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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(Overlay) - Method in class ij.gui.Overlay
Adds the ROIs in 'overlay2' to this overlay.
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, 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).
addEnumChoice(String, E[], E) - Method in class ij.gui.GenericDialog
Adds a group of choices to the dialog with menu items taken from the supplied array of enum elements.
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 current slice of 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
 
calibrateConversions - Static variable in class ij.Prefs
Calibrate image type conversions
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.
convertAndCalibrate(ImagePlus, String) - Static method in class ij.process.ImageConverter
 
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 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.Arrow
 
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() - Method in class ij.process.SignedShortProcessor
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
 
doInclude(String) - Static method in class ij.plugin.frame.Editor
Process optional #include statment at begining of macro.
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
 
enableLivePlot(boolean) - Method in class ij.gui.PlotWindow
Enables or disables live plotting.
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
provides interpolated function value at position xp
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
 
findMinAndMax() - Method in class ij.process.SignedShortProcessor
 
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
fixedScale - Variable in class ij.process.ShortProcessor
 
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
 
fullRange16bitInversions - Static variable in class ij.Prefs
Use full range for 16-bit inversions
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(int, int) - Method in class ij.process.SignedShortProcessor
 
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 default directory as a string ending in the separator character ("/" or "\"), or a 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
Returns the display range maximum of the current channel.
getDisplayRangeMin() - Method in class ij.CompositeImage
 
getDisplayRangeMin() - Method in class ij.ImagePlus
Returns the display range minimum of the current channel.
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 maximum 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 minimum 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) - Method in class ij.process.SignedShortProcessor
 
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(byte[], byte[], byte[]) - Static method in class ij.process.ImageProcessor
Returns a color model based on the colors of the input from 0 to 254 (inclusive).
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
 
GRAY10_UNSIGNED - Static variable in class ij.io.FileInfo
10-bit unsigned integer (0-1023).
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. 
hideRangeArrows() - Method in class ij.gui.PlotWindow
 
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.
ImagePanel(ImagePlus) - Constructor for class ij.gui.ImagePanel
 
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 or ROI is inverted using p=max-(p-min), where 'min' and 'max' are the minimum and maximum displayed pixel values.
invert() - Method in class ij.process.ImageProcessor
Inverts the image or ROI.
invert() - Method in class ij.process.ShortProcessor
If "Full range 16-bit inversions" (Prefs.fullRange16bitInversions) is set in Edit/Options/Conversions, the image or ROI is inverted using the full pixel value range (0-65535) or, if set, using the "Unsigned 16-bit range" in the "Set" option of the Image>Adjust>Brightness/Contrast dialog.
Otherwise, each pixel in the image or ROI is inverted using v2=max-(v1-min), where 'min' and 'max' are the image's minimum and maximum pixel values.
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.
isThreshold() - Method in class ij.process.ImageProcessor
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, 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 - Variable in class ij.process.ShortProcessor
 
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
 
MaximumFinder - Class in ij.plugin.filter
This ImageJ plug-in filter finds the maxima (or minima) of an image.
MaximumFinder() - Constructor for class ij.plugin.filter.MaximumFinder
 
MAXLOCAL - Static variable in class ij.plugin.Filters3D
 
maxMemory() - Static method in class ij.IJ
Returns the maximum amount of memory available to ImageJ or zero if ImageJ is unable to determine this limit.
maxMemory() - Method in class ij.plugin.Memory
Returns the maximum amount of memory this JVM will attempt to use.
maxPoints - Variable in class ij.gui.PolygonRoi
 
maxThreshold - Variable in class ij.process.ImageProcessor
 
maxValue() - Method in class ij.process.FloatProcessor
Returns the largest possible positive finite pixel value.
maxValue() - Method in class ij.process.ImageProcessor
Returns the maximum possible pixel value.
maxValue() - Method in class ij.process.ShortProcessor
Returns the maximum possible pixel value.
mean - Variable in class ij.process.ImageStatistics
 
Mean - ij.process.AutoThresholder.Method
 
MEAN - Static variable in interface ij.measure.Measurements
 
MEAN - Static variable in class ij.measure.ResultsTable
 
MEAN - Static variable in class ij.plugin.filter.RankFilters
 
MEAN - Static variable in class ij.plugin.Filters3D
 
measure() - Method in class ij.gui.MultiLineLabel
 
measure() - Method in class ij.plugin.filter.Analyzer
Measures the image or selection and adds the results to the default results table.
measure(ImagePlus) - Method in class ij.gui.Overlay
Measures the ROIs in this overlay on the specified image and returns the results as a ResultsTable.
Measurements - Interface in ij.measure
 
MeasurementsWriter - Class in ij.plugin
Saves a table as a csv or tab-delimited text file.
MeasurementsWriter() - Constructor for class ij.plugin.MeasurementsWriter
 
median - Variable in class ij.process.ImageStatistics
 
MEDIAN - Static variable in interface ij.measure.Measurements
 
MEDIAN - Static variable in class ij.measure.ResultsTable
 
MEDIAN - Static variable in class ij.plugin.Binner
 
MEDIAN - Static variable in class ij.plugin.filter.RankFilters
 
MEDIAN - Static variable in class ij.plugin.Filters3D
 
MEDIAN_FILTER - Static variable in class ij.process.ImageProcessor
 
MEDIAN_METHOD - Static variable in class ij.plugin.ZProjector
 
MedianCut - Class in ij.process
Converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.
MedianCut(int[], int, int) - Constructor for class ij.process.MedianCut
 
MedianCut(ColorProcessor) - Constructor for class ij.process.MedianCut
 
medianFilter() - Method in class ij.process.ByteProcessor
 
medianFilter() - Method in class ij.process.ColorProcessor
 
medianFilter() - Method in class ij.process.FloatProcessor
Not implemented.
medianFilter() - Method in class ij.process.ImageProcessor
A 3x3 median filter.
medianFilter() - Method in class ij.process.ShortProcessor
Not implemented.
medianSort() - Method in class ij.util.ArrayUtil
The median (sorted array)
Memory - Class in ij.plugin
This plugin implements the Edit/Options/Memory command.
Memory() - Constructor for class ij.plugin.Memory
 
MemoryMonitor - Class in ij.plugin.frame
This plugin continuously plots ImageJ's memory utilization.
MemoryMonitor() - Constructor for class ij.plugin.frame.MemoryMonitor
 
MENU_BAR - Static variable in class ij.plugin.frame.Editor
 
MENU_SIZE - Static variable in class ij.Prefs
 
Menus - Class in ij
This class installs and updates ImageJ's menus.
mergeChannels(ImagePlus[], boolean) - Static method in class ij.plugin.RGBStackMerge
 
mergeHyperstacks(ImagePlus[], boolean) - Method in class ij.plugin.RGBStackMerge
 
mergeStacks() - Method in class ij.plugin.RGBStackMerge
Combines up to seven grayscale stacks into one RGB or composite stack.
mergeStacks(int, int, int, ImageStack, ImageStack, ImageStack, boolean) - Method in class ij.plugin.RGBStackMerge
 
mergeStacks(ImageStack, ImageStack, ImageStack, boolean) - Static method in class ij.plugin.RGBStackMerge
 
MessageDialog - Class in ij.gui
A modal dialog box that displays information.
MessageDialog(Frame, String, String) - Constructor for class ij.gui.MessageDialog
 
META_DATA - Static variable in class ij.io.TiffDecoder
 
META_DATA_BYTE_COUNTS - Static variable in class ij.io.TiffDecoder
 
metaData - Variable in class ij.io.FileInfo
 
metaDataTypes - Variable in class ij.io.FileInfo
 
METAMORPH1 - Static variable in class ij.io.TiffDecoder
 
METAMORPH2 - Static variable in class ij.io.TiffDecoder
 
methods - Static variable in class ij.plugin.Thresholder
 
METHODS - Static variable in class ij.plugin.ZProjector
 
Mi - Variable in class ij.process.ColorSpaceConverter
XYZ to sRGB conversion matrix
micronSymbol - Static variable in class ij.IJ
 
min - Variable in class ij.io.ImageReader
 
min - Variable in class ij.process.ColorProcessor
 
min - Variable in class ij.process.ImageStatistics
 
min - Variable in class ij.process.LUT
 
min - Variable in class ij.process.ShortProcessor
 
min(double) - Method in class ij.process.FloatProcessor
 
min(double) - Method in class ij.process.ImageProcessor
Pixels less than 'value' are set to 'value'.
min(double) - Method in class ij.process.ShortProcessor
 
MIN - Static variable in class ij.measure.ResultsTable
 
MIN - Static variable in class ij.plugin.Binner
 
MIN - Static variable in class ij.plugin.filter.RankFilters
 
MIN - Static variable in class ij.plugin.Filters3D
 
MIN - Static variable in interface ij.process.Blitter
dst=min(dst,src)
MIN - Static variable in class ij.process.ImageProcessor
 
MIN_FERET - Static variable in class ij.measure.ResultsTable
 
MIN_FRAMEHEIGHT - Static variable in class ij.gui.Plot
minimum width of frame area in plot
MIN_FRAMEWIDTH - Static variable in class ij.gui.Plot
minimum width of frame area in plot
MIN_HEIGHT - Static variable in class ij.gui.ImageWindow
 
MIN_MAX - Static variable in interface ij.measure.Measurements
 
MIN_METHOD - Static variable in class ij.plugin.ZProjector
 
MIN_OF - Static variable in interface ij.macro.MacroConstants
 
MIN_PROJECTION - Static variable in class ij.process.ImageProcessor
Composite image projection modes.
MIN_THRESHOLD - Static variable in class ij.measure.ResultsTable
 
MIN_WIDTH - Static variable in class ij.gui.ImageWindow
 
MinError - ij.process.AutoThresholder.Method
 
minimize() - Method in class ij.gui.ImageWindow
 
minimize(double[], double[]) - Method in class ij.measure.Minimizer
Perform minimization with the gradient-enhanced simplex method once or a few times, depending on the value of 'restarts'.
minimizeOnce(double[], double[]) - Method in class ij.measure.Minimizer
Perform minimization with the simplex method once, including re-initialization until we have a stable solution.
Minimizer - Class in ij.measure
Minimizer based on Nelder-Mead simplex method (also known as polytope method), including the 'outside contraction' as described in: J.C.
Minimizer() - Constructor for class ij.measure.Minimizer
 
Minimum - ij.process.AutoThresholder.Method
 
minimumLayoutSize(Container) - Method in class ij.gui.ImageLayout
Returns the minimum dimensions for this layout.
minMaxSet - Variable in class ij.process.ImageProcessor
 
minor - Variable in class ij.process.EllipseFitter
Length of minor axis
minor - Variable in class ij.process.ImageStatistics
Length of minor axis of fitted ellipse
MINOR - Static variable in class ij.measure.ResultsTable
 
minThreshold - Variable in class ij.process.ImageProcessor
 
MINUS_EQUAL - Static variable in interface ij.macro.MacroConstants
 
MINUS_MINUS - Static variable in interface ij.macro.MacroConstants
 
minValue() - Method in class ij.process.FloatProcessor
Returns the smallest possible positive nonzero pixel value.
minValue() - Method in class ij.process.ImageProcessor
Returns the minimum possible pixel value.
mode - Variable in class ij.process.ImageStatistics
Mode of 256 bin histogram (counts limited to 2^31-1)
MODE - Static variable in interface ij.measure.Measurements
 
MODE - Static variable in class ij.measure.ResultsTable
 
MODE_KEY - Static variable in class ij.plugin.frame.ThresholdAdjuster
 
MODIFIED - Static variable in interface ij.gui.RoiListener
 
modifiers(int) - Static method in class ij.ImageJ
Return the current list of modifier keys.
Moments - ij.process.AutoThresholder.Method
 
MONOSPACED - Static variable in class ij.plugin.frame.Editor
 
MontageMaker - Class in ij.plugin
Implements the Image/Stacks/Make Montage command.
MontageMaker() - Constructor for class ij.plugin.MontageMaker
 
mouseClicked(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
 
mouseClicked(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mouseClicked(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseClicked(MouseEvent) - Method in class ij.ImageJ
 
mouseClicked(MouseEvent) - Method in class ij.plugin.CommandFinder
 
mouseClicked(MouseEvent) - Method in class ij.plugin.frame.Editor
 
mouseClicked(MouseEvent) - Method in class ij.plugin.frame.RoiManager
 
mouseClicked(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
Propagate mouse clicked events to all synchronized windows.
mouseClicked(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseClicked(MouseEvent) - Method in class ij.text.TextPanel
 
mouseDownInHandle(int, int, int) - Method in class ij.gui.Line
 
mouseDownInHandle(int, int, int) - Method in class ij.gui.PolygonRoi
 
mouseDownInHandle(int, int, int) - Method in class ij.gui.Roi
 
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.ArrowTool
 
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.BrushTool
 
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.OverlayBrushTool
 
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PixelInspectionTool
 
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
 
mouseDragged(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.RoiRotationTool
 
mouseDragged(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mouseDragged(MouseEvent) - Method in class ij.gui.Roi
 
mouseDragged(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseDragged(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
Propagate mouse dragged events to all synchronized windows.
mouseDragged(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseDragged(MouseEvent) - Method in class ij.text.TextPanel
 
mouseEntered(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
 
mouseEntered(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mouseEntered(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseEntered(MouseEvent) - Method in class ij.ImageJ
 
mouseEntered(MouseEvent) - Method in class ij.plugin.CommandFinder
 
mouseEntered(MouseEvent) - Method in class ij.plugin.frame.Editor
 
mouseEntered(MouseEvent) - Method in class ij.plugin.frame.RoiManager
 
mouseEntered(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
Propagate mouse entered events to all synchronized windows.
mouseEntered(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseEntered(MouseEvent) - Method in class ij.text.TextPanel
 
mouseExited(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
 
mouseExited(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mouseExited(MouseEvent) - Method in class ij.gui.PlotCanvas
overrides ImageCanvas.mouseExited; removes 'range' arrows
mouseExited(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseExited(MouseEvent) - Method in class ij.ImageJ
 
mouseExited(MouseEvent) - Method in class ij.plugin.CommandFinder
 
mouseExited(MouseEvent) - Method in class ij.plugin.frame.Editor
 
mouseExited(MouseEvent) - Method in class ij.plugin.frame.RoiManager
 
mouseExited(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
Propagate mouse exited events to all synchronized windows.
mouseExited(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseExited(MouseEvent) - Method in class ij.text.TextPanel
 
mouseMoved(int, int) - Method in class ij.gui.HistogramWindow
 
mouseMoved(int, int) - Method in class ij.gui.ImageWindow
This method is called by ImageCanvas.mouseMoved(MouseEvent).
mouseMoved(int, int) - Method in class ij.gui.PlotWindow
Updates the X and Y values when the mouse is moved and, if appropriate, shows/hides the overlay with the triangular buttons for changing the axis range limits.
mouseMoved(int, int) - Method in class ij.ImagePlus
Displays the cursor coordinates and pixel value in the status bar.
mouseMoved(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
 
mouseMoved(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mouseMoved(MouseEvent) - Method in class ij.gui.Line
 
mouseMoved(MouseEvent) - Method in class ij.gui.PolygonRoi
 
mouseMoved(MouseEvent) - Method in class ij.gui.Roi
 
mouseMoved(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseMoved(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
Draws the "synchronize" cursor in each of the synchronized windows.
mouseMoved(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseMoved(MouseEvent) - Method in class ij.text.TextPanel
 
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.ArrowTool
 
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.BrushTool
 
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.OverlayBrushTool
 
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PixelInspectionTool
 
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
 
mousePressed(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.RoiRotationTool
 
mousePressed(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mousePressed(MouseEvent) - Method in class ij.gui.PlotCanvas
overrides ImageCanvas.mousePressed: no further processing of clicks on 'range' arrows
mousePressed(MouseEvent) - Method in class ij.gui.Toolbar
 
mousePressed(MouseEvent) - Method in class ij.ImageJ
 
mousePressed(MouseEvent) - Method in class ij.plugin.CommandFinder
 
mousePressed(MouseEvent) - Method in class ij.plugin.frame.Editor
 
mousePressed(MouseEvent) - Method in class ij.plugin.frame.RoiManager
 
mousePressed(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
Propagate mouse pressed events to all synchronized windows.
mousePressed(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mousePressed(MouseEvent) - Method in class ij.text.TextPanel
 
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.ArrowTool
 
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.BrushTool
 
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.OverlayBrushTool
 
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.PlugInTool
 
mouseReleased(ImagePlus, MouseEvent) - Method in class ij.plugin.tool.RoiRotationTool
 
mouseReleased(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mouseReleased(MouseEvent) - Method in class ij.gui.PlotCanvas
Overrides ImageCanvas.mouseReleased, handles clicks on 'range' arrows
mouseReleased(MouseEvent) - Method in class ij.gui.Roi
 
mouseReleased(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseReleased(MouseEvent) - Method in class ij.ImageJ
 
mouseReleased(MouseEvent) - Method in class ij.plugin.CommandFinder
 
mouseReleased(MouseEvent) - Method in class ij.plugin.frame.Editor
 
mouseReleased(MouseEvent) - Method in class ij.plugin.frame.RoiManager
 
mouseReleased(MouseEvent) - Method in class ij.plugin.frame.SyncWindows
Propagate mouse released events to all synchronized windows.
mouseReleased(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseReleased(MouseEvent) - Method in class ij.text.TextPanel
 
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.ImageWindow
 
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.PlotWindow
Mouse wheel: zooms when shift or ctrl is pressed, scrolls in x if space bar down, in y otherwise.
mouseWheelMoved(MouseWheelEvent) - Method in class ij.gui.StackWindow
 
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.frame.RoiManager
 
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
 
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseWheelMoved(MouseWheelEvent) - Method in class ij.text.TextPanel
 
MOVE_TO - Static variable in interface ij.macro.MacroConstants
 
moveCursor - Static variable in class ij.gui.ImageCanvas
 
MOVED - Static variable in interface ij.gui.RoiListener
 
moveHandle(int, int) - Method in class ij.gui.EllipseRoi
 
moveHandle(int, int) - Method in class ij.gui.Line
 
moveHandle(int, int) - Method in class ij.gui.OvalRoi
 
moveHandle(int, int) - Method in class ij.gui.PolygonRoi
 
moveHandle(int, int) - Method in class ij.gui.Roi
 
moveHandle(int, int) - Method in class ij.gui.RotatedRectRoi
 
moveRoisToOverlay(ImagePlus) - Method in class ij.plugin.frame.RoiManager
Moves all the ROIs to the specified image's overlay.
moveTo(int, int) - Method in class ij.process.ImageProcessor
Sets the current drawing location.
moveToMisc - Static variable in class ij.Prefs
Move isolated plugins to Miscellaneous submenu.
MOVING - Static variable in class ij.gui.Roi
 
MOVING_HANDLE - Static variable in class ij.gui.Roi
 
MUL_EQUAL - Static variable in interface ij.macro.MacroConstants
 
multiCrop(String, String) - Method in class ij.plugin.frame.RoiManager
 
MultiLineLabel - Class in ij.gui
Custom component for displaying multiple lines.
MultiLineLabel(String) - Constructor for class ij.gui.MultiLineLabel
 
MultiLineLabel(String, int) - Constructor for class ij.gui.MultiLineLabel
 
multiMeasure(ImagePlus) - Method in class ij.plugin.frame.RoiManager
This method measures the selected ROIs, or all ROIs if none are selected, on all the slices of a stack and returns a ResultsTable arranged with one row per slice.
multiMeasure(ImagePlus, Roi[], boolean) - Static method in class ij.plugin.frame.RoiManager
 
multiply(double) - Method in class ij.process.FloatProcessor
 
multiply(double) - Method in class ij.process.ImageProcessor
Multiplies each pixel in the image or ROI by 'value'.
multiply(double) - Method in class ij.process.ShortProcessor
 
multiply(ImagePlus, ImageProcessor) - Static method in class ij.plugin.FFT
Multiplies a Fourier domain image by a filter
multiply(FHT) - Method in class ij.process.FHT
Returns the image resulting from the point by point Hartley multiplication of this image and the specified image.
MULTIPLY - Static variable in interface ij.process.Blitter
dst=src*src
multiPointMode - Static variable in class ij.Prefs
Use MultiPoint tool.

N

n(double) - Method in class ij.plugin.filter.Analyzer
Converts a number to a formatted string with a tab at the end.
N_COORDINATES - Static variable in class ij.io.RoiDecoder
 
name - Variable in class ij.macro.ExtensionDescriptor
 
NAME_LENGTH - Static variable in class ij.io.RoiDecoder
 
NAME_OFFSET - Static variable in class ij.io.RoiDecoder
 
nameKey - Static variable in class ij.process.LUT
 
NaN - Static variable in interface ij.macro.MacroConstants
 
NaN_EMPTY_CELLS - Static variable in interface ij.measure.Measurements
 
nBins - Static variable in class ij.gui.HistogramWindow
 
nBins - Variable in class ij.process.ImageStatistics
 
nChannels - Variable in class ij.ImagePlus
 
nCoordinates - Variable in class ij.process.EllipseFitter
Initialized by makeRoi()
NEAREST_NEIGHBOR - Static variable in class ij.process.ImageProcessor
Interpolation methods
NEQ - Static variable in interface ij.macro.MacroConstants
 
NEW_ARRAY - Static variable in interface ij.macro.MacroConstants
 
NEW_IMAGE - Static variable in interface ij.macro.MacroConstants
 
NEW_MENU - Static variable in interface ij.macro.MacroConstants
 
NEW_SUBFILE_TYPE - Static variable in class ij.io.TiffDecoder
 
newDescriptor(String, MacroExtension) - Static method in class ij.macro.ExtensionDescriptor
 
newDescriptor(String, MacroExtension, int) - Static method in class ij.macro.ExtensionDescriptor
 
newDescriptor(String, MacroExtension, int[]) - Static method in class ij.macro.ExtensionDescriptor
 
newDescriptor(String, MacroExtension, int, int) - Static method in class ij.macro.ExtensionDescriptor
 
newDescriptor(String, MacroExtension, int, int, int) - Static method in class ij.macro.ExtensionDescriptor
 
newDescriptor(String, MacroExtension, int, int, int, int) - Static method in class ij.macro.ExtensionDescriptor
 
newDescriptor(String, MacroExtension, Integer[]) - Static method in class ij.macro.ExtensionDescriptor
 
newDialog(String) - Static method in class ij.gui.NonBlockingGenericDialog
Obsolete, replaced by GUI.newNonBlockingDialog(String).
newDialog(String, ImagePlus) - Static method in class ij.gui.NonBlockingGenericDialog
Obsolete, replaced by GUI.newNonBlockingDialog(String,ImagePlus).
newImage(String, String, int, int, int) - Static method in class ij.IJ
Opens a new image.
NewImage - Class in ij.gui
New image dialog box plus several static utility methods for creating images.
NewImage() - Constructor for class ij.gui.NewImage
 
newMaxCount - Variable in class ij.gui.HistogramWindow
 
newNonBlockingDialog(String) - Static method in class ij.gui.GUI
Returns a new NonBlockingGenericDialog with the given title, except when Java is running in headless mode, in which case a GenericDialog is be returned.
newNonBlockingDialog(String, ImagePlus) - Static method in class ij.gui.GUI
Returns a new NonBlockingGenericDialog with the given title if Prefs.nonBlockingFilterDialogs is 'true' and 'imp' is displayed, otherwise returns a GenericDialog.
newPixels - Variable in class ij.process.ImageProcessor
 
NewPlugin - Class in ij.plugin
This class creates a new macro or the Java source for a new plugin.
NewPlugin() - Constructor for class ij.plugin.NewPlugin
 
newWindowCreated - Static variable in class ij.plugin.Converter
obsolete
next() - Method in class ij.gui.Line.PointIterator
 
NextImageOpener - Class in ij.plugin
 
NextImageOpener() - Constructor for class ij.plugin.NextImageOpener
 
nFrames - Variable in class ij.ImagePlus
 
NIH_IMAGE_HDR - Static variable in class ij.io.TiffDecoder
 
nImages - Variable in class ij.io.FileInfo
 
NIMAGES - Static variable in interface ij.macro.MacroConstants
 
NO_CHANGES - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter makes no changes to the pixel data and does not require undo.
NO_COMPRESSION - Static variable in class ij.plugin.filter.AVI_Writer
 
NO_IMAGE_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter does not require that an image be open.
NO_LUT_UPDATE - Static variable in class ij.process.ImageProcessor
 
NO_RESET - Static variable in class ij.plugin.frame.ThresholdAdjuster
 
NO_SHOW - Static variable in class ij.ImageJ
Run embedded and invisible in another application.
NO_THRESHOLD - Static variable in class ij.process.ImageProcessor
Value returned by getMinThreshold() when image is not thresholded.
NO_UNDO - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter does not require undo.
NO_UNDO_RESET - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag to prevent Undo from being reset when processing a stack.
NO_WINDOW - Static variable in class ij.process.FHT
 
noBorder - Static variable in class ij.Prefs
Do not draw black border around image.
noClickToGC - Static variable in class ij.Prefs
Don't run garbage collector when user clicks in status bar
noErrorBars() - Method in class ij.gui.PlotContentsDialog
Avoids showing a selection for the error bars; must be called before showDialog.
noGridLines - Static variable in class ij.gui.PlotWindow
Have axes with no grid lines.
noImage() - Static method in class ij.IJ
Displays a "no images are open" dialog box.
noise(double) - Method in class ij.process.ByteProcessor
Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
noise(double) - Method in class ij.process.ColorProcessor
 
noise(double) - Method in class ij.process.FloatProcessor
 
noise(double) - Method in class ij.process.ImageProcessor
Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
noise(double) - Method in class ij.process.ShortProcessor
Adds pseudorandom, Gaussian ("normally") distributed values, with mean 0.0 and the specified standard deviation, to this image or ROI.
NOISE_SD - Static variable in class ij.Prefs
 
nonBatchMacroRunning() - Static method in class ij.macro.Interpreter
 
nonBlockingFilterDialogs - Static variable in class ij.Prefs
Use NonBlockingGenericDialogs in filters
NonBlockingGenericDialog - Class in ij.gui
This is an extension of GenericDialog that is non-modal.
NonBlockingGenericDialog(String) - Constructor for class ij.gui.NonBlockingGenericDialog
 
