand: This is a variation of legacy autoOutline that uses int threshold arguments.
autoRun() - Static method in class ij.plugin.MacroInstaller: Runs the StartupMacros AutoRun macro on the current thread.
autoRunExamples - Static variable in class ij.Prefs: Automatically run examples in Help/Examples menu.
autoThreshold() - Method in class ij.process.ColorProcessor
autoThreshold() - Method in class ij.process.FloatProcessor: Not implemented.
autoThreshold() - Method in class ij.process.ImageProcessor: Converts the image to binary using an automatically determined threshold.
AutoThresholder - Class in ij.process: Autothresholding methods (limited to 256 bin histograms) from the Auto_Threshold plugin (http://fiji.sc/Auto_Threshold) by G.Landini at bham dot ac dot uk).
AutoThresholder() - Constructor for class ij.process.AutoThresholder
AutoThresholder.Method - Enum in ij.process
AVERAGE - Static variable in class ij.plugin.Binner
AVERAGE - Static variable in interface ij.process.Blitter: dst=(dst+src)/2
AVG_METHOD - Static variable in class ij.plugin.ZProjector
AVI - Static variable in class ij.io.Opener
AVI_Reader - Class in ij.plugin: ImageJ Plugin for reading an AVI file into an image stack (one slice per video frame) Restrictions and Notes: - Only few formats supported: - uncompressed 8 bit with palette (=LUT) - uncompressed 8 & 16 bit grayscale - uncompressed 24 & 32 bit RGB (alpha channel ignored) - uncompressed 32 bit AYUV (alpha channel ignored) - various YUV 4:2:2 and 4:2:0 compressed formats (i.e., formats with full luminance resolution, but reduced chroma resolution - png or jpeg-encoded individual frames.
AVI_Reader() - Constructor for class ij.plugin.AVI_Reader
AVI_Writer - Class in ij.plugin.filter: This plugin implements the File/Save As/AVI command.
AVI_Writer() - Constructor for class ij.plugin.filter.AVI_Writer
avoidResliceInterpolation - Static variable in class ij.Prefs: Avoid interpolation when re-slicing
AXIS_OPTIONS - Static variable in class ij.gui.PlotDialog: Types of dialog.

B

BACKGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
backgroundColor - Static variable in class ij.ImageJ
backgrounds - Static variable in class ij.plugin.Thresholder
BackgroundSubtracter - Class in ij.plugin.filter: Implements ImageJ's Subtract Background command.
BackgroundSubtracter() - Constructor for class ij.plugin.filter.BackgroundSubtracter
BAR - Static variable in class ij.gui.Arrow
BAR - Static variable in class ij.gui.Plot: Draw a histogram bar for each point (bars touch each other unless the x axis has categories set via the axis label.
BARE_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
BARG - Static variable in class ij.io.FileInfo: 32-bit interleaved BARG (MCID).
baseCM - Variable in class ij.process.ImageProcessor
BatchConverter - Class in ij.plugin: This plugin implements the File/ /Convert command, which converts the images in a folder to a specified format.
BatchConverter() - Constructor for class ij.plugin.BatchConverter
BatchMeasure - Class in ij.plugin: This plugin implements the File/Batch/Measure command, which measures all the images in a user-specified folder.
BatchMeasure() - Constructor for class ij.plugin.BatchMeasure
batchMode - Static variable in class ij.macro.Interpreter
BatchProcessor - Class in ij.plugin: This plugin implements the File/Batch/Macro and File/Batch/Virtual Stack commands.
BatchProcessor() - Constructor for class ij.plugin.BatchProcessor
BCOLOR - Static variable in class ij.Prefs
beep() - Static method in class ij.IJ: Emits an audio beep.
BEEP - Static variable in interface ij.macro.MacroConstants
Benchmark - Class in ij.plugin: Implements the Plugins/Utilities/Run Benchmark command.
Benchmark - Class in ij.plugin.filter: Implements the Plugins/Utilities/Run Benchmark command when the current image is 512x512 and RGB.
Benchmark() - Constructor for class ij.plugin.Benchmark
Benchmark() - Constructor for class ij.plugin.filter.Benchmark
BGR - Static variable in class ij.io.FileInfo: 24-bit interleaved BGR.
BICUBIC - Static variable in class ij.process.ImageProcessor: Interpolation methods
BILINEAR - Static variable in class ij.process.ImageProcessor: Interpolation methods
bin(int) - Method in class ij.process.ImageProcessor: Returns a copy of this image that has been reduced in size using binning.
Binary - Class in ij.plugin.filter: Implements the Erode, Dilate, Open, Close, Outline, Skeletonize and Fill Holes commands in the Process/Binary submenu.
Binary() - Constructor for class ij.plugin.filter.Binary
BinaryInterpolator - Class in ij.process
BinaryInterpolator() - Constructor for class ij.process.BinaryInterpolator
BinaryProcessor - Class in ij.process: This class processes binary images.
BinaryProcessor(ByteProcessor) - Constructor for class ij.process.BinaryProcessor: Creates a BinaryProcessor from a ByteProcessor.
Binner - Class in ij.plugin: This plugin implements the Image/Transform/Bin command.
Binner() - Constructor for class ij.plugin.Binner
binSize - Variable in class ij.process.ImageStatistics
BIT_DEPTH - Static variable in interface ij.macro.MacroConstants
BitBuffer - Class in ij.io: A class for reading arbitrary numbers of bits from a byte array.
BitBuffer(byte[]) - Constructor for class ij.io.BitBuffer
BITMAP - Static variable in class ij.io.FileInfo: 1-bit black and white.
BITS_PER_SAMPLE - Static variable in class ij.io.TiffDecoder
BLACK - Static variable in class ij.process.ImageProcessor: Value of pixels included in masks.
BLACK_AND_WHITE_LUT - Static variable in class ij.process.ImageProcessor
blackBackground - Static variable in class ij.Prefs: Backgound is black in binary images
blackCanvas - Static variable in class ij.Prefs: Use black image border.
Blitter - Interface in ij.process: ImageJ bit blitting classes must implement this interface.
blue - Variable in class ij.plugin.filter.RGBStackSplitter
blues - Variable in class ij.io.FileInfo
blur(ImagePlus, double, double, double) - Static method in class ij.plugin.GaussianBlur3D
blur(ImageProcessor, double) - Method in class ij.plugin.filter.GaussianBlur: Deprecated.
BLUR_MORE - Static variable in class ij.process.ImageProcessor
blur1Direction(FloatProcessor, double, double, boolean, int) - Method in class ij.plugin.filter.GaussianBlur: Blur an image in one direction (x or y) by a Gaussian, using multiple threads on multiprocessor machines
blurFloat(FloatProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur: Gaussian Filtering of a FloatProcessor.
blurGaussian(double) - Method in class ij.process.ImageProcessor: Blurs the image by convolving with a Gaussian function.
blurGaussian(ImageProcessor, double) - Method in class ij.plugin.filter.GaussianBlur: Gaussian Filtering of an ImageProcessor
blurGaussian(ImageProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur: Gaussian Filtering of an ImageProcessor
bLUT1 - Variable in class ij.process.ImageProcessor
bLUT2 - Variable in class ij.process.ImageProcessor
BMP - Static variable in class ij.io.FileInfo
BMP - Static variable in class ij.io.Opener
BMP_Reader - Class in ij.plugin: This plugin reads BMP files.
BMP_Reader() - Constructor for class ij.plugin.BMP_Reader
BMP_Writer - Class in ij.plugin: Implements the File/Save As/BMP command.
BMP_Writer() - Constructor for class ij.plugin.BMP_Writer
boldFont - Variable in class ij.process.ImageProcessor
BOTTOM - Static variable in class ij.io.RoiDecoder
BOTTOM_LEFT - Static variable in class ij.gui.Plot: Legend positions
BOTTOM_MARGIN - Static variable in class ij.gui.Plot: Deprecated.
Not a fixed value any more, use getDrawingFrame() to get the drawing area
BOTTOM_RIGHT - Static variable in class ij.gui.Plot: Legend positions
boundingRect(int, int, int, int) - Method in class ij.plugin.frame.SyncWindows: Compute bounding rectangle given current and old cursor locations.
BOX - Static variable in class ij.gui.Plot: Display points using a square box-shaped mark.
BOX - Static variable in class ij.gui.PlotWindow: Deprecated.
BREAK - Static variable in interface ij.macro.MacroConstants
BRIGHT_OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
BrowserLauncher - Class in ij.plugin: This plugin implements the File/Import/URL command and the commands in the Help menu that open web pages.
BrowserLauncher() - Constructor for class ij.plugin.BrowserLauncher
BRUSH_ROI - Static variable in class ij.gui.Toolbar
BrushTool - Class in ij.plugin.tool: This class implements the Paintbrush Tool, which allows the user to draw on an image, or on an Overlay if "Paint on overlay" is enabled.
BrushTool() - Constructor for class ij.plugin.tool.BrushTool
bSyncAll - Variable in class ij.plugin.frame.SyncWindows: Buttons for user control.
BUILD - Static variable in class ij.ImageJ
buildControlDialog(int, int) - Method in class ij.plugin.ZProjector: Builds dialog to query users for projection parameters.
buildControlPanel() - Method in class ij.plugin.frame.SyncWindows: Builds panel containing control buttons.
buildWindowList() - Method in class ij.plugin.frame.SyncWindows: Builds list of open ImageWindows
builtInTools - Static variable in class ij.gui.Toolbar
bUnsyncAll - Variable in class ij.plugin.frame.SyncWindows: Buttons for user control.
button - Variable in class ij.gui.MessageDialog
button - Variable in class ij.gui.WaitForUserDialog
BYTE - Static variable in class ij.plugin.filter.EDM: Output type: new 8-bit image
BYTE_OVERWRITE - Static variable in class ij.plugin.filter.EDM: Output type: overwrite current 8-bit image
ByteBlitter - Class in ij.process: This class does bit blitting of byte images.
ByteBlitter(ByteProcessor) - Constructor for class ij.process.ByteBlitter: Constructs a ByteBlitter from a ByteProcessor.
ByteProcessor - Class in ij.process: This is an 8-bit image and methods that operate on that image.
ByteProcessor(int, int) - Constructor for class ij.process.ByteProcessor: Creates a blank ByteProcessor of the specified dimensions.
ByteProcessor(int, int, byte[]) - Constructor for class ij.process.ByteProcessor: Creates a ByteProcessor from a byte array.
ByteProcessor(int, int, byte[], ColorModel) - Constructor for class ij.process.ByteProcessor: Creates a ByteProcessor from a pixel array and IndexColorModel.
ByteProcessor(ImageProcessor, boolean) - Constructor for class ij.process.ByteProcessor: Creates a ByteProcessor from an ImageProcessor.
ByteProcessor(Image) - Constructor for class ij.process.ByteProcessor: Creates a ByteProcessor from an AWT Image.
ByteProcessor(BufferedImage) - Constructor for class ij.process.ByteProcessor: Creates a ByteProcessor from a TYPE_BYTE_GRAY BufferedImage.
ByteStatistics - Class in ij.process: 8-bit image statistics, including histogram.
ByteStatistics(ImageProcessor) - Constructor for class ij.process.ByteStatistics: Construct an ImageStatistics object from a ByteProcessor using the standard measurement options (area, mean, mode, min and max) and no calibration.
ByteStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ByteStatistics: Constructs a ByteStatistics object from a ByteProcessor using the specified measurement and calibration.

C

C_POSITION - Static variable in class ij.io.RoiDecoder
c2hex(Color) - Static method in class ij.util.Tools: Converts a Color to an 7 byte hex string starting with '#'.
cachedMask - Variable in class ij.gui.Roi
cal - Variable in class ij.gui.HistogramWindow
cal - Variable in class ij.process.ImageStatistics
calculate(String, ImagePlus, ImagePlus) - Method in class ij.plugin.ImageCalculator: Deprecated.
replaced by run(String,ImagePlus,ImagePlus)
calculateDistance(int, int, int, int) - Static method in class ij.gui.Plot
CALCULATOR - Static variable in interface ij.macro.MacroConstants
calibrate(ImagePlus) - Method in class ij.plugin.filter.Calibrator: Calibrate an image with the function type defined previously.
CALIBRATE - Static variable in interface ij.macro.MacroConstants
calibrated() - Method in class ij.measure.Calibration: Returns true if this image is density calibrated.
Calibration - Class in ij.measure: Calibration objects contain an image's spatial and density calibration data.
Calibration() - Constructor for class ij.measure.Calibration: Constructs a new Calibration object using the default values.
Calibration(ImagePlus) - Constructor for class ij.measure.Calibration: Constructs a new Calibration object using the default values.
CalibrationBar - Class in ij.plugin: This plugin implements the Analyze/Tools/Calibration Bar command.
CalibrationBar() - Constructor for class ij.plugin.CalibrationBar
calibrationFunction - Variable in class ij.io.FileInfo
Calibrator - Class in ij.plugin.filter: Implements the Analyze/Calibrate command.
Calibrator() - Constructor for class ij.plugin.filter.Calibrator
CALL - Static variable in interface ij.macro.MacroConstants
cancelButton - Variable in class ij.gui.WaitForUserDialog
CANCELED - Static variable in class ij.IJ
cancelPressed() - Method in class ij.gui.SaveChangesDialog: Returns true if the user dismissed dialog by pressing "Cancel".
cancelPressed() - Method in class ij.gui.YesNoCancelDialog: Returns true if the user dismissed dialog by pressing "Cancel".
canEnlarge(int, int) - Method in class ij.gui.ImageCanvas: Returns the size to which the window can be enlarged, or null if it can't be enlarged.
canImport(JComponent, DataFlavor[]) - Method in class ij.io.DragAndDropHandler: Returns whether any of the transfer flavors is supported
CanvasResizer - Class in ij.plugin: This plugin implements the Image/Adjust/Canvas Size command.
CanvasResizer() - Constructor for class ij.plugin.CanvasResizer
captureImage() - Method in class ij.plugin.ScreenGrabber: Captures the active image window and returns it as an ImagePlus.
captureScreen() - Method in class ij.plugin.ScreenGrabber: Captures the entire screen and returns it as an ImagePlus.
caSnapshot() - Method in class ij.process.ColorProcessor: Used by the ContrastAdjuster
caSnapshot(boolean) - Method in class ij.process.ColorProcessor: Used by the ContrastAdjuster
cChannel - Variable in class ij.plugin.frame.SyncWindows: Checkboxes for user control.
cCoords - Variable in class ij.plugin.frame.SyncWindows: Checkboxes for user control.
cCursor - Variable in class ij.plugin.frame.SyncWindows: Checkboxes for user control.
center - Variable in class ij.gui.Roi
center(Window) - Static method in class ij.gui.GUI
center(Window, Component) - Static method in class ij.gui.GUI: Positions the specified window in the center of the screen that contains target.
CENTER - Static variable in class ij.gui.Plot: Text justification.
CENTER - Static variable in class ij.gui.TextRoi
CENTER_JUSTIFY - Static variable in class ij.process.ImageProcessor: Center justify text.
CENTER_OF_MASS - Static variable in interface ij.measure.Measurements
centerDialog(boolean) - Method in class ij.gui.GenericDialog: Display dialog centered on the primary screen.
centerNextImage() - Static method in class ij.gui.ImageWindow: Causes the next image to be opened to be centered on the screen and displayed without informational text above the image.
centerOnImageJScreen(Window) - Static method in class ij.gui.GUI: Positions the specified window in the center of the screen containing the "ImageJ" window.
CENTROID - Static variable in interface ij.measure.Measurements
cFrame - Variable in class ij.plugin.frame.SyncWindows: Checkboxes for user control.
CHANGE_VALUES - Static variable in interface ij.macro.MacroConstants
changeFont(Font) - Method in class ij.gui.Plot
changeFont(Font) - Method in class ij.gui.PlotWindow: Deprecated.
use the corresponding method of the Plot class
changes - Variable in class ij.ImagePlus: True if any changes have been made to this image.
changes - Variable in class ij.plugin.frame.Editor
CHANNEL - Static variable in class ij.measure.ResultsTable
ChannelArranger - Class in ij.plugin: This plugin implements the Image/Colors/Arrange Channels command, which allows the user to change the order of channels.
ChannelArranger() - Constructor for class ij.plugin.ChannelArranger
channelLuts - Variable in class ij.io.FileInfo
Channels - Class in ij.plugin.frame: Displays the ImageJ "Channels" dialog.
Channels() - Constructor for class ij.plugin.frame.Channels
ChannelSplitter - Class in ij.plugin: This plugin implements the Image/Color/Split Channels command.
ChannelSplitter() - Constructor for class ij.plugin.ChannelSplitter
CHAPMAN - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
CHAR_CODE_AT - Static variable in interface ij.macro.MacroConstants
CHECK_AVAILABLE_MEMORY - Static variable in class ij.gui.NewImage
checkArguments(Object[]) - Method in class ij.macro.ExtensionDescriptor
checkbox - Variable in class ij.gui.GenericDialog
checkForDuplicateName - Static variable in class ij.WindowManager
choice - Variable in class ij.gui.GenericDialog
chromaD50 - Variable in class ij.process.ColorSpaceConverter: reference white in xyY coordinates
chromaD55 - Variable in class ij.process.ColorSpaceConverter
chromaD65 - Variable in class ij.process.ColorSpaceConverter
chromaD75 - Variable in class ij.process.ColorSpaceConverter
chromaWhitePoint - Variable in class ij.process.ColorSpaceConverter
CIRCLE - Static variable in class ij.gui.Plot: Display points using a circle (5 pixels in diameter if line thickness<=1, otherwise 7).
CIRCLE - Static variable in class ij.gui.PlotWindow: Deprecated.
CIRCLE - Static variable in class ij.gui.PointRoi
CIRCULARITY - Static variable in interface ij.measure.Measurements
CIRCULARITY - Static variable in class ij.measure.ResultsTable
CircularRoiMaker - Class in ij.plugin: This class implements the Process/FFT/Make Circular Selection command.
CircularRoiMaker() - Constructor for class ij.plugin.CircularRoiMaker
ClassChecker - Class in ij.plugin: Checks for duplicate class and JAR files in the plugins folders.
ClassChecker() - Constructor for class ij.plugin.ClassChecker
clear() - Method in class ij.gui.Overlay: Removes all the ROIs in this Overlay.
clear() - Method in class ij.text.TextPanel: Deletes all the lines.
clear() - Method in class ij.util.FloatArray: Removes all elements form this FloatArray.
clear(ImageProcessor) - Method in class ij.gui.TextRoi
clear(ImageProcessor) - Method in class ij.plugin.filter.Filler
CLEAR_WORKSHEET - Static variable in class ij.plugin.filter.ParticleAnalyzer: Clear "Results" window before starting.
clearOutside(ImageProcessor) - Method in class ij.plugin.filter.Filler: Deprecated.
replaced by ImageProcessor.fillOutside(Roi)
clearSelection() - Method in class ij.text.TextPanel: Deletes the selected lines.
clipboard - Variable in class ij.gui.Roi
Clipboard - Class in ij.plugin: Copies/pastes images to/from the system clipboard.
Clipboard() - Constructor for class ij.plugin.Clipboard
clipHeight - Variable in class ij.gui.Roi
clipRectMargin() - Method in class ij.gui.Arrow
clipRectMargin() - Method in class ij.gui.Line
clipRectMargin() - Method in class ij.gui.PolygonRoi
clipRectMargin() - Method in class ij.gui.Roi
clipWidth - Variable in class ij.gui.Roi
clipX - Variable in class ij.gui.Roi
clipXMax - Variable in class ij.process.ImageProcessor
clipXMin - Variable in class ij.process.ImageProcessor
clipY - Variable in class ij.gui.Roi
clipYMax - Variable in class ij.process.ImageProcessor
clipYMin - Variable in class ij.process.ImageProcessor
clone() - Method in class ij.gui.ImageRoi
clone() - Method in class ij.gui.PointRoi: Returns a copy of this PointRoi.
clone() - Method in class ij.gui.PolygonRoi: Returns a copy of this PolygonRoi.
clone() - Method in class ij.gui.Roi: Returns a copy of this roi.
clone() - Method in class ij.gui.ShapeRoi: Returns a deep copy of this.
clone() - Method in class ij.gui.TextRoi: Returns a copy of this TextRoi.
clone() - Method in class ij.ImagePlus: Returns a shallow copy of this ImagePlus.
clone() - Method in class ij.io.FileInfo
clone() - Method in class ij.macro.Variable
clone() - Method in class ij.measure.Calibration
clone() - Method in class ij.measure.ResultsTable: Duplicates this ResultsTable.
clone() - Method in class ij.process.ImageProcessor: Returns a shallow copy of this ImageProcessor, where this image and the copy share pixel data.
clone() - Method in class ij.process.LUT
close() - Method in class ij.CompositeImage
close() - Method in class ij.gui.ImageWindow: Removes this window from the window list and disposes of it.
close() - Method in class ij.gui.StackWindow
close() - Method in class ij.gui.WaitForUserDialog
close() - Method in class ij.ImagePlus: Closes this image and sets the ImageProcessor to null.
close() - Method in class ij.io.LogStream
close() - Method in class ij.io.RandomAccessStream
close() - Method in class ij.macro.FunctionFinder
close() - Method in class ij.plugin.frame.Channels
close() - Method in class ij.plugin.frame.ColorPicker
close() - Method in class ij.plugin.frame.ColorThresholder
close() - Method in class ij.plugin.frame.Commands: Overrides PlugInFrame.close().
close() - Method in class ij.plugin.frame.ContrastAdjuster: Overrides close() in PlugInDialog.
close() - Method in class ij.plugin.frame.Editor: Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.LineWidthAdjuster: Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.MemoryMonitor
close() - Method in class ij.plugin.frame.PasteController
close() - Method in class ij.plugin.frame.PlugInDialog: Closes this window.
close() - Method in class ij.plugin.frame.PlugInFrame: Closes this window.
close() - Method in class ij.plugin.frame.Recorder
close() - Method in class ij.plugin.frame.RoiManager: Overrides PlugInFrame.close().
close() - Method in class ij.plugin.frame.SyncWindows
close() - Method in class ij.plugin.frame.ThresholdAdjuster: Overrides close() in PlugInFrame.
close() - Method in class ij.text.TextWindow
close(boolean) - Method in class ij.text.TextWindow: Closes this TextWindow.
CLOSE - Static variable in interface ij.macro.MacroConstants
CLOSE - Static variable in class ij.plugin.filter.RankFilters
closeAll() - Static method in class ij.plugin.Commands: Closes all image windows, or returns 'false' if the user cancels the unsaved changes dialog box.
closeAllWindows() - Static method in class ij.WindowManager: Closes all windows.
closeAndRefocus() - Method in class ij.macro.FunctionFinder
closed - Variable in class ij.gui.ImageWindow
CLOSED - Static variable in class ij.ImagePlus
closingAll - Static variable in class ij.Prefs: "Close All" command running
cm - Variable in class ij.process.ImageProcessor
cm2 - Variable in class ij.process.ImageProcessor
CMDS_KEY - Static variable in class ij.plugin.frame.Commands
CMYK - Static variable in class ij.io.FileInfo: 32-bit interleaved CMYK.
coefficients - Variable in class ij.io.FileInfo
COLOR - Static variable in class ij.CompositeImage: Display modes (note: TRANSPARENT mode has not yet been implemented)
COLOR - Static variable in class ij.IJ: Image display modes
COLOR - Static variable in interface ij.macro.MacroConstants
COLOR_256 - Static variable in class ij.ImagePlus: 8-bit indexed color
COLOR_MAP - Static variable in class ij.io.TiffDecoder
COLOR_PICKER_CLOSED - Static variable in interface ij.IJEventListener
COLOR_RGB - Static variable in class ij.ImagePlus: 32-bit RGB color
COLOR8 - Static variable in class ij.io.FileInfo: 8-bit unsigned integer with color lookup table.
ColorBlitter - Class in ij.process: This class does bit blitting of RGB images.
ColorBlitter(ColorProcessor) - Constructor for class ij.process.ColorBlitter: Constructs a ColorBlitter from a ColorProcessor.
ColorChooser - Class in ij.gui: Displays a dialog that allows the user to select a color using three sliders.
ColorChooser(String, Color, boolean) - Constructor for class ij.gui.ColorChooser: Constructs a ColorChooser using the specified title and initial color.
ColorChooser(String, Color, boolean, Frame) - Constructor for class ij.gui.ColorChooser
ColorPicker - Class in ij.plugin.frame: Implements the Image/Color/Color Picker command.
ColorPicker() - Constructor for class ij.plugin.frame.ColorPicker
ColorProcessor - Class in ij.process: This is an 32-bit RGB image and methods that operate on that image..
ColorProcessor(int, int) - Constructor for class ij.process.ColorProcessor: Creates a blank ColorProcessor of the specified dimensions.
ColorProcessor(int, int, int[]) - Constructor for class ij.process.ColorProcessor: Creates a ColorProcessor from a pixel array.
ColorProcessor(Image) - Constructor for class ij.process.ColorProcessor: Creates a ColorProcessor from an AWT Image or BufferedImage.
colors - Static variable in class ij.CompositeImage
colors - Static variable in class ij.plugin.Colors
Colors - Class in ij.plugin: This plugin implements most of the Edit/Options/Colors command.
Colors() - Constructor for class ij.plugin.Colors
ColorSpaceConverter - Class in ij.process: ColorSpaceConverter
ColorSpaceConverter() - Constructor for class ij.process.ColorSpaceConverter: Default constructor; uses D65 for the white point
ColorSpaceConverter(String) - Constructor for class ij.process.ColorSpaceConverter: Constructor for setting a non-default white point
ColorStatistics - Class in ij.process: RGB image statistics, including histogram.
ColorStatistics(ImageProcessor) - Constructor for class ij.process.ColorStatistics: Construct an ImageStatistics object from a ColorProcessor using the standard measurement options (area, mean, mode, min and max).
ColorStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ColorStatistics: Constructs a ColorStatistics object from a ColorProcessor using the specified measurement options.
ColorThresholder - Class in ij.plugin.frame: Selects pixels according to hsb or rgb components.
ColorThresholder() - Constructor for class ij.plugin.frame.ColorThresholder
colorToString(Color) - Static method in class ij.plugin.Colors: Converts a Color into a lowercase string ("red", "green", "#aa55ff", etc.).
colorToString2(Color) - Static method in class ij.plugin.Colors: Converts a Color into a string ("Red", "Green", #aa55ff, etc.).
COLUMN_IN_USE - Static variable in class ij.measure.ResultsTable
COLUMN_NOT_FOUND - Static variable in class ij.measure.ResultsTable
columnDeleted() - Method in class ij.measure.ResultsTable
columnExists(int) - Method in class ij.measure.ResultsTable: Returns 'true' if the specified column exists and is not empty.
columnExists(String) - Method in class ij.measure.ResultsTable: Returns 'true' if the specified column exists and is not emptly.
combineHorizontally(ImageStack, ImageStack) - Method in class ij.plugin.StackCombiner
combineVertically(ImageStack, ImageStack) - Method in class ij.plugin.StackCombiner
COMMAND_IN_USE - Static variable in class ij.Menus
COMMAND_NOT_FOUND - Static variable in class ij.Menus
commandExecuting(String) - Method in interface ij.CommandListener
commandExecuting(String) - Method in class ij.plugin.EventListener
commandExecuting(String) - Method in class ij.plugin.frame.Commands
commandExecuting(String) - Method in class ij.plugin.frame.SyncWindows
commandExecuting(String) - Method in class ij.plugin.Orthogonal_Views
CommandFinder - Class in ij.plugin
CommandFinder() - Constructor for class ij.plugin.CommandFinder
commandInUse(String) - Static method in class ij.Menus
commandLineMacro() - Static method in class ij.Prefs
CommandListener - Interface in ij: Plugins that implement this interface are notified when ImageJ is about to run a menu command.
CommandLister - Class in ij.plugin: This class is used by the Plugins/Shortcuts/List Shortcuts command to display a list keyboard shortcuts.
CommandLister() - Constructor for class ij.plugin.CommandLister
commandPrefix - Static variable in class ij.plugin.MacroInstaller
Commands - Class in ij.plugin: Runs miscellaneous File and Window menu commands.
Commands - Class in ij.plugin.frame: This plugin implements the Plugins>Utiltiees>Recent Commands command.
Commands() - Constructor for class ij.plugin.Commands
Commands() - Constructor for class ij.plugin.frame.Commands
Compiler - Class in ij.plugin: Compiles and runs plugins using the javac compiler.
Compiler() - Constructor for class ij.plugin.Compiler
COMPLETED - Static variable in interface ij.gui.RoiListener
completeReset() - Method in class ij.CompositeImage
COMPOSITE - Static variable in class ij.CompositeImage: Display modes (note: TRANSPARENT mode has not yet been implemented)
COMPOSITE - Static variable in class ij.gui.Roi
COMPOSITE - Static variable in class ij.IJ: Image display modes
COMPOSITE_ROIS - Static variable in class ij.plugin.filter.ParticleAnalyzer: Use composite ROIs for particles with holes.
CompositeConverter - Class in ij.plugin: This plugin implements the Image/Color/Make Composite command.
CompositeConverter() - Constructor for class ij.plugin.CompositeConverter
compositeImage - Variable in class ij.ImagePlus
CompositeImage - Class in ij
CompositeImage(ImagePlus) - Constructor for class ij.CompositeImage
CompositeImage(ImagePlus, int) - Constructor for class ij.CompositeImage
compositeRois - Variable in class ij.plugin.filter.ParticleAnalyzer
COMPOUND_FILTER - Static variable in class ij.Undo
COMPOUND_FILTER_DONE - Static variable in class ij.Undo
compression - Variable in class ij.io.FileInfo
COMPRESSION - Static variable in class ij.io.TiffDecoder
COMPRESSION_NONE - Static variable in class ij.io.FileInfo
COMPRESSION_UNKNOWN - Static variable in class ij.io.FileInfo
concatenate(ImagePlus[], boolean) - Method in class ij.plugin.Concatenator: Concatenates two or more images or stacks.
concatenate(ImagePlus, ImagePlus, boolean) - Method in class ij.plugin.Concatenator: Concatenate two images or stacks.
concatenateHyperstacks(ImagePlus[], String, boolean) - Method in class ij.plugin.Concatenator: Obsolete, replaced by concatenate(images,keep) and Concatenator.run(images).
Concatenator - Class in ij.plugin: This plugin, which concatenates two or more images or stacks, implements the Image/Stacks/Tools/Concatenate command.
Concatenator() - Constructor for class ij.plugin.Concatenator
conjugateMultiply(FHT) - Method in class ij.process.FHT: Returns the image resulting from the point by point Hartley conjugate multiplication of this image and the specified image.
CONNECTED_CIRCLES - Static variable in class ij.gui.Plot: Draw black lines between the dots and a circle with the given color at each dot
constrain - Variable in class ij.gui.Roi
CONSTRUCTING - Static variable in class ij.gui.Roi
containedPoints(Roi) - Method in class ij.gui.PointRoi: Returns the points of this Roi that are contained in the specified area ROI.
contains(double, double) - Method in class ij.process.FloatPolygon: Returns 'true' if the point (x,y) is inside this polygon.
contains(float, float) - Method in class ij.process.FloatPolygon: A version of contains() that accepts float arguments.
contains(int, int) - Method in class ij.gui.Arrow
contains(int, int) - Method in class ij.gui.Line
contains(int, int) - Method in class ij.gui.OvalRoi: Tests whether the center of the specified pixel is inside the boundary of this OvalRoi.
contains(int, int) - Method in class ij.gui.PointRoi: Returns true if (x,y) is one of the points in this collection.
contains(int, int) - Method in class ij.gui.PolygonRoi: Returns whether the center of pixel (x,y) is contained in the Roi.
contains(int, int) - Method in class ij.gui.Roi: Returns whether the center of pixel (x,y) is contained in the Roi.
contains(int, int) - Method in class ij.gui.ShapeRoi: Checks whether the center of the specified pixel inside of this ROI's shape boundaries.
contains(Roi) - Method in class ij.gui.Overlay: Returns 'true' if this Overlay contains the specified ROI.
containsPoint(double, double) - Method in class ij.gui.OvalRoi: Returns whether coordinate (x,y) is contained in the Roi.
containsPoint(double, double) - Method in class ij.gui.PolygonRoi: Returns whether coordinate (x,y) is contained in the Roi.
containsPoint(double, double) - Method in class ij.gui.Roi: Returns whether coordinate (x,y) is contained in the Roi.
containsPoint(double, double) - Method in class ij.gui.ShapeRoi: Returns whether coordinate (x,y) is contained in the Roi.
containsRegex(String, String, boolean) - Static method in class ij.plugin.FolderOpener
CONTINUE - Static variable in interface ij.macro.MacroConstants
ContrastAdjuster - Class in ij.plugin.frame: This plugin implements the Brightness/Contrast, Window/level and Color Balance commands, all in the Image/Adjust sub-menu.
ContrastAdjuster() - Constructor for class ij.plugin.frame.ContrastAdjuster
ContrastEnhancer - Class in ij.plugin: Implements ImageJ's Process/Enhance Contrast command.
ContrastEnhancer() - Constructor for class ij.plugin.ContrastEnhancer
controlKeyDown() - Static method in class ij.IJ: Returns true if the control key is down.
controlPanel() - Method in class ij.plugin.frame.SyncWindows: Build window list display and button controls.
ControlPanel - Class in ij.plugin: ControlPanel.
ControlPanel() - Constructor for class ij.plugin.ControlPanel
convert(int) - Method in class ij.process.MedianCut: Uses Heckbert's median-cut algorithm to divide the color space defined by "hist" into "maxcubes" cubes.
convert(ImageProcessor) - Method in class ij.plugin.filter.ThresholdToSelection: Returns a selection created from the thresholded pixels in the specified image, or null if there are no thresholded pixels.
convert(String) - Method in class ij.plugin.Converter: Converts the ImagePlus to the specified image type.
CONVERT_TO_FLOAT - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag to have the ImageProcessor that is passed to the run() method converted to a FloatProcessor.
Converter - Class in ij.plugin: Implements the conversion commands in the Image/Type submenu.
Converter() - Constructor for class ij.plugin.Converter
convertGrayJpegTo8Bits(ImagePlus) - Static method in class ij.io.Opener: Converts the specified RGB image to 8-bits if the 3 channels are identical.
convertHSB32ToRGB() - Method in class ij.process.ImageConverter: Converts a 3-slice (hue, saturation, brightness) 32-bit stack to RGB.
convertHSBToRGB() - Method in class ij.process.ImageConverter: Converts a 3-slice (hue, saturation, brightness) 8-bit stack to RGB.
convertHyperstack(ImagePlus, ImagePlus) - Method in class ij.plugin.RGBStackConverter
convertImagesToStack() - Method in class ij.plugin.ImagesToStack
convertImagesToStack() - Method in class ij.plugin.StackEditor
convertIndexToPosition(int) - Method in class ij.ImagePlus: Converts the stack index 'n' (one-based) into a hyperstack position (channel, slice, frame).
convertLabToRGB() - Method in class ij.process.ImageConverter: Converts a Lab stack to RGB.
convertLineToArea(Roi) - Static method in class ij.gui.Roi: Converts a line selection into an area (polygon or composite) selection.
Author: Michael Schmid
convertOutputType(Variable, Object) - Static method in class ij.macro.ExtensionDescriptor
convertRGBStackToRGB() - Method in class ij.process.ImageConverter: Converts a 2 or 3 slice 8-bit stack to RGB.
convertRGBtoIndexedColor(int) - Method in class ij.process.ImageConverter: Converts an RGB image to 8-bits indexed color.
convertShortcutToCode(String) - Static method in class ij.Menus
convertStackToImages(ImagePlus) - Method in class ij.plugin.StackEditor
convertToByte() - Method in class ij.process.TypeConverter: Converts processor to a ByteProcessor.
convertToByte(boolean) - Method in class ij.process.ImageProcessor: Returns an 8-bit version of this image as a ByteProcessor.
convertToByte(int) - Method in class ij.process.MedianCut: This is a version of convert that returns a ByteProcessor.
convertToByteProcessor() - Method in class ij.process.ImageProcessor: Returns an 8-bit version of this image as a ByteProcessor.
convertToByteProcessor(boolean) - Method in class ij.process.ImageProcessor: Returns an 8-bit version of this image as a ByteProcessor.
convertToColorProcessor() - Method in class ij.process.ImageProcessor: Returns an RGB version of this image as a ColorProcessor.
convertToFloat() - Method in class ij.ImageStack: Creates a float version of this stack.
convertToFloat() - Method in class ij.process.ImageProcessor: Returns a 32-bit float version of this image as a FloatProcessor.
convertToFloat(float[]) - Method in class ij.process.TypeConverter: Converts processor to a FloatProcessor.
convertToFloatProcessor() - Method in class ij.process.ImageProcessor: Returns a 32-bit float version of this image as a FloatProcessor.
convertToGray16() - Method in class ij.process.ImageConverter: Converts this ImagePlus to 16-bit grayscale.
convertToGray16() - Method in class ij.process.StackConverter: Converts this Stack to 16-bit grayscale.
convertToGray32() - Method in class ij.process.ImageConverter: Converts this ImagePlus to 32-bit grayscale.
convertToGray32() - Method in class ij.process.StackConverter: Converts this Stack to 32-bit (float) grayscale.
convertToGray8() - Method in class ij.process.ImageConverter: Converts this ImagePlus to 8-bit grayscale.
convertToGray8() - Method in class ij.process.StackConverter: Converts this Stack to 8-bit grayscale.
convertToHSB() - Method in class ij.process.ImageConverter: Converts an RGB image to a HSB (hue, saturation and brightness) stack.
convertToHSB32() - Method in class ij.process.ImageConverter: Converts an RGB image to a 32-bit HSB (hue, saturation and brightness) stack.
convertToHSB32Hyperstack() - Method in class ij.process.StackConverter: Converts the stack (which must be RGB) to a 3 channel (hue, saturation and brightness) 32-bit hyperstack.
convertToHSBHyperstack() - Method in class ij.process.StackConverter: Converts the stack (which must be RGB) to a 3 channel (hue, saturation and brightness) hyperstack.
convertToImageProcessor(BufferedImage, int) - Static method in class ij.ImagePlus: Extract pixels as an an ImageProcessor from a single band of a BufferedImage.
convertToIndexedColor(int) - Method in class ij.process.StackConverter: Converts the stack to 8-bits indexed color.
convertToLab() - Method in class ij.process.ImageConverter: Converts an RGB image to a Lab stack.
convertToLabHyperstack() - Method in class ij.process.StackConverter: Converts the stack (which must be RGB) to a 3 channel Lab hyperstack.
convertToMicrons - Static variable in class ij.Prefs: Convert tiff units to microns if pixel width is less than 0.0001 cm.
convertToPolygon() - Method in class ij.gui.Roi: Deprecated.
convertToRGB() - Method in class ij.process.ImageConverter: Converts this ImagePlus to RGB.
convertToRGB() - Method in class ij.process.ImageProcessor: Returns an RGB version of this image as a ColorProcessor.
convertToRGB() - Method in class ij.process.StackConverter: Converts the Stack to RGB.
convertToRGB() - Method in class ij.process.TypeConverter: Converts processor to a ColorProcessor.
convertToRGB(ImagePlus) - Static method in class ij.plugin.RGBStackConverter: Converts the specified multi-channel (composite) image to RGB.
convertToRGBHyperstack() - Method in class ij.process.StackConverter: Converts the stack (which must be RGB) to a 3 channel (red, green and blue) hyperstack.
convertToRGBStack() - Method in class ij.process.ImageConverter: Converts an RGB image to an RGB (red, green and blue) stack.
convertToShort() - Method in class ij.process.TypeConverter: Converts processor to a ShortProcessor.
convertToShort(boolean) - Method in class ij.process.ImageProcessor: Returns a 16-bit version of this image as a ShortProcessor.
convertToShortProcessor() - Method in class ij.process.ImageProcessor: Returns a 16-bit version of this image as a ShortProcessor.
convertToShortProcessor(boolean) - Method in class ij.process.ImageProcessor: Returns a 16-bit version of this image as a ShortProcessor.
convertVariable(Interpreter, int, Variable) - Static method in class ij.macro.ExtensionDescriptor
convolve(float[], int, int) - Method in class ij.process.ByteProcessor: Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ColorProcessor: Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.FloatProcessor: Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ImageProcessor: Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ShortProcessor: Performs a convolution operation using the specified kernel.
convolve(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver: Convolves ip with a kernel of width kw and height kh.
CONVOLVE - Static variable in class ij.process.ImageProcessor
convolve3x3(int[]) - Method in class ij.process.ByteProcessor
convolve3x3(int[]) - Method in class ij.process.ColorProcessor: 3x3 convolution contributed by Glynne Casteel.
convolve3x3(int[]) - Method in class ij.process.FloatProcessor: Does 3x3 convolution.
convolve3x3(int[]) - Method in class ij.process.ImageProcessor: Convolves the image or ROI with the specified 3x3 integer convolution kernel.
convolve3x3(int[]) - Method in class ij.process.ShortProcessor: Does 3x3 convolution.
convolveFloat(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver: Convolves the float image ip with a kernel of width kw and height kh.
convolveFloat1D(FloatProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver: Convolves the image ip with a kernel of width kw and height kh.
convolveFloat1D(FloatProcessor, float[], int, int, double) - Method in class ij.plugin.filter.Convolver: Convolves the image ip with a kernel of width kw and height kh.
Convolver - Class in ij.plugin.filter: This plugin convolves images using user user defined kernels.
Convolver() - Constructor for class ij.plugin.filter.Convolver
Coordinates - Class in ij.plugin: The plugin implements the Image/Adjust/Coordinates command.
Coordinates() - Constructor for class ij.plugin.Coordinates
COORDINATES - Static variable in class ij.io.RoiDecoder
copy - Variable in class ij.gui.HistogramWindow
copy() - Method in class ij.ImagePlus: Copies the contents of the current selection, or the entire image if there is no selection, to the internal clipboard.
copy() - Method in class ij.measure.Calibration: Returns a clone of this object.
copy(boolean) - Method in class ij.gui.ImageWindow: Copies the current ROI to the clipboard.
copy(boolean) - Method in class ij.ImagePlus: Copies the contents of the current selection to the internal clipboard.
COPY - Static variable in interface ij.process.Blitter: dst=src
COPY_AXIS_STYLE - Static variable in class ij.gui.Plot: Flag for copying from a template: copy axis style
COPY_CONTENTS_STYLE - Static variable in class ij.gui.Plot: Flag for copying from a template: copy contents style
COPY_EXTRA_OBJECTS - Static variable in class ij.gui.Plot: Flag for copying PlotObjects (curves...) from a template if the template has more PlotObjects than the Plot to copy to.
COPY_INVERTED - Static variable in interface ij.process.Blitter: dst=255-src (8-bits and RGB)
COPY_LABELS - Static variable in class ij.gui.Plot: Flag for copying from a template: copy style & text of axis labels
COPY_LEGEND - Static variable in class ij.gui.Plot: Flag for copying from a template: copy legend
COPY_SIZE - Static variable in class ij.gui.Plot: Flag for copying from a template: copy plot size
COPY_TRANSPARENT - Static variable in interface ij.process.Blitter: Copies with white pixels transparent.
COPY_ZERO_TRANSPARENT - Static variable in interface ij.process.Blitter: Copies with zero pixels transparent.
copyAttributes(Roi) - Method in class ij.gui.PointRoi
copyAttributes(Roi) - Method in class ij.gui.Roi: Copy the attributes (outline color, fill color, outline width) of 'roi2' to the this selection.
copyAttributes(ImagePlus) - Method in class ij.ImagePlus: Used internally.
copyBits(ImageStack, int, int, int) - Method in class ij.process.StackProcessor
copyBits(ImageProcessor, int, int, int) - Method in interface ij.process.Blitter: Copies the image in 'src' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteBlitter: Copies the byte image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteProcessor: Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorBlitter: Copies the RGB image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorProcessor: Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatBlitter: Copies the float image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatProcessor: Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ImageProcessor: Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortBlitter: Copies the 16-bit image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortProcessor: Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.StackProcessor
copyColumnHeaders - Static variable in class ij.Prefs: Include column headers when copying tables to clipboard.
copyFile(File, File) - Static method in class ij.macro.Functions
copyFile(String, String) - Static method in class ij.util.Tools: Copies the contents of the file at 'path1' to 'path2', returning an error message (as a non-empty string) if there is an error.
copyLuts(ImagePlus) - Method in class ij.CompositeImage: Copies the LUTs and display mode of 'imp' to this image.
copyScale(ImagePlus) - Method in class ij.ImagePlus: Copies the calibration of the specified image to this image.
copySelection() - Method in class ij.text.TextPanel: Copies the current selection to the system clipboard.
copyToClipboard() - Method in class ij.gui.HistogramWindow
copyToSystem() - Method in class ij.ImagePlus: Copies the contents of the current selection, or the entire image if there is no selection, to the system clipboard.
copyToSystem(ImagePlus) - Static method in class ij.plugin.Clipboard: Copies the contents of the specified image, or selection, to the system clicpboard.
CORNER_DIAMETER - Static variable in class ij.gui.Toolbar
COS - Static variable in interface ij.macro.MacroConstants
count - Variable in class ij.gui.HistogramWindow
COUNT - Static variable in class ij.plugin.filter.MaximumFinder: Do not create an image, just count maxima and add count to Results table
COUNTERS_OFFSET - Static variable in class ij.io.RoiDecoder
create() - Method in class ij.gui.Overlay: Returns a new Overlay that has the same properties as this one.
create(double, double, double, double) - Static method in class ij.gui.Line: Creates a new straight line selection using the specified starting and ending offscreen coordinates.
create(double, double, double, double) - Static method in class ij.gui.OvalRoi: Creates an OvalRoi.
create(double, double, double, double) - Static method in class ij.gui.Roi: Creates a rectangular ROI.
create(double, double, double, double, int) - Static method in class ij.gui.Roi: Creates a rounded rectangular ROI.
create(double, double, String, Font) - Static method in class ij.gui.TextRoi: Obsolete.
create(int, int, int, int) - Static method in class ij.ImageStack: Creates a new ImageStack.
create(ImagePlus[]) - Static method in class ij.ImageStack: Creates an ImageStack from an ImagePlus array.
create(String, double, double, Font) - Static method in class ij.gui.TextRoi: Creates a TextRoi using the specified text and location.
create(String, String) - Method in class ij.plugin.frame.Editor
createBlankImage(int, int) - Static method in class ij.gui.GUI: Obsolete
createByteImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createColorModel(FileInfo) - Method in class ij.io.FileOpener: Returns an IndexColorModel for the image specified by this FileInfo.
createComposite(int, int, int, ImageStack[], boolean) - Method in class ij.plugin.RGBStackMerge: Deprecated; replaced by mergeChannels().
CREATED - Static variable in interface ij.gui.RoiListener
createEmptyStack() - Method in class ij.ImagePlus: Returns an empty image stack that has the same width, height and color table as this image.
createFloatImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createGrayscaleColorModel(boolean) - Static method in class ij.LookUpTable
createHyperStack(String, int, int, int, int) - Method in class ij.ImagePlus: This method has been replaced by IJ.createHyperStack().
createHyperStack(String, int, int, int, int, int, int) - Static method in class ij.IJ: Creates a new hyperstack.
createImage() - Method in class ij.process.ByteProcessor
createImage() - Method in class ij.process.ColorProcessor
createImage() - Method in class ij.process.FloatProcessor: Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage() - Method in class ij.process.ImageProcessor: Returns a copy of this image is the form of an AWT Image.
createImage() - Method in class ij.process.IntProcessor: Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage() - Method in class ij.process.ShortProcessor: Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage(IndexColorModel) - Static method in class ij.plugin.LutLoader: Creates a 256x32 image from an IndexColorModel.
createImage(String, int, int, int, int) - Static method in class ij.IJ: Creates a new image.
createImage(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
createImage(String, String, int, int, int) - Static method in class ij.IJ: Creates a new imagePlus.
createImage(String, String, int, int, int, int, int) - Static method in class ij.IJ: Creates a new hyperstack.
createImagePlus() - Method in class ij.ImagePlus: Returns a new ImagePlus with this image's attributes (e.g.
createInputStream(FileInfo) - Method in class ij.io.FileOpener: Returns an InputStream for the image described by this FileInfo.
createIntImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createInvertedLut() - Method in class ij.process.LUT
createLut() - Method in class ij.ImagePlus: Creates a LookUpTable object that corresponds to this image.
createLutFromColor(Color) - Method in class ij.CompositeImage
createLutFromColor(Color) - Static method in class ij.process.LUT: Creates a color LUT from a Color.
createMacro(String) - Method in class ij.plugin.NewPlugin
createMacro(String, String) - Method in class ij.plugin.frame.Editor
createMask() - Method in class ij.process.ByteProcessor: Returns a binary mask, or null if a threshold is not set.
createMask() - Method in class ij.process.FloatProcessor: Returns a binary mask, or null if a threshold is not set.
createMask() - Method in class ij.process.ImageProcessor: Returns a binary mask, or null if a threshold is not set or this is an RGB image.
createMask() - Method in class ij.process.ShortProcessor: Returns a binary mask, or null if a threshold is not set.
createMask(ImagePlus) - Static method in class ij.plugin.Thresholder: Returns an 8-bit binary (0 and 255) threshold mask that has the same dimensions as this image.
createNewRoi(int, int) - Method in class ij.ImagePlus: Starts the process of creating a new selection, where sx and sy are the starting screen coordinates.
createOverlay() - Static method in class ij.plugin.OverlayLabels: Creates an empty Overlay that has the current label settings.
createPlugin(String, int, String) - Method in class ij.plugin.NewPlugin
createProcessor(int, int) - Method in class ij.process.ByteProcessor: Returns a new, blank ByteProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ColorProcessor: Returns a new, blank ColorProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.FloatProcessor: Returns a new, blank FloatProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ImageProcessor: Returns a new, blank processor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ShortProcessor: Returns a new, blank ShortProcessor with the specified width and height.
createRGBImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
createRoiMask() - Method in class ij.ImagePlus: Returns an 8-bit binary (foreground=255, background=0) ROI or overlay mask that has the same dimensions as this image.
createShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage: Creates an unsigned short image.
createStackOverlay(Roi[]) - Static method in class ij.gui.Overlay
createSubtitle() - Method in class ij.gui.ImageWindow: Creates the subtitle.
createSubtitle() - Method in class ij.gui.StackWindow
createTableFromImage(ImageProcessor) - Static method in class ij.measure.ResultsTable: Creates a ResultsTable from an image or image selection.
createThreadArray() - Static method in class ij.util.ThreadUtil
createThreadArray(int) - Static method in class ij.util.ThreadUtil
createThresholdMask() - Method in class ij.ImagePlus: Returns an 8-bit binary threshold mask (foreground=255, background=0) that has the same dimensions as this image.
createUnsignedShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage: Deprecated.
Short images are always unsigned.
createWindow() - Method in class ij.gui.ProfilePlot: Displays this profile plot in a window.
crop() - Method in class ij.ImagePlus: Returns a copy this image or stack slice, cropped if there is an ROI.
crop() - Method in class ij.process.ByteProcessor
crop() - Method in class ij.process.ColorProcessor
crop() - Method in class ij.process.FloatProcessor
crop() - Method in class ij.process.ImageProcessor: Returns a new processor containing an image that corresponds to the current ROI.
crop() - Method in class ij.process.ShortProcessor
crop(int, int) - Method in class ij.gui.Overlay: Removes ROIs having positions outside of the interval defined by firstSlice and lastSlice.
crop(int, int, int, int) - Method in class ij.process.StackProcessor: Crops the stack to the specified rectangle.
crop(int, int, int, int, int, int) - Method in class ij.gui.Overlay: Removes ROIs having a C, Z or T coordinate outside the volume defined by firstC, lastC, firstZ, lastZ, firstT and lastT.
crop(int, int, int, int, int, int) - Method in class ij.ImageStack: Creates a new stack by cropping this one.
crop(Roi) - Method in class ij.gui.PointRoi
crop(Roi[]) - Method in class ij.ImagePlus: Multi-roi cropping with default "slice" option.
crop(Roi[], String) - Method in class ij.ImagePlus: Returns an array of cropped images based on the provided list of rois.
crop(ImagePlus) - Method in class ij.plugin.Duplicator: Returns a copy the current image or stack slice, cropped if there is a selection.
crop(Rectangle) - Method in class ij.gui.Overlay
crop(String) - Method in class ij.ImagePlus: Returns a cropped copy this image or stack, where 'options' can be "stack", "slice", "whole-slice" or a range (e.g., "20-30").
cropAndSave(Roi[], String, String) - Method in class ij.ImagePlus: Saves the contents of the ROIs in this overlay as separate images, where 'directory' is the directory path and 'format' is "tif", "png" or "jpg".
cropOverlay(Overlay, Rectangle) - Static method in class ij.plugin.Duplicator
CROSS - Static variable in class ij.gui.Plot: Display points using an cross-shaped mark.
CROSS - Static variable in class ij.gui.PlotWindow: Deprecated.
CROSS - Static variable in class ij.gui.PointRoi
CROSSHAIR - Static variable in class ij.gui.PointRoi
CROSSHAIR - Static variable in class ij.gui.Toolbar
crosshairCursor - Static variable in class ij.gui.ImageCanvas
cScaling - Variable in class ij.plugin.frame.SyncWindows: Checkboxes for user control.
cSelector - Variable in class ij.gui.StackWindow
cSlice - Variable in class ij.plugin.frame.SyncWindows: Checkboxes for user control.
cTable - Variable in class ij.ImageStack
cTable - Variable in class ij.process.ImageProcessor
CTZ - Static variable in class ij.plugin.HyperStackConverter
cubic(double) - Static method in class ij.process.ImageProcessor
currentMacroEditor - Static variable in class ij.plugin.frame.Editor
currentMemory() - Static method in class ij.IJ: Returns the amount of memory currently being used by ImageJ.
currentSlice - Variable in class ij.ImagePlus
cursorOverImage() - Method in class ij.gui.ImageCanvas: Returns 'true' if the cursor is over this image.
CurveFitter - Class in ij.measure: Curve fitting class based on the Simplex method in the Minimizer class Notes on fitting polynomial functions: (i) The range of x values should not be too far from 0, especially for higher-order polynomials.
CurveFitter(double[], double[]) - Constructor for class ij.measure.CurveFitter: Construct a new CurveFitter.
CUSTOM - Static variable in class ij.gui.Plot: Draw shape using macro code
CUSTOM - Static variable in class ij.io.Opener
CUSTOM - Static variable in class ij.measure.Calibration
CUSTOM1 - Static variable in class ij.gui.Toolbar
CUSTOM2 - Static variable in class ij.gui.Toolbar
CUSTOM3 - Static variable in class ij.gui.Toolbar
CUSTOM4 - Static variable in class ij.gui.Toolbar
CUSTOM5 - Static variable in class ij.gui.Toolbar
CUSTOM6 - Static variable in class ij.gui.Toolbar
CUSTOM7 - Static variable in class ij.gui.Toolbar
cut() - Method in class ij.ImagePlus: Copies the contents of the current selection to the internal clipboard and then clears the selection.
cx - Variable in class ij.process.ImageProcessor
cy - Variable in class ij.process.ImageProcessor
CZT - Static variable in class ij.plugin.HyperStackConverter

