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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
 
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