NONE - Static variable in class ij.measure.Calibration
 
NONE - Static variable in class ij.process.ImageProcessor
Interpolation methods
nonScalable - Variable in class ij.gui.Roi
 
NOP - Static variable in interface ij.macro.MacroConstants
 
noPointLabels - Static variable in class ij.Prefs
Do not label multiple points created using point tool.
NORMAL - Static variable in class ij.gui.Roi
 
NORMAL_RETURN - Static variable in class ij.Menus
 
noRowNumbers - Static variable in class ij.Prefs
Do not include row numbers when copying tables to clipboard.
north(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
northeast(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
northwest(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
not(ShapeRoi) - Method in class ij.gui.ShapeRoi
Unary subtraction operator.
NOT_DEBUGGING - Static variable in interface ij.macro.Debugger
 
NOT_INSTALLED - Static variable in class ij.Menus
 
NOT_PASTING - Static variable in class ij.gui.Roi
 
NOTCHED - Static variable in class ij.gui.Arrow
 
NOTHING - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
NOTHING - Static variable in class ij.Undo
 
noTicks - Static variable in class ij.gui.PlotWindow
Have axes with no ticks.
notifyEventListeners(int) - Static method in class ij.IJ
 
notifyListeners(int) - Method in class ij.gui.Roi
 
notifyListeners(int) - Method in class ij.ImagePlus
 
npoints - Variable in class ij.gui.Wand
The number of points in the generated outline.
npoints - Variable in class ij.process.FloatPolygon
The number of points.
nPoints - Variable in class ij.gui.PolygonRoi
 
NRESULTS - Static variable in interface ij.macro.MacroConstants
 
nSlices - Variable in class ij.ImagePlus
 
NSLICES - Static variable in interface ij.macro.MacroConstants
 
nudge(int) - Method in class ij.gui.Roi
Nudge ROI one pixel on arrow key press.
nudgeCorner(int) - Method in class ij.gui.EllipseRoi
 
nudgeCorner(int) - Method in class ij.gui.Line
Nudge end point of line by one pixel.
nudgeCorner(int) - Method in class ij.gui.Roi
Nudge lower right corner of rectangular and oval ROIs by one pixel based on arrow key press.
nudgeCorner(int) - Method in class ij.gui.RotatedRectRoi
 
NUMBER - Static variable in interface ij.macro.MacroConstants
 
numberField - Variable in class ij.gui.GenericDialog
 
NUMERIC_FUNCTION - Static variable in interface ij.macro.MacroConstants
 
numericFunctionIDs - Static variable in interface ij.macro.MacroConstants
 
numericFunctions - Static variable in interface ij.macro.MacroConstants
 

O

offScreenX(int) - Method in class ij.gui.ImageCanvas
Converts a screen x-coordinate to an offscreen x-coordinate (nearest pixel center).
offScreenX(int) - Method in class ij.gui.Roi
Converts image canvas screen x coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offScreenX2(int) - Method in class ij.gui.ImageCanvas
Converts a screen x-coordinate to an offscreen x-coordinate (Roi coordinate of nearest pixel border).
offScreenXD(int) - Method in class ij.gui.ImageCanvas
Converts a screen x-coordinate to a floating-point offscreen x-coordinate.
offScreenXD(int) - Method in class ij.gui.Roi
Converts image canvas screen x coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offScreenY(int) - Method in class ij.gui.ImageCanvas
Converts a screen y-coordinate to an offscreen y-coordinate (nearest pixel center).
offScreenY(int) - Method in class ij.gui.Roi
Converts image canvas screen y coordinates to integer offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offScreenY2(int) - Method in class ij.gui.ImageCanvas
Converts a screen y-coordinate to an offscreen y-coordinate (Roi coordinate of nearest pixel border).
offScreenYD(int) - Method in class ij.gui.ImageCanvas
Converts a screen y-coordinate to a floating-point offscreen y-coordinate.
offScreenYD(int) - Method in class ij.gui.Roi
Converts image canvas screen y coordinates to floating-point offscreen image pixel coordinates, depending on whether this roi uses the line or area convention for coordinates.
offset - Variable in class ij.io.FileInfo
 
OJJ - Static variable in class ij.io.Opener
 
okForFits(ImagePlus) - Static method in class ij.io.FileSaver
 
okForGif(ImagePlus) - Static method in class ij.io.FileSaver
 
okForJpeg(ImagePlus) - Static method in class ij.io.FileSaver
Always returns true.
okToDeleteRoi() - Method in class ij.ImagePlus
 
oldHeight - Variable in class ij.gui.Roi
 
oldWidth - Variable in class ij.gui.Roi
 
oldX - Variable in class ij.gui.Roi
 
oldX - Variable in class ij.plugin.frame.SyncWindows
 
oldY - Variable in class ij.gui.Roi
 
oldY - Variable in class ij.plugin.frame.SyncWindows
 
ONE - Static variable in class ij.plugin.filter.EDM
Unit in old make16bitEDM: this pixel value corresponds to a distance of one pixel.
onePixelWide - Static variable in class ij.gui.Roi
 
open() - Static method in class ij.IJ
Displays a file open dialog box and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file selected by the user.
open() - Method in class ij.io.FileOpener
Opens the image and displays it.
open() - Method in class ij.io.Opener
Displays a file open dialog box and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file selected by the user.
open() - Method in class ij.plugin.TextReader
Displays a file open dialog and opens the specified text file as a float image.
open(boolean) - Method in class ij.io.FileOpener
Obsolete, replaced by openImage() and open().
open(InputStream) - Static method in class ij.plugin.LutLoader
Opens an ImageJ LUT using an InputStream and returns it as an IndexColorModel.
open(String) - Static method in class ij.IJ
Opens and displays a tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file.
open(String) - Method in class ij.io.Opener
Opens and displays the specified tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file.
open(String) - Static method in class ij.io.RoiDecoder
Opens the Roi at the specified path.
open(String) - Static method in class ij.Macro
 
open(String) - Static method in class ij.measure.ResultsTable
Opens a tab or comma delimited text file and returns it as a ResultsTable.
open(String) - Static method in class ij.plugin.BrowserLauncher
Opens the specified URL in the default browser.
open(String) - Method in class ij.plugin.DICOM
Opens the specified file as a DICOM.
open(String) - Static method in class ij.plugin.FolderOpener
Opens the images in the specified directory as a stack.
open(String) - Method in class ij.plugin.frame.RoiManager
Opens a single .roi file or a ZIP-compressed set of ROIs.
open(String) - Static method in class ij.plugin.LutLoader
Opens the specified ImageJ LUT and returns it as an IndexColorModel.
open(String) - Method in class ij.plugin.TextReader
Opens the specified text file as a float image.
open(String, boolean) - Static method in class ij.plugin.AVI_Reader
Opens an AVI file as a stack in memory or a virtual stack.
open(String, int) - Static method in class ij.IJ
Opens and displays the nth image in the specified tiff stack.
open(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
 
open(String, int, int, String) - Static method in class ij.plugin.FolderOpener
Opens the images in the specified directory as a widthxheight stack.
open(String, FileInfo) - Static method in class ij.plugin.Raw
Opens the image at 'filePath' using the format specified by 'fi'.
open(String, String) - Static method in class ij.plugin.AVI_Reader
Opens an AVI file, where 'options' can contain 'virtual' (open as virtual stack), 'convert' (convert color images to grayscale) or 'flip' (flip vertically).
open(String, String) - Static method in class ij.plugin.FolderOpener
Opens the images in the specified directory as a stack.
open(String, String) - Method in class ij.plugin.frame.Editor
Opens a file and replaces the text (if any) by the contents of the file.
OPEN - Static variable in class ij.gui.Arrow
 
OPEN - Static variable in interface ij.macro.MacroConstants
 
OPEN - Static variable in class ij.plugin.filter.RankFilters
 
open100Percent - Static variable in class ij.Prefs
Open images at 100% magnification
open16bitAsciiImage(StreamTokenizer, int, int) - Method in class ij.plugin.PGM_Reader
 
open16bitRawImage(InputStream, int, int) - Method in class ij.plugin.PGM_Reader
 
open2(String) - Static method in class ij.measure.ResultsTable
Opens a tab or comma delimited text file and returns it as a ResultsTable, without requiring a try/catch statement.
openAll(String, FileInfo) - Static method in class ij.plugin.Raw
Opens all the images in the specified directory as a stack, using the format specified by 'fi'.
openAllVirtual(String, FileInfo) - Static method in class ij.plugin.Raw
Opens all the images in the specified directory as a virtual stack, using the format specified by 'fi'.
openAndAddToRecent(String) - Method in class ij.io.Opener
Opens the specified file and adds it to the File/Open Recent menu.
openAsByteBuffer(String) - Static method in class ij.IJ
 
openAsciiImage(StreamTokenizer, int, byte[]) - Method in class ij.plugin.PGM_Reader
 
openAsString(String) - Static method in class ij.IJ
Opens a text file as a string.
openAsVirtualStack(boolean) - Method in class ij.plugin.FolderOpener
 
OpenDialog - Class in ij.io
This class displays a dialog window from which the user can select an input file.
OpenDialog(String) - Constructor for class ij.io.OpenDialog
Displays a file open dialog with 'title' as the title.
OpenDialog(String, String) - Constructor for class ij.io.OpenDialog
Displays a file open dialog with 'title' as the title.
OpenDialog(String, String, String) - Constructor for class ij.io.OpenDialog
Displays a file open dialog, using the specified default directory and file name.
openDicomsAsFloat - Static variable in class ij.Prefs
Open DICOMs as 32-bit float images
OPENED - Static variable in class ij.ImagePlus
 
Opener - Class in ij.io
Opens tiff (and tiff stacks), dicom, fits, pgm, jpeg, bmp or gif images, and look-up tables, using a file open dialog or a path.
Opener() - Constructor for class ij.io.Opener
 
openExample(String) - Static method in class ij.plugin.frame.Editor
Opens an example from the Help/Examples menu and runs if "Autorun Exampes" is checked.
openFile(File) - Method in class ij.plugin.DragAndDrop
Open a file.
openFile(String) - Method in class ij.plugin.PGM_Reader
 
openFolder(String) - Method in class ij.plugin.FolderOpener
Opens the images in the specified directory as a stack.
openFromByteArray(byte[]) - Static method in class ij.io.RoiDecoder
Opens an ROI from a byte array.
openFromIJJar(String) - Method in class ij.plugin.MacroInstaller
Returns a text file contained in ij.jar.
openFromIJJarAsString(String) - Static method in class ij.util.Tools
Opens a text file in ij.jar as a String (example path: "/macros/Circle_Tool.txt").
openHeader(StreamTokenizer) - Method in class ij.plugin.PGM_Reader
 
openImage() - Static method in class ij.IJ
Opens an image using a file open dialog and returns it as an ImagePlus object.
openImage() - Method in class ij.io.FileOpener
Opens the image and returns it has an ImagePlus object.
openImage() - Method in class ij.io.ImportDialog
Displays the dialog and opens the specified image or images.
openImage(String) - Static method in class ij.IJ
Opens the specified file as a tiff, bmp, dicom, fits, pgm, gif, jpeg or text image and returns an ImagePlus object if successful.
openImage(String) - Method in class ij.io.Opener
Opens, but does not display, the specified image file and returns an ImagePlus object object if successful, or returns null if the file is not in a supported format or is not found.
openImage(String, int) - Static method in class ij.IJ
Opens the nth image of the specified tiff stack.
openImage(String, int) - Method in class ij.io.Opener
Open the nth image of the specified tiff stack.
openImage(String, String) - Method in class ij.io.Opener
Attempts to open the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg image.
openLut(String) - Static method in class ij.io.Opener
Opens a lookup table (LUT) and returns it as a LUT object, or returns null if there is an error.
openLut(String) - Static method in class ij.plugin.LutLoader
Opens a LUT and returns it as a LUT object.
openMacroFromJar(String) - Static method in class ij.plugin.BatchProcessor
 
openMultiple() - Method in class ij.io.Opener
Displays a JFileChooser and then opens the tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text files selected by the user.
openNextDir - Variable in class ij.io.FileInfo
 
openNextName - Variable in class ij.io.FileInfo
 
openProcessor() - Method in class ij.io.FileOpener
 
openRawImage(InputStream, int, byte[]) - Method in class ij.plugin.PGM_Reader
 
openResultsTable(String) - Static method in class ij.io.Opener
Opens a tab or comma delimited text file in the Results window.
openRoi(String) - Method in class ij.io.Opener
Attempts to open the specified ROI, returning null if unsuccessful.
openRoi(String, String) - Method in class ij.plugin.RoiReader
 
openTable(String) - Static method in class ij.io.Opener
Opens a tab or comma delimited text file.
openTempImage(String, String) - Method in class ij.io.Opener
 
openTextImage(String, String) - Method in class ij.io.Opener
Opens the specified text file as a float image.
openTiff(InputStream, String) - Method in class ij.io.Opener
Attempts to open the specified inputStream as a TIFF, returning an ImagePlus object if successful.
openTiff(String, int) - Method in class ij.io.Opener
Opens the nth image of the specified TIFF stack.
openTiff(String, String) - Method in class ij.io.Opener
Attempts to open the specified file as a tiff.
openTiffStack(FileInfo[]) - Method in class ij.io.Opener
Attemps to open a tiff file as a stack.
openURL(String) - Method in class ij.io.Opener
Attempts to open the specified url as a tiff, zip compressed tiff, dicom, gif or jpeg.
openURL(String) - Static method in class ij.plugin.BrowserLauncher
Attempts to open the default web browser to the given URL.
openUrlAsString(String) - Static method in class ij.IJ
Opens a URL and returns the contents as a string.
openUsingBioFormats(String) - Static method in class ij.io.Opener
Opens an image file using the Bio-Formats plugin.
openUsingImageIO(String) - Static method in class ij.io.Opener
 
openVirtual(String) - Static method in class ij.IJ
Opens the specified tiff file as a virtual stack.
openVirtual(String) - Static method in class ij.plugin.AVI_Reader
Opens an AVI file as a virtual stack.
openVirtual(String) - Static method in class ij.plugin.FileInfoVirtualStack
Opens the specified tiff file as a virtual stack.
openWithHandleExtraFileTypes(String, int[]) - Method in class ij.io.Opener
 
openZip(String) - Method in class ij.io.Opener
Opens a single TIFF or DICOM contained in a ZIP archive, or a ZIPed collection of ".roi" files created by the ROI manager.
Options - Class in ij.plugin
This plugin implements most of the commands in the Edit/Options sub-menu.
Options() - Constructor for class ij.plugin.Options
 
OPTIONS - Static variable in class ij.io.RoiDecoder
 
OPTIONS - Static variable in class ij.Prefs
 
OPTIONS2 - Static variable in class ij.Prefs
 
or(int) - Method in class ij.process.FloatProcessor
 
or(int) - Method in class ij.process.ImageProcessor
Binary OR of each pixel in the image or ROI with 'value'.
or(int) - Method in class ij.process.ShortProcessor
 
or(ShapeRoi) - Method in class ij.gui.ShapeRoi
Unary union operator.
OR - Static variable in interface ij.process.Blitter
dst=dst OR src
ORIENTATION - Static variable in class ij.io.TiffDecoder
 
originalBitDepth - Variable in class ij.process.FHT
Used by the FFT class.
originalColorModel - Variable in class ij.process.FHT
Used by the FFT class.
originalHeight - Variable in class ij.process.FHT
Used by the FFT class.
originalWidth - Variable in class ij.process.FHT
Used by the FFT class.
Orthogonal_Views - Class in ij.plugin
This plugin projects dynamically orthogonal XZ and YZ views of a stack.
Orthogonal_Views() - Constructor for class ij.plugin.Orthogonal_Views
 
OtherInstance - Class in ij
 
OtherInstance() - Constructor for class ij.OtherInstance
 
Otsu - ij.process.AutoThresholder.Method
 
out(ImagePlus) - Static method in class ij.plugin.Zoom
 
OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
 
outline() - Method in class ij.process.BinaryProcessor
 
outline() - Method in class ij.process.ByteProcessor
 
OUTLINE - Static variable in class ij.io.RoiDecoder
 
OUTLINE_KEY - Static variable in class ij.gui.Arrow
 
OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
outOfMemory(String) - Static method in class ij.IJ
Displays an "out of memory" message to the "Log" window.
OVAL - Static variable in class ij.gui.Roi
 
OVAL - Static variable in class ij.gui.Toolbar
 
OVAL_ROI - Static variable in class ij.gui.Toolbar
 
OvalRoi - Class in ij.gui
Oval region of interest
OvalRoi(double, double, double, double) - Constructor for class ij.gui.OvalRoi
Creates an OvalRoi using double arguments.
OvalRoi(int, int, int, int) - Constructor for class ij.gui.OvalRoi
Creates an OvalRoi.
OvalRoi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
Deprecated. 
OvalRoi(int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
Starts the process of creating a user-defined OvalRoi.
OvalRoi(double, double, double, double) - Static method in class ij.IJ
Creates an OvalRoi.
OVER_UNDER_LUT - Static variable in class ij.process.ImageProcessor
 
overlay - Variable in class ij.gui.Roi
 
overlay - Variable in class ij.io.FileInfo
 
Overlay - Class in ij.gui
An Overlay is a list of ROIs that can be drawn non-destructively on an Image.
Overlay() - Constructor for class ij.gui.Overlay
Constructs an empty Overlay.
Overlay(Roi) - Constructor for class ij.gui.Overlay
Constructs an Overlay and adds the specified ROI.
OVERLAY - Static variable in interface ij.macro.MacroConstants
 
OVERLAY - Static variable in class ij.plugin.filter.ParticleAnalyzer
Use "Overlay" checkbox to display overlay.
OVERLAY_ADDITION - Static variable in class ij.Undo
 
OVERLAY_BACKGROUNDS - Static variable in class ij.io.RoiDecoder
 
OVERLAY_BOLD - Static variable in class ij.io.RoiDecoder
 
OVERLAY_FONT_SIZE - Static variable in class ij.io.RoiDecoder
 
OVERLAY_LABEL_COLOR - Static variable in class ij.io.RoiDecoder
 
OVERLAY_LABELS - Static variable in class ij.io.RoiDecoder
 
OVERLAY_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
OVERLAY_NAMES - Static variable in class ij.io.RoiDecoder
 
OVERLAY_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
OverlayBrushTool - Class in ij.plugin.tool
 
OverlayBrushTool() - Constructor for class ij.plugin.tool.OverlayBrushTool
 
OverlayCommands - Class in ij.plugin
This plugin implements the commands in the Image/Overlay menu.
OverlayCommands() - Constructor for class ij.plugin.OverlayCommands
 
OverlayLabels - Class in ij.plugin
This plugin implements the Image/Overlay/Labels command.
OverlayLabels() - Constructor for class ij.plugin.OverlayLabels
 

P

PACK_BITS - Static variable in class ij.io.FileInfo
 
packBitsUncompress(byte[], int) - Method in class ij.io.ImageReader
Based on the Bio-Formats PackbitsCodec written by Melissa Linkert.
pad(int, int) - Static method in class ij.IJ
Pad 'n' with leading zeros to the specified number of digits.
pad(String, int) - Static method in class ij.IJ
Pad 's' with leading zeros to the specified number of digits.
padEdges - Static variable in class ij.Prefs
Extend the borders to foreground for binary erosions and closings.
paint(Graphics) - Method in class ij.gui.GenericDialog
 
paint(Graphics) - Method in class ij.gui.ImageCanvas
 
paint(Graphics) - Method in class ij.gui.ImagePanel
 
paint(Graphics) - Method in class ij.gui.ImageWindow
 
paint(Graphics) - Method in class ij.gui.MultiLineLabel
 
paint(Graphics) - Method in class ij.gui.ProgressBar
 
paint(Graphics) - Method in class ij.gui.Toolbar
 
paint(Graphics) - Method in class ij.gui.YesNoCancelDialog
 
paintDoubleBuffered - Static variable in class ij.Prefs
Aways paint images using double buffering
panel - Variable in class ij.plugin.frame.SyncWindows
Panel for GUI
PARALLELIZE_IMAGES - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if images may be processed in parallel threads.
PARALLELIZE_STACKS - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the slices of a stack may be processed in parallel threads
PARSE_FLOAT - Static variable in interface ij.macro.MacroConstants
 
PARSE_INT - Static variable in interface ij.macro.MacroConstants
 
parseDouble(String) - Method in class ij.gui.GenericDialog
 
parseDouble(String) - Static method in class ij.util.Tools
Returns a double containg the value represented by the specified String.
parseDouble(String, double) - Static method in class ij.util.Tools
Returns a double containg the value represented by the specified String.
parseMenu(String, Menu) - Method in class ij.plugin.CommandFinder
 
ParticleAnalyzer - Class in ij.plugin.filter
Implements ImageJ's Analyze Particles command.
ParticleAnalyzer() - Constructor for class ij.plugin.filter.ParticleAnalyzer
Default constructor
ParticleAnalyzer(int, int, ResultsTable, double, double) - Constructor for class ij.plugin.filter.ParticleAnalyzer
Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1).
ParticleAnalyzer(int, int, ResultsTable, double, double, double, double) - Constructor for class ij.plugin.filter.ParticleAnalyzer
Constructs a ParticleAnalyzer.
particleAnalyzerFill(int, int, double, double, ImageProcessor, Rectangle) - Method in class ij.process.FloodFiller
This method is used by the particle analyzer to remove interior holes from particle masks.
paste() - Method in class ij.gui.ImageWindow
 
paste() - Method in class ij.ImagePlus
Inserts the contents of the internal clipboard into this image.
paste(int, int) - Method in class ij.ImagePlus
Inserts the contents of the internal clipboard at the specified location, without updating the display.
paste(int, int, String) - Method in class ij.ImagePlus
Copies the contents of the internal clipboard to the specified location using the specified transfer mode ("Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide").
PASTE - Static variable in class ij.Undo
 
PasteController - Class in ij.plugin.frame
Implements ImageJ's Paste Control window.
PasteController() - Constructor for class ij.plugin.frame.PasteController
 
pasteMode - Static variable in class ij.gui.Roi
 
path - Variable in class ij.io.PluginClassLoader
 
Percentile - ij.process.AutoThresholder.Method
 
PERIMETER - Static variable in interface ij.measure.Measurements
 
PERIMETER - Static variable in class ij.measure.ResultsTable
 
PGM - Static variable in class ij.io.FileInfo
 
PGM - Static variable in class ij.io.Opener
 
PGM_Reader - Class in ij.plugin
This plugin opens PxM format images.
PGM_Reader() - Constructor for class ij.plugin.PGM_Reader
 
ph - Variable in class ij.process.ImageStatistics
 
PHOTO_INTERP - Static variable in class ij.io.TiffDecoder
 
PI - Static variable in interface ij.macro.MacroConstants
 
pixelCount - Variable in class ij.process.ImageStatistics
Int pixel count (limited to 2^31-1)
pixelDepth - Variable in class ij.io.FileInfo
 
pixelDepth - Variable in class ij.measure.Calibration
Pixel depth in 'unit's
pixelHeight - Variable in class ij.io.FileInfo
 
pixelHeight - Variable in class ij.measure.Calibration
Pixel height in 'unit's
PixelInspectionTool - Class in ij.plugin.tool
This plugin continuously displays the pixel values of the cursor and its surroundings.
PixelInspectionTool() - Constructor for class ij.plugin.tool.PixelInspectionTool
 
pixels - Variable in class ij.io.FileInfo
 
pixels - Variable in class ij.process.ByteProcessor
 
pixels - Variable in class ij.process.ColorProcessor
 
pixels - Variable in class ij.process.ShortProcessor
 
pixels8 - Variable in class ij.process.FloatProcessor
 
pixels8 - Variable in class ij.process.ShortProcessor
 
pixelWidth - Variable in class ij.io.FileInfo
 
pixelWidth - Variable in class ij.measure.Calibration
Pixel width in 'unit's
PLANAR_CONFIGURATION - Static variable in class ij.io.TiffDecoder
 
plot - Variable in class ij.io.FileInfo
 
plot(CurveFitter) - Static method in class ij.plugin.frame.Fitter
 
plot(CurveFitter, boolean) - Static method in class ij.plugin.frame.Fitter
 
Plot - Class in ij.gui
This class creates an image that line graphs, scatter plots and plots of vector fields (arrows) can be drawn on and displayed.
Plot(ImagePlus, InputStream) - Constructor for class ij.gui.Plot
Constructs a new plot from an InputStream and closes the stream.
Plot(String, String, String) - Constructor for class ij.gui.Plot
Constructs a new Plot with the default options.
Plot(String, String, String, double[], double[]) - Constructor for class ij.gui.Plot
Deprecated. 
Plot(String, String, String, double[], double[], int) - Constructor for class ij.gui.Plot
Deprecated. 
Plot(String, String, String, float[], float[]) - Constructor for class ij.gui.Plot
Deprecated. 
Plot(String, String, String, float[], float[], int) - Constructor for class ij.gui.Plot
Deprecated. 
Plot(String, String, String, int) - Constructor for class ij.gui.Plot
This version of the constructor has a 'flags' argument for controlling whether ticks, grid, etc.
Plot(String, String, String, String, float[], float[]) - Constructor for class ij.gui.Plot
Deprecated. 
PLOT - Static variable in interface ij.macro.MacroConstants
 