D

d2s(double) - Static method in class ij.IJ: Converts a number to a formatted string using 2 digits to the right of the decimal point.
d2s(double, int) - Static method in class ij.IJ: Converts a number to a rounded formatted string.
d2s(double, int) - Static method in class ij.measure.ResultsTable: This is a version of IJ.d2s() that uses scientific notation for small numbes that would otherwise display as zero.
d2s(double, int, int) - Static method in class ij.IJ: Converts a number to a rounded formatted string.
D2S - Static variable in interface ij.macro.MacroConstants
D50 - Variable in class ij.process.ColorSpaceConverter: reference white in XYZ coordinates
D55 - Variable in class ij.process.ColorSpaceConverter
D65 - Variable in class ij.process.ColorSpaceConverter
D75 - Variable in class ij.process.ColorSpaceConverter
DARK_BACKGROUND - Static variable in class ij.plugin.frame.ThresholdAdjuster
DARK_OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
darkBlue - Static variable in class ij.plugin.filter.Analyzer
DATE_TIME - Static variable in class ij.io.TiffDecoder
debug(Interpreter, int) - Method in interface ij.macro.Debugger
debug(Interpreter, int) - Method in class ij.plugin.frame.Editor
DEBUG - Static variable in class ij.ImageJ: Run ImageJ in debug mode.
DEBUG - Static variable in interface ij.macro.MacroConstants
DEBUG_LOC_KEY - Static variable in class ij.text.TextWindow
Debugger - Interface in ij.macro
debugInfo - Variable in class ij.io.FileInfo
debugMode - Static variable in class ij.IJ: Use setDebugMode(boolean) to enable/disable debug mode.
debugMode - Variable in class ij.io.TiffDecoder
decimalPlaces - Variable in class ij.gui.HistogramWindow
decode(String) - Static method in class ij.plugin.Colors: Converts a String with the color name or the hexadecimal representation of a color with 6 or 8 hex digits to a Color.
decode(String, Color) - Static method in class ij.plugin.Colors: Converts a String with the color name or the hexadecimal representation of a color with 6 or 8 hex digits to a Color.
decodeDescriptionString(FileInfo) - Method in class ij.io.FileOpener
decodeEscaped(String, char) - Static method in class ij.util.Tools: Decodes backslash-escaped characters from the String until the character 'delim' is found.
decodeToken(int) - Method in class ij.macro.Program
Default - ij.process.AutoThresholder.Method
DEFAULT_FLAGS - Static variable in class ij.gui.Plot: The default axisFlags, will be modified by PlotWindow.noGridLines and PlotWindow.noTicks (see getDefaultFlags)
DEFAULT_JPEG_QUALITY - Static variable in class ij.io.FileSaver
DEFAULT_PORT - Static variable in class ij.ImageJ: Address of socket where Image accepts commands
DEFAULT_QUALITY - Static variable in class ij.plugin.JpegWriter
DEFAULT_VALUE_UNIT - Static variable in class ij.measure.Calibration
defaultChoiceIndexes - Variable in class ij.gui.GenericDialog
defaultColor - Static variable in class ij.gui.Roi
defaultColorModel - Static variable in class ij.process.ImageProcessor
defaultCursor - Static variable in class ij.gui.ImageCanvas
defaultDirectory - Static variable in class ij.gui.HistogramWindow
defaultFillColor - Static variable in class ij.gui.Roi
defaultResultsExtension() - Static method in class ij.Prefs
defaultStrings - Variable in class ij.gui.GenericDialog
defaultText - Variable in class ij.gui.GenericDialog
defaultValues - Variable in class ij.gui.GenericDialog
degreeSymbol - Static variable in class ij.IJ
deleteColumn(String) - Method in class ij.measure.ResultsTable: Deletes the specified column.
DELETED - Static variable in interface ij.gui.RoiListener
deleteHandle(double, double) - Method in class ij.gui.PolygonRoi
deleteLastSlice() - Method in class ij.ImageStack: Deletes the last slice in the stack.
deleteLastSlice() - Method in class ij.VirtualStack: Deletes the last slice in the stack.
deletePoint(int) - Method in class ij.gui.PointRoi
deletePoint(int) - Method in class ij.gui.PolygonRoi
deleteRoi() - Method in class ij.ImagePlus: Deletes the current region of interest.
deleteRow(int) - Method in class ij.measure.ResultsTable: Deletes the specified row.
deleteRows(int, int) - Static method in class ij.IJ: Deletes 'row1' through 'row2' of the "Results" window, where 'row1' and 'row2' must be in the range 0-Analyzer.getCounter()-1.
deleteRows(int, int) - Method in class ij.measure.ResultsTable: Deletes the specified rows.
deleteSlice(int) - Method in class ij.gui.PlotVirtualStack: Deletes the specified slice, where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.ImageStack: Deletes the specified slice, where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.plugin.AVI_Reader: Deletes the specified image from this virtual stack (if it is one), where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.plugin.FileInfoVirtualStack: Deletes the specified image, where 1<=n<=nImages.
deleteSlice(int) - Method in class ij.plugin.ListVirtualStack: Deletes the specified image, where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.VirtualStack: Deletes the specified slice, where 1<=n<=nslices.
descaleX(int) - Method in class ij.gui.Plot: Converts pixels to calibrated coordinates.
descaleY(int) - Method in class ij.gui.Plot: Converts pixels to calibrated coordinates.
description - Variable in class ij.io.FileInfo
deselect() - Method in class ij.plugin.frame.RoiManager
deselect(Roi) - Method in class ij.plugin.frame.RoiManager: Deselect the specified ROI if it is the only one selected.
deserialize(byte[]) - Method in class ij.io.Opener: Deserialize a byte array that was serialized using the FileSaver.serialize().
DESPECKLE - Static variable in class ij.plugin.filter.RankFilters
destroy() - Method in class ij.ImageJApplet
dfht3(float[], int, boolean, int) - Method in class ij.process.FHT: Performs an optimized 1D FHT of an array or part of an array.
DIALOG - Static variable in interface ij.macro.MacroConstants
dialogCancelButtonOnRight - Static variable in class ij.Prefs: Dialog "Cancel" button is on right on Linux
dialogItemChanged(GenericDialog, AWTEvent) - Method in interface ij.gui.DialogListener: This method is invoked by a Generic Dialog if any of the inputs have changed (CANCEL does not trigger it; OK and running the dialog from a macro only trigger the first DialogListener added to a GenericDialog).
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.gui.PlotContentsDialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.gui.PlotDialog: This method is called when the user changes something in the dialog.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.gui.RoiDefaultsDialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.measure.ResultsTableMacros
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.AppearanceOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.ArrowToolOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.CircularRoiMaker
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.Coordinates
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.BackgroundSubtracter
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Binary
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Convolver
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.GaussianBlur: Listener to modifications of the input fields of the dialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.ImageMath
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.MaximumFinder: Read the parameters (during preview or after showing the dialog)
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.PlugInFilterRunner: The listener to any change in the dialog.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.RankFilters
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Rotator
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.StackLabeler
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Translator
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.UnsharpMask
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.Grid
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.HyperStackReducer
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.OverlayLabels
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.PointToolOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RectToolOptions
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RGBStackConverter
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RoiEnlarger
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.SpecifyROI
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.Text
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.WandToolOptions
DialogListener - Interface in ij.gui: PlugIns or PlugInFilters that want to listen to changes in a GenericDialog without adding listeners for each dialog field should implementthis method.
DIAMOND - Static variable in class ij.gui.Plot: Display points using an diamond-shaped mark.
DICOM - Class in ij.plugin: This plugin decodes DICOM files.
DICOM - Static variable in class ij.io.FileInfo
DICOM - Static variable in class ij.io.Opener
DICOM() - Constructor for class ij.plugin.DICOM: Default constructor.
DICOM(BufferedInputStream) - Constructor for class ij.plugin.DICOM: Constructs a DICOM reader that using an BufferredInputStream.
DICOM(InputStream) - Constructor for class ij.plugin.DICOM: Constructs a DICOM reader that using an InputStream.
DicomTools - Class in ij.util: DICOM utilities
DicomTools() - Constructor for class ij.util.DicomTools
DIFFERENCE - Static variable in interface ij.process.Blitter: dst=abs(dst-src)
digits - Variable in class ij.gui.HistogramWindow
dilate() - Method in class ij.process.ByteProcessor
dilate() - Method in class ij.process.ColorProcessor
dilate() - Method in class ij.process.FloatProcessor: Not implemented.
dilate() - Method in class ij.process.ImageProcessor: Dilates the image or ROI using a 3x3 minimum filter.
dilate() - Method in class ij.process.ShortProcessor: Not implemented.
dilate(int, int) - Method in class ij.process.ByteProcessor
dimensionsSet - Variable in class ij.ImagePlus
DIR_IMAGE - Static variable in class ij.Prefs
directory - Variable in class ij.io.FileInfo
DirectoryChooser - Class in ij.io: This class displays a dialog box that allows the user can select a directory.
DirectoryChooser(String) - Constructor for class ij.io.DirectoryChooser: Display a dialog using the specified title.
disableChromaSubsampling(boolean) - Static method in class ij.plugin.JpegWriter
disableCommandRecording() - Static method in class ij.plugin.frame.Recorder
disableDensityCalibration() - Method in class ij.measure.Calibration
disablePathRecording() - Static method in class ij.plugin.frame.Recorder: Temporarily disables path recording.
disablePopupMenu(boolean) - Method in class ij.gui.ImageCanvas: Disable/enable popup menu.
disableReset(boolean) - Method in class ij.plugin.filter.Analyzer: Used by RoiManager.multiMeasure() to suppress save as dialogs.
disableRowLabels() - Method in class ij.measure.ResultsTable: Set the row label column to null if the column label is "Label".
disableUndo - Static variable in class ij.Prefs: Disable Edit/Undo command.
dispatch(Functions) - Method in class ij.macro.ExtensionDescriptor
display(String, String) - Method in class ij.plugin.frame.Editor
DISPLAY_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer: Display a summary.
displayChanged(DisplayChangeEvent) - Method in class ij.plugin.frame.SyncWindows: Method to pass on changes of the z-slice of a stack.
displayComplex - Static variable in class ij.plugin.FFT
displayCounts() - Method in class ij.gui.PointRoi
displayDialog(boolean) - Method in class ij.plugin.AVI_Reader
displayFHT - Static variable in class ij.plugin.FFT
displayRanges - Variable in class ij.io.FileInfo
displayRawPS - Static variable in class ij.plugin.FFT
displayResults() - Method in class ij.plugin.filter.Analyzer: Writes the last row in the system results table to the Results window.
displaySummary - Variable in class ij.plugin.filter.ParticleAnalyzer
dispose() - Method in class ij.gui.GenericDialog: Closes the dialog; records the options
dispose() - Method in class ij.gui.HTMLDialog
dispose() - Method in class ij.gui.NonBlockingGenericDialog
dispose() - Method in class ij.gui.Plot: Releases the ImageProcessor and ImagePlus associated with the plot.
dispose() - Method in class ij.gui.PlotWindow: Releases the resources used by this PlotWindow
Distribution - Class in ij.plugin: This plugin implements the Analyze/Distribution command.
Distribution() - Constructor for class ij.plugin.Distribution
DIV_BY_ZERO_VALUE - Static variable in class ij.Prefs
DIV_EQUAL - Static variable in interface ij.macro.MacroConstants
divide(FHT) - Method in class ij.process.FHT: Returns the image resulting from the point by point Hartley division of this image by the specified image.
DIVIDE - Static variable in interface ij.process.Blitter: dst=dst/src
divideByZeroValue - Static variable in class ij.process.FloatBlitter
dmode - Variable in class ij.process.ImageStatistics: Mode
DO - Static variable in interface ij.macro.MacroConstants
DO_COMMAND - Static variable in interface ij.macro.MacroConstants
DO_WAND - Static variable in interface ij.macro.MacroConstants
doClear() - Method in class ij.text.TextPanel: Implements the Clear command.
doCommand(ImagePlus, String) - Static method in class ij.IJ: Runs a menu command on a separete thread, using the specified image.
doCommand(String) - Static method in class ij.IJ: Runs a menu command on a separete thread and returns immediately.
doCustomFit(UserFunction, int, String, double[], double[], boolean) - Method in class ij.measure.CurveFitter: Fit a function defined in a user plugin implementing the UserFunction interface Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doCustomFit(String, double[], boolean) - Method in class ij.measure.CurveFitter: Fit a function defined as a macro String like "y = a + b*x + c*x*x".
DOES_16 - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter handles 16-bit images.
DOES_32 - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter handles float images.
DOES_8C - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter handles 8-bit indexed color images.
DOES_8G - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter handles 8-bit grayscale images.
DOES_ALL - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter handles all types of images.
DOES_RGB - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter handles RGB images.
DOES_STACKS - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter wants its run() method to be called for all the slices in a stack.
doFit(int) - Method in class ij.measure.CurveFitter: Perform curve fitting with one of the built-in functions doFit(fitType) does the fit quietly Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doFit(int) - Method in class ij.plugin.frame.Fitter: Fit data in the textArea, show result in log and create plot.
doFit(int, boolean) - Method in class ij.measure.CurveFitter: Perform curve fitting with one of the built-in functions doFit(fitType, true) pops up a dialog allowing the user to set the initial fit parameters and various numbers controlling the Minimizer Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doHyperStackProjection(boolean) - Method in class ij.plugin.ZProjector
doMath(ImagePlus, ImagePlus) - Method in class ij.plugin.FFTMath
done - Variable in class ij.gui.StackWindow
done() - Method in class ij.macro.Interpreter
DONE - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the filter does not want its run method called.
doNotSaveWindowLocations - Static variable in class ij.Prefs: Enable this option to workaround a bug with some Linux window managers that causes windows to wander down the screen.
dontSaveHeaders - Static variable in class ij.Prefs: Don't save Results table column headers
dontSaveRowNumbers - Static variable in class ij.Prefs: Don't save Results table row numbers
doOptions() - Method in class ij.plugin.Profiler
doProjection() - Method in class ij.plugin.ZProjector: Performs actual projection using specified method.
doProjection(boolean) - Method in class ij.plugin.ZProjector: Performs actual projection using specified method.
doRGBProjection() - Method in class ij.plugin.ZProjector
doRGBProjection(boolean) - Method in class ij.plugin.ZProjector
DOT - Static variable in class ij.gui.Plot: Display points using a single pixel.
DOT - Static variable in class ij.gui.PointRoi
DOUBLE_CLICK_THRESHOLD - Static variable in class ij.gui.Toolbar
DOUBLE_HEADED - Static variable in class ij.io.RoiDecoder
DOUBLE_HEADED_KEY - Static variable in class ij.gui.Arrow
doubleBuffer - Static variable in class ij.Prefs: No longer used
doWand(int, int) - Static method in class ij.IJ: Equivalent to clicking on the current image at (x,y) with the wand tool.
doWand(int, int, double, String) - Static method in class ij.IJ: Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel at the starting location.
doWand(ImagePlus, int, int, double, String) - Static method in class ij.IJ: This version of doWand adds an ImagePlus argument.
download(String, String) - Static method in class ij.plugin.PluginInstaller
downloadJar(String) - Static method in class ij.plugin.Macro_Runner
DownsizeTable - Class in ij.process: A table for easier downsizing by convolution with a kernel.
DragAndDrop - Class in ij.plugin: This class opens images, roi's, luts and text files dragged and dropped on the "ImageJ" window.
DragAndDrop() - Constructor for class ij.plugin.DragAndDrop
DragAndDropHandler - Class in ij.io: This class handles drag&drop onto JFileChoosers.
DragAndDropHandler(JFileChooser) - Constructor for class ij.io.DragAndDropHandler: Given a JFileChooser 'fc', this is how to use this class:
dragEnter(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
dragExit(DropTargetEvent) - Method in class ij.plugin.DragAndDrop
dragOver(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
draw() - Method in class ij.gui.Plot: Draws the plot specified for the first time.
draw() - Method in class ij.gui.PlotWindow: Displays the plot.
draw() - Method in class ij.ImagePlus: Draws the image.
draw(int, int, int, int) - Method in class ij.ImagePlus: Draws image and roi outline using a clip rect.
draw(Roi) - Method in class ij.process.ImageProcessor: Draws the specified ROI on this image using the line width and color defined by ip.setLineWidth() and ip.setColor().
draw(ImagePlus, int, double, double, int) - Method in class ij.gui.HistogramPlot: Plots a histogram using the specified title, number of bins and histogram range.
draw(ImagePlus, ImageStatistics) - Method in class ij.gui.HistogramPlot: Draws the histogram using the specified title and ImageStatistics.
draw(ImageProcessor) - Method in class ij.plugin.filter.Filler: Deprecated.
replaced by ImageProcessor.draw(Roi)
draw(Graphics) - Method in class ij.gui.Arrow: Draws this arrow on the image.
draw(Graphics) - Method in class ij.gui.EllipseRoi
draw(Graphics) - Method in class ij.gui.ImageRoi
draw(Graphics) - Method in class ij.gui.Line: Draws this line on the image.
draw(Graphics) - Method in class ij.gui.OvalRoi
draw(Graphics) - Method in class ij.gui.PointRoi: Draws the points on the image.
draw(Graphics) - Method in class ij.gui.PolygonRoi
draw(Graphics) - Method in class ij.gui.Roi
draw(Graphics) - Method in class ij.gui.RotatedRectRoi
draw(Graphics) - Method in class ij.gui.ShapeRoi: Non-destructively draws the shape of this object on the associated ImagePlus.
draw(Graphics) - Method in class ij.gui.TextRoi: Draws the text on the screen, clipped to the ROI.
draw(String, ImagePlus, int) - Method in class ij.gui.HistogramPlot: Plots a histogram using the specified title and number of bins.
DRAW_LINE - Static variable in interface ij.macro.MacroConstants
DRAW_OFFSET - Static variable in class ij.io.RoiDecoder
DRAW_OVAL - Static variable in interface ij.macro.MacroConstants
DRAW_RECT - Static variable in interface ij.macro.MacroConstants
DRAW_STRING - Static variable in interface ij.macro.MacroConstants
drawArrow(int, int, int, int, double) - Method in class ij.gui.Plot: Deprecated.
Use as a public method is not supported any more because it is incompatible with rescaling
drawBackgrounds(boolean) - Method in class ij.gui.Overlay
drawColorBar(Graphics, int, int, int, int) - Method in class ij.LookUpTable
drawDot(int, int) - Method in class ij.process.ImageProcessor: Draws a dot using the current line width and fill/draw value.
drawDot2(int, int) - Method in class ij.process.ImageProcessor: Deprecated.
drawDottedLine(double, double, double, double, int) - Method in class ij.gui.Plot: Draws a line using the coordinate system defined by setLimits().
drawEllipse(ImageProcessor) - Method in class ij.process.EllipseFitter: Draws the ellipse on the specified image.
drawEllipse(ImageProcessor) - Method in class ij.process.ImageStatistics
drawHistogram(ImageProcessor, boolean) - Method in class ij.gui.HistogramPlot
drawHistogram(ImageProcessor, boolean) - Method in class ij.gui.HistogramWindow
drawInfo(Graphics) - Method in class ij.gui.ImageWindow: Draws the subtitle.
drawingColor - Variable in class ij.process.ImageProcessor
drawLabel(ImagePlus, ImageProcessor, int, Rectangle) - Method in class ij.plugin.filter.Filler
drawLabels(boolean) - Method in class ij.gui.Overlay
drawLabels(boolean) - Static method in class ij.plugin.filter.Analyzer
drawLine(double, double, double, double) - Method in class ij.gui.Plot: Draws a line using the coordinate system defined by setLimits().
drawLine(int, int) - Method in class ij.gui.Line
drawLine(int, int, int, int) - Method in class ij.process.ImageProcessor: Draws a line from (x1,y1) to (x2,y2).
drawLine4(int, int, int, int) - Method in class ij.process.ImageProcessor
drawNames(boolean) - Method in class ij.gui.Overlay
drawNormalizedLine(double, double, double, double) - Method in class ij.gui.Plot: Draws a line using a normalized 0-1, 0-1 coordinate system, with (0,0) at the top left and (1,1) at the lower right corner.
drawOval(int, int, int, int) - Method in class ij.process.ImageProcessor: Draws an elliptical shape.
drawOverlay(Overlay) - Method in class ij.process.ImageProcessor: Draws the specified Overlay on this image.
drawOverlay(Graphics) - Method in class ij.gui.Roi
drawOverlay(Graphics) - Method in class ij.gui.TextRoi
drawParticle(ImageProcessor, Roi, ImageStatistics, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer: Draws a selected particle in a separate image.
drawPixel(int, int) - Method in class ij.process.ByteProcessor: Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ColorProcessor: Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.FloatProcessor: Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ImageProcessor: Sets the pixel at (x,y) to the current fill/draw value.
drawPixel(int, int) - Method in class ij.process.ShortProcessor: Draws a pixel in the current foreground color.
drawPixels() - Method in class ij.gui.Roi: Deprecated.
replaced by drawPixels(ImageProcessor)
drawPixels(ImageProcessor) - Method in class ij.gui.Arrow
drawPixels(ImageProcessor) - Method in class ij.gui.Line: If the width of this line is less than or equal to one, draws the line.
drawPixels(ImageProcessor) - Method in class ij.gui.OvalRoi: Draws an outline of this OvalRoi on the image.
drawPixels(ImageProcessor) - Method in class ij.gui.PointRoi
drawPixels(ImageProcessor) - Method in class ij.gui.PolygonRoi
drawPixels(ImageProcessor) - Method in class ij.gui.Roi: Draws the selection outline on the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.ShapeRoi: Draws the shape of this object onto the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.TextRoi: Renders the text on the image.
drawPlot(Plot) - Method in class ij.gui.PlotWindow: Draws a new plot in this window.
drawPolygon(Polygon) - Method in class ij.process.ImageProcessor: Draws a polygon.
drawRect(int, int, int, int) - Method in class ij.process.ImageProcessor: Draws a rectangle.
drawRoi(Roi) - Method in class ij.process.ImageProcessor: Draws the specified ROI on this image using the stroke width, stroke color and fill color defined by roi.setStrokeWidth, roi.setStrokeColor() and roi.setFillColor().
drawRoiBrush(Graphics) - Method in class ij.gui.ShapeRoi
drawShapes(String, ArrayList) - Method in class ij.gui.Plot: Adds a set of 'shapes' such as boxes and whiskers
drawSphere(double, int, int, int) - Method in class ij.ImageStack: Experimental
drawString(String) - Method in class ij.process.ImageProcessor: Draws a string at the current drawing location using the current fill/draw value.
drawString(String, int, int) - Method in class ij.process.ImageProcessor: Draws a string at the specified location using the current fill/draw value.
drawString(String, int, int, Color) - Method in class ij.process.ImageProcessor: Draws a string at the specified location with a filled background.
drawUnscaledColorBar(ImageProcessor, int, int, int, int) - Method in class ij.LookUpTable
drawVectors(double[], double[], double[], double[]) - Method in class ij.gui.Plot: Adds a set of points that will be drawn as ARROWs.
drawVectors(ArrayList, ArrayList, ArrayList, ArrayList) - Method in class ij.gui.Plot: Adds a set of vectors to the plot using double ArrayLists.
drop(DropTargetDropEvent) - Method in class ij.plugin.DragAndDrop
dropActionChanged(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
DROPPER - Static variable in class ij.gui.Toolbar
dstHeight - Variable in class ij.gui.ImageCanvas
dstWidth - Variable in class ij.gui.ImageCanvas
DUMP - Static variable in interface ij.macro.MacroConstants
dumpProgram() - Method in class ij.macro.Program
dumpSymbolTable() - Method in class ij.macro.Program
duplicate() - Method in class ij.gui.Overlay: Returns a clone of this Overlay.
duplicate() - Method in class ij.ImagePlus: Returns a copy of this image or stack.
duplicate() - Method in class ij.ImageStack: Duplicates this stack.
duplicate() - Method in class ij.process.ByteProcessor: Returns a duplicate of this image.
duplicate() - Method in class ij.process.ColorProcessor: Returns a duplicate of this image.
duplicate() - Method in class ij.process.FloatPolygon
duplicate() - Method in class ij.process.FloatProcessor: Returns a duplicate of this image.
duplicate() - Method in class ij.process.ImageProcessor: Returns a duplicate of this image.
duplicate() - Method in class ij.process.ShortProcessor: Returns a duplicate of this image.
Duplicater - Class in ij.plugin.filter: Deprecated.
replaced by ij.plugin.Duplicator class
Duplicater() - Constructor for class ij.plugin.filter.Duplicater: Deprecated.
duplicateStack(ImagePlus, String) - Method in class ij.plugin.filter.Duplicater: Deprecated.
duplicateSubstack(ImagePlus, String, int, int) - Method in class ij.plugin.filter.Duplicater: Deprecated.
Duplicator - Class in ij.plugin: This plugin implements the Image/Duplicate command.
Duplicator() - Constructor for class ij.plugin.Duplicator