PlotCanvas - Class in ij.gui
This subclass of ImageCanvas has special provisions for plots: - Zooming: sets the plot range - Scrolling: moves data area This behavior is suppressed if the plot is frozen
PlotCanvas(ImagePlus) - Constructor for class ij.gui.PlotCanvas
Creates a new PlotCanvas
PlotContentsDialog - Class in ij.gui
This class implements the Plot Window's Data>"Add from Plot", "Add form Table", "Add Fit" and "More>Contents Style" dialogs
PlotContentsDialog(Plot, int) - Constructor for class ij.gui.PlotContentsDialog
Prepares a new PlotContentsDialog for an existing plot.
PlotContentsDialog(Plot, String[], String[], ArrayList<float[]>) - Constructor for class ij.gui.PlotContentsDialog
Prepares a new PlotContentsDialog for adding data from float[] arrays to a plot.
PlotContentsDialog(String, ResultsTable) - Constructor for class ij.gui.PlotContentsDialog
Prepares a new PlotContentsDialog for creating a new plot using data from a ResultsTable.
PlotContentsDialog(String, String[], String[], ArrayList<float[]>) - Constructor for class ij.gui.PlotContentsDialog
Prepares a new PlotContentsDialog for creating a new plot using float[] arrays as data.
PlotDialog - Class in ij.gui
 
PlotDialog(Plot, int) - Constructor for class ij.gui.PlotDialog
Constructs a new PlotDialog for a given plot and sets the type of dialog
plotHeight - Static variable in class ij.gui.PlotWindow
The height of the plot in pixels.
plotHistogram() - Method in class ij.ImagePlus
Plots a 256 bin histogram of this image and returns the PlotWindow.
plotHistogram(int) - Method in class ij.ImagePlus
Plots a histogram of this image using the specified number of bins and returns the PlotWindow.
PlotMaker - Interface in ij.gui
Plugins that generate "Live" profile plots (Profiler and ZAxisProfiler) displayed in PlotWindows implement this interface.
plotScale - Variable in class ij.gui.HistogramWindow
 
PlotVirtualStack - Class in ij.gui
This is a virtual stack of frozen plots.
PlotVirtualStack(int, int) - Constructor for class ij.gui.PlotVirtualStack
 
plotWidth - Static variable in class ij.gui.PlotWindow
The width of the plot (without frame) in pixels.
PlotWindow - Class in ij.gui
This class implements the Analyze/Plot Profile command.
PlotWindow(ImagePlus, Plot) - Constructor for class ij.gui.PlotWindow
Creates a PlotWindow from a given ImagePlus with a Plot object.
PlotWindow(String, String, String, double[], double[]) - Constructor for class ij.gui.PlotWindow
Deprecated.
replaced by the Plot class.
PlotWindow(String, String, String, float[], float[]) - Constructor for class ij.gui.PlotWindow
Deprecated.
replaced by the Plot class.
PlugIn - Interface in ij.plugin
Plugins that acquire images or display windows should implement this interface.
PLUGIN - Static variable in class ij.plugin.NewPlugin
 
PLUGIN_FILTER - Static variable in class ij.plugin.NewPlugin
 
PLUGIN_FRAME - Static variable in class ij.plugin.NewPlugin
 
PLUGIN_TOOL - Static variable in class ij.plugin.NewPlugin
 
PluginClassLoader - Class in ij.io
ImageJ uses this class loader to load plugins and resources from the plugins directory and immediate subdirectories.
PluginClassLoader(String) - Constructor for class ij.io.PluginClassLoader
Creates a new PluginClassLoader that searches in the directory path passed as a parameter.
PluginClassLoader(String, boolean) - Constructor for class ij.io.PluginClassLoader
This version of the constructor is used when ImageJ is launched using Java WebStart.
PlugInDialog - Class in ij.plugin.frame
This is a non-modal dialog that plugins can extend.
PlugInDialog(String) - Constructor for class ij.plugin.frame.PlugInDialog
 
PlugInFilter - Interface in ij.plugin.filter
ImageJ plugins that process an image should implement this interface.
PlugInFilterRunner - Class in ij.plugin.filter
 
PlugInFilterRunner(Object, String, String) - Constructor for class ij.plugin.filter.PlugInFilterRunner
The constructor runs a PlugInFilter or ExtendedPlugInFilter by calling its setup, run, etc.
PlugInFrame - Class in ij.plugin.frame
This is a closeable window that plugins can extend.
PlugInFrame(String) - Constructor for class ij.plugin.frame.PlugInFrame
 
PluginInstaller - Class in ij.plugin
Installs plugins dragged and dropped on the "ImageJ" window, or plugins, macros or scripts opened using the Plugins/Install command.
PluginInstaller() - Constructor for class ij.plugin.PluginInstaller
 
PlugInInterpreter - Class in ij.plugin
Plugins that run scripts (e.g., BeanShell, Jython) extend this class.
PlugInInterpreter() - Constructor for class ij.plugin.PlugInInterpreter
 
pluginName - Variable in class ij.plugin.Concatenator
 
PLUGINS_MENU - Static variable in class ij.Menus
 
PlugInTool - Class in ij.plugin.tool
 
PlugInTool() - Constructor for class ij.plugin.tool.PlugInTool
 
PLUS_EQUAL - Static variable in interface ij.macro.MacroConstants
 
PLUS_PLUS - Static variable in interface ij.macro.MacroConstants
 
PNG - Static variable in class ij.io.Opener
 
PNG_COMPRESSION - Static variable in class ij.plugin.filter.AVI_Writer
 
PNG_Writer - Class in ij.plugin
Saves in PNG format using the ImageIO classes.
PNG_Writer() - Constructor for class ij.plugin.PNG_Writer
 
PNM_Writer - Class in ij.plugin
 
PNM_Writer() - Constructor for class ij.plugin.PNM_Writer
 
POINT - Static variable in class ij.gui.Roi
 
POINT - Static variable in class ij.gui.Toolbar
 
POINT_SELECTION - Static variable in class ij.plugin.filter.MaximumFinder
Do not create image, only mark points
POINT_TYPE - Static variable in class ij.io.RoiDecoder
 
pointAddToManager - Static variable in class ij.Prefs
Add points to ROI Manager.
pointAddToOverlay - Static variable in class ij.Prefs
Add points to overlay.
pointAutoMeasure - Static variable in class ij.Prefs
Point tool auto-measure mode.
pointAutoNextSlice - Static variable in class ij.Prefs
Point tool auto-next slice mode (not saved in IJ_Prefs).
PointIterator(double, double, double, double) - Constructor for class ij.gui.Line.PointIterator
 
PointIterator(Line) - Constructor for class ij.gui.Line.PointIterator
 
PointRoi - Class in ij.gui
This class represents a collection of points that can be associated with counters.
PointRoi() - Constructor for class ij.gui.PointRoi
 
PointRoi(double, double) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified offscreen double coordinates.
PointRoi(double, double, String) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified coordinates and options.
PointRoi(float[], float[]) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified float arrays of offscreen coordinates.
PointRoi(float[], float[], int) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified float arrays of offscreen coordinates.
PointRoi(float[], float[], String) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified coordinate arrays and options.
PointRoi(int[], int[], int) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified int arrays of offscreen coordinates.
PointRoi(int, int) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified offscreen int coordinates.
PointRoi(int, int, ImagePlus) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified screen coordinates.
PointRoi(FloatPolygon) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi from a FloatPolygon.
PointRoi(Polygon) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi from a Polygon.
PointToolOptions - Class in ij.plugin
This plugin implements the Edit/Options/Point Tool command.
PointToolOptions() - Constructor for class ij.plugin.PointToolOptions
 
POLY2 - Static variable in class ij.measure.Calibration
 
POLY2 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POLY3 - Static variable in class ij.measure.Calibration
 
POLY3 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POLY4 - Static variable in class ij.measure.Calibration
 
POLY4 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POLY5 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POLY6 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POLY7 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POLY8 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POLYGON - Static variable in class ij.gui.Roi
 
POLYGON - Static variable in class ij.gui.Toolbar
 
PolygonFiller - Class in ij.process
This class fills polygons using the scan-line filling algorithm described at "http://www.cs.rit.edu/~icss571/filling/".
PolygonFiller() - Constructor for class ij.process.PolygonFiller
Constructs a PolygonFiller.
PolygonFiller(float[], float[], int, double, double) - Constructor for class ij.process.PolygonFiller
Constructs a PolygonFiller using the specified polygon with floating-point coordinates.
PolygonFiller(int[], int[], int) - Constructor for class ij.process.PolygonFiller
Constructs a PolygonFiller using the specified polygon with integer coordinates.
PolygonRoi - Class in ij.gui
This class represents a polygon region of interest or polyline of interest.
PolygonRoi(float[], float[], int) - Constructor for class ij.gui.PolygonRoi
Creates a new polygon or polyline ROI from float x and y arrays.
PolygonRoi(float[], float[], int, int) - Constructor for class ij.gui.PolygonRoi
Creates a new polygon or polyline ROI from float x and y arrays.
PolygonRoi(int[], int[], int, int) - Constructor for class ij.gui.PolygonRoi
Creates a new polygon or polyline ROI from x and y coordinate arrays.
PolygonRoi(int[], int[], int, ImagePlus, int) - Constructor for class ij.gui.PolygonRoi
Deprecated. 
PolygonRoi(int, int, ImagePlus) - Constructor for class ij.gui.PolygonRoi
Starts the process of creating a new user-generated polygon or polyline ROI.
PolygonRoi(FloatPolygon, int) - Constructor for class ij.gui.PolygonRoi
Creates a new polygon or polyline ROI from a FloatPolygon.
PolygonRoi(Polygon, int) - Constructor for class ij.gui.PolygonRoi
Creates a new polygon or polyline ROI from a Polygon.
POLYLINE - Static variable in class ij.gui.Roi
 
POLYLINE - Static variable in class ij.gui.Toolbar
 
populateList(String) - Method in class ij.macro.FunctionFinder
 
populateList(String) - Method in class ij.plugin.CommandFinder
 
POSITION - Static variable in class ij.io.RoiDecoder
 
positionWindow() - Method in class ij.plugin.frame.Editor
 
POW - Static variable in interface ij.macro.MacroConstants
 
POWER - Static variable in class ij.measure.Calibration
 
POWER - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
POWER_REGRESSION - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
powerOf2Size() - Method in class ij.process.FHT
Returns true of this FHT contains a square image with a width that is a power of two.
powerSpectrumMean - Variable in class ij.process.FHT
Used by the FFT class.
precision - Static variable in class ij.plugin.filter.Analyzer
 
PREDEFINED_FUNCTION - Static variable in interface ij.macro.MacroConstants
 
PREDICTOR - Static variable in class ij.io.TiffDecoder
 
preferredLayoutSize(Container) - Method in class ij.gui.ImageLayout
Returns the preferred dimensions for this layout.
Prefs - Class in ij
This class contains the ImageJ preferences, which are loaded from the "IJ_Props.txt" and "IJ_Prefs.txt" files.
Prefs() - Constructor for class ij.Prefs
 
PREFS_NAME - Static variable in class ij.Prefs
 
previewLUT() - Method in class ij.plugin.CommandFinder
 
previewRunning(boolean) - Method in class ij.gui.GenericDialog
Used by PlugInFilterRunner to provide visable feedback whether preview is running or not by switching from "Preview" to "wait..."
previousRoi - Static variable in class ij.gui.Roi
Get using getPreviousRoi() and set using setPreviousRoi()
print(Graphics, PageFormat, int) - Method in class ij.plugin.filter.Printer
 
PRINT - Static variable in interface ij.macro.MacroConstants
 
Printer - Class in ij.plugin.filter
This plugin implements the File/Page Setup and File/Print commands.
Printer() - Constructor for class ij.plugin.filter.Printer
 
process(int, double) - Method in class ij.process.ShortProcessor
 
process(int, double) - Method in class ij.process.SignedShortProcessor
 
processStack - Variable in class ij.plugin.filter.ParticleAnalyzer
 
processWindowEvent(WindowEvent) - Method in class ij.plugin.frame.RoiManager
 
processWindowEvent(WindowEvent) - Method in class ij.text.TextWindow
 
profile - Variable in class ij.gui.ProfilePlot
 
ProfilePlot - Class in ij.gui
Creates a density profile plot of a rectangular selection or line selection.
ProfilePlot() - Constructor for class ij.gui.ProfilePlot
 
ProfilePlot(ImagePlus) - Constructor for class ij.gui.ProfilePlot
 
ProfilePlot(ImagePlus, boolean) - Constructor for class ij.gui.ProfilePlot
 
Profiler - Class in ij.plugin
Implements the Analyze/Plot Profile and Edit/Options/Profile Plot Options commands.
Profiler() - Constructor for class ij.plugin.Profiler
 
Program - Class in ij.macro
An object of this type is a tokenized macro file and the associated symbol table.
Program() - Constructor for class ij.macro.Program
 
ProgressBar - Class in ij.gui
This is the progress bar that is displayed in the lower right hand corner of the ImageJ window.
ProgressBar(int, int) - Constructor for class ij.gui.ProgressBar
This constructor is called once by ImageJ at startup.
Projector - Class in ij.plugin
This plugin creates a sequence of projections of a rotating volume (stack of slices) onto a plane using nearest-point (surface), brightest-point, or mean-value projection or a weighted combination of nearest- point projection with either of the other two methods (partial opacity).
Projector() - Constructor for class ij.plugin.Projector
 
PROMPT_BEFORE_DELETING - Static variable in class ij.io.RoiDecoder
 
promptBeforeDeleting() - Method in class ij.gui.PointRoi
 
promptBeforeDeleting(Boolean) - Method in class ij.gui.PointRoi
 
properties - Variable in class ij.io.FileInfo
 
PROPERTY - Static variable in interface ij.macro.MacroConstants
 
PROPERTY_KEY - Static variable in class ij.gui.Plot
key in ImagePlus properties to access the plot behind an ImagePlus
PROPS_NAME - Static variable in class ij.Prefs
 
protectStatusBar(boolean) - Static method in class ij.IJ
 
ProxySettings - Class in ij.plugin
This plugin implements the Plugins/Utilities/Proxy Settings command.
ProxySettings() - Constructor for class ij.plugin.ProxySettings
 
PUT_PIXEL - Static variable in interface ij.macro.MacroConstants
 
putBehind() - Static method in class ij.WindowManager
Activates the next image window on the window list.
putColumn(int, int, float[], int) - Method in class ij.process.ImageProcessor
Inserts the pixels contained in 'data' into a column starting at (x,y).
putColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
Inserts the pixels contained in 'data' into a column starting at (x,y).
putColumn(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
 
putPixel(int, int, int) - Method in class ij.process.ByteProcessor
Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.ColorProcessor
Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.FloatProcessor
Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.ImageProcessor
Stores the specified value at (x,y).
putPixel(int, int, int) - Method in class ij.process.ShortProcessor
Stores the specified value at (x,y).
putPixel(int, int, int[]) - Method in class ij.process.ColorProcessor
Sets a pixel in the image using a 3 element (R, G and B) int array of samples.
putPixel(int, int, int[]) - Method in class ij.process.FloatProcessor
Sets a pixel in the image using a one element int array.
putPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
Sets a pixel in the image using an int array of samples.
putPixelValue(int, int, double) - Method in class ij.process.ByteProcessor
Stores the specified real value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ColorProcessor
Stores the specified real grayscale value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.FloatProcessor
Stores the specified real value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ImageProcessor
Stores the specified value at (x,y).
putPixelValue(int, int, double) - Method in class ij.process.ShortProcessor
Stores the specified real value at (x,y).
putRow(int, int, float[], int) - Method in class ij.process.ImageProcessor
Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
putRow(int, int, int[], int) - Method in class ij.process.ImageProcessor
Inserts the pixels contained in 'data' into a horizontal line starting at (x,y).
putRow(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
 
putValue(int, float) - Method in class ij.util.ArrayUtil
put a value to a index
pw - Variable in class ij.process.ImageStatistics
 

Q

quadrantSwapNeeded - Variable in class ij.process.FHT
Used by the FFT class.
quit() - Method in class ij.ImageJ
Called by ImageJ when the user selects Quit.
quitting() - Method in class ij.ImageJ
Returns true if ImageJ is exiting.
quittingViaMacro() - Method in class ij.ImageJ
Returns true if ImageJ is quitting as a result of a run("Quit") macro call.

R

radioButtonGroups - Variable in class ij.gui.GenericDialog
 
rand(int, int) - Method in class ij.plugin.filter.SaltAndPepper
 
RANDOM - Static variable in interface ij.macro.MacroConstants
 
RandomAccessStream - Class in ij.io
This class uses a memory cache to allow seeking within an InputStream.
RandomAccessStream(InputStream) - Constructor for class ij.io.RandomAccessStream
Constructs a RandomAccessStream from an InputStream.
RandomAccessStream(RandomAccessFile) - Constructor for class ij.io.RandomAccessStream
Constructs a RandomAccessStream from an RandomAccessFile.
rank(double[]) - Static method in class ij.util.Tools
Returns a sorted list of indices of the specified double array.
rank(ImageProcessor, double, int) - Method in class ij.plugin.filter.RankFilters
Filters an image by any method except 'despecle', 'remove outliers', or top-hat
rank(ImageProcessor, double, int, int, float) - Method in class ij.plugin.filter.RankFilters
Filters an image by any method except 'despecle' and top-hat (for 'despeckle', use 'median' and radius=1)
rank(ImageProcessor, double, int, int, float, boolean, boolean) - Method in class ij.plugin.filter.RankFilters
Filters an image by any method except 'despecle' (for 'despeckle', use 'median' and radius=1)
rank(String[]) - Static method in class ij.util.Tools
Returns a sorted list of indices of the specified String array.
RankFilters - Class in ij.plugin.filter
This plugin implements the Mean, Minimum, Maximum, Variance, Median, Remove Outliers, Remove NaNs and Despeckle commands.
RankFilters() - Constructor for class ij.plugin.filter.RankFilters
 
raster - Variable in class ij.process.ImageProcessor
 
Raw - Class in ij.plugin
This plugin implements the File/Import/Raw command.
Raw() - Constructor for class ij.plugin.Raw
 
RAW - Static variable in class ij.io.FileInfo
 
RAW - Static variable in class ij.io.Opener
 
RAW_INTEGRATED_DENSITY - Static variable in class ij.measure.ResultsTable
 
RAW_VALUES - Static variable in class ij.plugin.frame.ThresholdAdjuster
 
rc2DFHT(float[], boolean, int) - Method in class ij.process.FHT
Performs a 2D FHT (Fast Hartley Transform).
read() - Method in class ij.io.RandomAccessStream
 
read(byte[], int, int) - Method in class ij.io.RandomAccessStream
 
readDouble() - Method in class ij.io.RandomAccessStream
 
readFloat() - Method in class ij.io.RandomAccessStream
 
readFully(byte[]) - Method in class ij.io.RandomAccessStream
 
readFully(byte[], int) - Method in class ij.io.RandomAccessStream
 
readInt() - Method in class ij.io.RandomAccessStream
 
readLong() - Method in class ij.io.RandomAccessStream
 
readPixels(InputStream) - Method in class ij.io.ImageReader
Reads the image from the InputStream and returns the pixel array (byte, short, int or float).
readPixels(InputStream, long) - Method in class ij.io.ImageReader
Skips the specified number of bytes, then reads an image and returns the pixel array (byte, short, int or float).
readPixels(String) - Method in class ij.io.ImageReader
Reads the image from a URL and returns the pixel array (byte, short, int or float).
readShort() - Method in class ij.io.RandomAccessStream
 
RecentOpener - Class in ij
Opens, in a separate thread, files selected from the File/Open Recent submenu.
record - Static variable in class ij.plugin.frame.Recorder
This variable is true if the recorder is running.
record() - Static method in class ij.process.ImageConverter
 
record(ImagePlus, int, int, int, int) - Static method in class ij.plugin.Scaler
 
record(String) - Static method in class ij.plugin.frame.Recorder
 
record(String, double, double) - Static method in class ij.plugin.frame.Recorder
 
record(String, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, int, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, int, int, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, int, int, int, int, double) - Static method in class ij.plugin.frame.Recorder
 
record(String, int, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, int, int, String) - Static method in class ij.plugin.frame.Recorder
 
record(String, String) - Static method in class ij.plugin.frame.Recorder
 
record(String, String, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, String, int, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, String, String) - Static method in class ij.plugin.frame.Recorder
 
record(String, String, String, int, int, int, int, int) - Static method in class ij.plugin.frame.Recorder
 
record(String, String, String, String) - Static method in class ij.plugin.frame.Recorder
 
RECORD_STARTS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Record starting coordinates so outline can be recreated later using doWand(x,y).
recordCall(String) - Static method in class ij.plugin.frame.Recorder
 
recordCall(String, boolean) - Static method in class ij.plugin.frame.Recorder
 
recordCall(String, String) - Static method in class ij.plugin.frame.Recorder
 
Recorder - Class in ij.plugin.frame
This is ImageJ's macro recorder.
Recorder() - Constructor for class ij.plugin.frame.Recorder
 
Recorder(boolean) - Constructor for class ij.plugin.frame.Recorder
 
recordInMacros - Static variable in class ij.plugin.frame.Recorder
Set this variable true to allow recording within IJ.run() calls.
recordOpen(String) - Static method in class ij.plugin.frame.Recorder
 
recordOption(String) - Static method in class ij.plugin.frame.Recorder
 
recordOption(String, String) - Static method in class ij.plugin.frame.Recorder
 
recordPath(String, String) - Static method in class ij.plugin.frame.Recorder
 
recordRoi(Roi) - Static method in class ij.plugin.frame.Recorder
 
recordRoi(Polygon, int) - Static method in class ij.plugin.frame.Recorder
 
recordScriptRoi(Polygon, int) - Static method in class ij.plugin.frame.Recorder
 
recordSetMinAndMax(double, double) - Static method in class ij.plugin.frame.ContrastAdjuster
 
recordStarts - Variable in class ij.plugin.filter.ParticleAnalyzer
 
recordString(String) - Static method in class ij.plugin.frame.Recorder
 
RECT - Static variable in interface ij.measure.Measurements
 
RECT_ROI - Static variable in class ij.gui.Toolbar
 
RECTANGLE - Static variable in class ij.gui.Roi
 
RECTANGLE - Static variable in class ij.gui.Toolbar
 
RectToolOptions - Class in ij.plugin
This plugin implements the rounded rectangle tool dialog box.
RectToolOptions() - Constructor for class ij.plugin.RectToolOptions
 
red - Variable in class ij.plugin.filter.RGBStackSplitter
 
RED_LUT - Static variable in class ij.process.ImageProcessor
 
redirectErrorMessages() - Static method in class ij.IJ
Causes IJ.error() output to be temporarily redirected to the "Log" window.
redirectErrorMessages(boolean) - Static method in class ij.IJ
Set 'true' and IJ.error() output will be temporarily redirected to the "Log" window.
redirectingErrorMessages() - Static method in class ij.IJ
Returns the state of the 'redirectErrorMessages' flag, which is set by File/Import/Image Sequence.
redirectSystem() - Static method in class ij.io.LogStream
Redirects all output sent to System.out and System.err to ImageJ's log console using the default prefixes.
redirectSystem(boolean) - Static method in class ij.io.LogStream
Redirects all output sent to System.out and System.err to ImageJ's log console using the default prefixes.
redirectSystemErr(String) - Static method in class ij.io.LogStream
Redirects all output sent to System.err to ImageJ's log console.
redirectSystemOut(String) - Static method in class ij.io.LogStream
Redirects all output sent to System.out to ImageJ's log console.
redrawGrid() - Method in class ij.gui.Plot
 
reds - Variable in class ij.io.FileInfo
 
reduce(int) - Method in class ij.plugin.ListVirtualStack
 
reduce(int) - Method in class ij.VirtualStack
Reduces the number of slices in this stack by a factor.
reduce(ImagePlus) - Method in class ij.plugin.HyperStackReducer
 
reduceHyperstack(ImagePlus, int, boolean) - Method in class ij.plugin.StackReducer
 
reduceStack(ImagePlus, int) - Method in class ij.plugin.StackReducer
 
reflexAngle - Static variable in class ij.Prefs
Angle tool measures reflex angle
register(Class) - Static method in class ij.IJ
Obsolete
register(Class) - Method in class ij.ImageJ
Adds the specified class to a Vector to keep it from being garbage collected, causing static fields to be reset.
registerExtensions(MacroExtension) - Static method in class ij.macro.Functions
 