E

east(ImageProcessor) - Method in class ij.plugin.filter.Shadows
Editor - Class in ij.plugin.frame: This is a simple TextArea based editor for editing and compiling plugins.
Editor() - Constructor for class ij.plugin.frame.Editor
Editor(int, int, int, int) - Constructor for class ij.plugin.frame.Editor
Editor(String) - Constructor for class ij.plugin.frame.Editor
EDM - Class in ij.plugin.filter: This plugin implements the Euclidean Distance Map (EDM), Watershed, Ultimate Eroded Points and Voronoi commands in the Process/Binary submenu.
EDM() - Constructor for class ij.plugin.filter.EDM
edPaste(String) - Method in class ij.macro.FunctionFinder
EIGHT_CONNECTED - Static variable in class ij.gui.Wand: Wand operation type: trace outline of 8-connected pixels
ELLIPSE - Static variable in class ij.io.RoiDecoder
ELLIPSE - Static variable in interface ij.measure.Measurements
ELLIPSE_ROI - Static variable in class ij.gui.Toolbar
EllipseFitter - Class in ij.process: This class fits an ellipse to an ROI.
EllipseFitter() - Constructor for class ij.process.EllipseFitter
EllipseRoi - Class in ij.gui: This class implements the ellipse selection tool.
EllipseRoi(double, double, double, double, double) - Constructor for class ij.gui.EllipseRoi
EllipseRoi(int, int, ImagePlus) - Constructor for class ij.gui.EllipseRoi
ELLIPSES - Static variable in class ij.plugin.filter.ParticleAnalyzer
ELSE - Static variable in interface ij.macro.MacroConstants
EMBEDDED - Static variable in class ij.ImageJ: Run embedded in another application.
enableDebugging() - Method in class ij.io.TiffDecoder
enableSubPixelResolution() - Method in class ij.gui.PolygonRoi
enableSubPixelResolution() - Method in class ij.gui.Roi
enableYesNoCancel() - Method in class ij.gui.GenericDialog: Make this a "Yes No Cancel" dialog.
enableYesNoCancel(String, String) - Method in class ij.gui.GenericDialog: Make this a "Yes No Cancel" dialog with custom labels.
endPaste() - Method in class ij.gui.Roi
ENDS_WITH - Static variable in interface ij.macro.MacroConstants
enhancedLineTool - Static variable in class ij.Prefs: Allow lines to be created with one click at start and another at the end
enhanceQuality(boolean) - Static method in class ij.plugin.JpegWriter: Enhance quality of JPEGs by disabing chroma subsampling.
enlarge(Roi, double) - Static method in class ij.plugin.RoiEnlarger
enlarge(ImagePlus, int) - Static method in class ij.plugin.RoiEnlarger
enlarge255(Roi, double) - Static method in class ij.plugin.RoiEnlarger
EOF - Static variable in interface ij.macro.MacroConstants
EQ - Static variable in interface ij.macro.MacroConstants
equalize(ImagePlus) - Method in class ij.plugin.ContrastEnhancer
equalize(ImageProcessor) - Method in class ij.plugin.ContrastEnhancer: Changes the tone curves of images.
equals(Calibration) - Method in class ij.measure.Calibration: Compares two Calibration objects for equality.
equals(Object) - Method in class ij.gui.Roi: Checks whether two rectangles are equal.
erf(double) - Static method in class ij.util.IJMath
ERF - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
erode() - Method in class ij.process.ByteProcessor
erode() - Method in class ij.process.ColorProcessor
erode() - Method in class ij.process.FloatProcessor: Not implemented.
erode() - Method in class ij.process.ImageProcessor: Erodes the image or ROI using a 3x3 maximum filter.
erode() - Method in class ij.process.ShortProcessor: Not implemented.
erode(int, int) - Method in class ij.process.ByteProcessor
error(String) - Static method in class ij.IJ: Displays a message in a dialog box titled "ImageJ".
error(String, String) - Static method in class ij.IJ: Displays a message in a dialog box with the specified title.
ERROR - Static variable in class ij.gui.PlotContentsDialog: Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
escapePressed() - Method in class ij.gui.HTMLDialog
escapePressed() - Method in class ij.gui.MessageDialog
escapePressed() - Static method in class ij.IJ: Returns true if the Esc key was pressed since the last ImageJ command started to execute or since resetEscape() was called.
escPressed() - Method in class ij.gui.WaitForUserDialog
eval(String) - Static method in class ij.Macro: Evaluates 'code' and returns the output, or any error, as a String (e.g., Macro.eval("2+2") returns "4").
eval(String) - Method in class ij.macro.Interpreter: Evaluates 'code' and returns the output, or any error, as a String.
eval(String) - Method in class ij.plugin.JavaScriptEvaluator
EVAL - Static variable in interface ij.macro.MacroConstants
evalSpline(double) - Method in class ij.measure.SplineFitter: Evalutes spline function at given point
evalSpline(float[], float[], int, double) - Method in class ij.measure.SplineFitter
evalSpline(int[], int[], int, double) - Method in class ij.measure.SplineFitter
evaluateScript(String) - Method in class ij.plugin.frame.Editor
EventListener - Class in ij.plugin: This plugin implements the Plugins/Utilities/Monitor Events command.
EventListener() - Constructor for class ij.plugin.EventListener
eventOccurred(int) - Method in interface ij.IJEventListener
eventOccurred(int) - Method in class ij.plugin.EventListener
ExceptionHandler() - Constructor for class ij.ImageJ.ExceptionHandler
EXCLUDE_EDGE_PARTICLES - Static variable in class ij.plugin.filter.ParticleAnalyzer: Do not measure particles touching edge of image.
excludedFileType(String) - Static method in class ij.plugin.FolderOpener
excludeEdgeParticles - Variable in class ij.plugin.filter.ParticleAnalyzer
EXEC - Static variable in interface ij.macro.MacroConstants
Executer - Class in ij: Runs ImageJ menu commands in a separate thread.
Executer(String) - Constructor for class ij.Executer: Create an Executer to run the specified menu command in this thread using the active image.
Executer(String, ImagePlus) - Constructor for class ij.Executer: Create an Executer that runs the specified menu command in a separate thread using the specified image, or using the active image if 'imp' is null.
exit() - Static method in class ij.IJ: Aborts any currently running JavaScript, or use IJ.error(string) to abort a JavaScript with a message.
EXIT - Static variable in interface ij.macro.MacroConstants
exitConstructingMode() - Method in class ij.gui.PolygonRoi
exitWhenQuitting(boolean) - Method in class ij.ImageJ: ImageJ calls System.exit() when qutting when 'exitWhenQuitting' is true.
exp() - Method in class ij.process.FloatProcessor
exp() - Method in class ij.process.ImageProcessor: Performs a exponential transform on the image or ROI.
exp() - Method in class ij.process.ShortProcessor
EXP - Static variable in interface ij.macro.MacroConstants
EXP_RECOVERY - Static variable in class ij.measure.Calibration
EXP_RECOVERY - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
EXP_RECOVERY_NOOFFSET - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
EXP_REGRESSION - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
EXP_WITH_OFFSET - Static variable in class ij.measure.Calibration
EXP_WITH_OFFSET - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
expandImage(ImageProcessor, int, int, int, int) - Method in class ij.plugin.CanvasResizer
expandStack(ImageStack, int, int, int, int) - Method in class ij.plugin.CanvasResizer
EXPONENTIAL - Static variable in class ij.measure.Calibration
EXPONENTIAL - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
EXT - Static variable in interface ij.macro.MacroConstants
EXTENDED - Static variable in interface ij.gui.RoiListener
ExtendedPlugInFilter - Interface in ij.plugin.filter: ImageJ plugins that process an image may implement this interface.
ExtensionDescriptor - Class in ij.macro
ExtensionDescriptor(String, int[], MacroExtension) - Constructor for class ij.macro.ExtensionDescriptor

F

f(double) - Method in class ij.measure.CurveFitter: Returns the formula value for parameters 'p' at 'x'.
f(double[], double) - Method in class ij.measure.CurveFitter: Returns the formula value for parameters 'p' at 'x'.
f(int, double[], double) - Static method in class ij.measure.CurveFitter: Returns value of built-in 'fitType' formula value for parameters "p" at "x"
f2hex(float) - Static method in class ij.util.Tools: Converts a float to an 9 byte hex string starting with '#'.
FALSE - Static variable in interface ij.macro.MacroConstants
FAST_TRACE - Static variable in interface ij.macro.Debugger
FCOLOR - Static variable in class ij.Prefs
FERET - Static variable in interface ij.measure.Measurements
FERET - Static variable in class ij.measure.ResultsTable
FERET_ANGLE - Static variable in class ij.measure.ResultsTable
FERET_ARRAY_POINTOFFSET - Static variable in class ij.gui.Roi
FERET_ARRAYSIZE - Static variable in class ij.gui.Roi
FERET_X - Static variable in class ij.measure.ResultsTable
FERET_Y - Static variable in class ij.measure.ResultsTable
FFT - Class in ij.plugin: This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands in the Process/FFT submenu.
FFT() - Constructor for class ij.plugin.FFT
FFTCustomFilter - Class in ij.plugin.filter: This class implements the Process/FFT/Custom Filter command.
FFTCustomFilter() - Constructor for class ij.plugin.filter.FFTCustomFilter
FFTFilter - Class in ij.plugin.filter: This class implements the Process/FFT/Bandpass Filter command.
FFTFilter() - Constructor for class ij.plugin.filter.FFTFilter
FFTMath - Class in ij.plugin: The class implements the Process/FFT/Math command.
FFTMath() - Constructor for class ij.plugin.FFTMath
FHT - Class in ij.process: This class contains a Java implementation of the Fast Hartley Transform.
FHT() - Constructor for class ij.process.FHT
FHT(ImageProcessor) - Constructor for class ij.process.FHT: Constructs a FHT object from an ImageProcessor.
FHT(ImageProcessor, boolean) - Constructor for class ij.process.FHT
FILE - Static variable in interface ij.macro.MacroConstants
fileChanged() - Method in class ij.plugin.frame.Editor
fileFormat - Variable in class ij.io.FileInfo
FileInfo - Class in ij.io: This class consists of public fields that describe an image file.
FileInfo() - Constructor for class ij.io.FileInfo: Creates a FileInfo object with all of its fields set to their default value.
FileInfoVirtualStack - Class in ij.plugin: This plugin opens a multi-page TIFF file, or a set of raw images, as a virtual stack.
FileInfoVirtualStack() - Constructor for class ij.plugin.FileInfoVirtualStack
FileInfoVirtualStack(FileInfo) - Constructor for class ij.plugin.FileInfoVirtualStack
FileInfoVirtualStack(FileInfo[]) - Constructor for class ij.plugin.FileInfoVirtualStack
FileInfoVirtualStack(FileInfo, boolean) - Constructor for class ij.plugin.FileInfoVirtualStack
fileName - Variable in class ij.io.FileInfo
fileName - Static variable in class ij.plugin.FFT
FileOpener - Class in ij.io: Opens or reverts an image specified by a FileInfo object.
FileOpener(FileInfo) - Constructor for class ij.io.FileOpener
FileSaver - Class in ij.io: Saves images in tiff, gif, jpeg, raw, zip and text format.
FileSaver(ImagePlus) - Constructor for class ij.io.FileSaver: Constructs a FileSaver from an ImagePlus.
fileType - Variable in class ij.io.FileInfo
fill() - Method in class ij.process.ColorProcessor: Fills the current rectangular ROI.
fill() - Method in class ij.process.FloatProcessor: Fills the current rectangular ROI.
fill() - Method in class ij.process.ImageProcessor: Fills the image or ROI bounding rectangle with the current fill/draw value.
fill() - Method in class ij.process.ShortProcessor: Fills the current rectangular ROI.
fill(int, int) - Method in class ij.process.FloodFiller: Does a 4-connected flood fill using the current fill/draw value, which is defined by ImageProcessor.setValue().
fill(Roi) - Method in class ij.process.ImageProcessor: Fills the ROI with the current fill/draw value.
fill(ImagePlus, Color, Color) - Method in class ij.gui.Overlay: Fills all the ROIs in this overlay with 'foreground' after clearing the the image to 'background' if it is not null.
fill(ImageProcessor) - Method in class ij.plugin.filter.Filler: Deprecated.
replaced by ImageProcessor.fill(Roi)
fill(ImageProcessor) - Method in class ij.process.ByteProcessor: Sets pixels that are within roi and part of the mask to the foreground color.
fill(ImageProcessor) - Method in class ij.process.ColorProcessor: Fills pixels that are within roi and part of the mask.
fill(ImageProcessor) - Method in class ij.process.FloatProcessor: Fills pixels that are within roi and part of the mask.
fill(ImageProcessor) - Method in class ij.process.ImageProcessor: Fills pixels that are within the ROI bounding rectangle and part of the mask (i.e.
fill(ImageProcessor) - Method in class ij.process.ShortProcessor: Fills pixels that are within roi and part of the mask.
fill(ImageProcessor, Rectangle) - Method in class ij.process.PolygonFiller: Fills the polygon using the ImageProcessor's current drawing color.
FILL - Static variable in interface ij.macro.MacroConstants
FILL_BLACK - Static variable in class ij.gui.NewImage
FILL_COLOR - Static variable in class ij.io.RoiDecoder
FILL_NOISE - Static variable in class ij.gui.NewImage
FILL_OVAL - Static variable in interface ij.macro.MacroConstants
FILL_RAMP - Static variable in class ij.gui.NewImage
FILL_RANDOM - Static variable in class ij.gui.NewImage
FILL_RECT - Static variable in interface ij.macro.MacroConstants
FILL_WHITE - Static variable in class ij.gui.NewImage
fill8(int, int) - Method in class ij.process.FloodFiller: Does a 8-connected flood fill using the current fill/draw value, which is defined by ImageProcessor.setValue().
fillByteProcessorMask(ByteProcessor) - Method in class ij.process.PolygonFiller: Fills the ByteProcessor with 255 inside the polygon
fillColor - Variable in class ij.gui.Roi
FILLED - Static variable in class ij.gui.Arrow
FILLED - Static variable in class ij.gui.Plot: Fill area between line plot and x-axis at y=0.
Filler - Class in ij.plugin.filter: This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.
Filler() - Constructor for class ij.plugin.filter.Filler
fillOutside(Roi) - Method in class ij.process.ImageProcessor: Fills outside an Roi.
fillOval(int, int, int, int) - Method in class ij.process.ImageProcessor: Fills an elliptical shape.
fillPolygon(Polygon) - Method in class ij.process.ImageProcessor: Fills a polygon.
fillRect(int, int, int, int) - Method in class ij.process.ImageProcessor: Fills a rectangle.
fillValueSet - Variable in class ij.process.ImageProcessor
fillValueSet() - Method in class ij.process.ImageProcessor: Returns 'true' if the fill/draw value has been set.
filter(int) - Method in class ij.process.ByteProcessor: Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ColorProcessor: A 3x3 filter operation, where the argument (ImageProcessor.BLUR_MORE, FIND_EDGES, MEDIAN_FILTER, MIN or MAX) determines the filter type.
filter(int) - Method in class ij.process.FloatProcessor: Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ImageProcessor: A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES, MEDIAN_FILTER, MIN or MAX) determines the filter type.
filter(int) - Method in class ij.process.ShortProcessor: Filters using a 3x3 neighborhood.
filter(ImagePlus, ImagePlus) - Static method in class ij.plugin.FFT: Version of filter() that accepts an ImagePlus for the filter.
filter(ImagePlus, ImageProcessor) - Static method in class ij.plugin.FFT: Does frequency domain fitering of the speciified image
filter(ImageStack, int, float, float, float) - Static method in class ij.plugin.Filters3D
FILTER - Static variable in class ij.Undo: Undo using ImageProcessor.snapshot.
FILTER_MAX - Static variable in class ij.process.StackProcessor
FILTER_MAXLOCAL - Static variable in class ij.process.StackProcessor
FILTER_MEAN - Static variable in class ij.process.StackProcessor
FILTER_MEDIAN - Static variable in class ij.process.StackProcessor
FILTER_MIN - Static variable in class ij.process.StackProcessor
FILTER_VAR - Static variable in class ij.process.StackProcessor
filter3D(ImageStack, float, float, float, int, int, int) - Method in class ij.process.StackProcessor: 3D filter using threads
filterRGB(int, double) - Method in class ij.process.ColorProcessor: Performs the specified filter on the red, green and blue planes of this image.
Filters - Class in ij.plugin.filter: This plugin implements the Invert, Smooth, Sharpen, Find Edges, and Add Noise commands.
Filters() - Constructor for class ij.plugin.filter.Filters
FILTERS_MENU - Static variable in class ij.Menus
Filters3D - Class in ij.plugin
Filters3D() - Constructor for class ij.plugin.Filters3D
FINAL_PROCESSING - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag if the setup method of the filter should be called again after the calls to the run(ip) have finished.
FIND_EDGES - Static variable in class ij.process.ImageProcessor
findAllMenuItems() - Method in class ij.plugin.CommandFinder
findEdges() - Method in class ij.process.ColorProcessor
findEdges() - Method in class ij.process.ImageProcessor: Finds edges in the image or ROI using a Sobel operator.
findMaxima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder
findMaxima(double[], double, int) - Static method in class ij.plugin.filter.MaximumFinder: Calculates peak positions of 1D array N.Vischer, 06-mar-2017
findMaxima(ImageProcessor, double, boolean, double, int, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder: Here the processing is done: Find the maxima of an image (does not find minima).
findMaxima(ImageProcessor, double, double, int, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder: Finds the maxima of an image (does not find minima).
findMaxima(ImageProcessor, double, int, boolean) - Method in class ij.plugin.filter.MaximumFinder: Find the maxima of an image.
findMinAndMax() - Method in class ij.process.FloatProcessor: Calculates the minimum and maximum pixel value for the entire image.
findMinAndMax() - Method in class ij.process.IntProcessor
findMinAndMax() - Method in class ij.process.ShortProcessor
findMinima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder: Returns minimum positions of array xx, sorted with decreasing strength
findMinima(double[], double, int) - Static method in class ij.plugin.filter.MaximumFinder
findNthLowestNumber(float[], int, int) - Static method in class ij.plugin.filter.RankFilters: Find the n-th lowest number in part of an array
fit(ImageProcessor, ImageStatistics) - Method in class ij.process.EllipseFitter: Fits an ellipse to the current ROI.
FIT - Static variable in interface ij.macro.MacroConstants
fitList - Static variable in class ij.measure.CurveFitter: Names of the built-in fit functions
FITS - Static variable in class ij.io.FileInfo
FITS - Static variable in class ij.io.Opener
FITS_Reader - Class in ij.plugin: Opens and displays FITS images.
FITS_Reader() - Constructor for class ij.plugin.FITS_Reader
FITS_Writer - Class in ij.plugin: This plugin saves a 16 or 32 bit image in FITS format.
FITS_Writer() - Constructor for class ij.plugin.FITS_Writer
fitSpline() - Method in class ij.gui.PolygonRoi: Fits a spline, which becomes the new shape of this Roi
fitSpline(int) - Method in class ij.gui.PolygonRoi: Fits a spline, which becomes the new shape of this Roi
fitSplineForStraightening() - Method in class ij.gui.PolygonRoi: Creates a spline fitted polygon with (roughly) one pixel segment lengths and sets it as the Roi shape.
Fitter - Class in ij.plugin.frame: ImageJ plugin that does curve fitting using the modified CurveFitter class.
Fitter() - Constructor for class ij.plugin.frame.Fitter
fitToWindow() - Method in class ij.gui.ImageCanvas
fitToWindow() - Method in class ij.gui.PlotCanvas: Resizes the plot (unless frozen) to fit the window
fix(Scrollbar) - Static method in class ij.gui.GUI: Lightens overly dark scrollbar background on Windows 8.
fixedDicomScaling - Static variable in class ij.Prefs: Assume DICOM volumes use identical RescaleSlope and RescaleIntercept across all slices
fixLineEndings() - Method in class ij.plugin.frame.Editor: Changes Windows (CRLF) line separators to line feeds (LF).
fixNewLines(String) - Static method in class ij.util.Tools: Converts carriage returns to line feeds.
fixPath(String) - Static method in class ij.plugin.frame.Recorder: Replaces '\' characters with '/'.
fixScrollbar(Scrollbar) - Static method in class ij.gui.GUI: Works around an OpenJDK bug on Windows that causes the scrollbar thumb color and background color to be almost identical.
fixString(String) - Static method in class ij.plugin.frame.Recorder: Replaces special characters in a String for creation of a quoted macro String.
flags - Variable in class ij.gui.ImageCanvas
flatten() - Method in class ij.ImagePlus: Returns a "flattened" version of this image, or stack slice, in RGB format.
flattenScale - Variable in class ij.gui.Roi
flattenStack() - Method in class ij.ImagePlus: Flattens all slices of this stack or HyperStack.
flattenTitle - Static variable in class ij.ImagePlus: Title of image used by Flatten command
FLATTOP - Static variable in class ij.process.FHT
flipHorizontal() - Method in class ij.process.ImageProcessor: Flips the image or ROI horizontally.
flipHorizontal() - Method in class ij.process.StackProcessor
flipImages(boolean) - Static method in class ij.plugin.FITS_Reader
flipStack(ImagePlus) - Method in class ij.plugin.StackReverser
flipVertical() - Method in class ij.process.ByteProcessor
flipVertical() - Method in class ij.process.ColorProcessor
flipVertical() - Method in class ij.process.FloatProcessor
flipVertical() - Method in class ij.process.ImageProcessor: Flips the image or ROI vertically.
flipVertical() - Method in class ij.process.ShortProcessor
flipVertical() - Method in class ij.process.StackProcessor
flipXZ - Static variable in class ij.Prefs: Rotate XZ orthogonal views 180 degrees
fList - Static variable in class ij.measure.CurveFitter: Equations of the built-in fit functions
FLOAT - Static variable in class ij.plugin.filter.EDM: Output type: new 32-bit image
FLOAT_PARAM - Static variable in class ij.io.RoiDecoder
FLOAT_STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
FloatArray - Class in ij.util: This class implements an expandable float array similar to an ArrayList or Vector but more efficient.
FloatArray() - Constructor for class ij.util.FloatArray: Creates a new expandable array with an initial capacity of 100.
FloatArray(int) - Constructor for class ij.util.FloatArray: Creates a new expandable array with specified initial capacity.
FloatBlitter - Class in ij.process: This class does bit blitting of 32-bit floating-point images.
FloatBlitter(FloatProcessor) - Constructor for class ij.process.FloatBlitter: Constructs a FloatBlitter from a FloatProcessor.
FloatPolygon - Class in ij.process: Used by the Roi classes to return float coordinate arrays and to determine if a point is inside or outside of spline fitted selections.
FloatPolygon() - Constructor for class ij.process.FloatPolygon: Constructs an empty FloatPolygon.
FloatPolygon(float[], float[]) - Constructor for class ij.process.FloatPolygon: Constructs a FloatPolygon from x and y arrays.
FloatPolygon(float[], float[], int) - Constructor for class ij.process.FloatPolygon: Constructs a FloatPolygon from x and y arrays.
FloatProcessor - Class in ij.process: This is an 32-bit floating-point image and methods that operate on that image.
FloatProcessor(float[][]) - Constructor for class ij.process.FloatProcessor: Creates a FloatProcessor from a 2D float array using the default LUT.
FloatProcessor(int[][]) - Constructor for class ij.process.FloatProcessor: Creates a FloatProcessor from a 2D int array.
FloatProcessor(int, int) - Constructor for class ij.process.FloatProcessor: Creates a blank FloatProcessor using the default grayscale LUT that displays zero as black.
FloatProcessor(int, int, double[]) - Constructor for class ij.process.FloatProcessor: Creates a FloatProcessor from a double array using the default grayscale LUT.
FloatProcessor(int, int, float[]) - Constructor for class ij.process.FloatProcessor: Creates a new FloatProcessor using the specified pixel array.
FloatProcessor(int, int, float[], ColorModel) - Constructor for class ij.process.FloatProcessor: Creates a new FloatProcessor using the specified pixel array and ColorModel.
FloatProcessor(int, int, int[]) - Constructor for class ij.process.FloatProcessor: Creates a FloatProcessor from an int array using the default grayscale LUT.
FloatStatistics - Class in ij.process: 32-bit (float) image statistics, including histogram.
FloatStatistics(ImageProcessor) - Constructor for class ij.process.FloatStatistics: Constructs an ImageStatistics object from a FloatProcessor using the standard measurement options (area, mean, mode, min and max).
FloatStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.FloatStatistics: Constructs a FloatStatistics object from a FloatProcessor using the specified measurement options.
FLOOD_FILL - Static variable in interface ij.macro.MacroConstants
floodFill - Variable in class ij.plugin.filter.ParticleAnalyzer
FloodFiller - Class in ij.process: This class, which does flood filling, is used by the floodFill() macro function and by the particle analyzer The Wikipedia at "http://en.wikipedia.org/wiki/Flood_fill" has a good description of the algorithm used here as well as examples in C and Java.
FloodFiller(ImageProcessor) - Constructor for class ij.process.FloodFiller
FLOOR - Static variable in interface ij.macro.MacroConstants
flush() - Method in class ij.ImagePlus: Sets the ImageProcessor, Roi, AWT Image and stack image arrays to null.
flush() - Method in class ij.io.LogStream
fMacro - Static variable in class ij.measure.CurveFitter: ImageJ Macro language code for the built-in functions
fmGraphics - Variable in class ij.process.ImageProcessor
fmImage - Variable in class ij.process.ImageProcessor
focusGained(FocusEvent) - Method in class ij.gui.GenericDialog
focusGained(FocusEvent) - Method in class ij.gui.ImageWindow
focusGained(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
focusGained(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
focusGained(FocusEvent) - Method in class ij.plugin.Scaler
focusGained(FocusEvent) - Method in class ij.text.TextWindow
focusLost(FocusEvent) - Method in class ij.gui.GenericDialog
focusLost(FocusEvent) - Method in class ij.gui.ImageWindow
focusLost(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
focusLost(FocusEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
focusLost(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
focusLost(FocusEvent) - Method in class ij.plugin.Scaler
focusLost(FocusEvent) - Method in class ij.text.TextWindow
FolderOpener - Class in ij.plugin: Implements the File/Import/Image Sequence command, which opens a folder of images as a stack.
FolderOpener() - Constructor for class ij.plugin.FolderOpener
font - Variable in class ij.process.ImageProcessor
font10 - Static variable in class ij.IJ: SansSerif, plain, 10-point font
font12 - Static variable in class ij.IJ: SansSerif, plain, 12-point font
font14 - Static variable in class ij.IJ: SansSerif, plain, 14-point font
fontMetrics - Variable in class ij.process.ImageProcessor
fontSize - Static variable in class ij.gui.PlotWindow: The plot text size, can be overridden by Plot.setFont, Plot.setFontSize, Plot.setXLabelFont etc.
FontUtil - Class in ij.util: This class contains static utility methods for replacing fonts that are not available on the current system.
FontUtil() - Constructor for class ij.util.FontUtil
FOR - Static variable in interface ij.macro.MacroConstants
FOREGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
forward(ImagePlus) - Static method in class ij.plugin.FFT: Performs a forward FHT transform.
FOUR_CONNECTED - Static variable in class ij.gui.Wand: Wand operation type: trace outline of 4-connected pixels
FOUR_CONNECTED - Static variable in class ij.plugin.filter.ParticleAnalyzer: Use 4-connected particle tracing.
fourier1D(float[], int) - Method in class ij.process.FHT: Calculates the Fourier amplitudes of an array, based on a 1D Fast Hartley Transform.
fps - Variable in class ij.measure.Calibration: Frame rate in frames per second
FPS - Static variable in class ij.Prefs
FractalBoxCounter - Class in ij.plugin.filter: Calculate the so-called "capacity" fractal dimension.
FractalBoxCounter() - Constructor for class ij.plugin.filter.FractalBoxCounter
frame - Variable in class ij.gui.HistogramWindow
FRAME - Static variable in class ij.measure.ResultsTable
frameInterval - Variable in class ij.io.FileInfo
frameInterval - Variable in class ij.measure.Calibration: Frame interval in 'timeUnit's
FreehandRoi - Class in ij.gui: Freehand region of interest or freehand line of interest
FreehandRoi(int, int, ImagePlus) - Constructor for class ij.gui.FreehandRoi
FREELINE - Static variable in class ij.gui.Roi
FREELINE - Static variable in class ij.gui.Toolbar
freeMemory() - Static method in class ij.IJ: Returns a string something like "64K of 256MB (25%)" that shows how much of the available memory is in use.
FREEROI - Static variable in class ij.gui.Roi
FREEROI - Static variable in class ij.gui.Toolbar
freeze() - Static method in class ij.gui.PlotWindow: Freezes the active plot window, so the image does not get redrawn for zooming, setting the range, etc.
FROM_CHAR_CODE - Static variable in interface ij.macro.MacroConstants
FUNCTION - Static variable in interface ij.macro.MacroConstants
FunctionFinder - Class in ij.macro: This class implements the text editor's Macros/Find Functions command.
FunctionFinder() - Constructor for class ij.macro.FunctionFinder
FunctionFinder(Editor) - Constructor for class ij.macro.FunctionFinder
functionIDs - Static variable in interface ij.macro.MacroConstants
functions - Static variable in interface ij.macro.MacroConstants
Functions - Class in ij.macro: This class implements the built-in macro functions.