REINITIALIZATION_FAILURE - Static variable in class ij.measure.Minimizer
Status returned: Could not reinitialize the simplex because all attempts to find restarting parameters resulted in the target function returning NaN.
remove() - Method in class ij.gui.Line.PointIterator
 
remove(int) - Method in class ij.gui.Overlay
Removes the ROI with the specified index from this Overlay.
remove(Roi) - Method in class ij.gui.Overlay
Removes the specified ROI from this Overlay.
remove(String) - Method in class ij.gui.Overlay
Removes all ROIs that have the specified name.
REMOVE_NAN - Static variable in class ij.plugin.filter.RankFilters
 
removeAdjustmentListener(AdjustmentListener) - Method in class ij.gui.ScrollbarWithLabel
 
removeBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
 
removeCommandListener(CommandListener) - Static method in class ij.Executer
Removes the specified command listener.
removeEventListener(IJEventListener) - Static method in class ij.IJ
 
removeImageListener(ImageListener) - Static method in class ij.ImagePlus
 
removeKeyListener(KeyListener) - Method in class ij.gui.ScrollbarWithLabel
 
removeLast(int) - Method in class ij.util.FloatArray
Deletes the last n element from this FloatArray.
removeLayoutComponent(Component) - Method in class ij.gui.ImageLayout
Not used by this class.
removeMacroTools() - Static method in class ij.gui.Toolbar
 
removeNaNs() - Method in class ij.gui.Plot
Removes NaNs from the xValues and yValues arrays of all plot objects.
removeRoiListener(RoiListener) - Static method in class ij.gui.Roi
 
removeScale() - Method in class ij.ImagePlus
Removes the spatial scaling of this image.
removeSplineFit() - Method in class ij.gui.PolygonRoi
 
removeWindow(Frame) - Static method in class ij.WindowManager
Removes the specified Frame from the Window menu.
removeWindow(Window) - Static method in class ij.WindowManager
Removes the specified window from the Window menu.
rename(int, String) - Method in class ij.plugin.frame.RoiManager
 
rename(String) - Method in class ij.text.TextWindow
 
RENAME - Static variable in interface ij.macro.MacroConstants
 
renameColumn(String, String) - Method in class ij.measure.ResultsTable
Changes the name of a column.
renameResults(String) - Static method in class ij.IJ
Renames a results window.
renameResults(String, String) - Static method in class ij.IJ
Changes the name of a table window from 'oldTitle' to 'newTitle'.
RenyiEntropy - ij.process.AutoThresholder.Method
 
repaint() - Method in class ij.gui.GenericDialog
 
repaintImageWindows() - Static method in class ij.WindowManager
Repaints all open image windows.
repaintOverlay() - Method in class ij.gui.ImageCanvas
 
repaintTool(int) - Static method in class ij.gui.Toolbar
 
repaintWindow() - Method in class ij.ImagePlus
Calls draw to draw the image and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.
replace(int, String, double[], double[]) - Method in class ij.gui.Plot
Replaces the specified plot object (curve or set of points).
REPLACE - Static variable in interface ij.macro.MacroConstants
 
requireControlKey - Static variable in class ij.Prefs
Require control or command key for keybaord shortcuts.
REQUIRES - Static variable in interface ij.macro.MacroConstants
 
resampleArray(double[], int) - Static method in class ij.util.Tools
Returns an array linearly resampled to a different length.
reset() - Method in class ij.CompositeImage
 
reset() - Method in class ij.measure.ResultsTable
 
reset() - Method in class ij.plugin.frame.RoiManager
Clears this RoiManager so that it contains no ROIs.
reset() - Method in class ij.process.ByteProcessor
Reset the image from snapshot.
reset() - Method in class ij.process.ColorProcessor
 
reset() - Method in class ij.process.FloatProcessor
 
reset() - Method in class ij.process.ImageProcessor
Restores the pixel data from the snapshot (undo) buffer.
reset() - Method in class ij.process.ShortProcessor
 
reset() - Static method in class ij.Undo
 
reset(ImageProcessor) - Method in class ij.process.ByteProcessor
Restore pixels that are within roi but not part of mask.
reset(ImageProcessor) - Method in class ij.process.ColorProcessor
 
reset(ImageProcessor) - Method in class ij.process.FloatProcessor
 
reset(ImageProcessor) - Method in class ij.process.ImageProcessor
Restores pixels from the snapshot buffer that are within the rectangular roi but not part of the mask.
reset(ImageProcessor) - Method in class ij.process.ShortProcessor
 
RESET - Static variable in interface ij.macro.MacroConstants
 
RESET_MIN_MAX - Static variable in interface ij.macro.MacroConstants
 
RESET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
 
resetBinaryThreshold() - Method in class ij.process.ImageProcessor
Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE.
resetBoundingRect() - Method in class ij.gui.PolygonRoi
 
resetClassLoader() - Static method in class ij.IJ
 
resetClipboard() - Static method in class ij.ImagePlus
Clears the internal clipboard.
resetCommandOptions() - Static method in class ij.plugin.frame.Recorder
Used by GenericDialog.notifyListeners() to clear the command options.
resetCounter - Variable in class ij.plugin.filter.ParticleAnalyzer
 
resetCounter() - Static method in class ij.plugin.filter.Analyzer
Sets the measurement counter to zero.
resetCounters() - Method in class ij.gui.GenericDialog
Reset the counters before reading the dialog parameters
resetCounters() - Method in class ij.gui.PointRoi
 
resetDefaultHandleSize() - Static method in class ij.gui.Roi
 
resetDisplayRange() - Method in class ij.CompositeImage
 
resetDisplayRange() - Method in class ij.ImagePlus
 
resetDisplayRanges() - Method in class ij.CompositeImage
 
resetDoubleBuffer() - Method in class ij.gui.ImageCanvas
 
resetEscape() - Static method in class ij.IJ
This method sets the Esc key to the "up" position.
resetMinAndMax() - Static method in class ij.IJ
Resets the minimum and maximum displayed pixel values of the current image to be the same as the min and max pixel values.
resetMinAndMax() - Method in class ij.process.ByteProcessor
Resets this image's LUT.
resetMinAndMax() - Method in class ij.process.FloatProcessor
Recalculates the min and max values used to scale pixel values to 0-255 for display.
resetMinAndMax() - Method in class ij.process.ImageProcessor
For short and float images, recalculates the min and max image values needed to correctly display the image.
resetMinAndMax() - Method in class ij.process.IntProcessor
 
resetMinAndMax() - Method in class ij.process.ShortProcessor
Recalculates the min and max values used to scale pixel values to 0-255 for display.
resetMinAndMax(ImagePlus) - Static method in class ij.IJ
Resets the minimum and maximum displayed pixel values of the specified image to be the same as the min and max pixel values.
resetMultiMeasureResults() - Static method in class ij.plugin.frame.RoiManager
 
resetOutOfRoi(ImageProcessor, int) - Static method in class ij.plugin.filter.GaussianBlur
Set the processed pixels above and below the roi rectangle back to their previous value (i.e., snapshot buffer).
resetPreferences() - Static method in class ij.Prefs
Delete the preferences file when ImageJ quits.
resetRoi() - Method in class ij.ImagePlus
Deletes the current region of interest.
resetRoi() - Method in class ij.process.ImageProcessor
Sets the ROI (Region of Interest) and clipping rectangle to the entire image.
resetSelection() - Method in class ij.text.TextPanel
Clears the selection, if any.
resetStack() - Method in class ij.ImagePlus
 
resetThreshold() - Static method in class ij.IJ
Disables thresholding on the current image.
resetThreshold() - Method in class ij.process.ImageProcessor
Disables thresholding.
resetThreshold(ImagePlus) - Static method in class ij.IJ
Disables thresholding on the specified image.
resize() - Method in class ij.ImageJ
 
resize(int) - Method in class ij.process.ImageProcessor
Returns a new ImageProcessor containing a scaled copy of this image or ROI, with the aspect ratio maintained.
resize(int, int) - Method in class ij.process.ByteProcessor
Creates a new ByteProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.ColorProcessor
Creates a new ColorProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.FloatProcessor
Creates a new FloatProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.ImageProcessor
Returns a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int, int) - Method in class ij.process.ShortProcessor
Creates a new ShortProcessor containing a scaled copy of this image or selection.
resize(int, int) - Method in class ij.process.StackProcessor
Creates a new stack with dimensions 'newWidth' x 'newHeight'.
resize(int, int, boolean) - Method in class ij.process.ImageProcessor
Returns a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int, int, boolean) - Method in class ij.process.StackProcessor
 
resize(int, int, int, String) - Method in class ij.ImagePlus
Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
resize(int, int, String) - Method in class ij.ImagePlus
Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
resize(ImagePlus, int, int, int, String) - Static method in class ij.plugin.Scaler
Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
resizeLinearly(int, int) - Method in class ij.process.ImageProcessor
Use linear interpolation to resize images that have a width or height of one.
Resizer - Class in ij.plugin
This plugin implements the Edit/Crop and Image/Adjust/Size commands.
Resizer() - Constructor for class ij.plugin.Resizer
 
RESIZING - Static variable in class ij.gui.Roi
 
reslice(ImagePlus) - Method in class ij.plugin.Slicer
 
RESOLUTION_UNIT - Static variable in class ij.io.TiffDecoder
 
RESTORE_PREVIOUS_TOOL - Static variable in interface ij.macro.MacroConstants
 
RESTORE_SETTINGS - Static variable in interface ij.macro.MacroConstants
 
restoreCentered(boolean) - Static method in class ij.plugin.frame.RoiManager
 
restorePlotObjects() - Method in class ij.gui.Plot
Restores the plot contents (not including axis formats etc) from the snapshot previously created by savePlotObjects().
restorePlotProperties() - Method in class ij.gui.Plot
Restores the plot properties (formatting, range etc., not PlotObjects such as data and corresponding curves etc.) from a snapshot previously created by savePlotPlotProperties.
restorePreviousTool() - Method in class ij.gui.Toolbar
 
restoreRoi() - Method in class ij.ImagePlus
 
restoreTools() - Static method in class ij.gui.Toolbar
 
ResultsTable - Class in ij.measure
This is a table for storing measurement results and strings as columns of values.
ResultsTable() - Constructor for class ij.measure.ResultsTable
Constructs an empty ResultsTable with the counter=0, no columns and the precision set to 3 or the "Decimal places" value in Analyze/Set Measurements if that value is higher than 3.
ResultsTable(Integer) - Constructor for class ij.measure.ResultsTable
Constructs a ResultsTable with 'nRows' rows.
ResultsTableMacros - Class in ij.measure
This class implements the Apply Macro command in tables.
ResultsTableMacros(ResultsTable) - Constructor for class ij.measure.ResultsTableMacros
 
RETURN - Static variable in interface ij.macro.MacroConstants
 
reverseNextPreviousOrder - Static variable in class ij.Prefs
Reverse channel-slice-frame priority used by Next Slice and Previous Slice commands.
revert() - Method in class ij.ImagePlus
Implements the File/Revert command.
revert() - Method in class ij.plugin.frame.Editor
 
revertSystem() - Static method in class ij.io.LogStream
Use this method to revert both System.out and System.err to their original output streams.
revertSystemErr() - Static method in class ij.io.LogStream
Use this method to revertSystem.err to the original output stream.
revertSystemOut() - Static method in class ij.io.LogStream
Use this method to revertSystem.out to the original output stream.
revertToSaved(ImagePlus) - Method in class ij.io.FileOpener
Restores the original version of the specified image.
rgb - Variable in class ij.gui.HistogramWindow
 
rgb - Variable in class ij.process.FHT
Used by the FFT class.
RGB - Static variable in class ij.gui.NewImage
 
RGB - Static variable in class ij.io.FileInfo
24-bit interleaved RGB.
RGB_DILATE - Static variable in class ij.process.ColorProcessor
 
RGB_ERODE - Static variable in class ij.process.ColorProcessor
 
RGB_FIND_EDGES - Static variable in class ij.process.ColorProcessor
 
RGB_MAX - Static variable in class ij.process.ColorProcessor
 
RGB_MEDIAN - Static variable in class ij.process.ColorProcessor
 
RGB_MIN - Static variable in class ij.process.ColorProcessor
 
RGB_NOISE - Static variable in class ij.process.ColorProcessor
 
RGB_PLANAR - Static variable in class ij.io.FileInfo
24-bit planer RGB.
RGB_RESIZE - Static variable in class ij.process.ColorProcessor
 
RGB_ROTATE - Static variable in class ij.process.ColorProcessor
 
RGB_SCALE - Static variable in class ij.process.ColorProcessor
 
RGB_THRESHOLD - Static variable in class ij.process.ColorProcessor
 
RGB_TRANSLATE - Static variable in class ij.process.ColorProcessor
 
RGB48 - Static variable in class ij.io.FileInfo
48-bit interleaved RGB.
RGB48_PLANAR - Static variable in class ij.io.FileInfo
48-bit planar RGB.
RGBStackConverter - Class in ij.plugin
Converts a 2 or 3 slice stack, or a hyperstack, to RGB.
RGBStackConverter() - Constructor for class ij.plugin.RGBStackConverter
 
RGBStackMerge - Class in ij.plugin
This plugin implements the Image/Color/Merge Channels command.
RGBStackMerge() - Constructor for class ij.plugin.RGBStackMerge
 
RGBStackSplitter - Class in ij.plugin.filter
Deprecated; replaced by ij.plugin.ChannelSplitter.
RGBStackSplitter() - Constructor for class ij.plugin.filter.RGBStackSplitter
 
RGBtoHSB(int[]) - Method in class ij.process.ColorSpaceConverter
 
RGBtoHSB(int, int, int) - Method in class ij.process.ColorSpaceConverter
 
RGBtoLab() - Static method in class ij.plugin.frame.ColorThresholder
Converts the current image from RGB to CIE L*a*b* and stores the results in the same RGB image R=L*, G=a*, B=b*.
RGBtoLAB(int) - Method in class ij.process.ColorSpaceConverter
 
RGBtoLAB(int[]) - Method in class ij.process.ColorSpaceConverter
 
RGBToLab(ImagePlus) - Method in class ij.process.ColorSpaceConverter
Converts an RGB image into a Lab stack.
RGBtoXYZ(int[]) - Method in class ij.process.ColorSpaceConverter
Convert RGB to XYZ
RGBtoXYZ(int, int, int) - Method in class ij.process.ColorSpaceConverter
Convert RGB to XYZ
RGBtoYUV() - Static method in class ij.plugin.frame.ColorThresholder
Converts the current image from RGB to YUV and stores the results in the same RGB image R=Y, G=U, B=V.
rh - Variable in class ij.process.ImageStatistics
 
RIGHT - Static variable in class ij.gui.Plot
Text justification.
RIGHT - Static variable in class ij.gui.TextRoi
 
RIGHT - Static variable in class ij.io.RoiDecoder
 
RIGHT_JUSTIFY - Static variable in class ij.process.ImageProcessor
Right justify text.
RIGHT_MARGIN - Static variable in class ij.gui.Plot
Deprecated.
Not a fixed value any more, use getDrawingFrame() to get the drawing area
rLUT1 - Variable in class ij.process.ImageProcessor
 
rLUT2 - Variable in class ij.process.ImageProcessor
 
rnd - Static variable in class ij.process.ImageProcessor
 
RODBARD - Static variable in class ij.measure.Calibration
 
RODBARD - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
RODBARD2 - Static variable in class ij.measure.Calibration
 
RODBARD2 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
roi - Variable in class ij.ImagePlus
 
roi - Variable in class ij.io.FileInfo
 
Roi - Class in ij.gui
A rectangular region of interest and superclass for the other ROI classes.
Roi(double, double, double, double) - Constructor for class ij.gui.Roi
Creates a rectangular ROI using double arguments.
Roi(double, double, double, double, int) - Constructor for class ij.gui.Roi
Creates a rounded rectangular ROI using double arguments.
Roi(int, int, int, int) - Constructor for class ij.gui.Roi
Creates a rectangular ROI.
Roi(int, int, int, int, int) - Constructor for class ij.gui.Roi
Creates a new rounded rectangular ROI.
Roi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Roi
Deprecated. 
Roi(int, int, ImagePlus) - Constructor for class ij.gui.Roi
Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
Roi(int, int, ImagePlus, int) - Constructor for class ij.gui.Roi
Starts the process of creating a user-defined rectangular Roi, where sx and sy are the starting screen coordinates.
Roi(Rectangle) - Constructor for class ij.gui.Roi
Creates a new rectangular Roi.
Roi(double, double, double, double) - Static method in class ij.IJ
Creates an Roi.
ROI - Static variable in class ij.io.Opener
 
ROI - Static variable in interface ij.macro.MacroConstants
 
ROI - Static variable in class ij.Undo
 
ROI_HEIGHT - Static variable in class ij.measure.ResultsTable
 
ROI_MANAGER - Static variable in interface ij.macro.MacroConstants
 
ROI_MANAGER2 - Static variable in interface ij.macro.MacroConstants
 
ROI_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
ROI_PROPS_LENGTH - Static variable in class ij.io.RoiDecoder
 
ROI_PROPS_OFFSET - Static variable in class ij.io.RoiDecoder
 
ROI_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter requires an ROI.
ROI_WIDTH - Static variable in class ij.measure.ResultsTable
 
ROI_X - Static variable in class ij.measure.ResultsTable
 
ROI_Y - Static variable in class ij.measure.ResultsTable
 
ROIColor - Static variable in class ij.gui.Roi
 
ROICOLOR - Static variable in class ij.Prefs
 
RoiDecoder - Class in ij.io
This class decodes an ImageJ .roi file.
RoiDecoder(byte[], String) - Constructor for class ij.io.RoiDecoder
Constructs an RoiDecoder using a byte array.
RoiDecoder(String) - Constructor for class ij.io.RoiDecoder
Constructs an RoiDecoder using a file path.
RoiDefaultsDialog - Class in ij.gui
This plugin implements the Edit/Options/Roi Defaults command.
RoiDefaultsDialog() - Constructor for class ij.gui.RoiDefaultsDialog
 
RoiEncoder - Class in ij.io
Saves an ROI to a file or stream.
RoiEncoder(OutputStream) - Constructor for class ij.io.RoiEncoder
Creates an RoiEncoder using the specified OutputStream.
RoiEncoder(String) - Constructor for class ij.io.RoiEncoder
Creates an RoiEncoder using the specified path.
RoiEnlarger - Class in ij.plugin
This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command.
RoiEnlarger() - Constructor for class ij.plugin.RoiEnlarger
 
roiHeight - Variable in class ij.process.ImageProcessor
 
roiHeight - Variable in class ij.process.ImageStatistics
 
RoiInterpolator - Class in ij.plugin
This class interpolates between ROIs in the ROI Manager.
RoiInterpolator() - Constructor for class ij.plugin.RoiInterpolator
 
RoiListener - Interface in ij.gui
Plugins that implement this interface are notified when an ROI is created, modified or deleted.
RoiManager - Class in ij.plugin.frame
This plugin implements the Analyze/Tools/ROI Manager command.
RoiManager() - Constructor for class ij.plugin.frame.RoiManager
Opens the "ROI Manager" window, or activates it if it is already open.
RoiManager(boolean) - Constructor for class ij.plugin.frame.RoiManager
Constructs an ROI Manager without displaying it.
roiManagerSelect(Roi, boolean) - Method in class ij.gui.ImageCanvas
 
roiModified(ImagePlus, int) - Method in class ij.gui.HistogramWindow
 
roiModified(ImagePlus, int) - Method in class ij.gui.PlotWindow
For live plots, update the plot if the ROI of the source image changes
roiModified(ImagePlus, int) - Method in interface ij.gui.RoiListener
 
roiModified(ImagePlus, int) - Method in class ij.plugin.EventListener
 
RoiProperties - Class in ij.gui
Displays a dialog that allows the user to specify ROI properties such as color and line width.
RoiProperties(String, Roi) - Constructor for class ij.gui.RoiProperties
Constructs a ColorChooser using the specified title and initial color.
RoiReader - Class in ij.plugin
Opens ImageJ, NIH Image and Scion Image for windows ROI outlines.
RoiReader() - Constructor for class ij.plugin.RoiReader
 
RoiRotationTool - Class in ij.plugin.tool
 
RoiRotationTool() - Constructor for class ij.plugin.tool.RoiRotationTool
 
RoiRotator - Class in ij.plugin
This plugin implements the Edit/Selection/Rotate command.
RoiRotator() - Constructor for class ij.plugin.RoiRotator
 
RoiScaler - Class in ij.plugin
This plugin implements the Edit/Selection/Scale command.
RoiScaler() - Constructor for class ij.plugin.RoiScaler
 
roiWidth - Variable in class ij.process.ImageProcessor
 
roiWidth - Variable in class ij.process.ImageStatistics
 
RoiWriter - Class in ij.plugin.filter
Saves the current ROI outline to a file.
RoiWriter() - Constructor for class ij.plugin.filter.RoiWriter
 
roiX - Variable in class ij.process.ImageProcessor
 
roiX - Variable in class ij.process.ImageStatistics
 
roiY - Variable in class ij.process.ImageProcessor
 
roiY - Variable in class ij.process.ImageStatistics
 
rollingBallBackground(ImageProcessor, double, boolean, boolean, boolean, boolean, boolean) - Method in class ij.plugin.filter.BackgroundSubtracter
Create or subtract a background, works for all image types.
rollingBallBrightnessBackground(ColorProcessor, double, boolean, boolean, boolean, boolean, boolean) - Method in class ij.plugin.filter.BackgroundSubtracter
Create or subtract a background, based on the brightness of an RGB image (keeping the hue of each pixel unchanged)
rotate(double) - Method in class ij.gui.ImageRoi
 
rotate(double) - Method in class ij.plugin.frame.RoiManager
 
rotate(double) - Method in class ij.process.ByteProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ColorProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.FloatProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ImageProcessor
Rotates the image or selection 'angle' degrees clockwise.
rotate(double) - Method in class ij.process.ShortProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(double, double, double) - Method in class ij.gui.Overlay
Returns a rotated version of this Overlay.
rotate(double, double, double) - Method in class ij.plugin.frame.RoiManager
 
rotate(Roi, double) - Static method in class ij.plugin.RoiRotator
 
rotate(Roi, double, double, double) - Static method in class ij.plugin.RoiRotator
 
ROTATED_RECT - Static variable in class ij.io.RoiDecoder
 
ROTATED_RECT_ROI - Static variable in class ij.gui.Toolbar
 
RotatedRectRoi - Class in ij.gui
This class implements the rotated rectangle selection tool.
RotatedRectRoi(double, double, double, double, double) - Constructor for class ij.gui.RotatedRectRoi
 
RotatedRectRoi(int, int, ImagePlus) - Constructor for class ij.gui.RotatedRectRoi
 
rotateLeft() - Method in class ij.process.ImageProcessor
Rotates the entire image 90 degrees counter-clockwise.
rotateLeft() - Method in class ij.process.StackProcessor
 
rotateLine(ImagePlus, int) - Method in class ij.plugin.Straightener
 
rotateRight() - Method in class ij.process.ImageProcessor
Rotates the entire image 90 degrees clockwise.
rotateRight() - Method in class ij.process.StackProcessor
 
rotateYZ - Static variable in class ij.Prefs
Rotate YZ orthogonal views 90 degrees
Rotator - Class in ij.plugin.filter
This plugin implements the Image/Rotate/Arbitrarily command.
Rotator() - Constructor for class ij.plugin.filter.Rotator
 
ROUND - Static variable in interface ij.macro.MacroConstants
 
ROUNDED_RECT_ARC_SIZE - Static variable in class ij.io.RoiDecoder
 
ROUNDED_RECT_ROI - Static variable in class ij.gui.Toolbar
 
ROUNDNESS - Static variable in class ij.measure.ResultsTable
 
rowIndex(int) - Method in class ij.text.TextPanel
Converts a y coordinate in pixels into a row index.
ROWS_PER_STRIP - Static variable in class ij.io.TiffDecoder
 
rowsPerStrip - Variable in class ij.io.FileInfo
 
rt - Variable in class ij.plugin.filter.ParticleAnalyzer
 
run() - Method in class ij.Executer
 
run() - Method in class ij.gui.HistogramWindow
 
run() - Method in class ij.gui.PlotWindow
 
run() - Method in class ij.gui.StackWindow
 
run() - Method in class ij.ImageJ
Quit using a separate thread, hopefully avoiding thread deadlocks.
run() - Method in class ij.macro.MacroRunner
Used to run the macro code in 'macro' on a separate thread.
run() - Method in class ij.macro.StartupRunner
 
run() - Method in class ij.measure.ResultsTableMacros
 
run() - Method in class ij.plugin.BatchProcessor
 
run() - Method in class ij.plugin.Concatenator
Displays a dialog requiring user to choose images and returns ImagePlus of concatenated images.
run() - Method in class ij.plugin.DragAndDrop
 
run() - Method in class ij.plugin.filter.PlugInFilterRunner
The dispatcher for the background threads
run() - Method in class ij.plugin.frame.ColorThresholder
 
run() - Method in class ij.plugin.frame.ContrastAdjuster
 
run() - Method in class ij.plugin.frame.Editor
Downloads BeanShell or Jython interpreter using a separate thread.
run() - Method in class ij.plugin.frame.LineWidthAdjuster
 
run() - Method in class ij.plugin.frame.ThresholdAdjuster
 
run() - Method in class ij.plugin.JavaScriptEvaluator
 
run() - Method in class ij.plugin.Orthogonal_Views
 
run() - Method in class ij.plugin.tool.BrushTool
 
run() - Method in class ij.plugin.tool.OverlayBrushTool
 
run() - Method in class ij.RecentOpener
Open the file and move the path to top of the submenu.
run() - Method in class ij.text.TextPanel
For better performance, open double-clicked files on separate thread instead of on event dispatch thread.
run(boolean) - Method in class ij.macro.StartupRunner
Runs the RunAtStartup and AutoRun macros, on the current thread if 'batchMode' true, otherwise on a separate thread.
run(int) - Method in class ij.macro.Interpreter
Runs an existing macro starting at the specified program counter location.
run(ImagePlus) - Method in class ij.plugin.Duplicator
Returns a copy of the image, stack or hyperstack contained in the specified ImagePlus.
run(ImagePlus) - Static 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.
run(ImagePlus[]) - Static method in class ij.plugin.Concatenator
Concatenates two or more images, stacks or hyperstacks.
run(ImagePlus[]) - Static method in class ij.plugin.ImagesToStack
Converts the images in 'images' to a stack, using the default settings ("copy center" and "titles as labels").
run(ImagePlus, int[]) - Static method in class ij.plugin.ChannelArranger
Changes the order of the channels in a hyperstack.
run(ImagePlus, int, int) - Method in class ij.plugin.Duplicator
Returns a new stack containing a subrange of the specified stack.
run(ImagePlus, int, int, int, int, int, int) - Method in class ij.plugin.Duplicator
Returns a new hyperstack containing a possibly reduced version of the input image.
run(ImagePlus, Roi[]) - Method in class ij.process.BinaryInterpolator
 
run(ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
Concatenates two images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
Concatenates three images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
Concatenates four images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus, ImagePlus, ImagePlus) - Static method in class ij.plugin.Concatenator
Concatenates five images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, String) - Static method in class ij.plugin.ImageCalculator
Performs arithmetic options on two images and returns the result, where 'operation' ("add","subtract", "multiply","divide", "and", "or", "xor", "min", "max", "average", "difference" or "copy") specifies the operation.
run(ImagePlus, String) - Static method in class ij.plugin.SubstackMaker
Extracts selected slices from a stack to make a new substack.
run(ImagePlus, String) - Static method in class ij.plugin.ZProjector
Performs projection on the entire stack using the specified method and returns the result, where 'method' is "avg", "min", "max", "sum", "sd" or "median".
run(ImagePlus, String, int, int) - Static method in class ij.plugin.ZProjector
Performs projection using the specified method and stack range, and returns the result, where 'method' is "avg", "min", "max", "sum", "sd" or "median".
run(ImagePlus, String, String) - Static method in class ij.IJ
Runs an ImageJ command using the specified image and options.
run(ImageStack) - Method in class ij.process.BinaryInterpolator
 
run(Interpreter, String, String) - Static method in class ij.IJ
The macro interpreter uses this method to run commands.
run(Program) - Method in class ij.macro.Interpreter
Interprets the specified tokenized macro file starting at location 0.
run(Program, int, String) - Method in class ij.macro.MacroRunner
Runs a tokenized macro on the current thread.
run(ResultsTable) - Method in class ij.plugin.Distribution
 
run(ImageProcessor) - Method in class ij.plugin.filter.Analyzer
 
run(ImageProcessor) - Method in class ij.plugin.filter.AVI_Writer
Asks for the compression type and filename; then saves as AVI file
run(ImageProcessor) - Method in class ij.plugin.filter.BackgroundSubtracter
Background for any image type
run(ImageProcessor) - Method in class ij.plugin.filter.Benchmark
 
run(ImageProcessor) - Method in class ij.plugin.filter.Binary
 
run(ImageProcessor) - Method in class ij.plugin.filter.Calibrator
 
run(ImageProcessor) - Method in class ij.plugin.filter.Convolver
 
run(ImageProcessor) - Method in class ij.plugin.filter.Duplicater
Deprecated.
 
run(ImageProcessor) - Method in class ij.plugin.filter.EDM
Called by the PlugInFilterRunner to process the image or one frame of a stack
run(ImageProcessor) - Method in class ij.plugin.filter.FFTCustomFilter
 
run(ImageProcessor) - Method in class ij.plugin.filter.FFTFilter
 
run(ImageProcessor) - Method in class ij.plugin.filter.Filler
 
run(ImageProcessor) - Method in class ij.plugin.filter.Filters
 
run(ImageProcessor) - Method in class ij.plugin.filter.FractalBoxCounter
 
run(ImageProcessor) - Method in class ij.plugin.filter.GaussianBlur
This method is invoked for each slice during execution
run(ImageProcessor) - Method in class ij.plugin.filter.ImageMath
 
run(ImageProcessor) - Method in class ij.plugin.filter.ImageProperties
 
run(ImageProcessor) - Method in class ij.plugin.filter.Info
Deprecated.
 
run(ImageProcessor) - Method in class ij.plugin.filter.LineGraphAnalyzer
 
run(ImageProcessor) - Method in class ij.plugin.filter.LutApplier
 
run(ImageProcessor) - Method in class ij.plugin.filter.LutViewer
 
run(ImageProcessor) - Method in class ij.plugin.filter.MaximumFinder
The plugin is inferred from ImageJ by this method
run(ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
 
run(ImageProcessor) - Method in interface ij.plugin.filter.PlugInFilter
Filters use this method to process the image.
run(ImageProcessor) - Method in class ij.plugin.filter.Printer
 
run(ImageProcessor) - Method in class ij.plugin.filter.RankFilters
 
run(ImageProcessor) - Method in class ij.plugin.filter.RGBStackSplitter
 
run(ImageProcessor) - Method in class ij.plugin.filter.RoiWriter
 
run(ImageProcessor) - Method in class ij.plugin.filter.Rotator
 
run(ImageProcessor) - Method in class ij.plugin.filter.SaltAndPepper
 
run(ImageProcessor) - Method in class ij.plugin.filter.ScaleDialog
 
run(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
run(ImageProcessor) - Method in class ij.plugin.filter.StackLabeler
 
run(ImageProcessor) - Method in class ij.plugin.filter.ThresholdToSelection
 
run(ImageProcessor) - Method in class ij.plugin.filter.Transformer
 
run(ImageProcessor) - Method in class ij.plugin.filter.Translator
 
run(ImageProcessor) - Method in class ij.plugin.filter.UnsharpMask
This method is invoked for each slice or color channel.
run(ImageProcessor) - Method in class ij.plugin.filter.Writer
Deprecated.
 
run(ImageProcessor) - Method in class ij.plugin.filter.XYWriter
 
run(String) - Method in class ij.gui.RoiDefaultsDialog
 
run(String) - Static method in class ij.IJ
Runs an ImageJ command.
run(String) - Method in class ij.macro.Interpreter
Interprets the specified string.
run(String) - Method in class ij.macro.MacroRunner
Runs the specified macro code.
run(String) - Method in class ij.plugin.AboutBox
 
run(String) - Method in class ij.plugin.Animator
Set 'arg' to "set" to display a dialog that allows the user to specify the animation speed.
run(String) - Method in class ij.plugin.AppearanceOptions
 
run(String) - Method in class ij.plugin.ArrowToolOptions
 
run(String) - Method in class ij.plugin.AVI_Reader
The plugin is invoked by ImageJ using this method.
run(String) - Method in class ij.plugin.BatchConverter
 
run(String) - Method in class ij.plugin.BatchMeasure
 
run(String) - Method in class ij.plugin.BatchProcessor
 
run(String) - Method in class ij.plugin.Benchmark
 
run(String) - Method in class ij.plugin.Binner
 
run(String) - Method in class ij.plugin.BMP_Reader
 
run(String) - Method in class ij.plugin.BMP_Writer
 
run(String) - Method in class ij.plugin.BrowserLauncher
Opens the specified URL (default is the ImageJ home page).
run(String) - Method in class ij.plugin.CalibrationBar
 
run(String) - Method in class ij.plugin.CanvasResizer
 
run(String) - Method in class ij.plugin.ChannelArranger
 
run(String) - Method in class ij.plugin.ChannelSplitter
 
run(String) - Method in class ij.plugin.CircularRoiMaker
 
run(String) - Method in class ij.plugin.ClassChecker
 
run(String) - Method in class ij.plugin.Clipboard
 
run(String) - Method in class ij.plugin.Colors
 
run(String) - Method in class ij.plugin.CommandFinder
Displays the Command Finder dialog.
run(String) - Method in class ij.plugin.CommandLister
 
run(String) - Method in class ij.plugin.Commands
 
run(String) - Method in class ij.plugin.Compiler
 
run(String) - Method in class ij.plugin.CompositeConverter
 
run(String) - Method in class ij.plugin.Concatenator
Optional string argument sets the name dialog boxes if called from another plugin.
run(String) - Method in class ij.plugin.ContrastEnhancer
 
run(String) - Method in class ij.plugin.ControlPanel
Creates a panel with the hierarchical tree structure of ImageJ's commands.
run(String) - Method in class ij.plugin.Converter
 
run(String) - Method in class ij.plugin.Coordinates
 
run(String) - Method in class ij.plugin.DICOM
 
run(String) - Method in class ij.plugin.Distribution
 
run(String) - Method in class ij.plugin.DragAndDrop
 
run(String) - Method in class ij.plugin.Duplicator
 
run(String) - Method in class ij.plugin.EventListener
 
run(String) - Method in class ij.plugin.FFT
 
run(String) - Method in class ij.plugin.FFTMath
 
run(String) - Method in class ij.plugin.FileInfoVirtualStack
 
run(String) - Method in class ij.plugin.Filters3D
 
run(String) - Method in class ij.plugin.FITS_Reader
 
run(String) - Method in class ij.plugin.FITS_Writer
 
run(String) - Method in class ij.plugin.FolderOpener
 
run(String) - Method in class ij.plugin.frame.ContrastAdjuster
 
run(String) - Method in class ij.plugin.frame.PlugInDialog
 
run(String) - Method in class ij.plugin.frame.PlugInFrame
 
run(String) - Method in class ij.plugin.GaussianBlur3D
 
run(String) - Method in class ij.plugin.GelAnalyzer
 
run(String) - Method in class ij.plugin.GIF_Reader
 
run(String) - Method in class ij.plugin.GifWriter
 
run(String) - Method in class ij.plugin.Grid
 
run(String) - Method in class ij.plugin.GroupedZProjector
 
run(String) - Method in class ij.plugin.Histogram
 
run(String) - Method in class ij.plugin.Hotkeys
 
run(String) - Method in class ij.plugin.HyperStackConverter
 
run(String) - Method in class ij.plugin.HyperStackMaker
 
run(String) - Method in class ij.plugin.HyperStackReducer
 
run(String) - Method in class ij.plugin.ImageCalculator
 
run(String) - Method in class ij.plugin.ImageInfo
 
run(String) - Method in class ij.plugin.ImageJ_Updater
 
run(String) - Method in class ij.plugin.ImagesToStack
 
run(String) - Method in class ij.plugin.JavaProperties
 
run(String) - Method in class ij.plugin.JavaScriptEvaluator
 
run(String) - Method in class ij.plugin.JpegWriter
 
run(String) - Method in class ij.plugin.ListVirtualStack
 
run(String) - Method in class ij.plugin.LUT_Editor
 
run(String) - Method in class ij.plugin.LutLoader
If 'arg'="", displays a file open dialog and opens the specified LUT.
run(String) - Method in class ij.plugin.Macro_Runner
Opens and runs the specified macro file (.txt or .ijm) or script file (.js, .bsh or .py) on the current thread.
run(String) - Method in class ij.plugin.MacroInstaller
 
run(String) - Method in class ij.plugin.MeasurementsWriter
 
run(String) - Method in class ij.plugin.Memory
 
run(String) - Method in class ij.plugin.MontageMaker
 
run(String) - Method in class ij.plugin.NewPlugin
 
run(String) - Method in class ij.plugin.NextImageOpener
 
run(String) - Method in class ij.plugin.Options
 
run(String) - Method in class ij.plugin.Orthogonal_Views
 
run(String) - Method in class ij.plugin.OverlayCommands
 
run(String) - Method in class ij.plugin.OverlayLabels
 
run(String) - Method in class ij.plugin.PGM_Reader
 
run(String) - Method in interface ij.plugin.PlugIn
This method is called when the plugin is loaded.
run(String) - Method in class ij.plugin.PluginInstaller
 
run(String) - Method in class ij.plugin.PlugInInterpreter
Run script on separate thread.
run(String) - Method in class ij.plugin.PNG_Writer
 
run(String) - Method in class ij.plugin.PNM_Writer
 
run(String) - Method in class ij.plugin.PointToolOptions
 
run(String) - Method in class ij.plugin.Profiler
 
run(String) - Method in class ij.plugin.Projector
 
run(String) - Method in class ij.plugin.ProxySettings
 
run(String) - Method in class ij.plugin.Raw
 
run(String) - Method in class ij.plugin.RectToolOptions
 
run(String) - Method in class ij.plugin.Resizer
 
run(String) - Method in class ij.plugin.RGBStackConverter
 
run(String) - Method in class ij.plugin.RGBStackMerge
 
run(String) - Method in class ij.plugin.RoiEnlarger
 
run(String) - Method in class ij.plugin.RoiInterpolator
 
run(String) - Method in class ij.plugin.RoiReader
 
run(String) - Method in class ij.plugin.RoiRotator
 
run(String) - Method in class ij.plugin.RoiScaler
 
run(String) - Method in class ij.plugin.ScaleBar
This method is called when the plugin is loaded.
run(String) - Method in class ij.plugin.Scaler
 
run(String) - Method in class ij.plugin.ScreenGrabber
 
run(String) - Method in class ij.plugin.Selection
 
run(String) - Method in class ij.plugin.SimpleCommands
 
run(String) - Method in class ij.plugin.Slicer
 
run(String) - Method in class ij.plugin.SpecifyROI
 
run(String) - Method in class ij.plugin.Stack_Statistics
 
run(String) - Method in class ij.plugin.StackCombiner
 
run(String) - Method in class ij.plugin.StackEditor
 
run(String) - Method in class ij.plugin.StackInserter
 
run(String) - Method in class ij.plugin.StackMaker
 
run(String) - Method in class ij.plugin.StackPlotter
 
run(String) - Method in class ij.plugin.StackReducer
 
run(String) - Method in class ij.plugin.StackReverser
 
run(String) - Method in class ij.plugin.StackWriter
 
run(String) - Method in class ij.plugin.Startup
 
run(String) - Method in class ij.plugin.Straightener
 
run(String) - Method in class ij.plugin.SubHyperstackMaker
 
run(String) - Method in class ij.plugin.SubstackMaker
 
run(String) - Method in class ij.plugin.SurfacePlotter
 
run(String) - Method in class ij.plugin.Text
 
run(String) - Method in class ij.plugin.TextFileReader
 
run(String) - Method in class ij.plugin.TextReader
 
run(String) - Method in class ij.plugin.TextWriter
 
run(String) - Method in class ij.plugin.ThreadLister
 
run(String) - Method in class ij.plugin.Thresholder
 
run(String) - Method in class ij.plugin.tool.BrushTool
 
run(String) - Method in class ij.plugin.tool.PlugInTool
 
run(String) - Method in class ij.plugin.URLOpener
If 'urlOrName' is a URL, opens the image at that URL.
run(String) - Method in class ij.plugin.WandToolOptions
 
run(String) - Method in class ij.plugin.WindowOrganizer
 
run(String) - Method in class ij.plugin.XY_Reader
 
run(String) - Method in class ij.plugin.XYCoordinates
 
run(String) - Method in class ij.plugin.ZAxisProfiler
 
run(String) - Method in class ij.plugin.Zoom
 
run(String) - Method in class ij.plugin.ZProjector
 
run(String, ImagePlus, ImagePlus) - Method in class ij.plugin.ImageCalculator
 
run(String, String) - Static method in class ij.IJ
Runs an ImageJ command, with options that are passed to the GenericDialog and OpenDialog classes.
run(String, String) - Method in class ij.macro.Interpreter
Runs the specified macro, passing it a string argument and returning a string value.
run(String, String) - Method in class ij.plugin.JavaScriptEvaluator
 
run(String, String) - Method in class ij.plugin.PlugInInterpreter
Run script on current thread.
RUN - Static variable in interface ij.macro.MacroConstants
 
RUN_BAR - Static variable in class ij.plugin.frame.Editor
 
RUN_MACRO - Static variable in interface ij.macro.MacroConstants
 
RUN_TO_CARET - Static variable in interface ij.macro.Debugger
 
RUN_TO_COMPLETION - Static variable in interface ij.macro.Debugger
 
run2(ImagePlus, String) - Method in class ij.plugin.ZProjector
 
runBatchMacro(String, ImagePlus) - Method in class ij.macro.Interpreter
Runs Process/Batch/ macros.
runBeanShell(String, String) - Static method in class ij.plugin.Macro_Runner
Runs a BeanShell script on the current thread, passing a string argument, which the script can retrieve using the getArgument() function.
runCommand(ImagePlus, String) - Method in class ij.plugin.frame.RoiManager
Using the specified image, runs the ROI Manager "Add", "Add & Draw", "Update", "Delete", "Measure", "Draw", "Show All", "Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split", "Sort" or "Multi Measure" command.
runCommand(String) - Method in class ij.plugin.CommandFinder
 
runCommand(String) - Method in class ij.plugin.frame.RoiManager
Executes the ROI Manager "Add", "Add & Draw", "Update", "Delete", "Measure", "Draw", "Show All", "Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split", "Sort" or "Multi Measure" command.
runCommand(String, String) - Method in class ij.plugin.frame.RoiManager
Executes the ROI Manager "Open", "Save" or "Rename" command.
runCommand(String, String, double) - Method in class ij.plugin.frame.RoiManager
Adds the current selection to the ROI Manager, using the specified color (a 6 digit hex string) and line width.
runFilterPlugIn(Object, String, String) - Method in class ij.ImageJ
 
runFromLabel(String) - Method in class ij.macro.FunctionFinder
 
runJavaScript(String, String) - Method in class ij.plugin.Macro_Runner
Runs a JavaScript script on the current thread, passing a string argument, which the script can retrieve using the getArgument() function.
runMacro(Program, int, String) - Method in class ij.macro.Interpreter
Interprets the specified tokenized macro starting at the specified location.
runMacro(String) - Static method in class ij.IJ
Runs the macro contained in the string macro on the current thread.
runMacro(String) - Method in class ij.plugin.MacroInstaller
 
runMacro(String, Editor) - Method in class ij.plugin.MacroInstaller
 
runMacro(String, String) - Static method in class ij.IJ
Runs the macro contained in the string macro on the current thread.
runMacro(String, String) - Method in class ij.plugin.Macro_Runner
Runs the specified macro on the current thread.
runMacroCommand(String) - Static method in class ij.plugin.MacroInstaller
Runs a command in the Plugins/Macros submenu on the current thread.
runMacroFile(String) - Static method in class ij.IJ
Runs the specified macro file.
runMacroFile(String, String) - Static method in class ij.IJ
Runs the specified macro or script file in the current thread.
runMacroFile(String, String) - Method in class ij.plugin.Macro_Runner
Opens and runs the specified macro or script on the current thread.
runMacroFromIJJar(String, String) - Method in class ij.plugin.Macro_Runner
 
runMacroFromJar(String, String) - Static method in class ij.plugin.Macro_Runner
Runs the specified macro from a JAR file in the plugins folder, passing it the specified argument.
runMacroShortcut(String) - Static method in class ij.plugin.MacroInstaller
 
runMacroTool(String) - Method in class ij.plugin.MacroInstaller
 
runMacroTool(String) - Method in class ij.plugin.tool.MacroToolRunner
 
runMacroTool(String) - Method in class ij.plugin.tool.PlugInTool
These methods are overridden by MacroToolRunner.
runMenuTool(String, String) - Method in class ij.plugin.MacroInstaller
 
runMenuTool(String, String) - Method in class ij.plugin.tool.MacroToolRunner
 
runMenuTool(String, String) - Method in class ij.plugin.tool.PlugInTool
 
running - Variable in class ij.gui.ImageWindow
This variable is set false if the user presses the escape key or closes the window.
running2 - Variable in class ij.gui.ImageWindow
This variable is set false if the user clicks in this window, presses the escape key, or closes the window.
runPlugIn(ImagePlus, String, String) - Static method in class ij.IJ
Runs the specified plugin using the specified image.
runPlugIn(String, String) - Static method in class ij.IJ
Runs the specified plugin and returns a reference to it.
runPlugIn(String, String, String) - Static method in class ij.IJ
Runs the specified plugin and returns a reference to it.
runPython(String, String) - Static method in class ij.plugin.Macro_Runner
Runs a Python script on the current thread, passing a string argument, which the script can retrieve using the getArgument() function.
runShortcut(Program, int, String) - Method in class ij.macro.MacroRunner
Runs tokenized macro on current thread if pgm.queueCommands is true.
runSocketListener - Static variable in class ij.Prefs
Run the SocketListener.
runUserPlugIn(String, String, String, boolean) - Method in class ij.ImageJ
 
rw - Variable in class ij.process.ImageStatistics
 
rx - Variable in class ij.process.ImageStatistics
 
ry - Variable in class ij.process.ImageStatistics
 

S

s2ints(String) - Method in class ij.plugin.ControlPanel
Breaks the specified string into an array of ints.
s2ints(String) - Method in class ij.plugin.filter.FractalBoxCounter
Breaks the specified string into an array of ints.
SaltAndPepper - Class in ij.plugin.filter
Implements ImageJ's Process/Noise/Salt and Pepper command.
SaltAndPepper() - Constructor for class ij.plugin.filter.SaltAndPepper
 
SAMPLE_FORMAT - Static variable in class ij.io.TiffDecoder
 
sampleModel - Variable in class ij.process.ImageProcessor
 
SAMPLES_PER_PIXEL - Static variable in class ij.io.TiffDecoder
 
samplesPerPixel - Variable in class ij.io.FileInfo
 
SansSerif12 - Static variable in class ij.ImageJ
SansSerif, 12-point, plain font.
SansSerif14 - Static variable in class ij.ImageJ
SansSerif, 14-point, plain font.
save - Variable in class ij.gui.HistogramWindow
 
save() - Method in class ij.io.FileSaver
Resaves the image.
save(Roi, String) - Static method in class ij.io.RoiEncoder
Saves the specified ROI as a file, returning 'true' if successful.
save(ImagePlus, String) - Static method in class ij.IJ
Saves the specified image, lookup table or selection to the specified file path.
save(ImagePlus, String) - Static method in class ij.plugin.GifWriter
Saves the specified image in GIF format or as an animated GIF if the image is a stack.
save(ImagePlus, String, int) - Static method in class ij.plugin.JpegWriter
Thread-safe method.
save(ImagePlus, String, String) - Static method in class ij.plugin.StackWriter
Saves the specified image as a sequence of images.
save(PrintWriter) - Method in class ij.text.TextPanel
Writes all the text in this TextPanel to a file.
save(String) - Static method in class ij.IJ
Saves the current image, lookup table, selection or text window to the specified file path.
save(String) - Method in class ij.measure.ResultsTable
Saves this ResultsTable as a tab or comma delimited text file.
save(String) - Method in class ij.plugin.frame.RoiManager
If one ROI is selected, it is saved as a .roi file, if multiple (or no) ROIs are selected, they are saved as a .zip ROI set.
save(String) - Method in class ij.plugin.MeasurementsWriter
 
SAVE - Static variable in interface ij.macro.MacroConstants
 
SAVE_AS - Static variable in interface ij.macro.MacroConstants
 
SAVE_AS_MENU - Static variable in class ij.Menus
 
SAVE_SETTINGS - Static variable in interface ij.macro.MacroConstants
 
saveAndRename(String) - Method in class ij.measure.ResultsTable
 
saveAs() - Method in class ij.plugin.frame.Editor
 
saveAs(ImagePlus, String, String) - Static method in class ij.IJ
 
saveAs(String) - Static method in class ij.Macro
 
saveAs(String) - Method in class ij.measure.ResultsTable
 
saveAs(String) - Method in class ij.text.TextPanel
Saves the text in this TextPanel to a file.
saveAs(String, String) - Static method in class ij.IJ
 
saveAsBmp() - Method in class ij.io.FileSaver
Save the image in BMP format using a save file dialog.
saveAsBmp(String) - Method in class ij.io.FileSaver
Save the image in BMP format using the specified path.
saveAsByteArray(Roi) - Static method in class ij.io.RoiEncoder
Saves the specified ROI as a byte array.
saveAsFits() - Method in class ij.io.FileSaver
Save the image in FITS format using a save file dialog.
saveAsFits(String) - Method in class ij.io.FileSaver
Save the image in FITS format using the specified path.
saveAsGif() - Method in class ij.io.FileSaver
Save the image in GIF format using a save file dialog.
saveAsGif(String) - Method in class ij.io.FileSaver
Save the image in Gif format using the specified path.
saveAsJpeg() - Method in class ij.io.FileSaver
Save the image in JPEG format using a save file dialog.
saveAsJpeg(String) - Method in class ij.io.FileSaver
Save the image in JPEG format using the specified path.
saveAsLut() - Method in class ij.io.FileSaver
Save the current LUT using a save file dialog.
saveAsLut(String) - Method in class ij.io.FileSaver
Save the current LUT using the specified path.
saveAsPgm() - Method in class ij.io.FileSaver
Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using a save file dialog.
saveAsPgm(String) - Method in class ij.io.FileSaver
Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using the specified path.
saveAsPng() - Method in class ij.io.FileSaver
Save the image in PNG format using a save file dialog.
saveAsPng(String) - Method in class ij.io.FileSaver
Save the image in PNG format using the specified path.
saveAsRaw() - Method in class ij.io.FileSaver
Save the image or stack as raw data using a save file dialog.
saveAsRaw(String) - Method in class ij.io.FileSaver
Save the image as raw data using the specified path.
saveAsRawStack(String) - Method in class ij.io.FileSaver
Save the stack as raw data using the specified path.
saveAsText() - Method in class ij.io.FileSaver
Save the image as tab-delimited text using a save file dialog.
saveAsText(String) - Method in class ij.io.FileSaver
Save the image as tab-delimited text using the specified path.
saveAsTiff() - Method in class ij.io.FileSaver
Saves the image or stack in TIFF format using a save file dialog.
saveAsTiff(ImagePlus, String) - Static method in class ij.IJ
Saves the specified image in TIFF format.
saveAsTiff(String) - Method in class ij.io.FileSaver
Saves the image in TIFF format using the specified path.
saveAsTiffStack(String) - Method in class ij.io.FileSaver
Saves the stack as a multi-image TIFF using the specified path.
saveAsZip() - Method in class ij.io.FileSaver
Uses a save file dialog to save the image or stack as a TIFF in a ZIP archive.
saveAsZip(String) - Method in class ij.io.FileSaver
Save the image or stack in TIFF/ZIP format using the specified path.
saveBitmap(String, Image, int, int) - Method in class ij.plugin.BMP_Writer
 
saveChanges(int) - Method in class ij.VirtualStack
Currently not implemented
SaveChangesDialog - Class in ij.gui
A modal dialog box with a one line message and "Don't Save", "Cancel" and "Save" buttons.
SaveChangesDialog(Frame, String) - Constructor for class ij.gui.SaveChangesDialog
 
saveColumnHeaders(boolean) - Method in class ij.measure.ResultsTable
 
saveCommand() - Static method in class ij.plugin.frame.Recorder
Writes the current command and options to the Recorder window.
SAVED - Static variable in class ij.ImagePlus
 