G

gamma(double) - Method in class ij.process.FloatProcessor
gamma(double) - Method in class ij.process.ImageProcessor: Performs gamma correction of the image or ROI.
gamma(double) - Method in class ij.process.ShortProcessor
GAMMA_VARIATE - Static variable in class ij.measure.Calibration
GAMMA_VARIATE - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
gapBetweenImages - Variable in class ij.io.FileInfo
GAUSSIAN - Static variable in class ij.measure.Calibration
GAUSSIAN - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
GAUSSIAN_NOOFFSET - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
GaussianBlur - Class in ij.plugin.filter: This plug-in filter uses convolution with a Gaussian function for smoothing.
GaussianBlur() - Constructor for class ij.plugin.filter.GaussianBlur
GaussianBlur3D - Class in ij.plugin
GaussianBlur3D() - Constructor for class ij.plugin.GaussianBlur3D
GelAnalyzer - Class in ij.plugin: This plugin generates gel profile plots that can be analyzed using the wand tool.
GelAnalyzer() - Constructor for class ij.plugin.GelAnalyzer
GenericDialog - Class in ij.gui: This class is a customizable modal dialog box.
GenericDialog(String) - Constructor for class ij.gui.GenericDialog: Creates a new GenericDialog with the specified title.
GenericDialog(String, Frame) - Constructor for class ij.gui.GenericDialog: Creates a new GenericDialog using the specified title and parent frame.
get(int) - Method in class ij.gui.Overlay: Returns the ROI with the specified index or null if the index is invalid.
get(int) - Method in class ij.process.ByteProcessor
get(int) - Method in class ij.process.ColorProcessor
get(int) - Method in class ij.process.FloatProcessor
get(int) - Method in class ij.process.ImageProcessor
get(int) - Method in class ij.process.ShortProcessor
get(int) - Method in class ij.util.FloatArray: Returns the element at the specified position in this FloatArray.
get(int, int) - Method in class ij.process.ByteProcessor
get(int, int) - Method in class ij.process.ColorProcessor
get(int, int) - Method in class ij.process.FloatProcessor
get(int, int) - Method in class ij.process.ImageProcessor: This is a faster version of getPixel() that does not do bounds checking.
get(int, int) - Method in class ij.process.ShortProcessor
get(String) - Method in class ij.gui.Overlay: Returns the ROI with the specified name or null if not found.
get(String, boolean) - Static method in class ij.Prefs: Uses the keyword key to retrieve a boolean from the preferences file.
get(String, double) - Static method in class ij.Prefs: Uses the keyword key to retrieve a number from the preferences file.
get(String, String) - Static method in class ij.Prefs: Uses the keyword key to retrieve a string from the preferences file.
GET_ARGUMENT - Static variable in interface ij.macro.MacroConstants
GET_BOOLEAN - Static variable in interface ij.macro.MacroConstants
GET_BOUNDING_RECT - Static variable in interface ij.macro.MacroConstants
GET_BOUNDS - Static variable in interface ij.macro.MacroConstants
GET_COORDINATES - Static variable in interface ij.macro.MacroConstants
GET_COUNT - Static variable in interface ij.macro.MacroConstants
GET_CURSOR_LOC - Static variable in interface ij.macro.MacroConstants
GET_DATE_AND_TIME - Static variable in interface ij.macro.MacroConstants
GET_DIMENSIONS - Static variable in interface ij.macro.MacroConstants
GET_DIR - Static variable in interface ij.macro.MacroConstants
GET_DIRECTORY - Static variable in interface ij.macro.MacroConstants
GET_DISPLAYED_AREA - Static variable in interface ij.macro.MacroConstants
GET_FILE_LIST - Static variable in interface ij.macro.MacroConstants
GET_FONT_LIST - Static variable in interface ij.macro.MacroConstants
GET_HEIGHT - Static variable in interface ij.macro.MacroConstants
GET_HISTOGRAM - Static variable in interface ij.macro.MacroConstants
GET_ID - Static variable in interface ij.macro.MacroConstants
GET_IMAGE_INFO - Static variable in interface ij.macro.MacroConstants
GET_INFO - Static variable in interface ij.macro.MacroConstants
GET_LINE - Static variable in interface ij.macro.MacroConstants
GET_LIST - Static variable in interface ij.macro.MacroConstants
GET_LOCATION_AND_SIZE - Static variable in interface ij.macro.MacroConstants
GET_LUT - Static variable in interface ij.macro.MacroConstants
GET_METADATA - Static variable in interface ij.macro.MacroConstants
GET_MIN_AND_MAX - Static variable in interface ij.macro.MacroConstants
GET_NUMBER - Static variable in interface ij.macro.MacroConstants
GET_PIXEL - Static variable in interface ij.macro.MacroConstants
GET_PIXEL_SIZE - Static variable in interface ij.macro.MacroConstants
GET_PROFILE - Static variable in interface ij.macro.MacroConstants
GET_RAW_STATISTICS - Static variable in interface ij.macro.MacroConstants
GET_RESULT - Static variable in interface ij.macro.MacroConstants
GET_RESULT_LABEL - Static variable in interface ij.macro.MacroConstants
GET_RESULT_STRING - Static variable in interface ij.macro.MacroConstants
GET_SLICE_NUMBER - Static variable in interface ij.macro.MacroConstants
GET_STATISTICS - Static variable in interface ij.macro.MacroConstants
GET_STRING - Static variable in interface ij.macro.MacroConstants
GET_STRING_WIDTH - Static variable in interface ij.macro.MacroConstants
GET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
GET_TIME - Static variable in interface ij.macro.MacroConstants
GET_TITLE - Static variable in interface ij.macro.MacroConstants
GET_VALUE - Static variable in interface ij.macro.MacroConstants
GET_VERSION - Static variable in interface ij.macro.MacroConstants
GET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
GET_WIDTH - Static variable in interface ij.macro.MacroConstants
GET_ZOOM - Static variable in interface ij.macro.MacroConstants
get16BitBufferedImage() - Method in class ij.process.ShortProcessor: Returns a copy of this image as a TYPE_USHORT_GRAY BufferedImage.
get16bitRangeIndex() - Static method in class ij.plugin.frame.ContrastAdjuster
getActiveChannels() - Method in class ij.CompositeImage
getActiveTable() - Static method in class ij.measure.ResultsTable: Returns the active (front most) displayed ResultsTable.
getActiveTable() - Static method in class ij.WindowManager: Returns the Window containing the active table, or null.
getActiveWindow() - Static method in class ij.WindowManager: Returns the front most window or null.
getAdditionalFunctions() - Static method in class ij.macro.Interpreter
getAllNonImageWindows() - Static method in class ij.WindowManager: Returns an array containing a list of the non-image Frames and Dialogs.
getAllStatistics() - Method in class ij.ImagePlus: This method returns complete calibrated statistics for this image or ROI (with "Limit to threshold"), but it is up to 70 times slower than getStatistics().
getAngle() - Method in class ij.gui.Line
getAngle() - Method in class ij.gui.PolygonRoi: Returns the angle in degrees between the first two segments of this polyline.
getAngle() - Method in class ij.gui.Roi: Overridden by PolygonRoi (angle between first two points), TextRoi (text angle) and Line (line angle).
getAngle() - Method in class ij.gui.TextRoi
getAngle() - Static method in class ij.plugin.filter.Rotator: Returns the current angle.
getAngle(int, int, int, int) - Method in class ij.gui.Roi: Returns the angle in degrees between the specified line and a horizontal line.
getAnimate() - Method in class ij.gui.StackWindow
getAntiAlias() - Method in class ij.gui.Roi
getAntialiased() - Method in class ij.gui.TextRoi: Returns the state of the 'antiAlias' instance variable.
getApplet() - Static method in class ij.IJ: Returns the Applet that created this ImageJ or null if running as an application.
getArgs() - Static method in class ij.ImageJ: Returns the command line arguments passed to ImageJ.
getAutoThreshold() - Method in class ij.process.ImageProcessor: Returns a pixel value (threshold) that can be used to divide the image into objects and background.
getAutoThreshold(int[]) - Method in class ij.process.ImageProcessor: This is a version of getAutoThreshold() that uses a histogram passed as an argument.
getBackgroundColor() - Static method in class ij.gui.Toolbar
getBackgroundValue() - Static method in class ij.gui.Toolbar
getBackgroundValue() - Method in class ij.process.ByteProcessor: Returns the background fill value.
getBackgroundValue() - Method in class ij.process.ColorProcessor: Returns the background fill value.
getBackgroundValue() - Method in class ij.process.FloatProcessor
getBackgroundValue() - Method in class ij.process.ImageProcessor: Returns the background fill value.
getBackgroundValue() - Method in class ij.process.ShortProcessor
getBatchModeImage(int) - Static method in class ij.macro.Interpreter
getBatchModeImageCount() - Static method in class ij.macro.Interpreter
getBatchModeImageIDs() - Static method in class ij.macro.Interpreter
getBatchModeRoiManager() - Static method in class ij.macro.Interpreter: Returns the batch mode RoiManager instance.
getBestIndex(Color) - Method in class ij.process.ColorProcessor: Always returns 0 since RGB images do not use LUTs.
getBestIndex(Color) - Method in class ij.process.ImageProcessor: Returns the LUT index that's the best match for this color.
getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.FloatProcessor: This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.ImageProcessor: This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
getBitDepth() - Method in class ij.gui.PlotVirtualStack: Returns either 24 (RGB) or 8 (grayscale).
getBitDepth() - Method in class ij.ImagePlus: Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth is unknown.
getBitDepth() - Method in class ij.ImageStack: Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).
getBitDepth() - Method in class ij.process.ByteProcessor
getBitDepth() - Method in class ij.process.ColorProcessor
getBitDepth() - Method in class ij.process.FloatProcessor
getBitDepth() - Method in class ij.process.ImageProcessor: Returns the bit depth, 8, 16, 24 (RGB) or 32.
getBitDepth() - Method in class ij.process.ShortProcessor
getBitDepth() - Method in class ij.VirtualStack: Returns the bit depth (8, 16, 24 or 32), or 0 if the bit depth is not known.
getBits(int) - Method in class ij.io.BitBuffer
getBlockIncrement() - Method in class ij.gui.ScrollbarWithLabel
getBlue(String) - Static method in class ij.plugin.Colors
getBlues() - Method in class ij.LookUpTable
getBoolean(String, boolean) - Static method in class ij.Prefs: Retrieves a boolean from IJ_Props or IJ_Prefs.txt.
getBoundingRect() - Method in class ij.gui.Roi: Deprecated.
replaced by getBounds()
getBounds() - Method in class ij.gui.Arrow: Return the bounding rectangle of this arrow.
getBounds() - Method in class ij.gui.Roi: Returns this selection's bounding rectangle.
getBounds() - Method in class ij.process.FloatPolygon
getBrightness() - Method in class ij.process.ColorProcessor: Returns brightness as a FloatProcessor.
getBrushSize() - Static method in class ij.gui.Toolbar: Returns the size of the selection brush tool, or 0 if the brush tool is not enabled.
getBufferedImage() - Method in class ij.ImagePlus: Returns a copy of this image as an 8-bit or RGB BufferedImage.
getBufferedImage() - Method in class ij.process.ByteProcessor: Returns this image as a BufferedImage.
getBufferedImage() - Method in class ij.process.FloatProcessor: Returns this image as an 8-bit BufferedImage.
getBufferedImage() - Method in class ij.process.ImageProcessor: Returns this image as a BufferedImage.
getBufferedImage() - Method in class ij.process.IntProcessor: Returns this image as an 8-bit BufferedImage .
getBufferedImage() - Method in class ij.process.ShortProcessor: Returns this image as an 8-bit BufferedImage .
getButton() - Method in class ij.gui.WaitForUserDialog: Returns a reference to the 'OK' button
getButtons() - Method in class ij.gui.GenericDialog: Returns references to the "OK" ("Yes"), "Cancel", "No", and "Help" buttons as an array of length 4.
getButtonSize() - Static method in class ij.gui.Toolbar: Returns the button width (button spacing).
getBytes() - Method in class ij.process.LUT
getBytesPerPixel() - Method in class ij.ImagePlus: Returns the number of bytes per pixel.
getBytesPerPixel() - Method in class ij.io.FileInfo: Returns the number of bytes used per pixel.
getC() - Method in class ij.ImagePlus: Returns the current hyperstack channel position.
getCachedFont() - Static method in class ij.Menus
getCalibration() - Method in class ij.ImagePlus: Returns this image's calibration.
getCalibrationTable() - Method in class ij.process.ImageProcessor: Returns the calibration table or null.
getCanvas() - Method in class ij.gui.ImageWindow
getCanvas() - Method in class ij.ImagePlus: Returns the ImageCanvas being used to display this image, or null.
getCaseSensitive() - Method in class ij.util.WildcardMatch: Returns the current state of case sensitivity.
getChannel() - Method in class ij.ImagePlus
getChannel(int) - Method in class ij.process.ColorProcessor: Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a byte array.
getChannel(int, ByteProcessor) - Method in class ij.process.ColorProcessor: Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a ByteProcessor.
getChannel(ImagePlus, int) - Static method in class ij.plugin.ChannelSplitter: Returns, as an ImageStack, the specified channel, where 'c' must be greater than zero and less than or equal to the number of channels in the image.
getChannelColor() - Method in class ij.CompositeImage: Returns the color used to display the image subtitle and "B&C" histogram.
getChannelLut() - Method in class ij.CompositeImage
getChannelLut(int) - Method in class ij.CompositeImage
getChannelProcessor() - Method in class ij.CompositeImage
getChannelProcessor() - Method in class ij.ImagePlus: Returns a reference to the current ImageProcessor.
getCheckboxes() - Method in class ij.gui.GenericDialog: Returns the Vector containing the Checkboxes.
getChoices() - Method in class ij.gui.GenericDialog: Returns the Vector containing the Choices.
getClassLoader() - Static method in class ij.IJ: Returns the class loader ImageJ uses to run plugins or the system class loader if Menus.getPlugInsPath() returns null.
getClipboard() - Static method in class ij.ImagePlus: Returns the internal clipboard or null if the internal clipboard is empty.
getClosestPoint(double, double, FloatPolygon) - Method in class ij.gui.PointRoi
getClosestPoint(double, double, FloatPolygon) - Method in class ij.gui.PolygonRoi
getCode() - Method in class ij.io.FileInfo: Returns JavaScript code that can be used to recreate this FileInfo.
getCode() - Method in class ij.macro.Program
getCoefficients() - Method in class ij.measure.Calibration: Returns the calibration function coefficients.
getColor() - Method in class ij.gui.ColorChooser: Displays a color selection dialog and returns the color selected by the user.
getColor() - Static method in class ij.gui.Roi: Returns the default (global) color used for drawing ROI outlines.
getColor() - Method in class ij.gui.Toolbar: Deprecated.
replaced by getForegroundColor()
getColor(int, int) - Method in class ij.process.ColorProcessor
getColor(String, Color) - Static method in class ij.plugin.Colors: For named colors, converts the name String to the corresponding color.
getColor(String, Color) - Static method in class ij.Prefs: Finds a color in IJ_Props or IJ_Prefs.txt.
getColorModel() - Method in class ij.ImageStack: Returns this stack's color model.
getColorModel() - Method in class ij.LookUpTable
getColorModel() - Method in class ij.process.ImageProcessor: Returns this processor's color model.
getColorModel() - Method in class ij.process.LUT
getColorName(Color, String) - Static method in class ij.plugin.Colors: For named colors, returns the name, or 'defaultName' if not a named color.
getColors(String...) - Static method in class ij.plugin.Colors: Returns an array of the color Strings in the argument(s) and the 13 predefined color names "Red", "Green", ...
getColumn(int) - Method in class ij.measure.ResultsTable: Returns a copy of the given column as a float array, or null if the column is empty.
getColumn(int, int, float[], int) - Method in class ij.process.ImageProcessor: Returns the pixel values down the column starting at (x,y).
getColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor: Returns the pixel values down the column starting at (x,y).
getColumn(String) - Method in class ij.measure.ResultsTable: Returns a copy of the given column as a double array, or null if the column is not found.
getColumnAsDoubles(int) - Method in class ij.measure.ResultsTable: Returns a copy of the given column as a double array, or null if the column is empty.
getColumnAsStrings(String) - Method in class ij.measure.ResultsTable: Returns a copy of the given column as a String array, or null if the column is not found.
getColumnAsVariables(String) - Method in class ij.measure.ResultsTable: Implements the Table.getColumn() macro function.
getColumnAverageProfile(Rectangle, ImageProcessor) - Static method in class ij.gui.ProfilePlot
getColumnHeading(int) - Method in class ij.measure.ResultsTable: Returns the heading of the specified column or null if the column is empty.
getColumnHeadings() - Method in class ij.measure.ResultsTable: Returns a tab or comma delimited string containing the column headings.
getColumnHeadings() - Method in class ij.text.TextPanel: Returns the column headings as a tab-delimited string.
getColumnIndex(String) - Method in class ij.measure.ResultsTable: Returns the index of the first column with the given heading.
getCommand() - Static method in class ij.Executer: Returns the last command executed.
getCommand() - Static method in class ij.plugin.frame.Recorder: Returns the name of the command currently being recorded, or null.
getCommandName() - Static method in class ij.ImageJ
getCommandOptions() - Static method in class ij.plugin.frame.Recorder: Used by GenericDialog to determine if any options have been recorded.
getCommands() - Static method in class ij.Menus: Returns the hashtable that associates commands with plugins.
getCompletedMinimizations() - Method in class ij.measure.Minimizer: Get number of minimizations completed (i.e.
getComplexTransform() - Method in class ij.process.FHT: Converts this FHT to a complex Fourier transform and returns it as a two slice stack.
getCompositeMode() - Method in class ij.ImagePlus: Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.
getContainedFloatPoints() - Method in class ij.gui.PointRoi: Returns the points as a FloatPolygon.
getContainedFloatPoints() - Method in class ij.gui.Roi: Returns the coordinates of the pixels inside this ROI as a FloatPolygon.
getContainedPoints() - Method in class ij.gui.PointRoi: Returns the points as an array of Points.
getContainedPoints() - Method in class ij.gui.Roi: Returns the coordinates of the pixels inside this ROI as an array of Points.
getContourCentroid() - Method in class ij.gui.Roi
getControlPanelProperties() - Static method in class ij.Prefs
getConvexHull() - Method in class ij.gui.Roi: Returns the convex hull of this Roi as a Polygon with integer coordinates by rounding the floating-point values.
getConvexHull() - Method in class ij.process.FloatPolygon: Uses the gift wrap algorithm to find the convex hull of all points in this FloatPolygon and returns it as a new FloatPolygon.
getCopy() - Method in class ij.process.FHT: Returns a clone of this FHT.
getCornerDiameter() - Method in class ij.gui.Roi: Returns the rounded rectangle corner diameter (pixels).
getCount() - Method in class ij.plugin.frame.RoiManager: Returns the ROI count.
getCount(int) - Method in class ij.gui.PointRoi: Returns the count associated with the specified counter index.
getCounter() - Method in class ij.gui.PointRoi: Returns the index of the current counter.
getCounter() - Method in class ij.measure.ResultsTable: Returns the current value of the measurement counter.
getCounter() - Static method in class ij.plugin.filter.Analyzer: Returns the current measurement count.
getCounter(int) - Method in class ij.gui.PointRoi: Returns the counter assocated with the specified point.
getCounterChoices() - Static method in class ij.gui.PointRoi
getCounterInfo() - Method in class ij.gui.PointRoi
getCounters() - Method in class ij.gui.PointRoi: Returns an array containing for each point: The counter number (0-100) in the lower 8 bits, and the slice number (or 0, if the point appears on all slices) in the higher 24 bits.
getCPosition() - Method in class ij.gui.Roi: Returns the channel position of this ROI, or zero if this ROI is not associated with a particular channel.
getCrossLoc() - Method in class ij.plugin.Orthogonal_Views
getCTable() - Method in class ij.measure.Calibration: Returns the calibration table.
getCurrentColorModel() - Method in class ij.process.ImageProcessor: Returns the current color model, which may have been modified by setMinAndMax() or setThreshold().
getCurrentErrStream() - Static method in class ij.io.LogStream: Returns the redirection stream for System.err if it exists.
getCurrentFont() - Method in class ij.gui.Plot: Returns the font currently used (e.g.
getCurrentFont() - Method in class ij.gui.TextRoi: Returns the current font.
getCurrentImage() - Static method in class ij.WindowManager: Returns a reference to the active image or null if there isn't one.
getCurrentOutStream() - Static method in class ij.io.LogStream: Returns the redirection stream for System.out if it exists.
getCurrentPasteMode() - Static method in class ij.gui.Roi: Returns the current paste transfer mode.
getCurrentSlice() - Method in class ij.ImagePlus: Returns the current stack index (one-based) or 1 if this is a single image.
getCurrentWindow() - Static method in class ij.WindowManager: Returns the active ImageWindow.
getCursorLoc() - Method in class ij.gui.ImageCanvas: Returns the current cursor location in image coordinates.
getCustomPrefsPath() - Static method in class ij.Prefs: Returns the custom preferences (IJ_Prefs.txt) file path.
getCustomPropsPath() - Static method in class ij.Prefs: Returns the custom properties (IJ_Props.txt) file path.
getCustomRoi() - Method in class ij.gui.ImageCanvas
getCValue(double) - Method in class ij.measure.Calibration: Converts a raw pixel value to a density calibrated value.
getCValue(int) - Method in class ij.measure.Calibration: Converts a raw pixel value to a density calibrated value.
getDataObjectArrays(int) - Method in class ij.gui.Plot: Get the data of the n-th Plot Object containing xy data in the sequence they were added (Other Plot Objects such as labels, arrows, lines, shapes and hidden PlotObjects are not counted).
getDataObjectDesignations() - Method in class ij.gui.Plot: Gets an array with human-readable designations of the PlotObjects containing xy data in the sequence they were added.
getDebugger() - Method in class ij.macro.Interpreter
getDebugInfo() - Method in class ij.gui.PolygonRoi
getDebugInfo() - Method in class ij.gui.Roi
getDecimalPlaces(double) - Static method in class ij.util.Tools: Returns the number of decimal places needed to display a number, or -2 if exponential notation should be used.
getDecimalPlaces(double, double) - Static method in class ij.util.Tools: Returns the number of decimal places needed to display two numbers, or -2 if exponential notation should be used.
getDefault16bitRange() - Static method in class ij.ImagePlus: Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 14, 15 or 16.
getDefaultColorModel() - Method in class ij.process.ImageProcessor: Returns the default grayscale IndexColorModel.
getDefaultCrossColor() - Static method in class ij.gui.PointRoi: Deprecated
getDefaultDirectory() - Static method in class ij.io.OpenDialog: Returns the current working directory as a string ending in the separator character ("/" or "\"), or an empty or null string.
getDefaultDirectory() - Static method in class ij.Prefs: Returns the default directory, if any, or null.
getDefaultDoubleHeaded() - Static method in class ij.gui.Arrow
getDefaultFillColor() - Static method in class ij.gui.Roi
getDefaultFlags() - Static method in class ij.gui.Plot: The default flags, taking PlotWindow.noGridLines, PlotWindow.noTicks into account
getDefaultFont() - Method in class ij.gui.Plot: Returns the default font for the plot
getDefaultFontName() - Static method in class ij.gui.TextRoi: Returns the name of the default font.
getDefaultFontSize() - Static method in class ij.gui.PlotWindow
getDefaultFontSize() - Static method in class ij.gui.TextRoi: Returns the default font size.
getDefaultFontStyle() - Static method in class ij.gui.TextRoi: Returns the default font style.
getDefaultGroup() - Static method in class ij.gui.Roi: Returns the group value assigned to newly created ROIs.
getDefaultHandleSize() - Static method in class ij.gui.Roi: Returns the default handle size.
getDefaultHeading(int) - Static method in class ij.measure.ResultsTable
getDefaultHeadings() - Static method in class ij.measure.ResultsTable: Returns the default headings ("Area","Mean","StdDev", etc.).
getDefaultHeadSize() - Static method in class ij.gui.Arrow
getDefaultMarkerSize() - Static method in class ij.gui.PointRoi: Deprecated.
getDefaultOutline() - Static method in class ij.gui.Arrow
getDefaultSize() - Static method in class ij.gui.PointRoi: Returns the default point size 0-6 (Tiny-XXXL).
getDefaultStrokeColor() - Static method in class ij.plugin.RectToolOptions
getDefaultStrokeWidth() - Static method in class ij.gui.Roi: Returns the default stroke width.
getDefaultStrokeWidth() - Static method in class ij.plugin.RectToolOptions
getDefaultStyle() - Static method in class ij.gui.Arrow
getDefaultType() - Static method in class ij.gui.PointRoi
getDefaultWidth() - Static method in class ij.gui.Arrow
getDescriptionString() - Method in class ij.io.FileSaver: Returns a string containing information about the specified image.
getDimensions() - Method in class ij.ImagePlus: Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.
getDimensions(boolean) - Method in class ij.ImagePlus
getDir(String) - Static method in class ij.IJ: Alias for getDirectory().
getDir(String) - Method in class ij.io.Opener
getDir(String) - Static method in class ij.Macro
getDirectory() - Method in class ij.io.DirectoryChooser: Returns the directory selected by the user.
getDirectory() - Method in class ij.io.OpenDialog: Returns the selected directory.
getDirectory() - Method in class ij.io.SaveDialog: Returns the selected directory.
getDirectory() - Method in class ij.macro.Functions
getDirectory() - Method in class ij.plugin.FileInfoVirtualStack
getDirectory() - Method in class ij.VirtualStack: Returns the path to the directory containing the images.
getDirectory(String) - Static method in class ij.IJ: Returns the path to the specified directory if title is "home" ("user.home"), "downloads", "startup", "imagej" (ImageJ directory), "plugins", "macros", "luts", "temp", "current", "default", "image" (directory active image was loaded from), "file" (directory most recently used to open or save a file), "cwd" (current working directory) or "preferences" (location of "IJ_Prefs.txt" file), otherwise displays a dialog and returns the path to the directory selected by the user.
getDisplayList() - Method in class ij.gui.ImageCanvas: Deprecated.
replaced by ImagePlus.getOverlay()
getDisplayMode() - Method in class ij.ImagePlus: Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a composite color image, or 0 if it not.
getDisplayRangeMax() - Method in class ij.CompositeImage
getDisplayRangeMax() - Method in class ij.ImagePlus
getDisplayRangeMin() - Method in class ij.CompositeImage
getDisplayRangeMin() - Method in class ij.ImagePlus
getDoScaling() - Static method in class ij.process.ImageConverter: Returns true if scaling is enabled.
getDouble(String, double) - Static method in class ij.Prefs: Retrieves a number from IJ_Props or IJ_Prefs.txt.
getDoubleFromArrayList(ArrayList) - Method in class ij.gui.Plot
getDoubleHeaded() - Method in class ij.gui.Arrow
getDrawBackgrounds() - Method in class ij.gui.Overlay
getDrawingFrame() - Method in class ij.gui.Plot: Returns the rectangle where the data are plotted.
getDrawLabels() - Method in class ij.gui.Overlay
getDrawLabels() - Method in class ij.plugin.frame.RoiManager
getDrawNames() - Method in class ij.gui.Overlay
getDrawOffset() - Method in class ij.gui.Roi: Deprecated.
Drawoffset is not used any more.
getDrawStringMode() - Method in class ij.gui.TextRoi
getEditor() - Method in class ij.plugin.NewPlugin: Returns the Editor the newly created macro or plugin was opened in.
getErrorMessage() - Method in class ij.gui.GenericDialog: Returns an error message if getNextNumber was unable to convert a string into a number, otherwise, returns null.
getErrorMessage() - Static method in class ij.IJ: Returns the last error message written by IJ.error() or null if there was no error since the last time this method was called.
getErrorMessage() - Method in class ij.macro.Interpreter
getErrorMessage() - Static method in class ij.plugin.frame.RoiManager: Returns the most recent I/O error message, or null if there was no error.
getErrorText() - Method in class ij.plugin.AVI_Reader: Returns a description of the error reading the file with makeStack or null if no error
getEscapeChar() - Method in class ij.util.WildcardMatch: Returns the character used to escape the wildcard functionality of a wildcard character.
getExamplesMenu(ActionListener) - Static method in class ij.Menus
getExifData(ImagePlus) - Method in class ij.plugin.ImageInfo
getExtensionFunctions() - Method in interface ij.macro.MacroExtension
getf(int) - Method in class ij.process.ByteProcessor
getf(int) - Method in class ij.process.ColorProcessor
getf(int) - Method in class ij.process.FloatProcessor
getf(int) - Method in class ij.process.ImageProcessor
getf(int) - Method in class ij.process.ShortProcessor
getf(int, int) - Method in class ij.process.ByteProcessor
getf(int, int) - Method in class ij.process.ColorProcessor
getf(int, int) - Method in class ij.process.FloatProcessor
getf(int, int) - Method in class ij.process.ImageProcessor: Returns the value of the pixel at (x,y) as a float.
getf(int, int) - Method in class ij.process.ShortProcessor
getFeretsDiameter() - Method in class ij.gui.Roi: Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
getFeretValues() - Method in class ij.gui.EllipseRoi
getFeretValues() - Method in class ij.gui.OvalRoi: Feret (caliper width) values, see ij.gui.Roi.getFeretValues().
getFeretValues() - Method in class ij.gui.Roi: Returns an array with the following values:
[0] "Feret" (maximum caliper width)
[1] "FeretAngle" (angle of diameter with maximum caliper width, between 0 and 180 deg)
[2] "MinFeret" (minimum caliper width)
[3][4] , "FeretX" and "FeretY", the X and Y coordinates of the starting point (leftmost point) of the maximum-caliper-width diameter.
getFileFormat(String) - Static method in class ij.io.Opener
getFileInfo() - Method in class ij.ImagePlus: Returns a FileInfo object containing information, including the pixel array, needed to save this image.
getFileInfo() - Method in class ij.io.ImportDialog: Displays the dialog and returns a FileInfo object that can be used to open the image.
getFileName() - Method in class ij.io.OpenDialog: Returns the selected file name.
getFileName() - Method in class ij.io.SaveDialog: Returns the selected file name.
getFileName() - Static method in class ij.plugin.MacroInstaller
getFileName(int) - Method in class ij.plugin.FileInfoVirtualStack
getFileName(int) - Method in class ij.VirtualStack: Returns the file name of the specified slice, where 1<=n<=nslices.
getFilePath() - Method in class ij.io.FileInfo: Returns the file path.
getFilePath() - Static method in class ij.plugin.Macro_Runner: Returns the file path of the most recently loaded macro or script.
getFilePath(String) - Static method in class ij.IJ: Displays an open file dialog and returns the path to the choosen file, or returns null if the dialog is canceled.
getFilePointer() - Method in class ij.io.RandomAccessStream
getFileSeparator() - Static method in class ij.Prefs: Returns the file.separator system property.
getFileType(String) - Method in class ij.io.Opener: Attempts to determine the image file type by looking for 'magic numbers' and the file name extension.
getFillColor() - Method in class ij.gui.Roi: Returns the fill color used to display this ROI, or null if it is displayed transparently.
getFilteredList(String[], String, String) - Static method in class ij.plugin.FolderOpener
getFit() - Method in class ij.measure.CurveFitter: returns the code of the fit type of the fit performed
getFitCode(String) - Static method in class ij.measure.CurveFitter: Returns the code for a fit with given name as defined in fitList, or -1 if not found
getFitGoodness() - Method in class ij.measure.CurveFitter: Get a measure of "goodness of fit" where 1.0 is best.
getFixedMax() - Static method in class ij.gui.ProfilePlot: Returns the profile plot y-axis max.
getFixedMin() - Static method in class ij.gui.ProfilePlot: Returns the profile plot y-axis min.
getFlags() - Method in class ij.gui.Plot: Returns the flags that control the axes
getFloatAngle(double, double, double, double) - Method in class ij.gui.Roi: Returns the angle in degrees between the specified line and a horizontal line.
getFloatArray() - Method in class ij.process.ImageProcessor: Returns a copy of the pixel data as a 2D float array with dimensions [x=0..width-1][y=0..height-1].
getFloatBounds() - Method in class ij.gui.Roi: Returns this selection's bounding rectangle (with subpixel accuracy).
getFloatBounds() - Method in class ij.process.FloatPolygon
getFloatConvexHull() - Method in class ij.gui.Roi: Returns the convex hull of this Roi as a FloatPolygon.
getFloatConvexHull() - Method in class ij.gui.ShapeRoi
getFloatHeight() - Method in class ij.gui.Roi
getFloatPoints() - Method in class ij.gui.Line: Returns, as a FloatPolygon, the two points that define this line.
getFloatPolygon() - Method in class ij.gui.Line: If the width of this line is less than or equal to one, returns the starting and ending coordinates as a 2-point FloatPolygon, or, if the width is greater than one, returns an outline of the line as a 4-point FloatPolygon.
getFloatPolygon() - Method in class ij.gui.OvalRoi: Returns this OvalRoi as a FloatPolygon approximating the ellipse.
getFloatPolygon() - Method in class ij.gui.PolygonRoi: Returns this polygon or polyline as float arrays in image pixel coordinates.
getFloatPolygon() - Method in class ij.gui.Roi: Returns the outline of this selection as a FloatPolygon
getFloatPolygon() - Method in class ij.gui.ShapeRoi: Returns all vertex points of the shape as approximated by polygons, in image pixel coordinates
getFloatPolygon(double) - Method in class ij.gui.Line: Obsolete
getFloatPolygon(double, boolean, boolean, boolean) - Method in class ij.gui.ShapeRoi: Returns a FloatPolygon with all vertices of the flattened shape, i.e., the shape approximated by straight line segments.
getFloatPolygon(Shape, double, boolean, boolean, boolean) - Method in class ij.gui.ShapeRoi
getFloatPolygon(String) - Method in class ij.gui.Roi: Returns the outline in image pixel coordinates, where options may include "close" to add a point to close the outline if this is an area roi and the outline is not closed yet.
getFloatPolygon(String) - Method in class ij.gui.ShapeRoi: Returns all vertex points of the shape as approximated by polygons, where options may include "close" to add points to close each subpath, and "separate" to insert NaN values between subpaths (= individual polygons)
getFloatPolygon4() - Method in class ij.gui.OvalRoi: Returns this OvalRoi as a 4 point FloatPolygon (x,y,w,h).
getFloatWidth() - Method in class ij.gui.Roi
getFont() - Static method in class ij.gui.TextRoi: Deprecated.
Replaced by getDefaultFontName
getFont() - Static method in class ij.Menus
getFont() - Method in class ij.process.ImageProcessor: Returns the current font.
getFont(boolean) - Static method in class ij.Menus
getFont(char) - Method in class ij.gui.Plot: Gets the font for xLabel ('x'), yLabel('y'), numbers ('f' for 'frame') or the legend ('l').
getFont(String, int, float) - Static method in class ij.util.FontUtil: Returns a font with the given family name or, if not available, a similar font, e.g.
getFontMetrics() - Method in class ij.process.ImageProcessor: Returns the current FontMetrics.
getFontSize() - Static method in class ij.Menus: Returns the size (in points) used for the fonts in ImageJ menus.
getFontSize() - Method in class ij.plugin.frame.Editor
getForegroundColor() - Static method in class ij.gui.Toolbar
getForegroundValue() - Static method in class ij.gui.Toolbar
getForegroundValue() - Method in class ij.process.ByteProcessor: Returns the foreground fill/draw value.
getForegroundValue() - Method in class ij.process.ColorProcessor: Returns the foreground fill/draw value.
getForegroundValue() - Method in class ij.process.FloatProcessor: Returns the foreground fill/draw value.
getForegroundValue() - Method in class ij.process.ImageProcessor: Returns the default fill/draw value.
getForegroundValue() - Method in class ij.process.ShortProcessor: Returns the foreground fill/draw value.
getFormula() - Method in class ij.measure.CurveFitter: returns a String with the formula of the fit function used
getFrame() - Method in class ij.ImagePlus
getFrame(String) - Static method in class ij.WindowManager: Obsolete; replaced by getWindow().
getFrameRate() - Static method in class ij.plugin.Animator: Returns the current animation speed in frames per second.
getFreeColumn(String) - Method in class ij.measure.ResultsTable: Sets the heading of the the first available column and returns that column's index.
getFrontWindow() - Static method in class ij.WindowManager: Obsolete; replaced by getActiveWindow.
getFullVersion() - Static method in class ij.IJ: Returns the ImageJ version and build number as a String, for example "1.46n05", or 1.46n99 if there is no build number.
getFunction() - Method in class ij.measure.Calibration: Returns the calibration function ID.
getFunctionValue() - Method in class ij.measure.Minimizer: Get the value of the minimum, i.e.
getGap() - Method in class ij.io.FileInfo: Returns the gap between images as a long.
getGelImage() - Static method in class ij.plugin.GelAnalyzer
getGlobalCalibration() - Method in class ij.ImagePlus: Returns the system-wide calibration, or null.
getGlobalJustification() - Static method in class ij.gui.TextRoi: Returns the default text tool justification (LEFT, CENTER or RIGHT).
getGlobals() - Method in class ij.macro.Program
getGreen(String) - Static method in class ij.plugin.Colors
getGreens() - Method in class ij.LookUpTable
getGroup() - Method in class ij.gui.Roi: Returns the group attribute of this ROI.
getGroupName(int) - Static method in class ij.gui.Roi: Returns the group name associtated with the specified group.
getGroupNames() - Static method in class ij.gui.Roi: Returns the group names as a comma-delimeted string.
getGuiScale() - Static method in class ij.Prefs: Returns the GenericDialog and Command Finder text scale.
getHandleSize() - Method in class ij.gui.Roi: Returns the current handle size.
getHash(String, boolean, String) - Static method in class ij.util.Tools: Returns the checksum of a string or file, or "0" if no success.
getHashCode() - Method in class ij.gui.Roi: Returns a hashcode for this Roi that typically changes if it is moved, even though it is still the same object.
getHeader(ImagePlus) - Static method in class ij.plugin.FITS_Writer: Extracts the original FITS header from the Properties object of the ImagePlus image (or from the current slice label in the case of an ImageStack) and returns it as an array of String objects representing each card.
getHeadings() - Method in class ij.measure.ResultsTable: Returns the column headings as an array of Strings.
getHeadingsAsVariableNames() - Method in class ij.measure.ResultsTable: Returns the column headings; headings not suitable as variable names are converted to valid variable names by replacing non-fitting characters with underscores and adding underscores.
getHeadSize() - Method in class ij.gui.Arrow
getHeight() - Method in class ij.ImagePlus: Returns the height of this image in pixels.
getHeight() - Method in class ij.ImageStack
getHeight() - Method in class ij.plugin.AVI_Reader: Returns the image height of the virtual stack
getHeight() - Method in class ij.plugin.FileInfoVirtualStack
getHeight() - Method in class ij.plugin.ListVirtualStack
getHeight() - Method in class ij.process.ImageProcessor: Returns the height of this image in pixels.
getHideOverlay() - Method in class ij.ImagePlus
getHigherZoomLevel(double) - Static method in class ij.gui.ImageCanvas
getHistogram() - Method in class ij.gui.HistogramPlot
getHistogram() - Method in class ij.gui.HistogramWindow
getHistogram() - Method in class ij.process.ByteProcessor
getHistogram() - Method in class ij.process.ColorProcessor
getHistogram() - Method in class ij.process.FloatProcessor: Returns a 256 bin histogram of the current ROI or of the entire image if there is no ROI.
getHistogram() - Method in class ij.process.ImageProcessor: Returns the histogram of the image or ROI.
getHistogram() - Method in class ij.process.ImageStatistics: Returns the histogram as an array of longs.
getHistogram() - Method in class ij.process.ShortProcessor: Returns 65,536 bin histogram of the current ROI, which can be non-rectangular.
getHistogram(int) - Method in class ij.process.ImageProcessor: Returns the histogram of the image or ROI, using the specified number of bins.
getHistogram(ImageProcessor) - Method in class ij.process.ByteProcessor
getHistogram(ImageProcessor) - Method in class ij.process.ColorProcessor
getHistogramMax() - Method in class ij.process.ImageProcessor: Returns the maximum histogram value used for histograms of float images.
getHistogramMin() - Method in class ij.process.ImageProcessor: Returns the minimum histogram value used for histograms of float images.
getHistogramSize() - Method in class ij.process.ImageProcessor: Returns the number of float image histogram bins.
getHomeDir() - Static method in class ij.Prefs: Obsolete, replaced by getImageJDir(), which, unlike this method, returns a path that ends with File.separator.
getHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor: Returns hue, saturation and brightness in 3 byte arrays.
getHSB(float[], float[], float[]) - Method in class ij.process.ColorProcessor: Returns hue, saturation and brightness in 3 float arrays.
getHSB32Stack() - Method in class ij.process.ColorProcessor: Returns an ImageStack with three 32-bit slices, representing hue, saturation and brightness
getHSBStack() - Method in class ij.process.ColorProcessor: Returns an ImageStack with three 8-bit slices, representing hue, saturation and brightness
getID() - Method in class ij.ImagePlus: Returns this image's unique numeric ID.
getIDList() - Static method in class ij.WindowManager: Returns a list of the IDs of open images.
getImage() - Method in class ij.CompositeImage
getImage() - Method in class ij.gui.ImageCanvas: Returns the ImagePlus object that is associated with this ImageCanvas.
getImage() - Method in class ij.gui.Roi: Returns the ImagePlus associated with this ROI, or null.
getImage() - Static method in class ij.IJ: Returns a reference to the active image, or displays an error message and aborts the plugin or macro if no images are open.
getImage() - Method in class ij.ImagePlus: Returns this image as a AWT image.
getImage() - Static method in class ij.plugin.Orthogonal_Views
getImage(int) - Static method in class ij.WindowManager: For IDs less than zero, returns the ImagePlus with the specified ID.
getImage(Interpreter) - Static method in class ij.IJ: The macro interpreter uses this method to call getImage().
getImage(String) - Static method in class ij.WindowManager: Returns the first image that has the specified title or null if it is not found.
getImageArray() - Method in class ij.ImageStack: Returns the stack as an array of 1D pixel arrays.
getImageArray() - Method in class ij.VirtualStack: Returns null.
getImageCount() - Static method in class ij.WindowManager: Returns the number of open images.
getImageFromVector(int) - Method in class ij.plugin.frame.SyncWindows: Get ImagePlus from Windows-Vector vwins.
getImageID() - Method in class ij.gui.Roi: Returns the ID of the image associated with this ROI.
getImageID() - Static method in class ij.plugin.Orthogonal_Views
getImageIDs() - Static method in class ij.plugin.Orthogonal_Views: Returns the IDs of the XY, YZ and XZ images as an int array.
getImageInfo(ImagePlus) - Method in class ij.plugin.ImageInfo
getImageInfo(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.Info: Deprecated.
getImageJDir() - Static method in class ij.Prefs: Returns the path, ending in File.separator, to the ImageJ directory.
getImageJMenu(String) - Static method in class ij.Menus: Returns the specified ImageJ menu (e.g., "File>New") or null if it is not found.
getImagePlus() - Method in class ij.gui.ImageWindow
getImagePlus() - Method in class ij.gui.Plot: Returns the plot as an ImagePlus.
getImagePlus() - Method in class ij.plugin.AVI_Reader: Returns the ImagePlus opened by run().
getImageProperties() - Method in class ij.ImagePlus
getImageSize(ImagePlus) - Static method in class ij.gui.ImageWindow
getImageStack() - Method in class ij.ImagePlus: Returns the base image stack.
getImageStackSize() - Method in class ij.ImagePlus: If this is a stack, returns the actual number of images in the stack, else returns 1.
getImagesURL() - Static method in class ij.Prefs: Returns the URL of the directory that contains the ImageJ sample images.
getImageTitleFromVector(int) - Method in class ij.plugin.frame.SyncWindows: Get the title of image n from Windows-Vector vwins.
getImageTitles() - Static method in class ij.WindowManager: Returns a list of the titles of all open images.
getImports() - Method in class ij.plugin.PlugInInterpreter: Returns the import statements that are added to the script.
getIndex(String) - Method in class ij.gui.Overlay: Returns the index of the ROI with the specified name, or -1 if not found.
getIndex(String) - Method in class ij.plugin.frame.RoiManager: Returns the index of the first ROI with the specified name, or -1 if no ROI has that name.
getIndexes() - Method in class ij.plugin.frame.RoiManager: Returns an array of the selected indexes or all indexes if none are selected.
getIndexesAsString() - Static method in class ij.plugin.frame.RoiManager: This is a macro-callable version of getSelectedIndexes().
getIndexOfImage(ImagePlus) - Method in class ij.plugin.frame.SyncWindows: Get index of "image" in vector of synchronized windows, if image is in vector.
getIndexSampleModel() - Method in class ij.process.ImageProcessor
getInfo() - Method in class ij.ImageJ
getInfo(String) - Method in class ij.plugin.DICOM: Returns the DICOM tags of the specified file as a string.
getInfoProperty() - Method in class ij.ImagePlus: Returns the "Info" property string, or null if it is not found.
getInitialMagnification() - Method in class ij.gui.ImageWindow
getInsets() - Method in class ij.gui.GenericDialog
getInsets() - Method in class ij.gui.ImageWindow: Override Container getInsets() to make room for some text above the image.
getInsets() - Method in class ij.plugin.frame.SyncWindows
getInstance() - Static method in class ij.gui.GenericDialog
getInstance() - Static method in class ij.gui.Toolbar: Returns a reference to the ImageJ toolbar.
getInstance() - Static method in class ij.IJ: Returns a reference to the "ImageJ" frame.
getInstance() - Static method in class ij.macro.Interpreter
getInstance() - Static method in class ij.plugin.frame.Channels: Obsolete; always returns null.
getInstance() - Static method in class ij.plugin.frame.Editor
getInstance() - Static method in class ij.plugin.frame.Recorder
getInstance() - Static method in class ij.plugin.frame.RoiManager: Returns a reference to the ROI Manager, or null if it is not open and a batch mode macro is not running.
getInstance() - Static method in class ij.plugin.frame.SyncWindows
getInstance() - Static method in class ij.plugin.Orthogonal_Views
getInstance2() - Static method in class ij.plugin.frame.RoiManager: Returns a reference to the ROI Manager window or to the macro batch mode RoiManager, or null if neither exists.
getInt(String, int) - Static method in class ij.Prefs: Retrieves a number from IJ_Props or IJ_Prefs.txt.
getInt(Properties, String) - Static method in class ij.OtherInstance
getIntArray() - Method in class ij.process.ImageProcessor: Returns a copy of the pixel data as a 2D int array with dimensions [x=0..width-1][y=0..height-1].
getInterpolate() - Method in class ij.process.ImageProcessor: Returns the value of the interpolate field.
getInterpolatedPixel(double, double) - Method in class ij.process.ByteProcessor: Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ColorProcessor: Calls getPixelValue(x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.FloatProcessor: Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ImageProcessor: Uses the current interpolation method (bilinear or bicubic) to find the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ShortProcessor: Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPolygon() - Method in class ij.gui.Roi: Returns, as a FloatPolygon, an interpolated version of this selection that has points spaced 1.0 pixel apart.
getInterpolatedPolygon(double, boolean) - Method in class ij.gui.PolygonRoi
getInterpolatedPolygon(double, boolean) - Method in class ij.gui.Roi: Returns, as a FloatPolygon, an interpolated version of this selection with points spaced 'interval' pixels apart.
getInterpolatedPolygon(FloatPolygon, double, boolean) - Method in class ij.gui.Roi: Returns, as a FloatPolygon, an interpolated version of this selection with points spaced abs('interval') pixels apart.
getInterpolatedRGBPixel(double, double) - Method in class ij.process.ColorProcessor: Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedValue(double, double) - Method in class ij.process.ImageProcessor: Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolationMethod() - Method in class ij.process.ImageProcessor: Returns the current interpolation method (NONE, BILINEAR or BICUBIC).
getInterpolationMethods() - Static method in class ij.process.ImageProcessor
getInverse(ImagePlus) - Method in class ij.gui.Roi: Returns the inverted roi, or null if this is not an area roi or cannot be converted to a ShapeRoi.
getInvertY() - Method in class ij.measure.Calibration: Returns the 'invertY' flag.
getIterations() - Method in class ij.measure.CurveFitter: Get number of iterations performed.
getIterations() - Method in class ij.measure.Minimizer: Get number of iterations performed (includes all restarts).
getJarFileForMenuEntry(String) - Static method in class ij.Menus
getJpegQuality() - Static method in class ij.io.FileSaver: Returns the current JPEG quality setting (0-100).
getJSPrefix(String) - Static method in class ij.plugin.frame.Editor
getJustification() - Method in class ij.gui.TextRoi: Returns the value of the 'justification' instance variable (LEFT, CENTER or RIGHT).
getLab(ImageProcessor, byte[], byte[], byte[]) - Static method in class ij.plugin.frame.ColorThresholder: Returns Lab in 3 byte arrays.
getLabel() - Method in class ij.gui.GenericDialog: Returns a reference to the label of the most recently added numeric field, string field, choice or slider.
getLabel(char) - Method in class ij.gui.Plot: Gets the label String of the xLabel ('x'), yLabel('y') or the legend ('l').
getLabel(int) - Method in class ij.measure.ResultsTable: Returns the label of the specified row.
getLabelColor() - Method in class ij.gui.Overlay
getLabelFont() - Method in class ij.gui.Overlay
getLast() - Method in class ij.util.FloatArray: Returns the last element of this FloatArray.
getLastBatchModeImage() - Static method in class ij.macro.Interpreter
getLastColumn() - Method in class ij.measure.ResultsTable: Returns the index of the last used column, or -1 if no columns are used.
getLastCounter() - Method in class ij.gui.PointRoi: Returns the index of the last counter.
getLastDirectory() - Static method in class ij.io.OpenDialog: Returns the path to the directory that contains the last file opened or saved, or null if a file has not been opened or saved.
getLastFileInfo() - Static method in class ij.io.ImportDialog: Returns the FileInfo object used to import the last raw image, or null if a raw image has not been imported.
getLastName() - Static method in class ij.io.OpenDialog: Returns the name of the last file opened by the user using a file open or file save dialog, or using drag and drop.
getLength() - Method in class ij.gui.EllipseRoi: Returns the perimeter of this ellipse.
getLength() - Method in class ij.gui.Line: Returns the length of this line.
getLength() - Method in class ij.gui.OvalRoi: Returns the perimeter length using Ramanujan's approximation for the circumference of an ellipse
getLength() - Method in class ij.gui.PolygonRoi: Returns the perimeter (for ROIs) or length (for lines).
getLength() - Method in class ij.gui.Roi: Returns the perimeter length.
getLength() - Method in class ij.gui.ShapeRoi: Returns the perimeter of this ShapeRoi.
getLength(boolean) - Method in class ij.process.FloatPolygon
getLimits() - Method in class ij.gui.Plot: Returns the current limits as an array xMin, xMax, yMin, yMax.
getLine(double, double, double, double) - Method in class ij.process.ImageProcessor: Returns an array containing the pixel values along the line starting at (x1,y1) and ending at (x2,y2).
getLine(int) - Method in class ij.text.TextPanel: Returns the specified line as a string.
getLineCount() - Method in class ij.text.TextPanel: Returns the number of lines of text in this TextPanel.
getLineNumber() - Method in class ij.macro.Interpreter
getLineWidth() - Method in class ij.process.ImageProcessor: Returns the current line width.
getList() - Method in class ij.plugin.frame.RoiManager: Deprecated.
getListenerCount() - Static method in class ij.Executer
getListeners() - Static method in class ij.gui.Roi
getListeners() - Static method in class ij.ImagePlus
getLoadRate(double, ImagePlus) - Static method in class ij.io.Opener
getLocalCalibration() - Method in class ij.ImagePlus: Returns this image's local calibration, ignoring the "Global" calibration flag.
getLocation(String) - Static method in class ij.Prefs: Uses the keyword key to retrieve a location from the preferences file.
getLocationAsString(int, int) - Method in class ij.ImagePlus: Converts the current cursor location to a string.
getLog() - Static method in class ij.IJ: Returns the contents of the Log window or null if the Log window is not open.
getLongFilePointer() - Method in class ij.io.RandomAccessStream
getLookAndFeel() - Static method in class ij.util.Java2: Returns the current Swing look and feel or null.
getLowerZoomLevel(double) - Static method in class ij.gui.ImageCanvas
getLut() - Method in class ij.process.ImageProcessor
getLut(String) - Static method in class ij.plugin.LutLoader: Returns the LUT 'name' as an IndexColorModel, where 'name' can be any entry in the Image/Lookup Tables menu.
getLuts() - Method in class ij.CompositeImage
getLuts() - Static method in class ij.IJ: Returns, as an array of strings, a list of the LUTs in the Image/Lookup Tables menu.
getLuts() - Method in class ij.ImagePlus: Returns an array containing the lookup tables used by this image, one per channel, or an empty array if this is an RGB image.
getLutUpdateMode() - Method in class ij.process.ImageProcessor: Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
getMacroCode() - Method in class ij.measure.CurveFitter: Returns macro code of the form "y = ...x" for the fit function used.
getMacroCode(String, ImagePlus) - Method in class ij.gui.TextRoi: Used by the Recorder for recording the text tool.
getMacroCount() - Method in class ij.Menus
getMacroCount() - Method in class ij.plugin.MacroInstaller
getMacroCount() - Method in class ij.plugin.tool.MacroToolRunner
getMacroProgram() - Method in class ij.plugin.tool.MacroToolRunner
getMacroProgram() - Method in class ij.plugin.tool.PlugInTool
getMacroShortcuts() - Static method in class ij.Menus: Returns the hashtable that associates keyboard shortcuts with macros.
getMacrosMenu() - Static method in class ij.Menus
getMacrosPath() - Static method in class ij.Menus: Returns the path to the macros directory or null if the macros directory was not found.
getMagnification() - Method in class ij.gui.ImageCanvas
getMagnification() - Method in class ij.gui.Roi
getMapSize() - Method in class ij.LookUpTable
getMask() - Method in class ij.gui.Arrow
getMask() - Method in class ij.gui.OvalRoi
getMask() - Method in class ij.gui.PointRoi
getMask() - Method in class ij.gui.PolygonRoi
getMask() - Method in class ij.gui.Roi: Always returns null for rectangular Roi's
getMask() - Method in class ij.gui.ShapeRoi: Returns this ROI's mask pixels as a ByteProcessor with pixels "in" the mask set to white (255) and pixels "outside" the mask set to black (0).
getMask() - Method in class ij.ImagePlus: For images with irregular ROIs, returns a byte mask, otherwise, returns null.
getMask() - Method in class ij.process.ImageProcessor: For images with irregular ROIs, returns a mask, otherwise, returns null.
getMask(int, int) - Method in class ij.process.PolygonFiller: Returns a byte mask containing a filled version of the polygon.
getMaskArray() - Method in class ij.process.ImageProcessor: Returns a reference to the mask pixel array, or null if there is no mask.
getMatchingCoords(ImageCanvas, ImageCanvas, int, int) - Method in class ij.plugin.frame.SyncWindows: Get Screen Coordinates for ImageCanvas ic matching the OffScreen Coordinates of the current ImageCanvas.
getMax() - Method in class ij.gui.ProfilePlot: Returns the calculated maximum value.
getMax() - Method in class ij.process.ByteProcessor: Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ColorProcessor: Returns the largest displayed pixel value.
getMax() - Method in class ij.process.FloatProcessor: Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ImageProcessor: Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ShortProcessor: Returns the largest displayed pixel value.
getMax(double[]) - Static method in class ij.measure.CurveFitter: Gets index of highest value in an array.
getMaxima(ImageProcessor, double, boolean) - Method in class ij.plugin.filter.MaximumFinder: Finds the image maxima and returns them as a Polygon, where poly.npoints is the number of maxima.
getMaxima(ImageProcessor, double, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder: Finds the image maxima and returns them as a Polygon, where poly.npoints is the number of maxima.
getMaximum() - Method in class ij.gui.ScrollbarWithLabel
getMaximum() - Method in class ij.util.ArrayUtil: The maximum value
getMaximumBounds() - Method in class ij.gui.ImageWindow
getMaxIterations() - Method in class ij.measure.CurveFitter: Get maximum number of iterations allowed (sum of iteration count for all restarts)
getMaxIterations() - Method in class ij.measure.Minimizer: Get maximum number of iterations allowed.
getMaxRestarts() - Method in class ij.measure.Minimizer: Get maximum number of minimization restarts to do
getMaxThreshold() - Method in class ij.process.ImageProcessor: Returns the upper threshold level.
getMaxWindowBounds() - Static method in class ij.gui.GUI
getMaxWindowBounds(Component) - Static method in class ij.gui.GUI
getMaxWindowBounds(Point) - Static method in class ij.gui.GUI
getMean() - Method in class ij.util.ArrayUtil: Average value
getMeasurements() - Static method in class ij.plugin.filter.Analyzer
getMemorySetting() - Method in class ij.plugin.Memory
getMenuBar() - Static method in class ij.Menus
getMenus() - Method in class ij.macro.Program
getMessage() - Method in class ij.gui.GenericDialog: Returns a reference to the Label or MultiLineLabel created by the last addMessage() call.
getMethod() - Static method in class ij.plugin.frame.ThresholdAdjuster: Returns the current thresholding method ("Default", "Huang", etc).
getMethods() - Static method in class ij.process.AutoThresholder
getMin() - Method in class ij.gui.ProfilePlot: Returns the calculated minimum value.
getMin() - Method in class ij.process.ByteProcessor: Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ColorProcessor: Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.FloatProcessor: Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ImageProcessor: Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ShortProcessor: Returns the smallest displayed pixel value.
getMinimizer() - Method in class ij.measure.CurveFitter: Returns a reference to the Minimizer used, for accessing Minimizer methods directly.
getMinimum() - Method in class ij.gui.ScrollbarWithLabel
getMinimum() - Method in class ij.util.ArrayUtil: The minimum value
getMinimumSize() - Method in class ij.gui.ImagePanel
getMinimumSize() - Method in class ij.gui.MultiLineLabel
getMinimumSize() - Method in class ij.gui.Plot: The minimum plot size including borders, in pixels (at scale=1)
getMinimumSize() - Method in class ij.gui.ScrollbarWithLabel
getMinimumSize() - Method in class ij.gui.Toolbar
getMinimumSize() - Method in class ij.gui.TrimmedButton
getMinMax(double[]) - Static method in class ij.util.Tools: Determines the minimum and maximum value in the array a and returns them as 2-element array {minimum, maximum}.
getMinMax(float[]) - Static method in class ij.util.Tools: Determines the minimum and maximum value in the array a and returns them as 2-element array {minimum, maximum}.
getMinThreshold() - Method in class ij.process.ImageProcessor: Returns the lower threshold level.
getMode() - Method in class ij.CompositeImage
getMode() - Static method in class ij.plugin.frame.ThresholdAdjuster: Returns the current mode ("Red","B&W" or"Over/Under").
getMode() - Static method in class ij.plugin.WandToolOptions
getModeAsString() - Method in class ij.CompositeImage
getModifiers() - Method in class ij.gui.ImageCanvas: Returns the mouse event modifiers.
getMultipleWildcardChar() - Method in class ij.util.WildcardMatch: Returns the character used to specify any amount of characters.
getMultiPointMode() - Static method in class ij.gui.Toolbar: Returns 'true' if the multi-point tool is enabled.
getName() - Method in class ij.gui.Roi: Returns the name of this ROI, or null.
getName() - Method in class ij.measure.CurveFitter: returns the name of the fit function of the fit performed
getName() - Method in class ij.plugin.PlugInInterpreter: Returns the name of this PlugInInterpreter.
getName() - Method in class ij.plugin.TextReader: Returns the file name.
getName(int) - Method in class ij.plugin.frame.RoiManager: Returns the name of the ROI with the specified index, or null if the index is out of range.
getName(String) - Method in class ij.io.Opener
getName(String) - Static method in class ij.Macro
getName(String) - Static method in class ij.plugin.frame.RoiManager: Returns the name of the ROI with the specified index.
getNbCpus() - Static method in class ij.util.ThreadUtil
getNChannels() - Method in class ij.ImagePlus: Returns the number of channels.
getNChannels() - Method in class ij.process.ColorProcessor: Returns the number of color channels (3).
getNChannels() - Method in class ij.process.ImageProcessor: Returns the number of color channels in the image.
getNChannels() - Method in class ij.process.IntProcessor: Returns the number of channels (1).
getNCoordinates() - Method in class ij.gui.PolygonRoi: Returns the number of points that define this PolygonRoi.
getNCounters() - Method in class ij.gui.PointRoi: Returns the number of counters.
getNDimensions() - Method in class ij.ImagePlus: Returns the number of dimensions (2, 3, 4 or 5).
getNeighborhood(int, int, double[][]) - Method in class ij.process.ImageProcessor: Experimental
getNextBoolean() - Method in class ij.gui.GenericDialog: Returns the state of the next checkbox.
getNextChoice() - Method in class ij.gui.GenericDialog: Returns the selected item in the next popup menu.
getNextChoiceIndex() - Method in class ij.gui.GenericDialog: Returns the index of the selected item in the next popup menu.
getNextEnumChoice(Class<E>) - Method in class ij.gui.GenericDialog: Returns the selected item in the next enum choice menu.
getNextImage() - Method in class ij.gui.GenericDialog
getNextNumber() - Method in class ij.gui.GenericDialog: Returns the contents of the next numeric field, or NaN if the field does not contain a number.
getNextRadioButton() - Method in class ij.gui.GenericDialog: Returns the selected item in the next radio button group.
getNextString() - Method in class ij.gui.GenericDialog: Returns the contents of the next text field.
getNextText() - Method in class ij.gui.GenericDialog: Returns the contents of the next text area.
getNFrames() - Method in class ij.ImagePlus: Returns the number of frames (time-points).
getNonImageTitles() - Static method in class ij.WindowManager: Returns an array containing the titles of non-image Frames and Dialogs.
getNonImageWindows() - Static method in class ij.WindowManager: Returns an array containing a list of the non-image Frames.
getNonSplineCoordinates() - Method in class ij.gui.PolygonRoi
getNonSplineFloatPolygon() - Method in class ij.gui.PolygonRoi
getNScrollbars() - Method in class ij.gui.StackWindow
getNSlices() - Method in class ij.ImagePlus: Returns the image depth (number of z-slices).
getNthImageID(int) - Static method in class ij.WindowManager: Returns the ID of the Nth open image.
getNumber(String, double) - Static method in class ij.IJ: Allows the user to enter a number in a dialog box.
getNumberFromList(String, String) - Static method in class ij.util.Tools: Retrieves a number form a list of key-number pairs like "value1=1234.5 area=1.2e6".
getNumberFromList(String, String, double) - Static method in class ij.util.Tools
getNumericFields() - Method in class ij.gui.GenericDialog: Returns the Vector containing the numeric TextFields.
getNumericProp(String) - Method in class ij.ImagePlus: Returns the numeric property associated with the specified key or NaN if the property is not found.
getNumericProperty(String) - Method in class ij.ImagePlus: Returns the numeric value from the "Info" property string associated with 'key', or NaN if the key is not found or the value associated with the key is not numeric.
getNumParams() - Method in class ij.measure.CurveFitter: Get number of parameters for current fit formula Do not use before 'doFit', because the fit function would be undefined.
getNumParams(int) - Static method in class ij.measure.CurveFitter: Returns the number of parameters for a given fit type, except for the 'custom' fit, where the number of parameters is given by the equation: see getNumParams(String)
getNumParams(String) - Static method in class ij.measure.CurveFitter: Returns the number of parameters for a custom equation given as a macro String, like "y = a + b*x + c*x*x" .
getNumPlotObjects() - Method in class ij.gui.Plot: Returns the number of PlotObjects (curves, labels, ...) passed with the constructor or added by 'add' or 'draw' methods.
getNumTools() - Method in class ij.gui.Toolbar
getObjectFlags(char) - Method in class ij.gui.Plot: Gets the flags of the xLabel ('x'), yLabel('y') or the legend ('l').
getOffset() - Method in class ij.io.FileInfo: Returns the offset as a long.
getOpacity() - Method in class ij.gui.ImageRoi: Returns the current opacity.
getOpenAsHyperStack() - Method in class ij.ImagePlus
getOpenRecentMenu() - Static method in class ij.Menus
getOpenUsingPlugins() - Static method in class ij.io.Opener: Returns the state of the openUsingPlugins flag.
getOptions() - Static method in class ij.Macro: If a command started using run(name, options) is running, and the current thread is the same thread, returns the options string, otherwise, returns null.
getOrCreateResultsTable() - Method in class ij.text.TextPanel: Returns the ResultsTable associated with this TextPanel, or attempts to create one and returns the created table.
getOrientation() - Method in class ij.gui.ScrollbarWithLabel
getOriginalFileInfo() - Method in class ij.ImagePlus: Returns the FileInfo object that was used to open this image.
getOutline() - Method in class ij.gui.Arrow
getOutputImage() - Method in class ij.plugin.filter.ParticleAnalyzer: Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu.
getOutputType() - Static method in class ij.plugin.filter.EDM: Returns the current output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
getOvalToolType() - Static method in class ij.gui.Toolbar: Returns the oval tool type (OVAL_ROI, ELLIPSE_ROI or BRUSH_ROI).
getOverlay() - Method in class ij.gui.ImageCanvas: Use ImagePlus.getOverlay().
getOverlay() - Method in class ij.ImagePlus: Returns the current overly, or null if this image does not have an overlay.
getOverlay() - Method in class ij.process.ImageProcessor
getOverlay(ImagePlus) - Static method in class ij.io.FileSaver
getPaintPending() - Method in class ij.gui.ImageCanvas
getParams() - Method in class ij.gui.EllipseRoi: Returns x1, y1, x2, y2 and aspectRatio as a 5 element array.
getParams() - Method in class ij.gui.RotatedRectRoi: Returns x1, y1, x2, y2 and width as a 5 element array.
getParams() - Method in class ij.measure.CurveFitter: Get the result of fitting, i.e.
getParams() - Method in class ij.measure.Minimizer: Get the result, i.e., the set of parameter values (i.e., variable values) from the best corner of the simplex.
getPasteMode() - Method in class ij.gui.Roi: Returns the current paste transfer mode, or NOT_PASTING (-1) if no paste operation is in progress.
getPath() - Method in class ij.io.OpenDialog: Returns the selected file path or null if the dialog was canceled.
getPath(ImagePlus, String) - Static method in class ij.io.SaveDialog
getPixel(int, int) - Method in class ij.ImagePlus: Returns the pixel value at (x,y) as a 4 element array.
getPixel(int, int) - Method in class ij.process.ByteProcessor
getPixel(int, int) - Method in class ij.process.ColorProcessor
getPixel(int, int) - Method in class ij.process.FloatProcessor: Returns a pixel value that must be converted using Float.intBitsToFloat().
getPixel(int, int) - Method in class ij.process.ImageProcessor: Returns the value of the pixel at (x,y).
getPixel(int, int) - Method in class ij.process.ShortProcessor
getPixel(int, int, int[]) - Method in class ij.process.ColorProcessor: Returns the 3 samples for the pixel at (x,y) in an array of int.
getPixel(int, int, int[]) - Method in class ij.process.FloatProcessor: Returns the value of the pixel at (x,y) in a one element int array.
getPixel(int, int, int[]) - Method in class ij.process.ImageProcessor: Returns the samples for the pixel at (x,y) in an int array.
getPixelCount() - Method in class ij.process.ImageProcessor
getPixelInterpolated(double, double) - Method in class ij.process.ByteProcessor
getPixelInterpolated(double, double) - Method in class ij.process.ColorProcessor
getPixelInterpolated(double, double) - Method in class ij.process.FloatProcessor
getPixelInterpolated(double, double) - Method in class ij.process.ImageProcessor: Uses the current interpolation method to find the pixel value at real coordinates (x,y).
getPixelInterpolated(double, double) - Method in class ij.process.ShortProcessor
getPixels() - Method in class ij.gui.Line: Returns the pixel values along this line.
getPixels() - Method in class ij.process.ByteProcessor: Returns a reference to the byte array containing this image's pixel data.
getPixels() - Method in class ij.process.ColorProcessor: Returns a reference to the int array containing this image's pixel data.
getPixels() - Method in class ij.process.FloatProcessor: Returns a reference to the float array containing this image's pixel data.
getPixels() - Method in class ij.process.ImageProcessor: Returns a reference to this image's pixel array.
getPixels() - Method in class ij.process.ShortProcessor: Returns a reference to the short array containing this image's pixel data.
getPixels(int) - Method in class ij.gui.PlotVirtualStack: Returns the pixel array for the specified slice, where 1<=n<=nslices.
getPixels(int) - Method in class ij.ImageStack: Returns the pixel array for the specified slice, where 1<=n<=nslices.
getPixels(int) - Method in class ij.VirtualStack: Returns the pixel array for the specified slice, where 1<=n<=nslices.
getPixelsCopy() - Method in class ij.process.ByteProcessor: Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ColorProcessor: Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.FloatProcessor: Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ImageProcessor: Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ShortProcessor: Returns a copy of the pixel data.
getPixelValue(int, int) - Method in class ij.process.ByteProcessor
getPixelValue(int, int) - Method in class ij.process.ColorProcessor: Converts the specified pixel to grayscale using the formula g=(r+g+b)/3 and returns it as a float.
getPixelValue(int, int) - Method in class ij.process.FloatProcessor: Returns the value of the pixel at (x,y) as a float.
getPixelValue(int, int) - Method in class ij.process.ImageProcessor: Returns the value of the pixel at (x,y).
getPixelValue(int, int) - Method in class ij.process.IntProcessor
getPixelValue(int, int) - Method in class ij.process.ShortProcessor: Returns the value of the pixel at (x,y) as a float.
getPlot() - Method in class ij.gui.PlotCanvas: Returns the Plot displayed in this canvas
getPlot() - Method in interface ij.gui.PlotMaker: Returns a profile plot.
getPlot() - Method in class ij.gui.PlotWindow: Returns the Plot associated with this PlotWindow.
getPlot() - Method in class ij.gui.ProfilePlot
getPlot() - Method in class ij.ImagePlus
getPlot() - Method in class ij.measure.CurveFitter
getPlot() - Method in class ij.plugin.Profiler
getPlot() - Method in class ij.plugin.ZAxisProfiler
getPlot(int) - Method in class ij.measure.CurveFitter
getPlot(ImagePlus) - Static method in class ij.plugin.ZAxisProfiler: Returns a Plot of the selection mean gray value versus slice number.
getPlot(ImagePlus, String) - Static method in class ij.plugin.ZAxisProfiler: Returns a Plot of the selection mean versus slice number for the specified hyperstack, where 'options' can be "time" or "z-axis".
getPlotObjectDesignations() - Method in class ij.gui.Plot: Gets an array with human-readable designations of the PlotObjects (curves, labels, ...) in the sequence they were added (the object passed with the constructor is first, even though it is plotted last).
getPlotObjectIndex(float[][]) - Method in class ij.gui.Plot: Returns the index of the first plot object with x,y data (points, line) or arrows with all data equal to those given.
getPlotObjectLabel(int) - Method in class ij.gui.Plot: Get the label the i-th PlotObject (in the sequence how they were added, including hidden ones).
getPlotObjectStyle(int) - Method in class ij.gui.Plot: Get the style of the i-th PlotObject (curve, label, ...) in the sequence they were added (including hidden ones), as String with comma delimiters: Main Color, Secondary Color (or "none"), Line Width [, Symbol shape for XY_DATA] [,hidden] PlotObjects here refers to curves, arrows, labels etc.
getPlotSize() - Method in class ij.gui.ProfilePlot: Returns the size of the plot that createWindow() creates.
getPluginCount() - Method in class ij.Menus
getPlugins() - Static method in class ij.Menus: Returns a list of the plugins in the plugins menu.
getPluginsDirProperty() - Static method in class ij.Prefs
getPlugInsPath() - Static method in class ij.Menus: Returns the path to the user plugins directory or null if the plugins directory was not found.