SaveDialog - Class in ij.io
This class displays a dialog window from which the user can save a file.
SaveDialog(String, String, String) - Constructor for class ij.io.SaveDialog
Displays a file save dialog with 'title' as the title, 'defaultName' as the initial file name, and 'extension' (e.g.
SaveDialog(String, String, String, String) - Constructor for class ij.io.SaveDialog
Displays a file save dialog, using the specified default directory and file name and extension.
saveDisplayRangesAndLuts(ImagePlus, FileInfo) - Method in class ij.io.FileSaver
 
savedPoints - Static variable in class ij.gui.PointRoi
 
saveGlobals(Program) - Method in class ij.macro.Interpreter
Saves global variables.
saveGroupNames() - Static method in class ij.gui.Roi
 
saveImageDescription(byte[], FileInfo) - Method in class ij.io.TiffDecoder
Save the image description in the specified FileInfo.
saveLocation(String, Point) - Static method in class ij.Prefs
Saves the Point loc in the preferences file as a string using the keyword key.
saveMetadata(String, String) - Method in class ij.io.TiffDecoder
 
saveOutput(boolean) - Static method in class ij.plugin.BatchProcessor
 
saveOverlay(ImagePlus) - Static method in class ij.Undo
 
savePlotObjects() - Method in class ij.gui.Plot
Creates a snapshot of the plot contents (not including axis formats etc), for later undo by restorePlotObjects.
savePlotPlotProperties() - Method in class ij.gui.Plot
Creates a snapshot of the plot properties (formatting, range etc., not PlotObjects such as data and corresponding curves etc.), for later undo by restorePlotProperties.
savePreferences() - Static method in class ij.Prefs
Saves user preferences in the IJ_Prefs.txt properties file.
savePreferences(Properties) - Static method in class ij.gui.NewImage
Called when ImageJ quits.
savePreferences(Properties) - Static method in class ij.gui.PlotWindow
Called once when ImageJ quits.
savePreferences(Properties) - Method in class ij.ImageJ
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.io.ImportDialog
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.Menus
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.Analyzer
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.ParticleAnalyzer
Called once when ImageJ quits.
savePrefs(Properties, String) - Static method in class ij.Prefs
 
savePressed() - Method in class ij.gui.SaveChangesDialog
Returns true if the user dismissed dialog by pressing "Save".
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.Analyzer
Saves the measurements specified in the "Set Measurements" dialog, or by calling setMeasurements(), in the default results table.
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.ParticleAnalyzer
Saves statistics for one particle in a results table.
saveRoi() - Method in class ij.ImagePlus
 
saveRoi(ImagePlus) - Method in class ij.plugin.filter.RoiWriter
 
saveString(String, String) - Static method in class ij.IJ
Saves a string as a file.
saveThreshold(double, double, Calibration) - Method in class ij.process.ImageStatistics
 
saveXValues - Static variable in class ij.gui.PlotWindow
Write first X column when listing or saving.
saveXYCoordinates(ImagePlus) - Method in class ij.plugin.filter.XYWriter
 
scalableLabels() - Method in class ij.gui.Overlay
 
scale(double, double) - Method in class ij.gui.Overlay
Returns a scaled version of this Overlay.
scale(double, double) - Method in class ij.process.ByteProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ColorProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.FloatProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ImageProcessor
Scales the image by the specified factors.
scale(double, double) - Method in class ij.process.ShortProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.StackProcessor
 
scale(double, double, boolean) - Method in class ij.plugin.frame.RoiManager
 
scale(double, double, double) - Method in class ij.process.StackProcessor
 
scale(Roi, double, double, boolean) - Static method in class ij.plugin.RoiScaler
 
scale(Component) - Static method in class ij.gui.GUI
Scales an AWT component according to Prefs.getGuiScale().
scale(JComponent) - Static method in class ij.gui.GUI
Tries to detect if a Swing component is unscaled and scales it it according to #getGuiScale().
SCALE_LABELS - Static variable in class ij.io.RoiDecoder
 
SCALE_STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
 
SCALE_T - Static variable in class ij.plugin.Resizer
 
scaleAndSetThreshold(double, double, int) - Method in class ij.process.ImageProcessor
Set the threshold using a 0-255 range.
ScaleBar - Class in ij.plugin
This plugin implements the Analyze/Tools/Scale Bar command.
ScaleBar() - Constructor for class ij.plugin.ScaleBar
 
scaled() - Method in class ij.measure.Calibration
Returns 'true' if this image is spatially calibrated.
ScaleDialog - Class in ij.plugin.filter
Implements the Analyze/Set Scale command.
ScaleDialog() - Constructor for class ij.plugin.filter.ScaleDialog
 
scaledOrOffset() - Method in class ij.measure.Calibration
Returns 'true' if this image is spatially calibrated or has offsets.
scalePopupMenu(PopupMenu) - Static method in class ij.gui.GUI
 
Scaler - Class in ij.plugin
This plugin implements the Image/Scale command.
Scaler() - Constructor for class ij.plugin.Scaler
 
scaleXtoPxl(double) - Method in class ij.gui.Plot
Converts calibrated coordinates to pixel coordinates.
scaleYtoPxl(double) - Method in class ij.gui.Plot
Converts calibrated coordinates to pixel coordinates.
SCIENTIFIC_NOTATION - Static variable in interface ij.measure.Measurements
 
SCREEN_HEIGHT - Static variable in interface ij.macro.MacroConstants
 
SCREEN_WIDTH - Static variable in interface ij.macro.MacroConstants
 
ScreenGrabber - Class in ij.plugin
This plugin implements the Plugins/Utilities/Capture Screen and Plugins/Utilities/Capture Image commands.
ScreenGrabber() - Constructor for class ij.plugin.ScreenGrabber
 
screenX(int) - Method in class ij.gui.ImageCanvas
Converts an offscreen x-coordinate to a screen x-coordinate.
screenX(int) - Method in class ij.gui.Roi
 
screenXD(double) - Method in class ij.gui.ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenXD(double) - Method in class ij.gui.Roi
Converts an image pixel x (offscreen)coordinate to a screen x coordinate, taking the the line or area convention for coordinates into account
screenY(int) - Method in class ij.gui.ImageCanvas
Converts an offscreen y-coordinate to a screen y-coordinate.
screenY(int) - Method in class ij.gui.Roi
 
screenYD(double) - Method in class ij.gui.ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenYD(double) - Method in class ij.gui.Roi
Converts an image pixel y (offscreen)coordinate to a screen y coordinate, taking the the line or area convention for coordinates into account
scriptMode() - Static method in class ij.plugin.frame.Recorder
 
scroll(int, int) - Method in class ij.gui.ImageCanvas
 
scroll(int, int) - Method in class ij.gui.PlotCanvas
overrides ImageCanvas.scroll; if plot is not frozen, scrolling modifies the plot data range
ScrollbarWithLabel - Class in ij.gui
This class, based on Joachim Walter's Image5D package, adds "c", "z" labels and play-pause icons (T) to the stack and hyperstacks dimension sliders.
ScrollbarWithLabel() - Constructor for class ij.gui.ScrollbarWithLabel
 
ScrollbarWithLabel(StackWindow, int, int, int, int, char) - Constructor for class ij.gui.ScrollbarWithLabel
 
scrollToTop() - Method in class ij.text.TextPanel
 
SD_METHOD - Static variable in class ij.plugin.ZProjector
 
seed - Static variable in class ij.process.ImageProcessor
 
seek(int) - Method in class ij.io.RandomAccessStream
 
seek(long) - Method in class ij.io.RandomAccessStream
 
SEGMENTED - Static variable in class ij.plugin.filter.MaximumFinder
Output type watershed-segmented image
select(int) - Method in class ij.plugin.frame.RoiManager
Assigns the ROI at the specified index to the current image.
select(int, boolean, boolean) - Method in class ij.plugin.frame.RoiManager
 
select(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager
Assigns the ROI at the specified index to 'imp'.
SELECT - Static variable in interface ij.macro.MacroConstants
 
SELECT_IMAGE - Static variable in interface ij.macro.MacroConstants
 
selectable(boolean) - Method in class ij.gui.Overlay
Set 'false' to prevent ROIs in this overlay from being activated by clicking on their labels or by a long clicking.
selectAll() - Method in class ij.text.TextPanel
Selects all the lines in this TextPanel.
selectAndMakeVisible(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager
 
selected() - Method in class ij.plugin.frame.RoiManager
Returns the count of selected ROIs.
selectGroup(int) - Method in class ij.plugin.frame.RoiManager
Selects all ROIs of a given group.
selectGroup(String) - Static method in class ij.plugin.frame.RoiManager
Obsolete; replaced by RoiManager.selectGroup() macro function.
Selection - Class in ij.plugin
This plugin implements the commands in the Edit/Selection submenu.
Selection() - Constructor for class ij.plugin.Selection
 
SELECTION_CONTAINS - Static variable in interface ij.macro.MacroConstants
 
SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
 
SELECTION_TYPE - Static variable in interface ij.macro.MacroConstants
 
selectPosition(int, int, int) - Method in class ij.plugin.frame.RoiManager
Selects all ROIs at the specified position.
selectRow(Roi) - Static method in class ij.measure.ResultsTable
Selects the row in the "Results" table assocuiated with the specified Roi.
selectWindow(int) - Static method in class ij.IJ
For IDs less than zero, activates the image with the specified ID.
selectWindow(String) - Static method in class ij.IJ
Activates the window with the specified title.
sendArguments(String[]) - Static method in class ij.OtherInstance
 
SEPARATED_BAR - Static variable in class ij.gui.Plot
Draw a free-standing bar for each point.
separator - Static variable in class ij.Prefs
file.separator system property
serialize() - Method in class ij.io.FileSaver
Converts this image to a TIFF encoded array of bytes, which can be decoded using Opener.deserialize().
set(double) - Method in class ij.process.FloatProcessor
 
set(double) - Method in class ij.process.ImageProcessor
Assigns 'value' to each pixel in the image or ROI.
set(double) - Method in class ij.process.ShortProcessor
 
set(int, float) - Method in class ij.util.FloatArray
Replaces the element at the specified position with the value given.
set(int, int) - Method in class ij.process.ByteProcessor
 
set(int, int) - Method in class ij.process.ColorProcessor
 
set(int, int) - Method in class ij.process.FloatProcessor
 
set(int, int) - Method in class ij.process.ImageProcessor
 
set(int, int) - Method in class ij.process.ShortProcessor
 
set(int, int, int) - Method in class ij.process.ByteProcessor
 
set(int, int, int) - Method in class ij.process.ColorProcessor
 
set(int, int, int) - Method in class ij.process.FloatProcessor
 
set(int, int, int) - Method in class ij.process.ImageProcessor
This is a faster version of putPixel() that does not clip out of range values and does not do bounds checking.
set(int, int, int) - Method in class ij.process.ShortProcessor
 
set(Roi, int) - Method in class ij.gui.Overlay
Replaces the ROI at the specified index.
set(ImagePlus, double) - Static method in class ij.plugin.Zoom
 
set(ImagePlus, double, int, int) - Static method in class ij.plugin.Zoom
 
set(String, boolean) - Static method in class ij.Prefs
Saves the value of the boolean value in the preferences file using the keyword key.
set(String, double) - Static method in class ij.Prefs
Saves the value of the double value in the preferences file using the keyword key.
set(String, int) - Static method in class ij.Prefs
Saves the value of the integer value in the preferences file using the keyword key.
set(String, String) - Static method in class ij.Prefs
Saves the value of the string text in the preferences file using the keyword key.
SET_AUTO_THRESHOLD - Static variable in interface ij.macro.MacroConstants
 
SET_BACKGROUND - Static variable in interface ij.macro.MacroConstants
 
SET_BATCH_MODE - Static variable in interface ij.macro.MacroConstants
 
SET_COLOR - Static variable in interface ij.macro.MacroConstants
 
SET_FIRST_CHANNEL - Static variable in class ij.process.ImageProcessor
Composite image projection modes.
SET_FONT - Static variable in interface ij.macro.MacroConstants
 
SET_FOREGROUND - Static variable in interface ij.macro.MacroConstants
 
SET_JUSTIFICATION - Static variable in interface ij.macro.MacroConstants
 
SET_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
 
SET_LINE_WIDTH - Static variable in interface ij.macro.MacroConstants
 
SET_LOCATION - Static variable in interface ij.macro.MacroConstants
 
SET_LUT - Static variable in interface ij.macro.MacroConstants
 
SET_METADATA - Static variable in interface ij.macro.MacroConstants
 
SET_MIN_MAX - Static variable in interface ij.macro.MacroConstants
 
SET_OPTION - Static variable in interface ij.macro.MacroConstants
 
SET_PASTE_MODE - Static variable in interface ij.macro.MacroConstants
 
SET_PIXEL - Static variable in interface ij.macro.MacroConstants
 
SET_RANGE - Static variable in class ij.gui.PlotDialog
Types of dialog.
SET_RESULT - Static variable in interface ij.macro.MacroConstants
 
SET_RGB_WEIGHTS - Static variable in interface ij.macro.MacroConstants
 
SET_SELECTION_LOC - Static variable in interface ij.macro.MacroConstants
 
SET_SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
 
SET_SLICE - Static variable in interface ij.macro.MacroConstants
 
SET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
 
SET_TOOL - Static variable in interface ij.macro.MacroConstants
 
SET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
 
SET_Z_COORDINATE - Static variable in interface ij.macro.MacroConstants
 
set16bitRange(int) - Static method in class ij.plugin.frame.ContrastAdjuster
 
setActivated() - Method in class ij.ImagePlus
Called by ImageWindow.windowActivated(); to end waiting in waitTillActivated.
setActiveChannels(String) - Method in class ij.ImagePlus
Controls which channels in a composite color image are displayed, where 'channels' is a list of ones and zeros that specify the channels to display.
setAdditionalFunctions(String) - Static method in class ij.macro.Interpreter
Obsolete; replaced by the #include statement.
setAllPoints(boolean) - Static method in class ij.gui.Wand
Set 'true' and output will contain intermediate points for straight lines longer than one pixel.
setAngle(double) - Method in class ij.gui.ImageRoi
 
setAngle(double) - Method in class ij.gui.TextRoi
 
setAnimate(boolean) - Method in class ij.gui.StackWindow
 
setAntiAlias(boolean) - Method in class ij.gui.Roi
 
setAntialiased(boolean) - Method in class ij.gui.TextRoi
Sets the 'antiAlias' instance variable.
setAntialiased(boolean) - Static method in class ij.text.TextWindow
 
setAntialiased(Graphics, boolean) - Static method in class ij.util.Java2
 
setAntialiasedText(boolean) - Method in class ij.gui.Plot
Determines whether to use antialiased text (default true)
setAntialiasedText(boolean) - Static method in class ij.gui.TextRoi
Sets the state of the global 'antialiasedText' variable.
setAntialiasedText(boolean) - Method in class ij.process.ImageProcessor
Specifies whether or not text is drawn using antialiasing, which is enabled by default on macOS or when the font size is 14 or greater.
setAntialiasedText(Graphics, boolean) - Static method in class ij.util.Java2
 
setAntialiasRendering(boolean) - Method in class ij.ImagePlus
Enable/disable use of antialiasing by the flatten() method.
setApplyMacroTable(ResultsTable) - Method in class ij.macro.Interpreter
 
setAsRepeatCommand(String) - Static method in class ij.Executer
 
setAutoThreshold(int, int) - Method in class ij.process.ImageProcessor
Automatically sets the lower and upper threshold levels, where 'method' must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
setAutoThreshold(ImagePlus, String) - Static method in class ij.IJ
 
setAutoThreshold(AutoThresholder.Method, boolean) - Method in class ij.process.ImageProcessor
 
setAutoThreshold(AutoThresholder.Method, boolean, int) - Method in class ij.process.ImageProcessor
 
setAutoThreshold(String) - Method in class ij.process.ImageProcessor
Automatically sets the lower and upper threshold levels, where 'method' must be "Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData", "Li", "MaxEntropy", "Mean", "MinError", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag", "Triangle" or "Yen".
setAutoThreshold(String, boolean, int) - Method in class ij.process.ImageProcessor
 
setAverageWhenDownsizing(boolean) - Method in class ij.plugin.Resizer
 
setAxes(boolean, boolean, boolean, boolean, boolean, boolean, int, int) - Method in class ij.gui.Plot
Sets the properties of the axes.
setAxisLabelFont(int, float) - Method in class ij.gui.Plot
Sets the x and y label font size and style.
setAxisXLog(boolean) - Method in class ij.gui.Plot
Sets the X Axis format to Log or Linear.
setAxisYLog(boolean) - Method in class ij.gui.Plot
Sets the Y Axis format to Log or Linear.
setBackground(String) - Static method in class ij.plugin.Thresholder
 
setBackgroundColor(int, int, int) - Static method in class ij.IJ
Sets the background color.
setBackgroundColor(Color) - Method in class ij.gui.Plot
Set the plot frame background color.
setBackgroundColor(Color) - Static method in class ij.gui.Toolbar
 
setBackgroundColor(Color) - Static method in class ij.plugin.frame.Recorder
 
setBackgroundColor(Color) - Method in class ij.process.ByteProcessor
Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.ColorProcessor
Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.FloatProcessor
Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.ImageProcessor
Sets the background fill/draw color.
setBackgroundColor(Color) - Method in class ij.process.ShortProcessor
Sets the background fill/draw color.
setBackgroundColor(String) - Method in class ij.gui.Plot
Set the plot frame background color.
setBackgroundValue(double) - Static method in class ij.gui.Toolbar
Sets the background color to grayscale, where value is between 0 (black) and 255 (white).
setBackgroundValue(double) - Method in class ij.process.ByteProcessor
Sets the background fill value, where 0<=value<=255.
setBackgroundValue(double) - Method in class ij.process.ColorProcessor
Sets the background fill value, where value is interpreted as an RGB int.
setBackgroundValue(double) - Method in class ij.process.FloatProcessor
 
setBackgroundValue(double) - Method in class ij.process.ImageProcessor
Sets the background fill value used by the rotate() and scale() methods.
setBackgroundValue(double) - Method in class ij.process.ShortProcessor
 
setBatchMode(boolean) - Method in class ij.gui.ProgressBar
 
setBilinearInterpolation(Graphics, boolean) - Static method in class ij.util.Java2
 
setBinaryThreshold() - Method in class ij.process.ImageProcessor
 
setBitDepth(int) - Method in class ij.gui.PlotVirtualStack
 
setBitDepth(int) - Method in class ij.ImageStack
Sets the bit depth (8=byte, 16=short, 24=RGB, 32=float).
setBitDepth(int) - Method in class ij.VirtualStack
Sets the bit depth (8, 16, 24 or 32).
setBlackBackground() - Static method in class ij.plugin.frame.Recorder
 
setBlockIncrement(int) - Method in class ij.gui.ScrollbarWithLabel
 
setBorderColor(Color) - Method in class ij.ImagePlus
 
setBounds(Rectangle2D.Double) - Method in class ij.gui.Roi
Sets the bounds of rectangular, oval or text selections.
setBrightness(FloatProcessor) - Method in class ij.process.ColorProcessor
Updates the brightness using the pixels in the specified FloatProcessor).
setBrushSize(int) - Static method in class ij.gui.Toolbar
Set the size of the selection brush tool, in pixels.
setBrushWidth(int) - Static method in class ij.plugin.tool.BrushTool
 
setBufferSize(int) - Static method in class ij.io.FileSaver
Sets the BufferedOutputStream buffer size in bytes (default is 32K).
setC(int) - Method in class ij.ImagePlus
Sets the hyperstack channel position (one based).
setC(ImageWindow, int) - Static method in class ij.plugin.frame.SyncWindows
 
setCalibration(Calibration) - Method in class ij.ImagePlus
Sets this image's calibration.
setCalibrationTable(float[]) - Method in class ij.process.ImageProcessor
Set a lookup table used by getPixelValue(), getLine() and convertToFloat() to calibrate pixel values.
setCancelLabel(String) - Method in class ij.gui.GenericDialog
Sets a replacement label for the "Cancel" button.
setCaseSensitive(boolean) - Method in class ij.util.WildcardMatch
Makes pattern matching case insensitive.
setChannel(int, ByteProcessor) - Method in class ij.process.ColorProcessor
Sets the pixels of one color channel from a ByteProcessor.
setChannelColorModel(IndexColorModel) - Method in class ij.CompositeImage
 
setChannelLut(LUT) - Method in class ij.CompositeImage
 
setChannelLut(LUT, int) - Method in class ij.CompositeImage
 
setChannelsUpdated() - Method in class ij.CompositeImage
Deprecated
setClipRect(Rectangle) - Method in class ij.process.ImageProcessor
Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
setColor(double) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value.
setColor(int) - Method in class ij.process.ColorProcessor
Sets the fill/draw color, where color is an RGB int.
setColor(int) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value.
setColor(Color) - Method in class ij.gui.Plot
Changes the drawing color for the next objects that will be added to the plot.
setColor(Color) - Method in class ij.gui.PlotWindow
Deprecated.
use the corresponding method of the Plot class
setColor(Color) - Static method in class ij.gui.Roi
Sets the default (global) color used for ROI outlines.
setColor(Color) - Method in class ij.gui.Toolbar
Deprecated.
replaced by setForegroundColor()
setColor(Color) - Method in class ij.ImagePlus
Sets current foreground color.
setColor(Color) - Method in class ij.process.ByteProcessor
Sets the foreground drawing color.
setColor(Color) - Method in class ij.process.ColorProcessor
Sets the foreground color.
setColor(Color) - Method in class ij.process.FloatProcessor
Sets the foreground fill/draw color.
setColor(Color) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value to the pixel value closest to the specified color.
setColor(Color) - Method in class ij.process.ShortProcessor
Sets the foreground fill/draw color.
setColor(Color, Color) - Method in class ij.gui.Plot
Changes the drawing color for the next objects that will be added to the plot.
setColor(String) - Method in class ij.gui.Plot
 
setColor(String) - Method in class ij.process.ImageProcessor
Sets the fill/draw color, where 'color' is "white", "black", "blue", etc., or a hex value like "#ff0000".
setColor(String, String) - Method in class ij.gui.Plot
Sets the drawing colors for the next objects that will be added to the plot.
setColorModel(ColorModel) - Method in class ij.ImageStack
Assigns a new color model to this stack.
setColorModel(ColorModel) - Method in class ij.process.ColorProcessor
 
setColorModel(ColorModel) - Method in class ij.process.ImageProcessor
Sets the color model.
setColorModel(ColorModel) - Method in class ij.process.IntProcessor
 
setColumn(String, Variable[]) - Method in class ij.measure.ResultsTable
Implements the Table.setColumn() macro function.
setColumnHeadings(String) - Static method in class ij.IJ
Clears the "Results" window and sets the column headings to those in the tab-delimited 'headings' String.
setColumnHeadings(String) - Method in class ij.text.TextPanel
Clears this TextPanel and sets the column headings to those in the tab-delimited 'headings' String.
setCommand(String) - Static method in class ij.plugin.frame.Recorder
Starts recording a command.
setCommandName(String) - Static method in class ij.ImageJ
 
setComposite(Composite) - Method in class ij.gui.ImageRoi
Sets the composite mode.
setCornerDiameter(int) - Method in class ij.gui.Roi
Sets the rounded rectangle corner diameter (pixels).
setCounter(int) - Method in class ij.gui.PointRoi
 
setCounterInfo(int[]) - Method in class ij.gui.PointRoi
 
setCounters(int[]) - Method in class ij.gui.PointRoi
Sets the counter number and slice number for each point from an array, where the lower 8 bits are the counter number and the higher 24 bits contain the slice position of each point.
setCrossLoc(int, int, int) - Method in class ij.plugin.Orthogonal_Views
 
setCTable(float[], String) - Method in class ij.measure.Calibration
Sets the calibration table.
setCurrentFont(Font) - Method in class ij.gui.TextRoi
Deprecated.
Replaced by setFont(font)
setCurrentWindow(ImageWindow) - Static method in class ij.WindowManager
Makes the image contained in the specified window the active image.
setCursor(int, int, int, int) - Method in class ij.gui.ImageCanvas
Sets the cursor based on the current tool and cursor location.
setCursor(ImagePlus, Roi) - Method in class ij.plugin.frame.SyncWindows
 
setCursor(Cursor, int) - Static method in class ij.gui.ImageCanvas
Experimental
setCustomRoi(boolean) - Method in class ij.gui.ImageCanvas
Allows plugins (e.g., Orthogonal_Views) to create a custom ROI using a display list.
setDeactivated() - Method in class ij.ImagePlus
Called by new StackWindow(ImagePlus) before showing the StackWindow, to prepare for waitTillActivated().
setDebugger(Debugger) - Method in class ij.macro.Interpreter
 
setDebugMode(boolean) - Static method in class ij.IJ
Enable/disable debug mode.
setDebugMode(int) - Method in class ij.macro.Interpreter
 
setDecimalPlaces(int, int) - Method in class ij.measure.ResultsTable
 
setDefault16bitRange(int) - Static method in class ij.ImagePlus
Set the default 16-bit display range, where 'bitDepth' must be 0 (auto-scaling), 8 (0-255), 10 (0-1023), 12 (0-4095, 14 (0-16383), 15 (0-32767) or 16 (0-65535).
setDefaultAngle(double) - Static method in class ij.gui.TextRoi
Sets the default angle.
setDefaultColor(Color) - Static method in class ij.gui.Roi
Sets the default stroke color.
setDefaultCounter(int) - Static method in class ij.gui.PointRoi
 
setDefaultCrossColor(Color) - Static method in class ij.gui.PointRoi
Deprecated
setDefaultDirectory(String) - Static method in class ij.io.DirectoryChooser
Sets the default directory presented in the dialog.
setDefaultDirectory(String) - Static method in class ij.io.OpenDialog
Sets the default directory.
setDefaultDirectory(String) - Static method in class ij.plugin.frame.Editor
 
setDefaultDisplayRange(double, double) - Method in class ij.ImagePlus
 
setDefaultDoubleHeaded(boolean) - Static method in class ij.gui.Arrow
 
setDefaultFillColor(Color) - Static method in class ij.gui.Roi
 
setDefaultFillColor(Color) - Static method in class ij.gui.TextRoi
Sets the default fill (background) color.
setDefaultFont(Font) - Static method in class ij.gui.TextRoi
Sets the default font.
setDefaultFontSize(int) - Static method in class ij.gui.PlotWindow
 
setDefaultFontSize(int) - Static method in class ij.gui.TextRoi
Sets the default font size.
setDefaultGroup(int) - Static method in class ij.gui.Roi
Sets the group value assigned to newly created ROIs, and also sets the default ROI color to the group color.
setDefaultHeadings() - Method in class ij.measure.ResultsTable
Sets the headings used by the Measure command ("Area", "Mean", etc.).
setDefaultHeadings() - Static method in class ij.plugin.filter.Analyzer
Sets the default headings ("Area", "Mean", etc.).
setDefaultHeadSize(double) - Static method in class ij.gui.Arrow
 
setDefaultMarkerSize(String) - Static method in class ij.gui.PointRoi
Deprecated. 
setDefaultOutline(boolean) - Static method in class ij.gui.Arrow
 
setDefaultSize(int) - Static method in class ij.gui.PointRoi
Sets the default point size, where 'size' is 0-6 (Tiny-XXXL).
setDefaultString(int, String) - Method in class ij.gui.GenericDialog
 
setDefaultStrokeWidth(double) - Static method in class ij.gui.Roi
Sets the default stroke width.
setDefaultStyle(int) - Static method in class ij.gui.Arrow
 
setDefaultType(int) - Static method in class ij.gui.PointRoi
 
setDefaultWidth(double) - Static method in class ij.gui.Arrow
 
setDialog(GenericDialog) - Method in class ij.plugin.filter.PlugInFilterRunner
 
setDimensions(int, int, int) - Method in class ij.ImagePlus
Sets the 3rd, 4th and 5th dimensions, where nChannels*nSlices*nFrames must be equal to the stack size.
setDirectory(String) - Method in class ij.plugin.FolderOpener
Used by DragAndDrop when a directory is dragged onto the ImageJ window.
setDisplayList(Roi, Color) - Method in class ij.gui.ImageCanvas
Deprecated.
replaced by ImagePlus.setOverlay(Roi, Color, int, Color)
setDisplayList(Shape, Color, BasicStroke) - Method in class ij.gui.ImageCanvas
Deprecated.
replaced by ImagePlus.setOverlay(Shape, Color, BasicStroke)
setDisplayList(Vector) - Method in class ij.gui.ImageCanvas
Deprecated.
replaced by ImagePlus.setOverlay(ij.gui.Overlay)
setDisplayMode(int) - Method in class ij.ImagePlus
Sets the display mode of composite color images, where 'mode' should be IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE.
setDisplayRange(double, double) - Method in class ij.CompositeImage
 
setDisplayRange(double, double) - Method in class ij.ImagePlus
Sets the display range of the current channel.
setDisplayRange(double, double, int) - Method in class ij.ImagePlus
Sets the display range of specified channels in an RGB image, where 4=red, 2=green, 1=blue, 6=red+green, etc.
setDoScaling(boolean) - Static method in class ij.process.ImageConverter
Set true to scale to 0-255 when converting short to byte or float to byte and to 0-65535 when converting float to short.
setDoubleHeaded(boolean) - Method in class ij.gui.Arrow
 
setDraggable(boolean) - Method in class ij.gui.Overlay
Set 'false' to prevent ROIs in this overlay from being dragged by their labels.
setDrawingColor(int, int, boolean) - Method in class ij.gui.ImageCanvas
Sets the foreground drawing color (or background color if 'setBackground' is true) to the color of the pixel at (ox,oy).
setDrawingSize(int, int) - Method in class ij.gui.ImageCanvas
Obsolete; replaced by setSize()
setDrawOffset(boolean) - Method in class ij.gui.Roi
Deprecated.
This method was previously used to draw lines and polylines shifted by 0.5 pixels top the bottom and right, for better agreement with the position used by ProfilePlot, with the default taken from Prefs.subPixelResolution. Now the shift is independent of this setting and only depends on the ROI type (area or line/point ROI).
setDrawStringMode(boolean) - Method in class ij.gui.TextRoi
 
setEchoChar(char) - Method in class ij.gui.GenericDialog
Sets the echo character for the next string field.
setEditMode(ImagePlus, boolean) - Method in class ij.plugin.frame.RoiManager
 
setEditor(Editor) - Method in class ij.macro.MacroRunner
Use the specified Editor to run the macro in debug mode.
setEscapeChar(char) - Method in class ij.util.WildcardMatch
Sets the new character to be used as an escape character, overriding the the default of '\'.
setExceptionHandler(IJ.ExceptionHandler) - Static method in class ij.IJ
Installs a custom exception handler that overrides the handleException() method.
setExtension(String, String) - Static method in class ij.io.SaveDialog
 
setExtraArrayElements(int) - Method in class ij.measure.Minimizer
Add a given number of extra elements to array of parameters (independent vaiables) for private use in the user function.
setf(int, float) - Method in class ij.process.ByteProcessor
 
setf(int, float) - Method in class ij.process.ColorProcessor
 
setf(int, float) - Method in class ij.process.FloatProcessor
 
setf(int, float) - Method in class ij.process.ImageProcessor
 
setf(int, float) - Method in class ij.process.ShortProcessor
 
setf(int, int, float) - Method in class ij.process.ByteProcessor
 
setf(int, int, float) - Method in class ij.process.ColorProcessor
 
setf(int, int, float) - Method in class ij.process.FloatProcessor
 
setf(int, int, float) - Method in class ij.process.ImageProcessor
Sets the value of the pixel at (x,y) to 'value'.
setf(int, int, float) - Method in class ij.process.ShortProcessor
 
setFileInfo(FileInfo) - Method in class ij.ImagePlus
Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo().
setFileName(String) - Method in class ij.plugin.MacroInstaller
 
setFilePath(String) - Static method in class ij.plugin.Macro_Runner
 
setFillColor(Color) - Method in class ij.gui.Overlay
Sets the fill color of all the ROIs in this overlay.
setFillColor(Color) - Method in class ij.gui.Roi
Sets the fill color used to display this ROI, or set to null to display it transparently.
setFlattenScale(double) - Method in class ij.gui.Roi
 
setFloatArray(float[][]) - Method in class ij.process.ImageProcessor
Replaces the pixel data with contents of the specified 2D float array.
setFocusable(boolean) - Method in class ij.gui.ScrollbarWithLabel
 
setFont(char, Font) - Method in class ij.gui.Plot
Sets the font for xLabel ('x'), yLabel('y'), numbers ('f' for 'frame') or the legend ('l')
setFont(int, float) - Method in class ij.gui.Plot
Sets the font size and style for all following addLabel() etc.
setFont(Font) - Method in class ij.gui.GenericDialog
 
setFont(Font) - Method in class ij.gui.MultiLineLabel
 
setFont(Font) - Method in class ij.gui.Plot
Sets the font for all following addLabel() etc.
setFont(Font) - Method in class ij.gui.TextRoi
Sets the current font.
setFont(Font) - Method in class ij.plugin.frame.Editor
 
setFont(Font) - Method in class ij.process.ImageProcessor
Sets the font used by drawString().
setFont(Font, boolean) - Method in class ij.text.TextPanel
 
setFont(String, int, int) - Static method in class ij.gui.TextRoi
Sets the global font face, size and style that will be used by TextROIs interactively created using the text tool.
setFont(String, int, int) - Static method in class ij.text.TextWindow
 
setFont(String, int, int, boolean) - Static method in class ij.gui.TextRoi
Sets the font face, size, style and antialiasing mode that will be used by TextROIs interactively created using the text tool.
setFontColor(String) - Static method in class ij.plugin.filter.ParticleAnalyzer
Sets the color ("blue", "black", etc.) of the font used to label outlines in the next particle analyzer instance.
setFontSize(int) - Method in class ij.gui.Plot
Sets the font size for all following addLabel() etc.
setFontSize(int) - Method in class ij.gui.TextRoi
Sets the size of the current font.
setFontSize(int) - Static method in class ij.Menus
Set the size (in points) used for the fonts in ImageJ menus.
setFontSize(int) - Static method in class ij.plugin.filter.ParticleAnalyzer
Sets the size of the font used to label outlines in the next particle analyzer instance.
setFontSize(int) - Method in class ij.plugin.MontageMaker
 
setFontSize(int) - Method in class ij.process.ImageProcessor
Sets the size of the font used by drawString().
setForegroundColor(int, int, int) - Static method in class ij.IJ
Sets the foreground color.
setForegroundColor(Color) - Static method in class ij.gui.Toolbar
 
setForegroundColor(Color) - Static method in class ij.plugin.frame.Recorder
 
setForegroundValue(double) - Static method in class ij.gui.Toolbar
Sets the foreground color to grayscale, where value is between 0 (black) and 255 (white).
setFormatFlags(int) - Method in class ij.gui.Plot
Sets the flags that control the axes format.
setFrameSize(int, int) - Method in class ij.gui.Plot
Sets the plot frame size in (unscaled) pixels.
setFromFloatArrays(float[][]) - Method in class ij.process.ByteProcessor
 
setFromFloatProcessors(FloatProcessor[]) - Method in class ij.process.ByteProcessor
 
setFrozen(boolean) - Method in class ij.gui.Plot
Freezes or unfreezes the plot.
setFunction(int, double[], String) - Method in class ij.measure.Calibration
Sets the calibration function, coefficient table and unit (e.g.
setFunction(int, double[], String, boolean) - Method in class ij.measure.Calibration
 
setFunction(UserFunction, int) - Method in class ij.measure.Minimizer
Set the the target function, i.e.
setGlobalBackgroundColor() - Method in class ij.process.ImageProcessor
Sets the global (Color Picker) background color as the fill/draw color.
setGlobalCalibration(Calibration) - Method in class ij.ImagePlus
Sets the system-wide calibration.
setGlobalForegroundColor() - Method in class ij.process.ImageProcessor
Sets the global (Color Picker) foreground color as the fill/draw color.
setGlobalJustification(int) - Static method in class ij.gui.TextRoi
Sets the default text tool justification (LEFT, CENTER or RIGHT).
setGroup(int) - Method in class ij.gui.Roi
Sets the group of this Roi, and updates stroke color accordingly.
setGroup(int) - Method in class ij.plugin.frame.RoiManager
Sets the group for the selected ROIs.
setGroup(String) - Static method in class ij.plugin.frame.RoiManager
Obsolete; replaced by RoiManager.setGroup() macro function.
setGroupName(int, String) - Static method in class ij.gui.Roi
 
setGroupNames(String) - Static method in class ij.gui.Roi
Sets the group names from a comma-delimeted string.
setGuiScale(double) - Static method in class ij.Prefs
Sets the GenericDialog and Command Finder text scale (0.5 to 3.0).
setHandleSize(int) - Method in class ij.gui.Roi
Sets the current handle size.
setHeading(int, String) - Method in class ij.measure.ResultsTable
Deprecated.
Replaced by addValue(String,double) and setValue(String,int,double)
setHeadSize(double) - Method in class ij.gui.Arrow
 
setHelpLabel(String) - Method in class ij.gui.GenericDialog
Sets a replacement label for the "Help" button.
setHideLabels(boolean) - Method in class ij.gui.PointRoi
Deprecated. 
setHideOutputImage(boolean) - Method in class ij.plugin.filter.ParticleAnalyzer
Set 'hideOutputImage' true to not display the "Show:" image.
setHideOverlay(boolean) - Method in class ij.ImagePlus
 
setHistogramRange(double, double) - Method in class ij.process.ImageProcessor
Set the range used for histograms of float images.
setHistogramSize(int) - Method in class ij.process.ImageProcessor
Set the number of bins to be used for histograms of float images.
setHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Sets the current pixels from 3 byte arrays (hue, saturation and brightness).
setHSB(float[], float[], float[]) - Method in class ij.process.ColorProcessor
Sets the current pixels from 3 float arrays (hue, saturation and brightness).
setIcon(String, String) - Static method in class ij.gui.Toolbar
Sets the icon of the specified macro or plugin tool.
See: Help>Examples>Tool>Animated Icon Tool;
setIgnoreClipRect(boolean) - Method in class ij.gui.Roi
 
setIgnoreErrors(boolean) - Method in class ij.macro.Interpreter
 
setIgnoreFlush(boolean) - Method in class ij.ImagePlus
 
setIgnoreGlobalCalibration(boolean) - Method in class ij.ImagePlus
 
setIJMenuBar - Variable in class ij.ImagePlus
 
setIJMenuBar - Static variable in class ij.Prefs
Set MenuBar on Macs running Java 8.
setIJMenuBar() - Method in class ij.ImagePlus
 
setIJMenuBar(boolean) - Method in class ij.ImagePlus
 
setIm5D(boolean) - Method in class ij.plugin.Concatenator
 
setImage(ImagePlus) - Method in class ij.gui.ImageWindow
 
setImage(ImagePlus) - Method in class ij.gui.Roi
Sets the ImagePlus associated with this ROI.
setImage(ImagePlus) - Method in class ij.ImagePlus
Replaces this image with the specified ImagePlus.
setImage(ImagePlus) - Method in class ij.measure.Calibration
Disables the density calibation if the specified image has a differenent bit depth.
setImage(ImagePlus) - Method in class ij.plugin.ZProjector
Explicitly set image to be projected.
setImage(Image) - Method in class ij.ImagePlus
Replaces the image, if any, with the one specified.
setImageJMenuBar(ImageWindow) - Static method in class ij.gui.ImageWindow
 
setImagePlus(ImagePlus) - Method in class ij.gui.Plot
Sets the ImagePlus where the plot will be displayed.
setImagesURL(String) - Static method in class ij.Prefs
Sets the URL of the directory that contains the ImageJ sample images.
setImageUpdated() - Method in class ij.gui.ImageCanvas
ImagePlus.updateAndDraw calls this method to force the paint() method to update the image from the ImageProcessor.
setIndexes(int[]) - Method in class ij.VirtualStack
Sets the table that translates slice numbers of hyperstacks not in default CZT order.
setInitialParameters(double[]) - Method in class ij.measure.CurveFitter
Sets the initial parameters, which override the default initial parameters.
setInputEvent(InputEvent) - Static method in class ij.IJ
 
setInsets(int, int, int) - Method in class ij.gui.GenericDialog
Set the insets (margins), in pixels, that will be used for the next component added to the dialog (except components added to the same row with addToSameRow)
setInstanceColor(Color) - Method in class ij.gui.Roi
Deprecated.
replaced by setStrokeColor()
setIntArray(int[][]) - Method in class ij.process.ImageProcessor
Replaces the pixel data with contents of the specified 2D int array.
setInterpolate(boolean) - Method in class ij.process.ImageProcessor
This method has been replaced by setInterpolationMethod().
setInterpolationMethod(int) - Method in class ij.process.ImageProcessor
Use this method to set the interpolation method (NONE, BILINEAR or BICUBIC) used by scale(), resize() and rotate().
setInvertY(boolean) - Method in class ij.measure.Calibration
Sets the 'invertY' flag.
setIsCalibrationBar(boolean) - Method in class ij.gui.Overlay
 
setIsCursor(boolean) - Method in class ij.gui.Roi
 
setIsMacroWindow(boolean) - Method in class ij.plugin.frame.Editor
 
setIsResultsTable(boolean) - Method in class ij.measure.ResultsTable
 
setJpegQuality(int) - Static method in class ij.io.FileSaver
Specifies the image quality (0-100).
setJustification(int) - Method in class ij.gui.Plot
Sets the justification used by addLabel(), where justification is Plot.LEFT, Plot.CENTER or Plot.RIGHT.
setJustification(int) - Method in class ij.gui.TextRoi
Sets the 'justification' instance variable (LEFT, CENTER or RIGHT)
setJustification(int) - Method in class ij.process.ImageProcessor
Sets the justification used by drawString(), where justification is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY.
setKeyDown(int) - Static method in class ij.IJ
 
setKeyUp(int) - Static method in class ij.IJ
 
setLabel(int, String) - Method in class ij.gui.Plot
Sets the label for the plot object nuber 'index' in the sequence they were added.
setLabel(String, int) - Method in class ij.measure.ResultsTable
Adds a label to the beginning of the specified row, or updates an existing lable, where 0<=row
setLabelColor(Color) - Method in class ij.gui.Overlay
 
setLabelFont(Font) - Method in class ij.gui.Overlay
 
setLabelFont(Font, boolean) - Method in class ij.gui.Overlay
 
setLabelFontSize(int, String) - Method in class ij.gui.Overlay
Set the label font size with options.
setLastDirectory(String) - Static method in class ij.io.OpenDialog
Sets the path to the directory containing the last file opened by the user.
setLastName(String) - Static method in class ij.io.OpenDialog
Sets the name of the last file opened by the user.
setLegend(String, int) - Method in class ij.gui.Plot
Adds a legend.
setLimits(double[]) - Method in class ij.gui.Plot
Sets the current limits from an array xMin, xMax, yMin, yMax The array may be also longer or shorter, but should not contain NaN values.
setLimits(double, double, double, double) - Method in class ij.gui.Plot
Sets the x-axis and y-axis range.
setLimits(double, double, double, double) - Method in class ij.gui.PlotWindow
Deprecated.
use the corresponding method of the Plot class
setLimitsToDefaults(boolean) - Method in class ij.gui.Plot
Sets the plot range to the initial value determined from minima&maxima or given by setLimits.
setLimitsToFit(boolean) - Method in class ij.gui.Plot
Sets the plot range to encompass all data.
setLine(int, String) - Method in class ij.text.TextPanel
Replaces the contents of the specified line, where 'index' must be greater than or equal to zero and less than the value returned by getLineCount().
setLineWidth(float) - Method in class ij.gui.Plot
Changes the line width for the next objects that will be added to the plot.
setLineWidth(int) - Method in class ij.gui.Plot
Changes the line width for the next objects that will be added to the plot.
setLineWidth(int) - Method in class ij.gui.PlotWindow
Deprecated.
use the corresponding method of the Plot class
setLineWidth(int) - Method in class ij.gui.Roi
Deprecated.
replaced by setStrokeWidth(int)
setLineWidth(int) - Static method in class ij.plugin.filter.ParticleAnalyzer
Sets the outline line width for the next ParticleAnalyzer instance.
setLineWidth(int) - Method in class ij.process.ImageProcessor
Sets the line width used by lineTo() and drawDot().
setLocation(double, double) - Method in class ij.gui.Line
Sets the x coordinate of the leftmost and y coordinate of the topmost end point
setLocation(double, double) - Method in class ij.gui.PolygonRoi
 
setLocation(double, double) - Method in class ij.gui.Roi
Set the location of the ROI in image coordinates.
setLocation(int, int) - Method in class ij.gui.GenericDialog
 
setLocation(int, int) - Method in class ij.gui.ImageWindow
 
setLocation(int, int) - Method in class ij.gui.Line
 
setLocation(int, int) - Method in class ij.gui.Roi
Set the location of the ROI in image coordinates.
setLocation(int, int) - Method in class ij.gui.TextRoi
 
setLocationAndSize(int, int, int, int) - Method in class ij.gui.ImageWindow
Moves and resizes this window.
setLogScaleX() - Method in class ij.gui.Plot
Sets log scale in x.
setLogScaleY() - Method in class ij.gui.Plot
 
setLongClickDelay(int) - Static method in class ij.gui.ImageCanvas
Sets the context menu long click delay in milliseconds (default is 1000).
setLongClickDelay(int) - Static method in class ij.gui.Toolbar
Sets the tool menu long click delay in milliseconds (default is 600).
setLookAndFeel(LookAndFeel) - Static method in class ij.util.Java2
Sets the Swing look and feel.
setLoopBackAndForth(boolean) - Static method in class ij.measure.Calibration
Set the default state of the animation "Loop back and forth" flag
setLut(LUT) - Method in class ij.ImagePlus
Assigns a LUT (lookup table) to this image.
setLut(LUT) - Method in class ij.process.ImageProcessor
 
setLutAnimation(boolean) - Method in class ij.process.FloatProcessor
 
setLutAnimation(boolean) - Method in class ij.process.ImageProcessor
For 16 and 32 bit processors, set 'lutAnimation' true to have createImage() use the cached 8-bit version of the image.
setLutAnimation(boolean) - Method in class ij.process.ShortProcessor
 
setLuts(LUT[]) - Method in class ij.CompositeImage
 
setMagnification(double) - Method in class ij.gui.ImageCanvas
 
setMagnification(double) - Method in class ij.gui.PlotCanvas
The image of a PlotCanvas is always shown at 100% magnification unless the plot is frozen
setMask(ImageProcessor) - Method in class ij.process.ImageProcessor
Defines a byte mask that limits processing to an irregular ROI.
setMaxError(double) - Method in class ij.measure.CurveFitter
Set the maximum error.
setMaxError(double) - Method in class ij.measure.Minimizer
Sets the accuracy of convergence.
setMaxError(double, double) - Method in class ij.measure.Minimizer
Sets the accuracy of convergence.
setMaximum(int) - Method in class ij.gui.ScrollbarWithLabel
 
setMaximumThreads(int) - Method in class ij.measure.Minimizer
Call setMaximuThreads(1) to avoid multi-threaded execution (in case the user-provided target function does not allow moultithreading).
setMaxIntervals(int) - Method in class ij.gui.Plot
Sets the maximum number of intervals in a plot.
setMaxIterations(int) - Method in class ij.measure.CurveFitter
Set maximum number of iterations allowed (sum of iteration count for all restarts)
setMaxIterations(int) - Method in class ij.measure.Minimizer
Set maximum number of iterations allowed (including all restarts and all threads).
setMaxRestarts(int) - Method in class ij.measure.Minimizer
Set maximum number of minimization restarts to do.
setMeasurement(int, boolean) - Static method in class ij.plugin.filter.Analyzer
Sets the specified system-wide measurement option.
setMeasurements(int) - Static method in class ij.plugin.filter.Analyzer
Sets the system-wide measurement options.
setMenuBarCount - Static variable in class ij.Menus
 
setMenuBarTime - Static variable in class ij.gui.ImageWindow
 
setMethod(int) - Method in class ij.plugin.ZProjector
 
setMethod(String) - Static method in class ij.plugin.frame.ThresholdAdjuster
Sets the thresholding method ("Default", "Huang", etc).
setMethod(String) - Static method in class ij.plugin.Thresholder
 
setMinAndMax(double, double) - Static method in class ij.gui.ProfilePlot
Sets the y-axis min and max.
setMinAndMax(double, double) - Static method in class ij.IJ
Sets the display range (minimum and maximum displayed pixel values) of the current image.
setMinAndMax(double, double) - Method in class ij.process.ByteProcessor
Maps the entries in this image's LUT from min-max to 0-255.
setMinAndMax(double, double) - Method in class ij.process.ColorProcessor
Uses a table look-up to map the pixels in this image from min-max to 0-255.
setMinAndMax(double, double) - Method in class ij.process.FloatProcessor
Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double) - Method in class ij.process.ImageProcessor
This image will be displayed by mapping pixel values in the range min-max to screen values in the range 0-255.
setMinAndMax(double, double) - Method in class ij.process.ShortProcessor
Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double, int) - Static method in class ij.IJ
Sets the minimum and maximum displayed pixel values on the specified RGB channels, where 4=red, 2=green and 1=blue.
setMinAndMax(double, double, int) - Method in class ij.process.ColorProcessor
 