getPlugInTool() - Static method in class ij.gui.Toolbar
getPointPosition(int) - Method in class ij.gui.PointRoi: Returns the stack slice of the point with the given index, or 0 if no slice defined for this point
getPoints() - Method in class ij.gui.Line: Returns, as a Polygon, the two points that define this line.
getPointType() - Method in class ij.gui.PointRoi: Returns the point type (0=hybrid, 1=cross, 2=dot, 3=circle).
getPolygon() - Method in class ij.gui.Line: If the width of this line is less than or equal to one, returns the starting and ending coordinates as a 2-point Polygon, or, if the width is greater than one, returns an outline of the line as a 4-point Polygon.
getPolygon() - Method in class ij.gui.OvalRoi: Returns this OvalRoi as a Polygon that outlines the mask, in image pixel coordinates.
getPolygon() - Method in class ij.gui.PolygonRoi: Returns this PolygonRoi as a Polygon.
getPolygon() - Method in class ij.gui.Roi: Returns the outline of this selection as a Polygon.
getPolygon() - Method in class ij.gui.ShapeRoi
getPopupMenu() - Static method in class ij.Menus
getPort() - Static method in class ij.ImageJ: Returns the port that ImageJ checks on startup to see if another instance is running.
getPosition() - Method in class ij.gui.Roi: Returns the stack position (image number) of this ROI, or zero if the ROI is not associated with a particular stack image.
getPowerSpectrum() - Method in class ij.process.FHT: Returns an 8-bit power spectrum, log-scaled to 1-254.
getPrecision() - Static method in class ij.plugin.filter.Analyzer: Returns the number of digits displayed to the right of decimal point.
getPreferredLocation() - Method in class ij.ImageJ
getPreferredSize() - Method in class ij.gui.ImageCanvas
getPreferredSize() - Method in class ij.gui.ImagePanel
getPreferredSize() - Method in class ij.gui.MultiLineLabel
getPreferredSize() - Method in class ij.gui.ProgressBar
getPreferredSize() - Method in class ij.gui.ScrollbarWithLabel
getPreferredSize() - Method in class ij.gui.Toolbar
getPreferredSize() - Method in class ij.gui.TrimmedButton
getPrefsDir() - Static method in class ij.Prefs: Returns the path to the directory where the preferences file (IJPrefs.txt) is saved.
getPrefsDirectory() - Static method in class ij.OtherInstance
getPreviewCheckbox() - Method in class ij.gui.GenericDialog: Returns a reference to the Preview checkbox.
getPreviousRoi() - Static method in class ij.gui.Roi: Returns the Roi saved by setPreviousRoi().
getProcessor() - Method in class ij.gui.ImageRoi
getProcessor() - Method in class ij.gui.Plot: Draws the plot (if not done before) in an ImageProcessor and returns the ImageProcessor with the plot.
getProcessor() - Static method in class ij.IJ: Returns the active image or stack slice as an ImageProcessor, or displays an error message and aborts the plugin or macro if no images are open.
getProcessor() - Method in class ij.ImagePlus: Returns a reference to the current ImageProcessor.
getProcessor(int) - Method in class ij.CompositeImage
getProcessor(int) - Method in class ij.gui.PlotVirtualStack: Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProcessor(int) - Method in class ij.ImageStack: Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProcessor(int) - Method in class ij.plugin.AVI_Reader: Returns an ImageProcessor for the specified slice of this virtual stack (if it is one) where 1<=n<=nslices.
getProcessor(int) - Method in class ij.plugin.FileInfoVirtualStack: Returns an ImageProcessor for the specified image, where 1<=n<=nImages.
getProcessor(int) - Method in class ij.plugin.ListVirtualStack: Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProcessor(int) - Method in class ij.VirtualStack: Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProfile() - Method in class ij.gui.ProfilePlot: Returns the profile plot data.
getProgram() - Method in class ij.plugin.MacroInstaller
getProgressBar() - Method in class ij.ImageJ
getProgressIncrement(int, int) - Method in class ij.process.ImageProcessor
getProjection() - Method in class ij.plugin.ZProjector: Retrieve results of most recent projection operation.
getProp(String) - Method in class ij.ImagePlus: Returns as a string the image property associated with the specified key or null if the property is not found.
getProperties() - Method in class ij.gui.Roi
getProperties() - Method in class ij.ImagePlus: Returns this image's Properties.
getProperties() - Method in class ij.VirtualStack: Returns the ImagePlus Properties assoctated with the current slice, or null.
getPropertiesAsArray() - Method in class ij.ImagePlus: Used for saving string properties in TIFF header.
getProperty(String) - Method in class ij.gui.Roi
getProperty(String) - Static method in class ij.IJ: Returns the object in IJ.properties associated with 'key', or null if 'key' is not found.
getProperty(String) - Method in class ij.ImagePlus: Returns the property associated with 'key', or null if it is not found.
getPropertyCount() - Method in class ij.gui.Roi
getPropsInfo() - Method in class ij.ImagePlus: Returns information displayed by Image/Show Info command.
getPrototypeOverlay() - Method in class ij.gui.Roi
getQuality() - Static method in class ij.plugin.JpegWriter
getRadioButtonGroups() - Method in class ij.gui.GenericDialog: Returns the Vector that contains the RadioButtonGroups.
getRawInstance() - Static method in class ij.plugin.frame.RoiManager
getRawLength() - Method in class ij.gui.Line: Returns the length of this line in pixels.
getRawPowerSpectrum() - Method in class ij.process.FHT: Returns the unscaled 32-bit power spectrum.
getRawStatistics() - Method in class ij.ImagePlus
getRawType(int) - Static method in class ij.macro.ExtensionDescriptor
getRawValue(double) - Method in class ij.measure.Calibration: Converts a density calibrated value into a raw pixel value.
getRawX(double) - Method in class ij.measure.Calibration: Converts a x-coordinate in physical units to pixels.
getRawY(double) - Method in class ij.measure.Calibration: Converts a y-coodinate in physical units to pixels.
getRawY(double, int) - Method in class ij.measure.Calibration: Converts a y-coodinate in physical units to pixels, taking into account the 'invertY' flag.
getRawZ(double) - Method in class ij.measure.Calibration: Converts a z-coodinate in physical units to pixels.
getRectToolType() - Static method in class ij.gui.Toolbar: Returns the rectangle tool type (RECT_ROI, ROUNDED_RECT_ROI or ROTATED_RECT_ROI).
getRed(String) - Static method in class ij.plugin.Colors
getRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer: Returns the image selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog, or null if "None" is selected, the image was not found or the image is not the same size as currentImage.
getReds() - Method in class ij.LookUpTable
getRejectMacrosMsg() - Method in class ij.plugin.frame.Editor
getResiduals() - Method in class ij.measure.CurveFitter: Returns residuals array, i.e., differences between data and curve.
getRestarts() - Method in class ij.measure.CurveFitter: Get maximum number of simplex restarts to do.
getResultsTable() - Method in class ij.gui.HistogramWindow: Returns the histogram values as a ResultsTable.
getResultsTable() - Method in class ij.gui.Plot: Creates a ResultsTable with the plot data.
getResultsTable() - Method in class ij.gui.PlotWindow: Returns the plot values with simple headings (X, Y, Y1 etc, not the labels) as a ResultsTable.
getResultsTable() - Static method in class ij.measure.ResultsTable: Returns the ResultsTable used by the Measure command.
getResultsTable() - Static method in class ij.plugin.filter.Analyzer: Returns the default results table.
getResultsTable() - Method in class ij.text.TextPanel: Returns the ResultsTable associated with this TextPanel, or null.
getResultsTable() - Method in class ij.text.TextWindow: Returns the ResultsTable associated with this TextWindow, or null.
getResultsTable(boolean) - Method in class ij.gui.Plot: Creates a ResultsTable with the data of the plot.
getResultsTable(String) - Static method in class ij.measure.ResultsTable: Returns the ResultsTable with the specified title, or null if it does not exist,
getResultsTableWithLabels() - Method in class ij.gui.Plot: Creates a ResultsTable with the data of the plot.
getResultString() - Method in class ij.measure.CurveFitter: Get a string with detailed description of the curve fitting results (several lines, including the fit parameters).
getResultsWindow() - Static method in class ij.measure.ResultsTable: Obsolete.
getReturnValue() - Method in class ij.plugin.PlugInInterpreter: Returns the value returned by the script, if any, or null.
getRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor: Returns the red, green and blue planes as 3 byte arrays.
getRGBWeights() - Method in class ij.process.ColorProcessor: Returns the values set by setRGBWeights(), or null if setRGBWeights() has not been called.
getRoi() - Method in class ij.ImagePlus: Returns the current selection, or null if there is no selection.
getRoi() - Method in class ij.ImageStack
getRoi() - Method in class ij.io.RoiDecoder: Returns the ROI.
getRoi() - Method in class ij.process.ImageProcessor: Returns a Rectangle that represents the current region of interest.
getRoi(int) - Method in class ij.plugin.frame.RoiManager: Returns a reference to the ROI at the specified index.
getRoiIndex(Roi) - Method in class ij.plugin.frame.RoiManager: Returns the index of the specified Roi, or -1 if it is not found.
getRoiManager() - Static method in class ij.plugin.frame.RoiManager: Returns a reference to the ROI Manager if it open or opens it if it is not already open.
getRois() - Method in class ij.gui.ShapeRoi: Converts a Shape into Roi object(s).
getROIs() - Method in class ij.plugin.frame.RoiManager: Deprecated.
getRoisAsArray() - Method in class ij.plugin.frame.RoiManager: Returns the ROIs as an array.
getRoot() - Method in class ij.plugin.ControlPanel
getRotationCenter() - Method in class ij.gui.Line
getRotationCenter() - Method in class ij.gui.Roi
getRoundRectArcSize() - Method in class ij.gui.Roi: Obsolete; replaced by getCornerDiameter().
getRoundRectArcSize() - Static method in class ij.gui.Toolbar: Returns the rounded rectangle arc size, or 0 if the rounded rectangle tool is not enabled.
getRow(int, int, float[], int) - Method in class ij.process.ImageProcessor: Returns the pixel values along the horizontal line starting at (x,y).
getRow(int, int, int[], int) - Method in class ij.process.ImageProcessor: Returns the pixel values along the horizontal line starting at (x,y).
getRowAsString(int) - Method in class ij.measure.ResultsTable: Returns a tab or comma delimited string representing the given row, where 0<=row<=size()-1.
getRSquared() - Method in class ij.measure.CurveFitter: Returns R^2, where 1.0 is best.
getSampleImageNames() - Static method in class ij.plugin.URLOpener
getSaveAsMenu() - Static method in class ij.Menus
getScale(float[]) - Static method in class ij.plugin.filter.Convolver
getScaledStroke() - Method in class ij.gui.Roi
getScaleStrokeWidth() - Method in class ij.gui.Roi: Returns 'true' if the stroke width is scaled as images are zoomed.
getScaleToFit() - Method in class ij.gui.ImageCanvas
getScreenBounds() - Static method in class ij.gui.GUI
getScreenBounds(Component) - Static method in class ij.gui.GUI
getScreenBounds(Component, boolean) - Static method in class ij.gui.GUI: Get maximum bounds for the screen that contains a given component.
getScreenBounds(Point) - Static method in class ij.gui.GUI
getScreenBounds(Point, boolean) - Static method in class ij.gui.GUI: Get maximum bounds for the screen that contains a given point.
getScreenSize() - Static method in class ij.IJ: Returns the size, in pixels, of the primary display.
getSD() - Method in class ij.measure.CurveFitter: Returns the standard deviation of the residuals.
getSD() - Static method in class ij.plugin.filter.Filters: Returns the default standard deviation used by Process/Noise/Add Specified Noise.
getSelectedIndex() - Method in class ij.plugin.frame.RoiManager: Returns the index of the first selected ROI or -1 if no ROI is selected.
getSelectedIndexes() - Method in class ij.plugin.frame.RoiManager: Returns an array of the selected indexes.
getSelectedRoisAsArray() - Method in class ij.plugin.frame.RoiManager: Returns the selected ROIs as an array, or all the ROIs if none are selected.
getSelectionCoordinates() - Method in class ij.gui.ShapeRoi: Used by the getSelectionCoordinates macro function
getSelectionEnd() - Method in class ij.text.TextPanel: Returns the index of the last selected line, or -1 if there is no slection.
getSelectionStart() - Method in class ij.text.TextPanel: Returns the index of the first selected line, or -1 if there is no slection.
getSerializedImage() - Method in class ij.gui.ImageRoi: Returns a serialized version of the image.
getShape() - Method in class ij.gui.ShapeRoi: Returns a reference to the Shape object encapsulated by this ShapeRoi.
getShapeAsArray() - Method in class ij.gui.ShapeRoi: Retrieves the end points and control points of the path as a float array.
getShapeRoi() - Method in class ij.io.RoiDecoder
getShortcuts() - Static method in class ij.Menus: Returns the hashtable that associates shortcuts with commands.
getShortcuts() - Method in class ij.plugin.CommandLister
getShortSliceLabel(int) - Method in class ij.ImageStack: Returns a shortened version (up to the first 60 characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label.
getShortSliceLabel(int, int) - Method in class ij.ImageStack: Returns a shortened version (up to the first 'max' characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label.
getShortTitle() - Method in class ij.ImagePlus: If the image title is a file name, returns the name without the extension and with spaces removed, otherwise returns the title shortened to the first space.
getShowAllColor() - Static method in class ij.gui.ImageCanvas: Obsolete
getShowAllList() - Method in class ij.gui.ImageCanvas
getShowAllROIs() - Method in class ij.gui.ImageCanvas: Obsolete
getShowLabels() - Method in class ij.gui.PointRoi
getSimilarFontsList(String) - Static method in class ij.util.FontUtil: For a few basic font types, gets a list of replacement font families Note that java's 'SansSerif' has wider characters (significantly different metrics) than the other sans-serif fonts in the list; thus it should be considered a fallback option only.
getSingleWildcardChar() - Method in class ij.util.WildcardMatch: Returns the character used to specify exactly one character.
getSixteenBitRanges() - Static method in class ij.plugin.frame.ContrastAdjuster
getSize() - Method in class ij.gui.Plot: The size of the plot including borders with axis labels etc., in pixels
getSize() - Method in class ij.gui.PlotVirtualStack: Returns the number of slices in this stack.
getSize() - Method in class ij.gui.PointRoi: Returns the current point size 0-6 (Tiny-XXXL).
getSize() - Static method in class ij.gui.TextRoi: Deprecated.
Replaced by getDefaultFontSize
getSize() - Method in class ij.ImageStack
getSize() - Method in class ij.macro.Program
getSize() - Method in class ij.plugin.AVI_Reader: Returns the number of images in this virtual stack (if it is one)
getSize() - Method in class ij.plugin.FileInfoVirtualStack
getSize() - Method in class ij.plugin.ListVirtualStack: Returns the number of images in this stack.
getSize() - Method in class ij.VirtualStack
getSizeInBytes() - Method in class ij.ImagePlus: Returns the size of this image in bytes.
getSlice() - Method in class ij.ImagePlus
getSliceLabel(int) - Method in class ij.gui.PlotVirtualStack
getSliceLabel(int) - Method in class ij.ImageStack: Returns the label of the specified slice, where 1<=n<=nslices.
getSliceLabel(int) - Method in class ij.plugin.AVI_Reader: Returns the label of the specified slice in this virtual stack (if it is one).
getSliceLabel(int) - Method in class ij.plugin.FileInfoVirtualStack: Returns the label of the Nth image.
getSliceLabel(int) - Method in class ij.plugin.ListVirtualStack: Returns the name of the specified image.
getSliceLabel(int) - Method in class ij.VirtualStack: Returns the label of the Nth image.
getSliceLabels() - Method in class ij.ImageStack: Returns the slice labels as an array of Strings.
getSliceNumber() - Method in class ij.plugin.filter.PlugInFilterRunner: Return the slice number currently processed by the calling thread.
getSliceNumber() - Method in class ij.process.ImageProcessor
getSliceNumber(String) - Method in class ij.gui.ImageCanvas
getSliceNumber(String) - Method in class ij.plugin.frame.RoiManager: Returns the slice number associated with the specified name, or -1 if the name does not include a slice number.
getSliderHeight() - Method in class ij.gui.ImageWindow
getSliders() - Method in class ij.gui.GenericDialog: Returns the Vector containing the sliders (Scrollbars).
getSnapshotPixels() - Method in class ij.process.ByteProcessor
getSnapshotPixels() - Method in class ij.process.ColorProcessor: Returns a reference to the snapshot pixel array.
getSnapshotPixels() - Method in class ij.process.FloatProcessor
getSnapshotPixels() - Method in class ij.process.ImageProcessor: Returns a reference to the snapshot (undo) buffer, or null.
getSnapshotPixels() - Method in class ij.process.ShortProcessor
getSortedFitList() - Static method in class ij.measure.CurveFitter: Returns an array of fit names with nicer sorting
getSourceImage() - Method in interface ij.gui.PlotMaker: Returns the ImagePlus used to generate the profile plots.
getSourceImage() - Method in class ij.plugin.Profiler
getSourceImage() - Method in class ij.plugin.ZAxisProfiler
getSrcRect() - Method in class ij.gui.ImageCanvas
getStack() - Method in class ij.gui.Plot: Returns the virtual stack created by addToStack().
getStack() - Method in class ij.ImagePlus: Returns the image stack.
getStackIndex(int, int, int) - Method in class ij.ImagePlus: Returns that stack index (one-based) corresponding to the specified position.
getStackSize() - Method in class ij.ImagePlus: Returns the number of stack images.
getStartTime() - Method in class ij.ImagePlus: Returns the time in milliseconds when startTiming() was last called.
getStartupMacro() - Method in class ij.plugin.Startup
getState() - Method in class ij.gui.Roi
getStaticGlobalCalibration() - Static method in class ij.ImagePlus: This is a version of getGlobalCalibration() that can be called from a static context.
getStatistics() - Method in class ij.gui.Roi
getStatistics() - Method in class ij.ImagePlus: Get calibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation and mode.
getStatistics() - Method in class ij.process.ImageProcessor: Calculates and returns complete uncalibrated (raw) statistics for this image or ROI but it is up to 70 times slower than getStats().
getStatistics(double[]) - Static method in class ij.util.Tools
getStatistics(int) - Method in class ij.ImagePlus: Returns an ImageStatistics object generated using the specified measurement options.
getStatistics(int, int) - Method in class ij.ImagePlus: Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.
getStatistics(int, int, double, double) - Method in class ij.ImagePlus: Returns an ImageStatistics object generated using the specified measurement options, histogram bin count and histogram range.
getStatistics(ImageProcessor) - Static method in class ij.process.ImageStatistics: Calculates and returns uncalibrated (raw) statistics for the specified image, including histogram, area, mean, min and max, standard deviation and mode.
getStatistics(ImageProcessor, int, Calibration) - Static method in class ij.process.ImageStatistics: Calculates and returns statistics for the specified image using the specified measurent options and calibration.
getStats() - Method in class ij.process.ImageProcessor: Calculates and returns uncalibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation, and mode.
getStatus() - Method in class ij.measure.CurveFitter
getStatusBar() - Method in class ij.ImageJ
getStatusBarText() - Static method in class ij.ImageJ
getStatusString() - Method in class ij.measure.CurveFitter: Get a short text with a short description of the status.
getString() - Method in class ij.macro.Variable
getString(String) - Static method in class ij.Prefs: Retrieves a string from string in IJ_Props or IJ_Prefs.txt.
getString(String, String) - Static method in class ij.IJ: Allows the user to enter a string in a dialog box.
getString(String, String) - Static method in class ij.Prefs: Retrieves a string from IJ_Props or IJ_Prefs.txt.
getStringBounds(String) - Method in class ij.process.ImageProcessor: Returns a rectangle enclosing the pixels affected by drawString assuming it is drawn at (x=0, y=0).
getStringFields() - Method in class ij.gui.GenericDialog: Returns the Vector containing the string TextFields.
getStringFromList(String, String) - Static method in class ij.util.Tools: Retrieves a String form a list of key-number pairs like "value1="abc" str='the Text'".
getStringFromList(String, String, String) - Static method in class ij.util.Tools
getStringProperty(String) - Method in class ij.ImagePlus: Returns the string value from the "Info" property string associated with 'key', or null if the key is not found.
getStringValue(int, int) - Method in class ij.measure.ResultsTable: Returns the string value of the given column and row, where column must be less than or equal the value returned by getLastColumn() and row must be greater than or equal zero and less than the value returned by size().
getStringValue(String, int) - Method in class ij.measure.ResultsTable: Returns the string value of the given column and row, where row must be greater than or equal zero and less than the value returned by size().
getStringVariable(String) - Method in class ij.macro.Interpreter
getStringWidth(String) - Method in class ij.process.ImageProcessor: Returns the width in pixels of the specified string, including any background space (whitespace) between the x drawing coordinate and the string, not necessarily including all whitespace at the right.
getStringWidth(String, FontMetrics, Graphics) - Static method in class ij.util.Java2
getStroke() - Method in class ij.gui.Roi: Returns the Stroke used to draw this ROI, or null if no Stroke is used.
getStrokeColor() - Method in class ij.gui.Roi: Returns the the color used to draw the ROI outline or null if the default color is being used.
getStrokeWidth() - Method in class ij.gui.Roi: Returns the line width.
getStubPath() - Static method in class ij.OtherInstance
getStyle() - Method in class ij.gui.Arrow
getStyle() - Static method in class ij.gui.TextRoi: Deprecated.
Replaced by getDefaultFontStyle
getSumResidualsSqr() - Method in class ij.measure.CurveFitter: Returns the sum of the residuals (may be NaN if the minimizer could not start properly i.e., if getStatus() returns Minimizer.INITILIZATION_FAILURE).
getSymbolTable() - Method in class ij.macro.Program
getT() - Method in class ij.ImagePlus: Returns the current hyperstack frame position.
getTableAsImage() - Method in class ij.measure.ResultsTable: Returns the contents of this ResultsTable as a FloatProcessor.
getTag(ImagePlus, String) - Static method in class ij.util.DicomTools: Returns the value (as a string) of the specified DICOM tag id (in the form "0018,0050") of the specified image or stack slice.
getTagName(String) - Static method in class ij.plugin.DICOM: Returns the name of the specified DICOM tag id.
getTagName(String) - Static method in class ij.util.DicomTools: Returns the name of the specified DICOM tag id.
getTempCurrentImage() - Static method in class ij.WindowManager: Returns the temporary current image for this thread, or null.
getText() - Method in class ij.gui.TextRoi
getText() - Method in class ij.plugin.frame.Editor
getText() - Method in class ij.plugin.frame.Recorder
getText() - Method in class ij.text.TextPanel: Returns all the text as a string.
getTextArea() - Method in class ij.plugin.frame.Editor
getTextArea1() - Method in class ij.gui.GenericDialog: Returns a reference to textArea1.
getTextArea2() - Method in class ij.gui.GenericDialog: Returns a reference to textArea2.
getTextPanel() - Static method in class ij.IJ: Returns a reference to the "Results" window TextPanel.
getTextPanel() - Method in class ij.text.TextWindow: Returns a reference to this TextWindow's TextPanel.
getThread() - Method in class ij.macro.MacroRunner
getThreads() - Static method in class ij.Prefs: Returns the number of threads used by PlugInFilters to process images and stacks.
getThreshold(AutoThresholder.Method, int[]) - Method in class ij.process.AutoThresholder: Calculates and returns a threshold using the specified method and 256 bin histogram.
getThreshold(String, int[]) - Method in class ij.process.AutoThresholder
getThresholdColorModel() - Method in class ij.process.ImageProcessor
getTiffFileInfo(String) - Static method in class ij.io.Opener: Returns the FileInfo of the specified TIFF file.
getTiffInfo() - Method in class ij.io.TiffDecoder
getTimeUnit() - Method in class ij.measure.Calibration: Returns the distance unit (e.g.
getTitle() - Method in class ij.gui.Plot: Returns the title of the image showing the plot (if any) or title of the plot
getTitle() - Method in class ij.ImagePlus: Returns the image name.
getTitle() - Method in class ij.measure.ResultsTable
getTolerance() - Static method in class ij.plugin.WandToolOptions
getToolIcon() - Method in class ij.plugin.tool.ArrowTool
getToolIcon() - Method in class ij.plugin.tool.BrushTool
getToolIcon() - Method in class ij.plugin.tool.OverlayBrushTool
getToolIcon() - Method in class ij.plugin.tool.PixelInspectionTool
getToolIcon() - Method in class ij.plugin.tool.PlugInTool: Return the string encoding of the tool icon.
getToolIcon() - Method in class ij.plugin.tool.RoiRotationTool
getToolId() - Static method in class ij.gui.Toolbar: Returns the ID of the current tool (Toolbar.RECTANGLE, Toolbar.OVAL, etc.).
getToolId(String) - Method in class ij.gui.Toolbar: Returns the ID of the tool whose name (the description displayed in the status bar) starts with the specified string, or -1 if the tool is not found.
getToolName() - Static method in class ij.gui.Toolbar: Returns the name of the current tool.
getToolName() - Static method in class ij.IJ: Returns the name of the current tool.
getToolName() - Method in class ij.plugin.tool.ArrowTool
getToolName() - Method in class ij.plugin.tool.BrushTool
getToolName() - Method in class ij.plugin.tool.OverlayBrushTool
getToolName() - Method in class ij.plugin.tool.PixelInspectionTool
getToolName() - Method in class ij.plugin.tool.PlugInTool: Return the tool name.
getToolName() - Method in class ij.plugin.tool.RoiRotationTool
getTPosition() - Method in class ij.gui.Roi: Returns the frame position of this ROI, or zero if this ROI is not associated with a particular frame.
getTransferData(DataFlavor) - Method in class ij.plugin.Clipboard
getTransferDataFlavors() - Method in class ij.plugin.Clipboard
getTransparentIndex() - Static method in class ij.Prefs: Returns the transparent index (0-255), or -1 if transparency is disabled.
getType() - Method in class ij.gui.Roi
getType() - Method in class ij.ImagePlus: Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
getTypeAsString() - Method in class ij.gui.Roi: Convenience method that converts Roi type to a human-readable form.
getTypeName(int) - Static method in class ij.macro.ExtensionDescriptor
getTypes() - Method in class ij.gui.Plot: Returns an array of the available curve types ("Line", "Bar", "Circle", etc).
getUMeans() - Static method in class ij.plugin.filter.Analyzer: Returns an array containing the first 20 uncalibrated means.
getUncalibratedLength() - Method in class ij.gui.PolygonRoi
getUnionOfBounds() - Static method in class ij.gui.GUI
getUniqueName(ImagePlus, String) - Static method in class ij.WindowManager
getUniqueName(String) - Static method in class ij.WindowManager: Returns a unique name by adding, before the extension, -1, -2, etc.
getUnit() - Method in class ij.measure.Calibration: Returns the default length unit (e.g.
getUnitIncrement() - Method in class ij.gui.ScrollbarWithLabel
getUnits() - Method in class ij.measure.Calibration: Returns the plural form of the length unit (e.g.
getValue() - Method in class ij.gui.ScrollbarWithLabel
getValue() - Method in class ij.macro.Variable
getValue(int, int) - Method in class ij.measure.ResultsTable: Deprecated.
replaced by getValueAsDouble
getValue(int, int) - Method in class ij.process.ImageProcessor: Returns the value of the pixel at (x,y), a calibrated value from 8-bit and 16-bit images, an intensity value from RGB images and a double value from 32-bit images.
getValue(ImagePlus, String) - Static method in class ij.IJ: Returns a measurement result, where 'measurement' is "Area", "Mean", "StdDev", "Mode", "Min", "Max", "X", "Y", "XM", "YM", "Perim.", "BX", "BY", "Width", "Height", "Major", "Minor", "Angle", "Circ.", "Feret", "IntDen", "Median", "Skew", "Kurt", "%Area", "RawIntDen", "Ch", "Slice", "Frame", "FeretX", "FeretY", "FeretAngle", "MinFeret", "AR", "Round", "Solidity", "MinThr" or "MaxThr".
getValue(String) - Method in class ij.gui.GenericDialog
getValue(String, int) - Method in class ij.measure.ResultsTable: Returns the value of the specified column and row, where column is the column heading and row is a number greater than or equal zero and less than value returned by size().
getValue(String, String, String) - Static method in class ij.Macro
getValueAsDouble(int, int) - Method in class ij.measure.ResultsTable: Returns the value of the given column and row, where column must be less than or equal the value returned by getLastColumn() and row must be greater than or equal zero and less than the value returned by size().
getValueUnit() - Method in class ij.measure.Calibration: Returns the value unit.
getVariable(String) - Method in class ij.macro.Interpreter
getVariable2(String) - Method in class ij.macro.Interpreter
getVariableAsString(String) - Method in class ij.macro.Interpreter
getVariableNames() - Method in class ij.macro.Interpreter: Returns the names of all variables, without any annotation
getVariables() - Method in class ij.macro.Interpreter: Returns the names of all variables and functions with human-readable annotations
getVariance() - Method in class ij.util.ArrayUtil: Variance value
getVersion() - Static method in class ij.IJ: Returns the ImageJ version number as a string.
getVersion() - Method in class ij.plugin.PlugInInterpreter: Returns the version of ImageJ at the time this plugin was created.
getVisibleAmount() - Method in class ij.gui.ScrollbarWithLabel
getVoxel(int, int, int) - Method in class ij.ImageStack: Returns, as a double, the value of the specified voxel.
getVoxelDepth(ImageStack) - Static method in class ij.util.DicomTools: Calculates the voxel depth of the specified DICOM stack based on the distance between the first and last slices.
getVoxels(int, int, int, int, int, int, float[]) - Method in class ij.ImageStack
getVoxels(int, int, int, int, int, int, float[], int) - Method in class ij.ImageStack
getWeightingFactors() - Static method in class ij.process.ColorProcessor: Returns the three weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
getWidth() - Static method in class ij.gui.Line: Returns the default line width.
getWidth() - Method in class ij.ImagePlus: Returns the width of this image in pixels.
getWidth() - Method in class ij.ImageStack
getWidth() - Method in class ij.plugin.AVI_Reader: Returns the image width of the virtual stack
getWidth() - Method in class ij.plugin.FileInfoVirtualStack
getWidth() - Method in class ij.plugin.ListVirtualStack
getWidth() - Method in class ij.process.ImageProcessor: Returns the width of this image in pixels.
getWindow() - Method in class ij.ImagePlus: Returns the ImageWindow that is being used to display this image.
getWindow(String) - Static method in class ij.WindowManager: Returns the window (a Frame or a Dialog) with the specified title, or null if a window with that title is not found.
getWindowCount() - Static method in class ij.WindowManager: Returns the number of open image windows.
getX(double) - Method in class ij.measure.Calibration: Converts a x-coodinate in pixels to physical units (e.g.
getXBase() - Method in class ij.gui.Roi
getXCoordinates() - Method in class ij.gui.PolygonRoi: Obsolete; replaced by either getPolygon() or getFloatPolygon().
getXPoints() - Method in class ij.measure.CurveFitter: returns the array with the x data
getXUnit() - Method in class ij.measure.Calibration: Returns the X length unit.
getXUnits() - Method in class ij.measure.Calibration: Returns the plural form of the X length unit (e.g.
getXValues() - Method in class ij.gui.HistogramPlot
getXValues() - Method in class ij.gui.HistogramWindow
getXValues() - Method in class ij.gui.Plot: Get the x coordinates of the data set passed with the constructor (if not null) or otherwise of the data set of the first 'addPoints'.
getXValues() - Method in class ij.gui.PlotWindow
getXZImage() - Method in class ij.plugin.Orthogonal_Views
getY(double) - Method in class ij.measure.Calibration: Converts a y-coordinate in pixels to physical units (e.g.
getY(double, int) - Method in class ij.measure.Calibration: Converts a y-coordinate in pixels to physical units (e.g.
getYBase() - Method in class ij.gui.Roi
getYCoordinates() - Method in class ij.gui.PolygonRoi: Obsolete; replaced by either getPolygon() or getFloatPolygon().
getYPoints() - Method in class ij.measure.CurveFitter: returns the array with the y data
getYUnit() - Method in class ij.measure.Calibration: Returns the Y length unit, or the default unit if 'yunit' is null.
getYUnits() - Method in class ij.measure.Calibration: Returns the plural form of the Y length unit (e.g.
getYUV(ImageProcessor, byte[], byte[], byte[]) - Method in class ij.plugin.frame.ColorThresholder
getYValues() - Method in class ij.gui.Plot: Get the y coordinates of the data set passed with the constructor (if not null) or otherwise of the data set of the first 'addPoints'.
getYValues() - Method in class ij.gui.PlotWindow
getYZImage() - Method in class ij.plugin.Orthogonal_Views
getZ() - Method in class ij.ImagePlus: Returns the current hyperstack slice position.
getZ(double) - Method in class ij.measure.Calibration: Converts a z-coordinate in pixels to physical units (e.g.
getZeroBasedMaxBounds() - Static method in class ij.gui.GUI
getZeroTransparent() - Method in class ij.gui.ImageRoi
getZPosition() - Method in class ij.gui.Roi: Returns the slice position of this ROI, or zero if this ROI is not associated with a particular slice.
getZUnit() - Method in class ij.measure.Calibration: Returns the Z length unit, or the default unit if 'zunit' is null.
getZUnits() - Method in class ij.measure.Calibration: Returns the plural form of the Z length unit (e.g.
GIF - Static variable in class ij.io.Opener
GIF_OR_JPG - Static variable in class ij.io.FileInfo
GIF_Reader - Class in ij.plugin: This plugin opens GIFs and Animated GIFs.
GIF_Reader() - Constructor for class ij.plugin.GIF_Reader
GifWriter - Class in ij.plugin: Saves the active image in GIF format, or as an animated GIF if the image is a stack.
GifWriter() - Constructor for class ij.plugin.GifWriter
gLUT1 - Variable in class ij.process.ImageProcessor
gLUT2 - Variable in class ij.process.ImageProcessor
GRAY12_UNSIGNED - Static variable in class ij.io.FileInfo: 12-bit unsigned integer (0-4095).
GRAY16 - Static variable in class ij.gui.NewImage
GRAY16 - Static variable in class ij.ImagePlus: 16-bit grayscale (unsigned)
GRAY16_SIGNED - Static variable in class ij.io.FileInfo: 16-bit signed integer (-32768-32767).
GRAY16_UNSIGNED - Static variable in class ij.io.FileInfo: 16-bit unsigned integer (0-65535).
GRAY24_UNSIGNED - Static variable in class ij.io.FileInfo: 24-bit unsigned integer.
GRAY32 - Static variable in class ij.gui.NewImage
GRAY32 - Static variable in class ij.ImagePlus: 32-bit floating-point grayscale
GRAY32_FLOAT - Static variable in class ij.io.FileInfo: 32-bit floating-point.
GRAY32_INT - Static variable in class ij.io.FileInfo: 32-bit signed integer.
GRAY32_UNSIGNED - Static variable in class ij.io.FileInfo: 32-bit unsigned integer.
GRAY64_FLOAT - Static variable in class ij.io.FileInfo: 64-bit floating-point.
GRAY8 - Static variable in class ij.gui.NewImage
GRAY8 - Static variable in class ij.ImagePlus: 8-bit grayscale (unsigned)
GRAY8 - Static variable in class ij.io.FileInfo: 8-bit unsigned integer (0-255).
GRAYSCALE - Static variable in class ij.CompositeImage: Display modes (note: TRANSPARENT mode has not yet been implemented)
GRAYSCALE - Static variable in class ij.IJ: Image display modes
green - Variable in class ij.plugin.filter.RGBStackSplitter
greens - Variable in class ij.io.FileInfo
Grid - Class in ij.plugin: This class implements the Analyze/Tools/Grid command.
Grid() - Constructor for class ij.plugin.Grid
GRID - Static variable in class ij.plugin.filter.Rotator
GROUP - Static variable in class ij.io.RoiDecoder
GroupedZProjector - Class in ij.plugin: Implements the Image/Stacks/Tools/Grouped Z Project command.
GroupedZProjector() - Constructor for class ij.plugin.GroupedZProjector
groupZProject(ImagePlus, int, int) - Method in class ij.plugin.GroupedZProjector
grow(int, int) - Method in class ij.gui.EllipseRoi
grow(int, int) - Method in class ij.gui.FreehandRoi
grow(int, int) - Method in class ij.gui.Line
grow(int, int) - Method in class ij.gui.PolygonRoi
grow(int, int) - Method in class ij.gui.Roi
grow(int, int) - Method in class ij.gui.RotatedRectRoi
GT - Static variable in interface ij.macro.MacroConstants
GTE - Static variable in interface ij.macro.MacroConstants
GUI - Class in ij.gui: This class consists of static GUI utility methods.
GUI() - Constructor for class ij.gui.GUI
GUI_SCALE - Static variable in class ij.Prefs

H

HAMMING - Static variable in class ij.process.FHT
HAND - Static variable in class ij.gui.Toolbar
handCursor - Static variable in class ij.gui.ImageCanvas
handle(Throwable) - Method in interface ij.IJ.ExceptionHandler
handle(Throwable) - Method in class ij.ImageJ.ExceptionHandler
HANDLE_SIZE - Static variable in class ij.gui.Roi
handleColor - Variable in class ij.gui.Roi
handleException(String, Throwable) - Method in class ij.ImageJ.ExceptionHandler
handleException(Throwable) - Static method in class ij.IJ: Displays a stack trace.
handleExtension(String, Object[]) - Method in interface ij.macro.MacroExtension
handleMouseDown(int, int) - Method in class ij.gui.Arrow
handleMouseDown(int, int) - Method in class ij.gui.Line
handleMouseDown(int, int) - Method in class ij.gui.Roi
handleMouseDrag(int, int, int) - Method in class ij.gui.Roi
handleMouseUp(int, int) - Method in class ij.gui.EllipseRoi
handleMouseUp(int, int) - Method in class ij.gui.FreehandRoi
handleMouseUp(int, int) - Method in class ij.gui.Line
handleMouseUp(int, int) - Method in class ij.gui.PointRoi
handleMouseUp(int, int) - Method in class ij.gui.PolygonRoi: With segmented selections, ignore first mouse up and finalize when user double-clicks, control-clicks or clicks in start box.
handleMouseUp(int, int) - Method in class ij.gui.Roi
handleMouseUp(int, int) - Method in class ij.gui.RotatedRectRoi
handleMouseUp(int, int) - Method in class ij.gui.TextRoi
handlePopupMenu(MouseEvent) - Method in class ij.gui.ImageCanvas
handler - Variable in class ij.macro.ExtensionDescriptor
handleRoiMouseDown(MouseEvent) - Method in class ij.gui.ImageCanvas
HANN - Static variable in class ij.process.FHT
hasCustomLuts() - Method in class ij.CompositeImage
hasHyperStackPosition() - Method in class ij.gui.Roi: Returns 'true' if setPosition(C,Z,T) has been called.
hasImageStack() - Method in class ij.ImagePlus: Returns 'true' if this ImagePlus contains an ImageStack.
hasNext() - Method in class ij.gui.Line.PointIterator
hasVars() - Method in class ij.macro.Program
hasWord(String) - Method in class ij.macro.Program
HEADER2_OFFSET - Static variable in class ij.io.RoiDecoder
HEADLESS - Static variable in class ij.gui.Arrow
height - Variable in class ij.ImagePlus
height - Variable in class ij.io.FileInfo
height - Variable in class ij.process.ImageProcessor
height - Variable in class ij.process.ImageStatistics
HEIGHT - Static variable in class ij.gui.ProgressBar
HEIGHT_KEY - Static variable in class ij.text.TextWindow
HEIGHTD - Static variable in class ij.io.RoiDecoder
help - Static variable in class ij.plugin.frame.Channels
help - Static variable in class ij.plugin.PointToolOptions
hexDigits - Static variable in class ij.util.Tools: This array contains the 16 hex digits '0'-'F'.
hexToColor(String) - Static method in class ij.plugin.Colors: Converts a hex color (e.g., "ffff00") into "red", "green", "yellow", etc.
hexToColor2(String) - Static method in class ij.plugin.Colors: Converts a hex color (e.g., "ffff00" or "#ffff00") into a color name "Red", "Green", "Yellow", etc.
HGAP - Static variable in class ij.gui.ImageWindow
HI_RESOLUTION - Static variable in class ij.gui.PlotDialog: Types of dialog.
hide() - Method in class ij.ImagePlus: Closes the window, if any, that is displaying this image.
hideCancelButton() - Method in class ij.gui.GenericDialog: Do not display "Cancel" button.
hideErrorMessages() - Method in class ij.plugin.TextReader
hideProcessStackDialog - Static variable in class ij.IJ
hideProgress() - Method in class ij.process.ImageProcessor: Deprecated.
hideZoomIndicator(boolean) - Method in class ij.gui.ImageCanvas
histMax - Variable in class ij.process.ImageStatistics
histMin - Variable in class ij.process.ImageStatistics
histogram - Variable in class ij.gui.HistogramWindow
histogram - Variable in class ij.process.ImageStatistics: Use the hIstogram() method to get the histogram as a double array.
histogram() - Method in class ij.process.ImageStatistics: Returns the histogram as an array of doubles.
Histogram - Class in ij.plugin: This plugin implements the Analyze/Histogram command.
Histogram() - Constructor for class ij.plugin.Histogram
histogram16 - Variable in class ij.process.ImageStatistics: Bin width 1 histogram of 16-bit images
histogramMax - Variable in class ij.process.ImageProcessor
histogramMin - Variable in class ij.process.ImageProcessor
HistogramPlot - Class in ij.gui
HistogramPlot() - Constructor for class ij.gui.HistogramPlot
histogramSize - Variable in class ij.process.ImageProcessor
HistogramWindow - Class in ij.gui: This class is an extended ImageWindow that displays histograms.
HistogramWindow(HistogramPlot, ImagePlus) - Constructor for class ij.gui.HistogramWindow
HistogramWindow(ImagePlus) - Constructor for class ij.gui.HistogramWindow: Displays a histogram using the title "Histogram of ImageName".
HistogramWindow(String, ImagePlus, int) - Constructor for class ij.gui.HistogramWindow: Displays a histogram using the specified title and number of bins.
HistogramWindow(String, ImagePlus, int, double, double) - Constructor for class ij.gui.HistogramWindow: Displays a histogram using the specified title, number of bins and histogram range.
HistogramWindow(String, ImagePlus, int, double, double, int) - Constructor for class ij.gui.HistogramWindow: Displays a histogram using the specified title, number of bins, histogram range and yMax.
HistogramWindow(String, ImagePlus, ImageStatistics) - Constructor for class ij.gui.HistogramWindow: Displays a histogram using the specified title and ImageStatistics.
histYMax - Variable in class ij.process.ImageStatistics
HOST_COMPUTER - Static variable in class ij.io.TiffDecoder
Hotkeys - Class in ij.plugin: Implements the Plugins/Hotkeys/Create Shortcut and Remove commands.
Hotkeys() - Constructor for class ij.plugin.Hotkeys
HSBtoRGB(double[]) - Method in class ij.process.ColorSpaceConverter
HSBtoRGB(double, double, double) - Method in class ij.process.ColorSpaceConverter
HTMLDialog - Class in ij.gui: This is modal or non-modal dialog box that displays HTML formated text.
HTMLDialog(Dialog, String, String) - Constructor for class ij.gui.HTMLDialog
HTMLDialog(String, String) - Constructor for class ij.gui.HTMLDialog
HTMLDialog(String, String, boolean) - Constructor for class ij.gui.HTMLDialog
Huang - ij.process.AutoThresholder.Method
HYBRID - Static variable in class ij.gui.PointRoi
hyperlinkUpdate(HyperlinkEvent) - Method in class ij.gui.HTMLDialog
HyperStackConverter - Class in ij.plugin: Implements the "Stack to HyperStack", "RGB to HyperStack" and "HyperStack to Stack" commands.
HyperStackConverter() - Constructor for class ij.plugin.HyperStackConverter
HyperStackMaker - Class in ij.plugin: This plugin implements the File/New/Hyperstack command.
HyperStackMaker() - Constructor for class ij.plugin.HyperStackMaker
HyperStackReducer - Class in ij.plugin: Implements the Image/HyperStacks/Reduce Dimensionality command.
HyperStackReducer() - Constructor for class ij.plugin.HyperStackReducer: Default constructor
HyperStackReducer(ImagePlus) - Constructor for class ij.plugin.HyperStackReducer: Constructs a HyperStackReducer using the specified source image.

I

ic - Variable in class ij.gui.ImageWindow
ic - Variable in class ij.gui.Roi
IF - Static variable in interface ij.macro.MacroConstants
ignoreClipRect - Variable in class ij.gui.Roi
ignoreNextSelection() - Static method in class ij.plugin.Duplicator
ignoreNonImageWidths(boolean) - Method in class ij.gui.ImageLayout: Determines whether to ignore the width of non-image components when calculating the preferred width (default false, i.e.
ignoreRescaleSlope - Static variable in class ij.Prefs: Ignore Rescale Slope when opening DICOMs
ij - module ij
ij - package ij
ij - Variable in class ij.gui.ImageCanvas
ij - Variable in class ij.gui.ImageWindow
IJ - Class in ij: This class consists of static utility methods.
IJ() - Constructor for class ij.IJ
IJ_CALL - Static variable in interface ij.macro.MacroConstants
IJ_IsoData - ij.process.AutoThresholder.Method
IJ.ExceptionHandler - Interface in ij
ij.gui - package ij.gui
ij.io - package ij.io
ij.macro - package ij.macro
ij.measure - package ij.measure
ij.plugin - package ij.plugin
ij.plugin.filter - package ij.plugin.filter
ij.plugin.frame - package ij.plugin.frame
ij.plugin.tool - package ij.plugin.tool
ij.process - package ij.process
ij.text - package ij.text
ij.util - package ij.util
IJEventListener - Interface in ij: Plugins that implement this interface are notified when the user changes the foreground color, changes the background color, closes the color picker, closes the Log window or switches to another tool.
ijInstance - Variable in class ij.plugin.frame.SyncWindows: reference to current instance of ImageJ (to avoid repeated IJ.getInstance() s)
IJMath - Class in ij.util
IJMath() - Constructor for class ij.util.IJMath
image - Variable in class ij.process.ImageProcessor
IMAGE - Static variable in class ij.io.RoiDecoder
IMAGE - Static variable in interface ij.macro.MacroConstants
IMAGE_DESCRIPTION - Static variable in class ij.io.TiffDecoder
IMAGE_LENGTH - Static variable in class ij.io.TiffDecoder
IMAGE_OPACITY - Static variable in class ij.io.RoiDecoder
IMAGE_SIZE - Static variable in class ij.io.RoiDecoder
IMAGE_WIDTH - Static variable in class ij.io.TiffDecoder
ImageCalculator - Class in ij.plugin: This plugin implements the Process/Image Calculator command.
ImageCalculator() - Constructor for class ij.plugin.ImageCalculator
ImageCanvas - Class in ij.gui: This is a Canvas used to display images in a Window.
ImageCanvas(ImagePlus) - Constructor for class ij.gui.ImageCanvas
imageClosed(ImagePlus) - Method in class ij.gui.HistogramWindow
imageClosed(ImagePlus) - Method in class ij.gui.PlotWindow: For live plots, if either the source image or this image are closed, exit live mode
imageClosed(ImagePlus) - Method in interface ij.ImageListener
imageClosed(ImagePlus) - Method in class ij.plugin.EventListener
imageClosed(ImagePlus) - Method in class ij.plugin.frame.Recorder
imageClosed(ImagePlus) - Method in class ij.plugin.frame.SyncWindows: Implementation of ImageListener interface: update window list, if image is opened or closed
imageClosed(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
imageClosed(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
ImageConverter - Class in ij.process: This class converts an ImagePlus object to a different type.
ImageConverter(ImagePlus) - Constructor for class ij.process.ImageConverter: Constructs an ImageConverter based on an ImagePlus object.
imageHeight - Variable in class ij.gui.ImageCanvas
ImageInfo - Class in ij.plugin: This plugin implements the Image/Show Info command.
ImageInfo() - Constructor for class ij.plugin.ImageInfo
IMAGEIO - Static variable in class ij.io.FileInfo
ImageJ - Class in ij: This frame is the main ImageJ class.
ImageJ() - Constructor for class ij.ImageJ: Creates a new ImageJ frame that runs as an application.
ImageJ(int) - Constructor for class ij.ImageJ: Creates a new ImageJ frame that runs as an application in the specified mode.
ImageJ(Applet) - Constructor for class ij.ImageJ: Creates a new ImageJ frame that runs as an applet.
ImageJ(Applet, int) - Constructor for class ij.ImageJ: If 'applet' is not null, creates a new ImageJ frame that runs as an applet.
IMAGEJ_APP - Static variable in class ij.ImageJ: Run as the ImageJ application.
ImageJ_Updater - Class in ij.plugin: This plugin implements the Help/Update ImageJ command.
ImageJ_Updater() - Constructor for class ij.plugin.ImageJ_Updater
ImageJ.ExceptionHandler - Class in ij: Handles exceptions on the EDT.
ImageJApplet - Class in ij: Runs ImageJ as an applet and optionally opens up to nine images using URLs passed as a parameters.
ImageJApplet() - Constructor for class ij.ImageJApplet
ImageLayout - Class in ij.gui: This is a custom layout manager that supports resizing of zoomed images.
ImageLayout(ImageCanvas) - Constructor for class ij.gui.ImageLayout: Creates a new ImageLayout with center alignment.
ImageListener - Interface in ij: Plugins that implement this interface are notified when an image is opened, closed or updated.
ImageMath - Class in ij.plugin.filter: This plugin implements ImageJ's Process/Math submenu.
ImageMath() - Constructor for class ij.plugin.filter.ImageMath
imageOpened(ImagePlus) - Method in class ij.gui.HistogramWindow
imageOpened(ImagePlus) - Method in class ij.gui.PlotWindow
imageOpened(ImagePlus) - Method in interface ij.ImageListener
imageOpened(ImagePlus) - Method in class ij.plugin.EventListener
imageOpened(ImagePlus) - Method in class ij.plugin.frame.Recorder
imageOpened(ImagePlus) - Method in class ij.plugin.frame.SyncWindows: Implementation of ImageListener interface: update window list, if image is opened or closed
imageOpened(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
imageOpened(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
ImagePanel - Class in ij.gui: This class is used by GenericDialog to add images to dialogs.
ImagePlus - Class in ij: An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image).
ImagePlus() - Constructor for class ij.ImagePlus: Constructs an uninitialized ImagePlus.
ImagePlus(String) - Constructor for class ij.ImagePlus: Constructs an ImagePlus from a TIFF, BMP, DICOM, FITS, PGM, GIF or JPRG specified by a path or from a TIFF, DICOM, GIF or JPEG specified by a URL.
ImagePlus(String, ImageStack) - Constructor for class ij.ImagePlus: Constructs an ImagePlus from a stack.
ImagePlus(String, ImageProcessor) - Constructor for class ij.ImagePlus: Constructs an ImagePlus from an ImageProcessor.
ImagePlus(String, Image) - Constructor for class ij.ImagePlus: Constructs an ImagePlus from an Image or BufferedImage.
ImageProcessor - Class in ij.process: This abstract class is the superclass for classes that process the four data types (byte, short, float and RGB) supported by ImageJ.
ImageProcessor() - Constructor for class ij.process.ImageProcessor
ImageProperties - Class in ij.plugin.filter
ImageProperties() - Constructor for class ij.plugin.filter.ImageProperties
ImageReader - Class in ij.io: Reads raw 8-bit, 16-bit or 32-bit (float or RGB) images from a stream or URL.
ImageReader(FileInfo) - Constructor for class ij.io.ImageReader: Constructs a new ImageReader using a FileInfo object to describe the file to be read.
ImageRoi - Class in ij.gui: An ImageRoi is an Roi that overlays an image.
ImageRoi(int, int, ImageProcessor) - Constructor for class ij.gui.ImageRoi: Creates a new ImageRoi from a ImageProcessor.
ImageRoi(int, int, BufferedImage) - Constructor for class ij.gui.ImageRoi: Creates a new ImageRoi from a BufferedImage.
imageSaved - Variable in class ij.io.FileInfo
imageSaved(ImagePlus) - Method in class ij.plugin.EventListener
ImageStack - Class in ij: This class represents an expandable array of images.
ImageStack() - Constructor for class ij.ImageStack: Default constructor.
ImageStack(int, int) - Constructor for class ij.ImageStack: Creates a new, empty image stack.
ImageStack(int, int, int) - Constructor for class ij.ImageStack: Creates a new, empty image stack with a capacity of 'size'.
ImageStack(int, int, ColorModel) - Constructor for class ij.ImageStack: Creates a new, empty image stack using the specified color model.
ImageStatistics - Class in ij.process: Statistics, including the histogram, of an image or selection.
ImageStatistics() - Constructor for class ij.process.ImageStatistics
ImagesToStack - Class in ij.plugin: Implements the Image/Stacks/Images to Stack" command.
ImagesToStack() - Constructor for class ij.plugin.ImagesToStack
imageUpdate(Image, int, int, int, int, int) - Method in class ij.ImagePlus: Used by ImagePlus to monitor loading of images.
imageUpdated - Variable in class ij.gui.ImageCanvas
imageUpdated(ImagePlus) - Method in class ij.gui.HistogramWindow
imageUpdated(ImagePlus) - Method in class ij.gui.PlotWindow: For live plots, this method is called if the source image content is changed.
imageUpdated(ImagePlus) - Method in interface ij.ImageListener
imageUpdated(ImagePlus) - Method in class ij.plugin.EventListener
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.Recorder
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
imageUpdated(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
imageWidth - Variable in class ij.gui.ImageCanvas
ImageWindow - Class in ij.gui: A frame for displaying images.
ImageWindow(ImagePlus) - Constructor for class ij.gui.ImageWindow
ImageWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.ImageWindow
ImageWindow(String) - Constructor for class ij.gui.ImageWindow
ImageWriter - Class in ij.io: Writes a raw image described by a FileInfo object to an OutputStream.
ImageWriter(FileInfo) - Constructor for class ij.io.ImageWriter
img - Variable in class ij.ImagePlus
img - Variable in class ij.process.ImageProcessor
imp - Variable in class ij.gui.ImageCanvas
imp - Variable in class ij.gui.ImageWindow
imp - Variable in class ij.gui.ProfilePlot
imp - Variable in class ij.gui.Roi
imp - Variable in class ij.plugin.filter.ParticleAnalyzer
IMPORT_MENU - Static variable in class ij.Menus
importData(JComponent, Transferable) - Method in class ij.io.DragAndDropHandler: Imports the drag&drop file or list of files and sets the JFileChooser to this.
ImportDialog - Class in ij.io: This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.
ImportDialog() - Constructor for class ij.io.ImportDialog
ImportDialog(String, String) - Constructor for class ij.io.ImportDialog
in - Variable in class ij.io.TiffDecoder
in(ImagePlus) - Static method in class ij.plugin.Zoom
IN_PLACE - Static variable in class ij.plugin.Resizer
IN_SITU_SHOW - Static variable in class ij.plugin.filter.ParticleAnalyzer: Replace original image with masks.
IN_TOLERANCE - Static variable in class ij.plugin.filter.MaximumFinder: Output type all points around the maximum within the tolerance
INCLUDE_HOLES - Static variable in class ij.plugin.filter.ParticleAnalyzer: Flood fill to ignore interior holes.
incrementCounter() - Method in class ij.measure.ResultsTable: Adds a row to the table.
INDEX_OF - Static variable in interface ij.macro.MacroConstants
indexAt(int, int) - Method in class ij.gui.Overlay: Returns the index of the last ROI that contains the point (x,y) or null if no ROI contains the point.
indices - Variable in class ij.process.DownsizeTable: For each source point between srcStart and srcEnd, indices of destination points where the data should be added.
info - Variable in class ij.io.FileInfo
info - Variable in class ij.measure.Calibration: Plugin writers can use this string to store information about the image.
Info - Class in ij.plugin.filter: Deprecated.
replaced by ij.plugin.ImageInfo
Info() - Constructor for class ij.plugin.filter.Info: Deprecated.
init() - Method in class ij.gui.Toolbar
init() - Method in class ij.ImageJApplet: Starts ImageJ if it's not already running.
init(int, int) - Method in class ij.gui.ProgressBar
INITIALIZATION_FAILURE - Static variable in class ij.measure.Minimizer: Status returned: Could not initialize the simplex because either the initialParams resulted in the target function returning NaN or all attempts to find starting parameters for the other simplex points resulted in the target function returning NaN.
inputStream - Variable in class ij.io.FileInfo
insert(ImagePlus, ImagePlus, int, int) - Method in class ij.plugin.StackInserter
insert(ImageProcessor, int, int) - Method in class ij.process.ImageProcessor: Inserts the image contained in 'ip' at (xloc, yloc).
insertText(String) - Method in class ij.plugin.frame.Editor
inSituShow - Variable in class ij.plugin.filter.ParticleAnalyzer
install(String) - Method in class ij.plugin.MacroInstaller
install(String) - Method in class ij.plugin.PluginInstaller
install(String, Menu) - Method in class ij.plugin.MacroInstaller
INSTALL_BUTTON - Static variable in class ij.plugin.frame.Editor
installFile(String) - Method in class ij.plugin.MacroInstaller
installFromIJJar(String) - Method in class ij.plugin.MacroInstaller: Installs a macro set contained in ij.jar.
installFromJar(String) - Static method in class ij.plugin.MacroInstaller: Installs a macro set contained in ij.jar.
installLibrary(String) - Method in class ij.plugin.MacroInstaller
installPlugin(String, char, String, String, ImageJ) - Static method in class ij.Menus: Adds a plugin based command to the end of a specified menu.
installSingleTool(String) - Method in class ij.plugin.MacroInstaller
installStartupMacros(String) - Method in class ij.plugin.MacroInstaller: Installs startup macros and runs AutoRun macro on current thread.
installStartupMacrosTools() - Static method in class ij.gui.Toolbar
installStartupTools() - Method in class ij.gui.Toolbar
installTool(String) - Method in class ij.plugin.MacroInstaller
installUserPlugin(String, boolean) - Method in class ij.Menus
instance - Static variable in class ij.gui.GenericDialog
instanceColor - Variable in class ij.gui.Roi
int2hex(int, int) - Static method in class ij.util.Tools: Converts an int to a zero-padded hex string of fixed length 'digits'.
INTEGRATED_DENSITY - Static variable in interface ij.measure.Measurements
INTEGRATED_DENSITY - Static variable in class ij.measure.ResultsTable
intelByteOrder - Variable in class ij.io.FileInfo
intelByteOrder - Static variable in class ij.Prefs: Export TIFF and Raw using little-endian byte order.
INTERACTIVE_NAME - Static variable in class ij.plugin.frame.Editor
Intermodes - ij.process.AutoThresholder.Method
interpolate - Static variable in class ij.gui.PlotWindow: Interpolate line profiles.
interpolate - Variable in class ij.process.ImageProcessor
interpolateScaledImages - Static variable in class ij.Prefs: Display images scaled <100% using bilinear interpolation
interpolationMethod - Variable in class ij.process.ImageProcessor
Interpreter - Class in ij.macro: This is the recursive descent parser/interpreter for the ImageJ macro language.
Interpreter() - Constructor for class ij.macro.Interpreter
IntProcessor - Class in ij.process: This is an extended ColorProcessor that supports signed 32-bit int images.
IntProcessor(int, int) - Constructor for class ij.process.IntProcessor: Creates a blank IntProcessor with the specified dimensions.
IntProcessor(int, int, int[]) - Constructor for class ij.process.IntProcessor: Creates an IntProcessor from a pixel array.
INV_RODBARD - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
INVALID_SHORTCUT - Static variable in class ij.Menus
invalidNumber() - Method in class ij.gui.GenericDialog: Returns true if one or more of the numeric fields contained an invalid number.
inverse(ImagePlus) - Static method in class ij.plugin.FFT: Performs an inverse FHT transform.
inverseTransform() - Method in class ij.process.FHT: Performs an inverse transform, converting this image into the space domain.
inverseTransform1D(float[]) - Method in class ij.process.FHT: Performs an inverse 1D Fast Hartley Transform (FHT) of an array
inversionTested - Variable in class ij.process.ImageProcessor
invert() - Method in class ij.process.FloatProcessor: Each pixel in the image is inverted using p=max-(p-min), where 'min' and 'max' are the display range limits set using setMinAndMax().
invert() - Method in class ij.process.ImageProcessor: Inverts the image or ROI.
invert() - Method in class ij.process.ShortProcessor
invert() - Method in class ij.process.StackProcessor
INVERT - Static variable in interface ij.macro.MacroConstants
INVERT_PROJECTION - Static variable in class ij.process.ImageProcessor: Composite image projection modes.
INVERT_Y - Static variable in interface ij.measure.Measurements
invertedLut - Variable in class ij.process.ImageProcessor
invertLut() - Method in class ij.process.ColorProcessor: Does nothing since RGB images do not use LUTs.
invertLut() - Method in class ij.process.ImageProcessor: Inverts the values in this image's LUT (indexed color model).
ip - Variable in class ij.ImagePlus
IPLAB - Static variable in class ij.io.TiffDecoder
IS - Static variable in interface ij.macro.MacroConstants
IS_ACTIVE - Static variable in interface ij.macro.MacroConstants
IS_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
IS_NAN - Static variable in interface ij.macro.MacroConstants
IS_OPEN - Static variable in interface ij.macro.MacroConstants
is64Bit() - Static method in class ij.IJ: Returns true if ImageJ is running a 64-bit version of Java.
isActiveOverlayRoi() - Method in class ij.gui.Roi: Returns 'true' if this ROI is displayed and is also in an overlay.
isAntialiased() - Static method in class ij.gui.TextRoi: Returns the state of the global 'antialiasedText' variable, which is used by the "Fonts" widget.
isArea() - Method in class ij.gui.Roi: Returns 'true' if this is an area selection.
isAutoRunAndHide() - Method in class ij.plugin.MacroInstaller: Returns true if an "AutoRunAndHide" macro was run/installed.
isBatchMode() - Static method in class ij.macro.Interpreter
isBatchModeRoiManager() - Static method in class ij.macro.Interpreter: Returns true if there is an internal batch mode RoiManager.
isBinary() - Method in class ij.process.ByteProcessor: Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isBinary() - Method in class ij.process.ImageProcessor: Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isCalibrationBar() - Method in class ij.gui.Overlay
isClosed() - Method in class ij.gui.ImageWindow: Has this window been closed?
isColorLut() - Method in class ij.process.ImageProcessor: Returns true if this image uses a color LUT.
isComposite() - Method in class ij.ImagePlus: Returns true if this is a CompositeImage.
isCursor() - Method in class ij.gui.Roi
isDarkBackground() - Static method in class ij.plugin.frame.ThresholdAdjuster
isDataFlavorSupported(DataFlavor) - Method in class ij.plugin.Clipboard
isDefaultLut() - Method in class ij.process.ImageProcessor: Returns true if the image is using the default grayscale LUT.
isDisplayedHyperStack() - Method in class ij.ImagePlus: Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.
isDraggable() - Method in class ij.gui.Overlay: Returns 'true' if ROIs in this overlay can be dragged by their labels.
isDrawingTool() - Method in class ij.gui.Arrow
isDrawingTool() - Method in class ij.gui.Roi: Returns 'true' if this is an ROI primarily used from drawing (e.g., TextRoi or Arrow).
isDrawingTool() - Method in class ij.gui.TextRoi
isFrozen() - Method in class ij.gui.Plot
isFrozen() - Method in class ij.gui.PlotCanvas: Whether the plot is frozen, i.e.
isFullPath(String) - Static method in class ij.io.Opener
isGrayscale() - Method in class ij.LookUpTable: Returns true if this is a 256 entry grayscale LUT.
isGrayscale() - Method in class ij.process.ColorProcessor: Returns 'true' if this is a grayscale image.
isGrayscale() - Method in class ij.process.ImageProcessor: Returns 'true' if this is an image with a grayscale LUT or an RGB image with identical red, green and blue channels.
isHandle(int, int) - Method in class ij.gui.EllipseRoi
isHandle(int, int) - Method in class ij.gui.Line: Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.OvalRoi: Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.PointRoi: Returns a point index if it has been at least one second since the last point was added and the specified screen coordinates are inside or near a point, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.PolygonRoi: Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.Roi: Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.RotatedRectRoi
isHandle(int, int) - Method in class ij.gui.ShapeRoi: Always returns -1 since ShapeRois do not have handles.
isHSB() - Method in class ij.ImageStack: Returns true if this is a 3-slice HSB stack.
isHSB32() - Method in class ij.ImageStack: Returns true if this is a 3-slice 32-bit HSB stack.
isHyperStack() - Method in class ij.gui.StackWindow
isHyperStack() - Method in class ij.ImagePlus: Returns 'true' if this image has more than three dimensions.
isInteger(double) - Static method in class ij.gui.Roi: Returns whether a number is an integer
isInvertedLut() - Method in class ij.ImagePlus: Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.
isInvertedLut() - Method in class ij.process.ColorProcessor: Always returns false since RGB images do not use LUTs.
isInvertedLut() - Method in class ij.process.ImageProcessor: Returns true if this image uses an inverting LUT that displays zero as white and 255 as black.
isJava14() - Static method in class ij.IJ: Always returns true.
isJava15() - Static method in class ij.IJ: Always returns true.
isJava16() - Static method in class ij.IJ: Returns true if ImageJ is running on a Java 1.6 or greater JVM.
isJava17() - Static method in class ij.IJ: Returns true if ImageJ is running on a Java 1.7 or greater JVM.
isJava18() - Static method in class ij.IJ: Returns true if ImageJ is running on a Java 1.8 or greater JVM.
isJava19() - Static method in class ij.IJ: Returns true if ImageJ is running on a Java 1.9 or greater JVM.
isJava2() - Static method in class ij.IJ: Always returns true.
isKillable() - Method in class ij.process.ImageProcessor: Deprecated.
isLab() - Method in class ij.ImageStack: Returns true if this is a Lab stack.
isLine() - Method in class ij.gui.Roi: Returns 'true' if this is a line selection.
isLineOrPoint() - Method in class ij.gui.Roi: Return 'true' if this is a line or point selection.
isLinux() - Static method in class ij.IJ: Returns true if ImageJ is running on Linux.
isLocked() - Method in class ij.ImagePlus: Returns 'true' if the image is locked.
isLockedByAnotherThread() - Method in class ij.ImagePlus: Returns 'true' if the image was locked on another thread.
isMacintosh() - Static method in class ij.IJ: Returns true if this machine is a Macintosh.
isMacOSX() - Static method in class ij.IJ: Returns true if this machine is a Macintosh running OS X.
isMacro() - Method in class ij.gui.GenericDialog
isMacro() - Static method in class ij.IJ: Returns true if a macro is running, or if the run(), open() or newImage() method is executing.
isMacroCommand(String) - Static method in class ij.plugin.MacroInstaller: Returns 'true' if the macro command 'name' exists.
isMaximum(double) - Method in class ij.util.ArrayUtil
IsoData - ij.process.AutoThresholder.Method
ISODATA - Static variable in class ij.process.ImageProcessor: Isodata thresholding method
ISODATA2 - Static variable in class ij.process.ImageProcessor: Modified isodata method used in Image/Adjust/Threshold tool
isOptionalArg(int) - Static method in class ij.macro.ExtensionDescriptor
isOrthoViewsImage(ImagePlus) - Static method in class ij.plugin.Orthogonal_Views
isOutputArg(int) - Static method in class ij.macro.ExtensionDescriptor
isPowerOf2(int) - Static method in class ij.process.FHT
isPreviewActive() - Method in class ij.gui.GenericDialog: Returns 'true' if this dialog has a "Preview" checkbox and it is enabled.
isProcessor() - Method in class ij.ImagePlus
isPseudoColorLut() - Method in class ij.process.ImageProcessor: Returns true if this image uses a pseudocolor or grayscale LUT, in other words, is this an image that can be filtered.
isRedirectImage() - Static method in class ij.plugin.filter.Analyzer: Returns true if an image is selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog box.
isResultsTable - Variable in class ij.measure.ResultsTable
isResultsWindow() - Static method in class ij.IJ: Returns true if the "Results" window is open.
isRGB() - Method in class ij.ImagePlus
isRGB() - Method in class ij.ImageStack: Returns true if this is a 3-slice, 8-bit RGB stack.
isRMIEnabled() - Static method in class ij.OtherInstance
isSelectable() - Method in class ij.gui.Overlay: Returns 'true' if ROIs in this overlay can be activated by clicking on their labels or by a long press.
isSelected(int) - Method in class ij.plugin.frame.RoiManager: Returns 'true' if the index is valid and the indexed ROI is selected.
isSigned16Bit() - Method in class ij.measure.Calibration: Returns true if this is a signed 16-bit image.
isSigned16Bit() - Method in class ij.process.ImageProcessor: Returns 'true' if this is a signed 16-bit image.
isSigned16Bit() - Method in class ij.process.ShortProcessor: Returns 'true' if this is a signed 16-bit image.
isSplineFit() - Method in class ij.gui.PolygonRoi: Returns 'true' if this selection has been fitted with a spline.
isStack() - Method in class ij.ImagePlus: Deprecated.
Replaced by ImagePlus.hasImageStack()
isSupportedTransferFlavor(DataFlavor) - Method in class ij.io.DragAndDropHandler: Returns whether this transfer flavor is supported.
isThreshold() - Method in class ij.ImagePlus: Returns 'true' if this image is thresholded.
isVirtual() - Method in class ij.ImageStack: Returns true if this is a virtual (disk resident) stack.
isVirtual() - Method in class ij.VirtualStack: Always return true.
isVisible() - Method in class ij.gui.Roi: Returns true if this ROI is currently displayed on an image.
isVisible() - Method in class ij.ImagePlus: Returns true if this image is currently being displayed in a window.
isVista() - Static method in class ij.IJ: Obsolete; always returns false.
isWindows() - Static method in class ij.IJ: Returns true if this machine is running Windows.
itemStateChanged(ItemEvent) - Method in class ij.gui.GenericDialog
itemStateChanged(ItemEvent) - Method in class ij.gui.PlotWindow: Called if the user activates/deactivates a CheckboxMenuItem
itemStateChanged(ItemEvent) - Method in class ij.gui.Toolbar
itemStateChanged(ItemEvent) - Method in class ij.ImageJ: Handles CheckboxMenuItem state changes.
itemStateChanged(ItemEvent) - Method in class ij.macro.FunctionFinder
itemStateChanged(ItemEvent) - Method in class ij.plugin.BatchProcessor
itemStateChanged(ItemEvent) - Method in class ij.plugin.Colors: Callback listener for Choice modifications in the dialog
itemStateChanged(ItemEvent) - Method in class ij.plugin.CommandFinder
itemStateChanged(ItemEvent) - Method in class ij.plugin.Concatenator
itemStateChanged(ItemEvent) - Method in class ij.plugin.Duplicator
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Channels
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ColorThresholder
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Commands
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ContrastAdjuster
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Editor
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Fitter
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.PasteController
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Recorder
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.RoiManager
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.SyncWindows: Item Listener method
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
itemStateChanged(ItemEvent) - Method in class ij.plugin.Resizer
itemStateChanged(ItemEvent) - Method in class ij.plugin.Slicer
itemStateChanged(ItemEvent) - Method in class ij.plugin.Startup
itemStateChanged(ItemEvent) - Method in class ij.plugin.Thresholder
itemStateChanged(ItemEvent) - Method in class ij.text.TextWindow
iterator() - Method in class ij.gui.Line
iterator() - Method in class ij.gui.Overlay
iterator() - Method in class ij.gui.PointRoi: Custom iterator for points contained in a PointRoi.
iterator() - Method in class ij.gui.Roi: Required by the Iterable interface.
iterator() - Method in class ij.plugin.frame.RoiManager
IterFactor - Static variable in class ij.measure.CurveFitter: Deprecated.
now in the Minimizer class (since ImageJ 1.46f). (probably of not much value for anyone anyhow?)

J

JAVA_OR_TEXT - Static variable in class ij.io.Opener
Java2 - Class in ij.util: This class contains static methods that use the Java 2 API.
Java2() - Constructor for class ij.util.Java2
JavaProperties - Class in ij.plugin: Displays the Java system properties in a text window.
JavaProperties() - Constructor for class ij.plugin.JavaProperties
JAVASCRIPT - Static variable in class ij.plugin.NewPlugin
JavaScriptEvaluator - Class in ij.plugin: Implements the text editor's Macros/Run command, and the IJ.runMacroFile() method, when the file name ends with ".js".
JavaScriptEvaluator() - Constructor for class ij.plugin.JavaScriptEvaluator
JavaScriptIncludes - Static variable in class ij.plugin.frame.Editor: ImportPackage statements added in front of scripts.
javaVersion() - Static method in class ij.IJ: Returns the Java version (6, 7, 8, 9, 10, etc.).
jFileChooserSettingChanged - Static variable in class ij.Prefs: Use JFileChooser setting changed/
joinAll(Future[]) - Static method in class ij.util.ThreadUtil: Waits for completion of all Callables corresponding to the Futures given.
JPEG - Static variable in class ij.io.FileInfo
JPEG - Static variable in class ij.io.Opener
JPEG - Static variable in class ij.Prefs
JPEG_COMPRESSION - Static variable in class ij.plugin.filter.AVI_Writer
JPEG_TABLES - Static variable in class ij.io.TiffDecoder
JpegWriter - Class in ij.plugin: The File/Save As/Jpeg command (FileSaver.saveAsJpeg() method) uses this plugin to save images in JPEG format.
JpegWriter() - Constructor for class ij.plugin.JpegWriter
justification - Variable in class ij.process.ImageProcessor

K

KEEP_PREVIEW - Static variable in interface ij.plugin.filter.ExtendedPlugInFilter: Set this flag if the last preview image may be kept as a result.
KEEP_THRESHOLD - Static variable in interface ij.plugin.filter.PlugInFilter: Set this flag to keep the invisible binary threshold from being reset.
keepArrowSelections - Static variable in class ij.Prefs: Keep arrow selection after adding to overlay
keepUndoBuffers - Static variable in class ij.Prefs: Preserve undo (snapshot) buffers when switching images
kernel(double) - Method in class ij.process.DownsizeTable
kernelSize - Variable in class ij.process.DownsizeTable: Number of kernel points per source data point
KEY_PREFIX - Static variable in class ij.Prefs
keyPressed(KeyEvent) - Method in class ij.gui.GenericDialog
keyPressed(KeyEvent) - Method in class ij.gui.HTMLDialog
keyPressed(KeyEvent) - Method in class ij.gui.MessageDialog
keyPressed(KeyEvent) - Method in class ij.gui.NonBlockingGenericDialog
keyPressed(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyPressed(KeyEvent) - Method in class ij.gui.WaitForUserDialog
keyPressed(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyPressed(KeyEvent) - Method in class ij.ImageJ
keyPressed(KeyEvent) - Method in class ij.macro.FunctionFinder
keyPressed(KeyEvent) - Method in class ij.measure.ResultsTableMacros
keyPressed(KeyEvent) - Method in class ij.plugin.CommandFinder
keyPressed(KeyEvent) - Method in class ij.plugin.frame.Editor
keyPressed(KeyEvent) - Method in class ij.plugin.frame.Fitter
keyPressed(KeyEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
keyPressed(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
keyPressed(KeyEvent) - Method in class ij.text.TextPanel
keyReleased(KeyEvent) - Method in class ij.gui.GenericDialog
keyReleased(KeyEvent) - Method in class ij.gui.HTMLDialog
keyReleased(KeyEvent) - Method in class ij.gui.MessageDialog
keyReleased(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyReleased(KeyEvent) - Method in class ij.gui.WaitForUserDialog
keyReleased(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyReleased(KeyEvent) - Method in class ij.ImageJ
keyReleased(KeyEvent) - Method in class ij.macro.FunctionFinder
keyReleased(KeyEvent) - Method in class ij.measure.ResultsTableMacros
keyReleased(KeyEvent) - Method in class ij.plugin.CommandFinder
keyReleased(KeyEvent) - Method in class ij.plugin.frame.Editor
keyReleased(KeyEvent) - Method in class ij.plugin.frame.Fitter
keyReleased(KeyEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
keyReleased(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
keyReleased(KeyEvent) - Method in class ij.text.TextPanel
keyTyped(KeyEvent) - Method in class ij.gui.GenericDialog
keyTyped(KeyEvent) - Method in class ij.gui.HTMLDialog
keyTyped(KeyEvent) - Method in class ij.gui.MessageDialog
keyTyped(KeyEvent) - Method in class ij.gui.SaveChangesDialog
keyTyped(KeyEvent) - Method in class ij.gui.WaitForUserDialog
keyTyped(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
keyTyped(KeyEvent) - Method in class ij.ImageJ
keyTyped(KeyEvent) - Method in class ij.macro.FunctionFinder
keyTyped(KeyEvent) - Method in class ij.measure.ResultsTableMacros
keyTyped(KeyEvent) - Method in class ij.plugin.CommandFinder
keyTyped(KeyEvent) - Method in class ij.plugin.frame.Editor
keyTyped(KeyEvent) - Method in class ij.plugin.frame.Fitter
keyTyped(KeyEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
keyTyped(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
keyTyped(KeyEvent) - Method in class ij.text.TextPanel
keywordIDs - Static variable in interface ij.macro.MacroConstants
keywords - Static variable in interface ij.macro.MacroConstants
killPlotObjectsSnapshot() - Method in class ij.gui.Plot: Deletes the snapshot of the plot contents to make space
killPlotPropertiesSnapshot() - Method in class ij.gui.Plot: Deletes the snapshot of the plot properties to make space
killRoi() - Method in class ij.ImagePlus: Deletes the current region of interest.
killStack() - Method in class ij.ImagePlus
kurtosis - Variable in class ij.process.ImageStatistics
KURTOSIS - Static variable in interface ij.measure.Measurements
KURTOSIS - Static variable in class ij.measure.ResultsTable

L

label - Variable in class ij.gui.MessageDialog
label - Variable in class ij.gui.WaitForUserDialog
label(ImageProcessor) - Method in class ij.plugin.filter.Filler
labelHyperstack(ImagePlus) - Static method in class ij.plugin.HyperStackMaker
LABELS - Static variable in interface ij.measure.Measurements
LabToRGB(ImagePlus) - Method in class ij.process.ColorSpaceConverter: Converts a Lab stack into an RGB image.
LABtoRGB(double[]) - Method in class ij.process.ColorSpaceConverter
LABtoRGB(double, double, double) - Method in class ij.process.ColorSpaceConverter: Convert LAB to RGB.
LABtoXYZ(double[]) - Method in class ij.process.ColorSpaceConverter: Convert LAB to XYZ.
LABtoXYZ(double, double, double) - Method in class ij.process.ColorSpaceConverter: Convert LAB to XYZ.
LAST_HEADING - Static variable in class ij.measure.ResultsTable
LAST_INDEX_OF - Static variable in interface ij.macro.MacroConstants
lastZoomSX - Variable in class ij.gui.ImageCanvas: Screen coordinates where the last zoom operation was done (initialized to impossible value)
lastZoomSY - Variable in class ij.gui.ImageCanvas
layoutContainer(Container) - Method in class ij.gui.ImageLayout: Lays out the container and calls ImageCanvas.resizeCanvas() to adjust the image canvas size as needed.
LEFT - Static variable in class ij.gui.Plot: Text justification.
LEFT - Static variable in class ij.gui.TextRoi
LEFT - Static variable in class ij.io.RoiDecoder
LEFT_JUSTIFY - Static variable in class ij.process.ImageProcessor: Left justify text.
LEFT_MARGIN - Static variable in class ij.gui.Plot: Deprecated.
Not a fixed value any more, use getDrawingFrame() to get the drawing area
LEGACY_MODE - Static variable in class ij.gui.Wand: Wand operation type similar to that of ImageJ 1.42p and before; for backwards compatibility.
LEGEND - Static variable in class ij.gui.PlotDialog: Types of dialog.
LEGEND_BOTTOM_UP - Static variable in class ij.gui.Plot: Legend has its curves in bottom-to-top sequence (otherwise top to bottom)
LEGEND_TRANSPARENT - Static variable in class ij.gui.Plot: Legend erases background (otherwise transparent)
LENGTH_OF - Static variable in interface ij.macro.MacroConstants
Li - ij.process.AutoThresholder.Method
LIMIT - Static variable in interface ij.measure.Measurements
Line - Class in ij.gui: This class represents a straight line selection.
Line(double, double, double, double) - Constructor for class ij.gui.Line: Creates a new straight line selection using the specified starting and ending offscreen double coordinates.
Line(int, int, int, int) - Constructor for class ij.gui.Line: Creates a new straight line selection using the specified starting and ending offscreen integer coordinates.
Line(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Line: Deprecated.
replaced by Line(int, int, int, int)
Line(int, int, ImagePlus) - Constructor for class ij.gui.Line: Starts the process of creating a new user-generated straight line selection.
LINE - Static variable in class ij.gui.Plot: Connect points with solid lines.
LINE - Static variable in class ij.gui.PlotWindow: Deprecated.
LINE - Static variable in class ij.gui.Roi
LINE - Static variable in class ij.gui.Toolbar
LINE_TO - Static variable in interface ij.macro.MacroConstants
Line.PointIterator - Class in ij.gui: Dedicated point iterator for thin lines.
lineCircleIntersection(double, double, double, double, double, double, double, boolean) - Static method in class ij.gui.Roi: Calculates intersections of a line segment with a circle Author N.Vischer ax, ay, bx, by: points A and B of line segment cx, cy, rad: Circle center and radius.
LineGraphAnalyzer - Class in ij.plugin.filter: Implements ImageJ's Analyze/Tools/Analyze Line Graph command.
LineGraphAnalyzer() - Constructor for class ij.plugin.filter.LineGraphAnalyzer
lineTo(int, int) - Method in class ij.process.ImageProcessor: Draws a line from the current drawing location to (x2,y2).
lineToArea(Roi) - Static method in class ij.plugin.Selection: Converts a line selection into an area selection.
lineWidth - Static variable in class ij.gui.Roi
lineWidth - Variable in class ij.process.ImageProcessor
LineWidthAdjuster - Class in ij.plugin.frame: Adjusts the width of line selections.
LineWidthAdjuster() - Constructor for class ij.plugin.frame.LineWidthAdjuster
list - Variable in class ij.gui.HistogramWindow
LIST - Static variable in interface ij.macro.MacroConstants
LIST - Static variable in class ij.plugin.filter.MaximumFinder: Do not create an image, just list x, y of maxima in the Results table
listAllThreads(PrintWriter) - Static method in class ij.plugin.ThreadLister
listCommands() - Method in class ij.plugin.CommandLister
listRois(Roi[]) - Static method in class ij.plugin.OverlayCommands
listShortcuts() - Method in class ij.plugin.CommandLister
listValues - Static variable in class ij.gui.PlotWindow: Display the XY coordinates in a separate window.
ListVirtualStack - Class in ij.plugin: This plugin opens images specified by list of file paths as a virtual stack.
ListVirtualStack() - Constructor for class ij.plugin.ListVirtualStack
live - Variable in class ij.gui.HistogramWindow
ln() - Method in class ij.process.ImageProcessor: Does a natural logarithmic (base e) transform of the image or ROI.
load(BufferedReader) - Method in class ij.text.TextWindow: Appends the text in the specified file to the end of this TextWindow.
load(Object, Applet) - Static method in class ij.Prefs: Finds and loads the configuration file ("IJ_Props.txt") and the preferences file ("IJ_Prefs.txt").
loadLut(String) - Static method in class ij.Executer: Opens a .lut file from the ImageJ/luts directory and returns 'true' if successful.
loadPrefs() - Static method in class ij.OtherInstance
LOC_KEY - Static variable in class ij.gui.ImageWindow
LOC_KEY - Static variable in class ij.plugin.frame.Commands
LOC_KEY - Static variable in class ij.plugin.frame.ContrastAdjuster
LOC_KEY - Static variable in class ij.plugin.frame.LineWidthAdjuster
LOC_KEY - Static variable in class ij.plugin.frame.RoiManager
LOC_KEY - Static variable in class ij.plugin.frame.ThresholdAdjuster
LOC_KEY - Static variable in class ij.text.TextWindow
lock() - Method in class ij.ImagePlus: Locks the image so other threads can test to see if it is in use.
locked - Variable in class ij.ImagePlus
lockSilently() - Method in class ij.ImagePlus: Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.
log - Variable in class ij.gui.HistogramWindow
log() - Method in class ij.process.FloatProcessor
log() - Method in class ij.process.ImageProcessor: Does a natural logarithmic (base e) transform of the image or ROI.
log() - Method in class ij.process.ShortProcessor
log(String) - Static method in class ij.IJ
LOG - Static variable in interface ij.macro.MacroConstants
LOG - Static variable in class ij.measure.Calibration
LOG - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
LOG_HEIGHT_KEY - Static variable in class ij.text.TextWindow
LOG_LOC_KEY - Static variable in class ij.text.TextWindow
LOG_WIDTH_KEY - Static variable in class ij.text.TextWindow
LOG_WINDOW_CLOSED - Static variable in interface ij.IJEventListener
LOG2 - Static variable in class ij.measure.Calibration
LOG2 - Static variable in class ij.measure.CurveFitter: Constants for the built-in fit functions
LOGICAL_AND - Static variable in interface ij.macro.MacroConstants
LOGICAL_OR - Static variable in interface ij.macro.MacroConstants
logImageListeners() - Static method in class ij.ImagePlus: For debug purposes, writes all registered (and possibly, forgotten) ImageListeners to the log window
logProperties() - Method in class ij.plugin.ProxySettings
logScale - Variable in class ij.gui.HistogramWindow
LogStream - Class in ij.io: This class provides the functionality to divert output sent to the System.out and System.err streams to ImageJ's log console.
LogStream() - Constructor for class ij.io.LogStream
longGap - Variable in class ij.io.FileInfo
longHistogram - Variable in class ij.process.ImageStatistics: Long histogram; use getHIstogram() to retrieve.
longOffset - Variable in class ij.io.FileInfo
longPixelCount - Variable in class ij.process.ImageStatistics: Long pixel count
lookupPathVariable(String) - Static method in class ij.io.OpenDialog
LookUpTable - Class in ij: This class represents a color look-up table.
LookUpTable(Image) - Constructor for class ij.LookUpTable: Constructs a LookUpTable object from an AWT Image.
LookUpTable(ColorModel) - Constructor for class ij.LookUpTable: Constructs a LookUpTable object from a ColorModel.
loop - Variable in class ij.measure.Calibration
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.HistogramWindow
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.PlotWindow
lostOwnership(Clipboard, Transferable) - Method in class ij.plugin.frame.Editor
lostOwnership(Clipboard, Transferable) - Method in class ij.plugin.frame.Fitter
lostOwnership(Clipboard, Transferable) - Method in class ij.text.TextPanel
lowerThreshold - Variable in class ij.process.ImageStatistics: Minimum threshold when "Limit to threshold" enabled
LT - Static variable in interface ij.macro.MacroConstants
LTE - Static variable in interface ij.macro.MacroConstants
lut - Variable in class ij.gui.HistogramWindow
LUT - Class in ij.process: This is an indexed color model that allows an lower and upper bound to be specified.
LUT - Static variable in class ij.io.Opener
LUT(byte[], byte[], byte[]) - Constructor for class ij.process.LUT: Constructs a LUT from red, green and blue byte arrays, which must have a length of 256.
LUT(int, int, byte[], byte[], byte[]) - Constructor for class ij.process.LUT: Constructs a LUT from red, green and blue byte arrays, where 'bits' must be 8 and 'size' must be less than or equal to 256.
LUT(IndexColorModel, double, double) - Constructor for class ij.process.LUT
LUT_Editor - Class in ij.plugin
LUT_Editor() - Constructor for class ij.plugin.LUT_Editor
lutAnimation - Variable in class ij.process.ImageProcessor
LutApplier - Class in ij.plugin.filter: This plugin implements the Image/Lookup Tables/Apply LUT command.
LutApplier() - Constructor for class ij.plugin.filter.LutApplier
LutLoader - Class in ij.plugin: Opens NIH Image look-up tables (LUTs), 768 byte binary LUTs (256 reds, 256 greens and 256 blues), LUTs in text format, or generates the LUT specified by the string argument passed to the run() method.
LutLoader() - Constructor for class ij.plugin.LutLoader
lutMessage - Static variable in class ij.plugin.ZProjector
lutSize - Variable in class ij.io.FileInfo
lutUpdateMode - Variable in class ij.process.ImageProcessor
LutViewer - Class in ij.plugin.filter: Displays the active image's look-up table.
LutViewer() - Constructor for class ij.plugin.filter.LutViewer
LZW - Static variable in class ij.io.FileInfo
LZW_WITH_DIFFERENCING - Static variable in class ij.io.FileInfo
lzwUncompress(byte[]) - Method in class ij.io.ImageReader: Utility method for decoding an LZW-compressed image strip.

M

M - Variable in class ij.process.ColorSpaceConverter: sRGB to XYZ conversion matrix
Macro - Class in ij: The class contains static methods that perform macro operations.
Macro() - Constructor for class ij.Macro
MACRO - Static variable in interface ij.macro.MacroConstants
MACRO - Static variable in class ij.plugin.NewPlugin
MACRO - Static variable in class ij.Undo
MACRO_CANCELED - Static variable in class ij.Macro
MACRO_KEY - Static variable in class ij.plugin.filter.ImageMath
Macro_Runner - Class in ij.plugin: This class runs macros and scripts installed in the Plugins menu as well as macros and scripts opened using the Plugins/Macros/Run command.
Macro_Runner() - Constructor for class ij.plugin.Macro_Runner
MACRO_TOOL - Static variable in class ij.plugin.NewPlugin
MacroConstants - Interface in ij.macro
macroCount() - Method in class ij.macro.Program
MacroExtension - Interface in ij.macro
MacroInstaller - Class in ij.plugin: This plugin implements the Plugins/Macros/Install Macros command.
MacroInstaller() - Constructor for class ij.plugin.MacroInstaller
MacroRunner - Class in ij.macro: This class runs macros in a separate thread.
MacroRunner() - Constructor for class ij.macro.MacroRunner: Create a MacroRunner.
MacroRunner(Program, int, String) - Constructor for class ij.macro.MacroRunner: Runs a tokenized macro in a separate thread.
MacroRunner(Program, int, String, Editor) - Constructor for class ij.macro.MacroRunner: Runs a tokenized macro in debug mode if 'editor' is not null.
MacroRunner(Program, int, String, String) - Constructor for class ij.macro.MacroRunner: Runs a tokenized macro in a separate thread, passing a string argument.
MacroRunner(File) - Constructor for class ij.macro.MacroRunner: Interprets a macro file in a separate thread.
MacroRunner(String) - Constructor for class ij.macro.MacroRunner: Create a new object that interprets macro source in a separate thread.
MacroRunner(String, Editor) - Constructor for class ij.macro.MacroRunner: Create a new object that interprets macro source in debug mode if 'editor' is not null.
MacroRunner(String, String) - Constructor for class ij.macro.MacroRunner: Interprets macro source in a separate thread, passing a string argument.
macroRunning() - Static method in class ij.IJ: Returns true if the run(), open() or newImage() method is executing.
MACROS_MENU_ITEMS - Static variable in class ij.plugin.frame.Editor
MacroToolRunner - Class in ij.plugin.tool
MacroToolRunner(MacroInstaller) - Constructor for class ij.plugin.tool.MacroToolRunner
mag - Variable in class ij.gui.Roi
magnification - Variable in class ij.gui.ImageCanvas
magnification - Variable in class ij.gui.ProfilePlot
magnificationForSubPixel() - Method in class ij.gui.Roi: Returns whether a roi created interactively should have subpixel resolution, (if the roi type supports it), i.e., whether the magnification is high enough
magnificationForSubPixel(double) - Static method in class ij.gui.Roi
MAGNIFIER - Static variable in class ij.gui.Toolbar
main(String[]) - Static method in class ij.ImageJ
major - Variable in class ij.process.EllipseFitter: Length of major axis
major - Variable in class ij.process.ImageStatistics: Length of major axis of fitted ellipse
MAJOR - Static variable in class ij.measure.ResultsTable
MAKE_ARROW - Static variable in interface ij.macro.MacroConstants
MAKE_ELLIPSE - Static variable in interface ij.macro.MacroConstants
MAKE_LINE - Static variable in interface ij.macro.MacroConstants
MAKE_OVAL - Static variable in interface ij.macro.MacroConstants
MAKE_POINT - Static variable in interface ij.macro.MacroConstants
MAKE_POLYGON - Static variable in interface ij.macro.MacroConstants
MAKE_RECTANGLE - Static variable in interface ij.macro.MacroConstants
MAKE_ROTATED_RECT - Static variable in interface ij.macro.MacroConstants
MAKE_SELECTION - Static variable in interface ij.macro.MacroConstants
MAKE_TEXT - Static variable in interface ij.macro.MacroConstants
make16bitEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM: Calculates a 16-bit grayscale Euclidean Distance Map for a binary 8-bit image.
makeComposite(ImagePlus) - Static method in class ij.plugin.CompositeConverter
makeDefaultColorModel() - Method in class ij.process.ImageProcessor
makeFilePrivate(String) - Static method in class ij.OtherInstance
makeFloatEDM(ImageProcessor, int, boolean) - Method in class ij.plugin.filter.EDM: Creates the Euclidian Distance Map of a (binary) byte image.
makeFullPath(String) - Static method in class ij.io.Opener
makeGaussianKernel(double, double, int) - Method in class ij.plugin.filter.GaussianBlur: Create a 1-dimensional normalized Gaussian kernel with standard deviation sigma and the running sum over the kernel Note: this is one side of the kernel only, not the full kernel as used by the Convolver class of ImageJ.
makeHighResolution(String, float, boolean, boolean) - Method in class ij.gui.Plot: Creates a new high-resolution plot by scaling it and displays that plot if showIt is true.
makeKernel(double) - Method in class ij.plugin.filter.RankFilters: Deprecated.
Not needed any more, use the rank(ip, ...) method, which creates the kernel
makeLine(double, double, double, double) - Static method in class ij.IJ: Creates a straight line selection using floating point coordinates.
makeLine(int, int, int, int) - Static method in class ij.IJ: Creates a straight line selection.
makeLineRadii(double) - Method in class ij.plugin.filter.RankFilters: Create a circular kernel (structuring element) of a given radius.
makeMask(ImageProcessor, Rectangle) - Method in class ij.plugin.filter.Filler
makeMontage(ImagePlus) - Method in class ij.plugin.MontageMaker
makeMontage(ImagePlus, int, int, double, int, int, int, int, boolean) - Method in class ij.plugin.MontageMaker: Creates a montage and displays it.
makeMontage2(ImagePlus, int, int, double, int, int, int, int, boolean) - Method in class ij.plugin.MontageMaker: Creates a montage and returns it as an ImagePlus.
makeOval(double, double, double, double) - Static method in class ij.IJ: Creates an subpixel resolution oval selection.
makeOval(int, int, int, int) - Static method in class ij.IJ: Creates an oval selection.
makePoint(double, double) - Static method in class ij.IJ: Creates a point selection using floating point coordinates.
makePoint(int, int) - Static method in class ij.IJ: Creates a point selection using integer coordinates..
makeRectangle(double, double, double, double) - Static method in class ij.IJ: Creates a subpixel resolution rectangular selection.
makeRectangle(int, int, int, int) - Static method in class ij.IJ: Creates a rectangular selection.
makeRoi(ImageProcessor) - Method in class ij.process.EllipseFitter: Generates the xCoordinates, yCoordinates public arrays that can be used to create an ROI.
makeRow(String, CommandFinder.CommandAction) - Method in class ij.plugin.CommandFinder
makeStack(ImageProcessor, int, int, int) - Method in class ij.plugin.StackMaker
makeStack(String, int, int, boolean, boolean, boolean) - Method in class ij.plugin.AVI_Reader: Create an ImageStack from an avi file with given path.
makeSubhyperstack(ImagePlus, String, String, String) - Static method in class ij.plugin.SubHyperstackMaker
makeSubhyperstack(ImagePlus, List<Integer>, List<Integer>, List<Integer>) - Static method in class ij.plugin.SubHyperstackMaker
makeSubstack(ImagePlus, String) - Method in class ij.plugin.SubstackMaker
makeSurfacePlot(ImageProcessor) - Method in class ij.plugin.SurfacePlotter
makeThumbnail(int, int, double) - Method in class ij.process.ColorProcessor: Uses averaging to creates a new ColorProcessor containing a downsized copy of this image or selection.
makeUniqueName(String) - Static method in class ij.WindowManager: If 'name' is not unique, adds -1, -2, etc.
markWidth - Static variable in class ij.plugin.filter.Analyzer
MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
maskSizeError(ImageProcessor) - Method in class ij.process.ImageProcessor
match(String, String) - Method in class ij.util.WildcardMatch: Matches a string against a pattern with wildcards.
MATCHES - Static variable in interface ij.macro.MacroConstants
MATH - Static variable in interface ij.macro.MacroConstants
max - Variable in class ij.io.ImageReader
max - Variable in class ij.process.ColorProcessor
max - Variable in class ij.process.ImageStatistics
max - Variable in class ij.process.LUT
max(double) - Method in class ij.process.FloatProcessor
max(double) - Method in class ij.process.ImageProcessor: Pixels greater than 'value' are set to 'value'.
max(double) - Method in class ij.process.ShortProcessor
MAX - Static variable in class ij.measure.ResultsTable
MAX - Static variable in class ij.plugin.Binner
MAX - Static variable in class ij.plugin.filter.RankFilters
MAX - Static variable in class ij.plugin.Filters3D
MAX - Static variable in interface ij.process.Blitter: dst=max(dst,src)
MAX - Static variable in class ij.process.ImageProcessor
MAX_CHANNELS - Static variable in class ij.CompositeImage
MAX_COLUMNS - Static variable in class ij.measure.ResultsTable: Obsolete; use getLastColumn().
MAX_COMMANDS - Static variable in class ij.plugin.frame.Commands
MAX_COUNTERS - Static variable in class ij.gui.PointRoi
MAX_ITERATIONS_EXCEEDED - Static variable in class ij.measure.Minimizer: Status returned: no convergence detected after maximum iteration count
MAX_MACROS - Static variable in class ij.plugin.MacroInstaller
MAX_METHOD - Static variable in class ij.plugin.ZProjector
MAX_MOUSEMOVE_ZOOM - Static variable in class ij.gui.ImageCanvas: If the mouse moves less than this in screen pixels, successive zoom operations are on the same image pixel
MAX_OF - Static variable in interface ij.macro.MacroConstants
MAX_OPEN_RECENT_ITEMS - Static variable in class ij.Menus
MAX_PROJECTION - Static variable in class ij.process.ImageProcessor: Composite image projection modes.
MAX_RESTARTS_EXCEEDED - Static variable in class ij.measure.Minimizer: Status returned: not two equal solutions after maximum number of restarts
MAX_SIZE - Static variable in class ij.plugin.frame.Editor
MAX_SIZE - Static variable in class ij.plugin.MacroInstaller
MAX_STANDARDS - Static variable in interface ij.measure.Measurements: Maximum number of calibration standard (20)
MAX_THRESHOLD - Static variable in class ij.measure.ResultsTable
maxCount - Variable in class ij.process.ImageStatistics
maxEntries - Variable in class ij.plugin.Concatenator
MaxEntropy - ij.process.AutoThresholder.Method
maximize() - Method in class ij.gui.ImageWindow
maximize(ImagePlus) - Static method in class ij.plugin.Zoom
M