setMinAndMax(double, double, int) - Method in class ij.process.IntProcessor
 
setMinAndMax(ImagePlus, double, double) - Static method in class ij.IJ
Sets the display range (minimum and maximum displayed pixel values) of the specified image.
setMinimum(int) - Method in class ij.gui.ScrollbarWithLabel
 
setMinorTickLength(int) - Method in class ij.gui.Plot
Sets the length of the minor tick in pixels.
setMode(int) - Method in class ij.CompositeImage
 
setMode(String) - Static method in class ij.plugin.frame.ThresholdAdjuster
Sets the current mode ("Red","B&W" or"Over/Under").
setMonospaced(boolean) - Static method in class ij.text.TextWindow
 
setName(String) - Method in class ij.gui.Roi
Sets the name of this ROI.
setNaNEmptyCells(boolean) - Method in class ij.measure.ResultsTable
Set 'true' to initially fill data arrays with NaNs instead of zeros.
setNextLocation(int, int) - Static method in class ij.gui.ImageWindow
Causes the next image to be displayed at the specified location.
setNextLocation(int, int) - Static method in class ij.gui.WaitForUserDialog
Display the next WaitForUser dialog at the specified location.
setNextLocation(Point) - Static method in class ij.gui.ImageWindow
Causes the next image to be displayed at the specified location.
setNonScalable(boolean) - Method in class ij.gui.Roi
Set 'nonScalable' true to have TextRois in a display list drawn at a fixed location and size.
setNormalize(boolean) - Method in class ij.plugin.ContrastEnhancer
 
setNormalize(boolean) - Method in class ij.plugin.filter.Convolver
If 'normalize' is true (the default), the convolve(), convolveFloat() and convolveFloat1D() (4 argument version) methods divide each kernel coefficient by the sum of the coefficients, preserving image brightness.
setNPasses(int) - Method in class ij.plugin.filter.BackgroundSubtracter
 
setNPasses(int) - Method in class ij.plugin.filter.Binary
 
setNPasses(int) - Method in class ij.plugin.filter.Convolver
 
setNPasses(int) - Method in class ij.plugin.filter.EDM
Prepare the progress bar.
setNPasses(int) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
This method is called by ImageJ to inform the plugin-filter about the passes to its run method.
setNPasses(int) - Method in class ij.plugin.filter.GaussianBlur
Set the number of passes of the blur1Direction method.
setNPasses(int) - Method in class ij.plugin.filter.ImageMath
 
setNPasses(int) - Method in class ij.plugin.filter.MaximumFinder
Set his to the number of images to process (for the watershed progress bar only).
setNPasses(int) - Method in class ij.plugin.filter.RankFilters
This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar.
setNPasses(int) - Method in class ij.plugin.filter.Rotator
 
setNPasses(int) - Method in class ij.plugin.filter.StackLabeler
 
setNPasses(int) - Method in class ij.plugin.filter.Translator
 
setNPasses(int) - Method in class ij.plugin.filter.UnsharpMask
Since most computing time is spent in GaussianBlur, forward the information about the number of passes to Gaussian Blur.
setOffsetMultiplySlopeParams(int, int, int) - Method in class ij.measure.CurveFitter
For improved fitting performance when using a custom fit formula, one may specify parameters that can be calculated directly by linear regression.
setOKLabel(String) - Method in class ij.gui.GenericDialog
Sets a replacement label for the "OK" button.
setOpacity(double) - Method in class ij.gui.ImageRoi
Sets the composite mode using the specified opacity (alpha), in the range 0.0-1.0, where 0.0 is fully transparent and 1.0 is fully opaque.
setOpenAsHyperStack(boolean) - Method in class ij.ImagePlus
 
setOpenUsingPlugins(boolean) - Static method in class ij.io.Opener
Open all images using HandleExtraFileTypes.
setOption(String, boolean) - Static method in class ij.plugin.filter.Analyzer
 
setOptions(String) - Method in class ij.gui.Plot
Sets options for the plot.
setOptions(String) - Method in class ij.gui.PointRoi
 
setOptions(String) - Method in class ij.ImageStack
 
setOptions(String) - Static method in class ij.Macro
Define a set of Macro options for the current Thread.
setOptions(Thread, String) - Static method in class ij.Macro
Define a set of Macro options for a Thread.
setOutline(boolean) - Method in class ij.gui.Arrow
 
setOutputType(int) - Static method in class ij.plugin.filter.EDM
Sets the output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
setOverColor(int, int, int) - Static method in class ij.process.ImageProcessor
Sets the upper Over/Under threshold color.
setOverlay(Overlay) - Method in class ij.gui.ImageCanvas
Use ImagePlus.setOverlay(ij.gui.Overlay).
setOverlay(Overlay) - Method in class ij.ImagePlus
Installs a list of ROIs that will be drawn on this image as a non-destructive overlay.
setOverlay(Overlay) - Method in class ij.plugin.frame.RoiManager
 
setOverlay(Overlay) - Method in class ij.process.ImageProcessor
This method is used to display virtual stack overlays.
setOverlay(Roi, Color, int, Color) - Method in class ij.ImagePlus
Creates an Overlay from the specified ROI, and assigns it to this image.
setOverlay(Shape, Color, BasicStroke) - Method in class ij.ImagePlus
Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image.
setPaintPending(boolean) - Method in class ij.gui.ImageCanvas
 
setParamResolutions(double[]) - Method in class ij.measure.Minimizer
Set the resolution of the parameters, for problems where the target function is not smooth but suffers from numerical noise.
setPasteMode(int) - Static method in class ij.gui.Roi
Sets the Paste transfer mode.
setPasteMode(String) - Static method in class ij.IJ
Sets the transfer mode used by the Edit/Paste command, where mode is "Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide".
setPixels(int, FloatProcessor) - Method in class ij.process.ByteProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(int, FloatProcessor) - Method in class ij.process.ColorProcessor
Sets the pixels of one color channel from a FloatProcessor.
setPixels(int, FloatProcessor) - Method in class ij.process.FloatProcessor
Sets the pixels, and min&max values from a FloatProcessor.
setPixels(int, FloatProcessor) - Method in class ij.process.ImageProcessor
Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
setPixels(int, FloatProcessor) - Method in class ij.process.ShortProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object) - Method in class ij.process.ByteProcessor
 
setPixels(Object) - Method in class ij.process.ColorProcessor
 
setPixels(Object) - Method in class ij.process.FloatProcessor
 
setPixels(Object) - Method in class ij.process.ImageProcessor
Sets a new pixel array for the image.
setPixels(Object) - Method in class ij.process.ShortProcessor
 
setPixels(Object, int) - Method in class ij.gui.PlotVirtualStack
 
setPixels(Object, int) - Method in class ij.ImageStack
Assigns a pixel array to the specified slice, where 1<=n<=nslices.
setPixels(Object, int) - Method in class ij.VirtualStack
Assigns a pixel array to the specified slice, where 1<=n<=nslices.
setPlot(Plot) - Method in class ij.gui.PlotCanvas
Tells the PlotCanvas which plot to use for zooming etc.
setPlot(Plot) - Method in class ij.gui.PlotWindow
Sets the Plot object shown in this PlotWindow.
setPlot(Plot) - Method in class ij.ImagePlus
 
setPlotMaker(PlotMaker) - Method in class ij.gui.Plot
 
setPlotObjectLabel(int, String) - Method in class ij.gui.Plot
Set the label the i-th PlotObject (in the sequence how they were added, including hidden ones) PlotObjects here refers to curves, arrows, labels etc.
setPlotObjectStyle(int, String) - Method in class ij.gui.Plot
 
setPointType(int) - Method in class ij.gui.PointRoi
Sets the point type (0=hybrid, 1=cross, 2=dot, 3=circle).
setPolygon(float[], float[], int, double, double) - Method in class ij.process.PolygonFiller
Specifies the polygon to be filled in case of float coordinates.
setPolygon(int[], int[], int) - Method in class ij.process.PolygonFiller
Specifies the polygon to be filled.
setPosition(int) - Method in class ij.gui.Roi
Sets the stack position (image number) of this ROI.
setPosition(int) - Method in class ij.ImagePlus
Set the current hyperstack position based on the stack index 'n' (one-based).
setPosition(int) - Method in class ij.plugin.frame.RoiManager
Sets the position for the selected ROIs.
setPosition(int, int, int) - Method in class ij.gui.Roi
Sets the hyperstack position of this ROI.
setPosition(int, int, int) - Method in class ij.gui.StackWindow
 
setPosition(int, int, int) - Method in class ij.ImagePlus
Sets the current hyperstack position and updates the display, where 'channel', 'slice' and 'frame' are one-based indexes.
setPosition(ImagePlus) - Method in class ij.gui.Roi
Sets the position of this ROI based on the stack position of the specified image.
setPositionWithoutUpdate(int, int, int) - Method in class ij.ImagePlus
Sets the current hyperstack position without updating the display, where 'channel', 'slice' and 'frame' are one-based indexes.
setPrecision(int) - Method in class ij.measure.ResultsTable
Sets the decimal places (digits to the right of decimal point) that are used when this table is displayed.
setPrecision(int) - Static method in class ij.plugin.filter.Analyzer
Sets the number of digits displayed to the right of decimal point.
setPreviousMinMax() - Method in class ij.gui.Plot
reverts plot range to previous values and updates the image
setPreviousRoi(Roi) - Static method in class ij.gui.Roi
Saves 'roi' so it can be restored later using Edit/Selection/Restore Selection.
setPreviousTextRoi(Roi) - Method in class ij.gui.TextRoi
 
setProcessor(ImageProcessor) - Method in class ij.gui.ImageRoi
 
setProcessor(ImageProcessor) - Method in class ij.ImagePlus
Replaces the ImageProcessor with the one specified and updates the display.
setProcessor(ImageProcessor, int) - Method in class ij.ImageStack
Assigns the pixel array of an ImageProcessor to the specified slice, where 1<=n<=nslices.
setProcessor(String, ImageProcessor) - Method in class ij.ImagePlus
Replaces the ImageProcessor with the one specified and updates the display.
setProcessStack(boolean) - Method in class ij.plugin.ContrastEnhancer
 
setProgressBar(ProgressBar) - Method in class ij.process.ImageProcessor
Assigns a progress bar to this processor.
setProp(String, double) - Method in class ij.ImagePlus
Saves a persistent numeric propery.
setProp(String, String) - Method in class ij.ImagePlus
Adds a key-value pair to this image's string properties.
setProperties(String) - Method in class ij.gui.Roi
 
setProperties(String[]) - Method in class ij.ImagePlus
Creates a set of image properties from an array of strings.
setProperty(String, Object) - Static method in class ij.IJ
Adds a key-value pair to IJ.properties.
setProperty(String, Object) - Method in class ij.ImagePlus
Adds a key-value pair to this image's properties.
setProperty(String, String) - Method in class ij.gui.Roi
 
setPrototypeOverlay(Overlay) - Method in class ij.gui.Roi
 
setQuality(int) - Static method in class ij.plugin.JpegWriter
 
setRandomSeed(double) - Static method in class ij.process.ImageProcessor
 
setRandomSeed(int) - Method in class ij.measure.Minimizer
Set a seed to initialize the random number generator, which is used for initialization of the simplex.
setRawThreshold(ImagePlus, double, double) - Static method in class ij.IJ
This is a version of setThreshold() that uses raw (uncalibrated) values in the range 0-255 for 8-bit images and 0-65535 for 16-bit images and the "Red" LUT display mode.
setRawThreshold(ImagePlus, double, double, String) - Static method in class ij.IJ
This is a version of setThreshold() that always uses raw (uncalibrated) values in the range 0-255 for 8-bit images and 0-65535 for 16-bit images.
setRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer
Set the "Redirect To" image.
setRejectMacrosMsg(String) - Method in class ij.plugin.frame.Editor
 
setRenderingHint(Graphics2D) - Method in class ij.gui.Roi
 
setRestarts(int) - Method in class ij.measure.CurveFitter
Set maximum number of simplex restarts to do.
setResultsTable(ResultsTable) - Static method in class ij.plugin.filter.Analyzer
 
setResultsTable(ResultsTable) - Static method in class ij.plugin.filter.ParticleAnalyzer
Sets the ResultsTable to be used by the next ParticleAnalyzer instance.
setResultsTable(ResultsTable) - Method in class ij.text.TextPanel
Sets the ResultsTable associated with this TextPanel.
setRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Sets the current pixels from 3 byte arrays (reg, green, blue).
setRGBWeights(double[]) - Method in class ij.process.ColorProcessor
This is a thread-safe (non-static) version of setWeightingFactors().
setRGBWeights(double, double, double) - Method in class ij.process.ColorProcessor
This is a thread-safe (non-static) version of setWeightingFactors().
setRoi(int, int, int, int) - Method in class ij.ImagePlus
Creates a rectangular selection.
setRoi(int, int, int, int) - Method in class ij.process.ImageProcessor
Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoi(Roi) - Method in class ij.ImagePlus
Assigns the specified ROI to this image and displays it.
setRoi(Roi) - Method in class ij.process.ImageProcessor
Defines a non-rectangular region of interest that will consist of a rectangular ROI and a mask.
setRoi(Roi, boolean) - Method in class ij.ImagePlus
Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.
setRoi(Roi, int) - Method in class ij.plugin.frame.RoiManager
Replaces the ROI at the specified index.
setRoi(Polygon) - Method in class ij.process.ImageProcessor
Defines a polygonal region of interest that will consist of a rectangular ROI and a mask.
setRoi(Rectangle) - Method in class ij.ImagePlus
Creates a rectangular selection.
setRoi(Rectangle) - Method in class ij.ImageStack
 
setRoi(Rectangle) - Method in class ij.process.ImageProcessor
Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoiManager(RoiManager) - Static method in class ij.plugin.filter.ParticleAnalyzer
Sets the RoiManager to be used by the next ParticleAnalyzer instance.
setRotationCenter(double, double) - Method in class ij.gui.Roi
 
setRoundRectArcSize(int) - Method in class ij.gui.Roi
Obsolete; replaced by setCornerDiameter().
setRoundRectArcSize(int) - Static method in class ij.gui.Toolbar
Sets the rounded rectangle corner diameter (pixels).
setScale(float) - Method in class ij.gui.Plot
Sets the scale.
setScaleToFit(boolean) - Method in class ij.gui.ImageCanvas
 
setScaleWhenConverting(boolean) - Method in class ij.plugin.RGBStackMerge
 
setSelectedIndexes(int[]) - Method in class ij.plugin.frame.RoiManager
Selects multiple ROIs, where 'indexes' is an array of integers, each greater than or equal to 0 and less than the value returned by getCount().
setSelection(int, int) - Method in class ij.text.TextPanel
Creates a selection and insures it is visible.
setShowAllColor(Color) - Static method in class ij.gui.ImageCanvas
Obsolete
setShowAllList(Overlay) - Method in class ij.gui.ImageCanvas
 
setShowAllROIs(boolean) - Method in class ij.gui.ImageCanvas
Obsolete
setShowConflictMessage(boolean) - Static method in class ij.io.FileOpener
 
setShowCursorStatus(boolean) - Method in class ij.gui.ImageCanvas
Called by IJ.showStatus() to prevent status bar text from being overwritten until the cursor moves at least 12 pixels.
setShowLabels(boolean) - Method in class ij.gui.PointRoi
 
setShowProgress(boolean) - Method in class ij.process.FHT
Enables/disables display of the progress bar during transforms.
setSigned16BitCalibration() - Method in class ij.measure.Calibration
Sets up a calibration function that subtracts 32,768 from pixel values.
setSilentMode(boolean) - Method in class ij.io.Opener
The "Opening: path" status message is not displayed in silent mode.
setSize(int) - Method in class ij.gui.PointRoi
Sets the point size, where 'size' is 0-6 (Tiny-XXXL).
setSize(int) - Method in class ij.util.ArrayUtil
 
setSize(int, int) - Method in class ij.gui.ImageCanvas
 
setSize(int, int) - Method in class ij.gui.Plot
Sets the canvas size in (unscaled) pixels and sets the scale to 1.0.
setSlice(int) - Static method in class ij.IJ
Switches to the specified stack slice, where 1<='slice'<=stack-size.
setSlice(int) - Method in class ij.ImagePlus
Displays the specified stack image, where 1<=n<=stackSize.
setSliceLabel(String, int) - Method in class ij.ImageStack
Sets the label of the specified slice, where 1<=n<=nslices.
setSliceLabel(String, int) - Method in class ij.VirtualStack
Does nothing.
setSliceNumber(int) - Method in class ij.process.ImageProcessor
PlugInFilterRunner uses this method to set the slice number.
setSliceWithoutUpdate(int) - Method in class ij.ImagePlus
Displays the specified stack image (1<=n<=stackSize) without updating the display.
setSliderHeight(int) - Method in class ij.gui.ImageWindow
 
setSlidersEnabled(boolean) - Method in class ij.gui.StackWindow
Enables or disables the sliders.
setSmartRecording(boolean) - Method in class ij.gui.GenericDialog
Unchanged parameters are not recorder in 'smart recording' mode.
setSnapshotCopyMode(boolean) - Method in class ij.process.ImageProcessor
The getPixelsCopy() method returns a reference to the snapshot buffer if it is not null and 'snapshotCopyMode' is true.
setSnapshotPixels(Object) - Method in class ij.process.ByteProcessor
 
setSnapshotPixels(Object) - Method in class ij.process.ColorProcessor
 
setSnapshotPixels(Object) - Method in class ij.process.FloatProcessor
 
setSnapshotPixels(Object) - Method in class ij.process.ImageProcessor
Sets a new pixel array for the snapshot (undo) buffer.
setSnapshotPixels(Object) - Method in class ij.process.ShortProcessor
 
setSourceRect(Rectangle) - Method in class ij.gui.ImageCanvas
Sets the region of the image (in pixels) to be displayed.
setSourceRect(Rectangle) - Method in class ij.gui.PlotCanvas
Scrolling a PlotCanvas is updating the plot, not viewing part of the plot, unless the plot is frozen
setStack(ImageStack) - Method in class ij.ImagePlus
Replaces the image with the specified stack and updates the display.
setStack(ImageStack, int, int, int) - Method in class ij.ImagePlus
 
setStack(String, ImageStack) - Method in class ij.ImagePlus
Replaces the image with the specified stack and updates the display.
setStart(int, int) - Static method in class ij.plugin.WandToolOptions
 
setStartSlice(int) - Method in class ij.plugin.ZProjector
 
setStatusAndEsc(String, boolean) - Method in class ij.measure.CurveFitter
Create output on the number of iterations in the ImageJ Status line, e.g.
setStatusAndEsc(String, boolean) - Method in class ij.measure.Minimizer
Create output on the number of iterations in the ImageJ Status line, e.g.
setStopSlice(int) - Method in class ij.plugin.ZProjector
 
setStroke(BasicStroke) - Method in class ij.gui.Roi
Sets the Stroke used to draw this ROI.
setStrokeColor(Color) - Method in class ij.gui.Overlay
Sets the stroke color of all the ROIs in this overlay.
setStrokeColor(Color) - Method in class ij.gui.Roi
Sets the color used by this ROI to draw its outline.
setStrokeWidth(double) - Method in class ij.gui.Roi
This is a version of setStrokeWidth() that accepts a double argument.
setStrokeWidth(float) - Method in class ij.gui.Line
 
setStrokeWidth(float) - Method in class ij.gui.Roi
Sets the width of the line used to draw this ROI.
setStrokeWidth(Double) - Method in class ij.gui.Overlay
Sets the stroke width of all the ROIs in this overlay.
setStyle(int) - Method in class ij.gui.Arrow
 
setStyle(int, String) - Method in class ij.gui.Plot
Sets the style of the specified PlotObject (curve, label, etc.) from a comma-delimited string ("color1,color2,lineWidth[,symbol][,hidden]"), where "color2" can be "none" and "symbol" and "hidden" are optional.
setStyle(String) - Method in class ij.gui.Arrow
 
setSummaryTable(ResultsTable) - Static method in class ij.plugin.filter.ParticleAnalyzer
Sets the ResultsTable to be used by the next ParticleAnalyzer instance for the summary.
setSystemLookAndFeel() - Static method in class ij.util.Java2
Sets the Swing look and feel to the system look and feel (Windows only).
setT(int) - Method in class ij.ImagePlus
Sets the hyperstack frame position (one based).
setT(ImageWindow, int) - Static method in class ij.plugin.frame.SyncWindows
 
setTempCurrentImage(ImagePlus) - Static method in class ij.WindowManager
Makes the specified image temporarily the active image for this thread.
setTempCurrentImage(Thread, ImagePlus) - Static method in class ij.WindowManager
Sets a temporary image for the specified thread.
setTemporary() - Method in class ij.ImagePlus
 
setText(String) - Method in class ij.gui.MultiLineLabel
 
setText(String) - Method in class ij.gui.TextRoi
 
setTextPanel(TextPanel) - Static method in class ij.IJ
TextWindow calls this method with a null argument when the "Results" window is closed.
setThreads(int) - Static method in class ij.Prefs
Sets the number of threads (1-32) used by PlugInFilters to process stacks.
setThreshold(double, double) - Static method in class ij.IJ
Sets the lower and upper threshold levels and displays the image using red to highlight thresholded pixels.
setThreshold(double, double) - Method in class ij.process.ImageProcessor
Sets the lower and upper threshold levels using NO_LUT_UPDATE.
setThreshold(double, double, int) - Method in class ij.process.ByteProcessor
 
setThreshold(double, double, int) - Method in class ij.process.FloatProcessor
 
setThreshold(double, double, int) - Method in class ij.process.ImageProcessor
Sets the lower and upper threshold levels.
setThreshold(double, double, int) - Method in class ij.process.ShortProcessor
 
setThreshold(double, double, String) - Static method in class ij.IJ
Sets the lower and upper threshold levels and displays the image using the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
setThreshold(ImagePlus, double, double) - Static method in class ij.IJ
Sets the lower and upper threshold levels of the specified image.
setThreshold(ImagePlus, double, double, String) - Static method in class ij.IJ
Sets the lower and upper threshold levels of the specified image and updates the display using the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
setTickLength(int) - Method in class ij.gui.Plot
Sets the length of the major tick in pixels.
setTimeUnit(String) - Method in class ij.measure.Calibration
Sets the time unit (e.g.
setTitle(String) - Method in class ij.ImagePlus
Sets the image name.
setTitle(String) - Method in class ij.text.TextPanel
 
setTool(int) - Method in class ij.gui.Toolbar
 
setTool(int) - Static method in class ij.IJ
Switches to the specified tool, where id = Toolbar.RECTANGLE (0), Toolbar.OVAL (1), etc.
setTool(String) - Method in class ij.gui.Toolbar
 
setTool(String) - Static method in class ij.IJ
Switches to the specified tool, where 'name' is "rect", "elliptical", "brush", etc.
setTransparentColor(Color) - Method in interface ij.process.Blitter
Sets the transparent color used in the COPY_TRANSPARENT mode (default is Color.white).
setTransparentColor(Color) - Method in class ij.process.ByteBlitter
 
setTransparentColor(Color) - Method in class ij.process.ColorBlitter
 
setTransparentColor(Color) - Method in class ij.process.FloatBlitter
 
setTransparentColor(Color) - Method in class ij.process.ShortBlitter
 
setTransparentIndex(int) - Static method in class ij.Prefs
Sets the transparent index (0-255), or set to -1 to disable transparency.
setType(int) - Method in class ij.ImagePlus
 
setTypeToColor256() - Method in class ij.ImagePlus
 
setUnderColor(int, int, int) - Static method in class ij.process.ImageProcessor
Set the lower Over/Under thresholding color.
setUnit(String) - Method in class ij.measure.Calibration
Sets the default length unit (e.g.
setUnitIncrement(int) - Method in class ij.gui.ScrollbarWithLabel
 
setUnsavedMeasurements(boolean) - Static method in class ij.plugin.filter.Analyzer
 
setUnscalableStrokeWidth(double) - Method in class ij.gui.Roi
Sets the width of the line used to draw this ROI and prevents the width from increasing when the image is zoomed.
setup() - Method in class ij.gui.GenericDialog
 
setup() - Method in class ij.gui.HistogramWindow
 
setup(int, ImagePlus) - Static method in class ij.Undo
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Analyzer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.AVI_Writer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.BackgroundSubtracter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Benchmark
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Binary
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Calibrator
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Convolver
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Duplicater
Deprecated.
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.EDM
Prepare for processing; also called at the very end with argument 'final' to show any newly created output image.
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTCustomFilter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTFilter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filler
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filters
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.FractalBoxCounter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.GaussianBlur
Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageMath
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageProperties
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Info
Deprecated.
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutApplier
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutViewer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.MaximumFinder
Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
 
setup(String, ImagePlus) - Method in interface ij.plugin.filter.PlugInFilter
This method is called once when the filter is loaded.
setup(String, ImagePlus) - Method in class ij.plugin.filter.Printer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.RankFilters
Setup of the PlugInFilter.
setup(String, ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.RoiWriter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Rotator
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.SaltAndPepper
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ScaleDialog
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Shadows
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.StackLabeler
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ThresholdToSelection
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Transformer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Translator
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.UnsharpMask
Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.Writer
Deprecated.
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.XYWriter
 
SETUP_UNDO - Static variable in interface ij.macro.MacroConstants
 
setupDialog(ImagePlus, int) - Static method in class ij.IJ
Displays a "Process all images?" dialog.
setupScroll(int, int) - Method in class ij.gui.ImageCanvas
 
setupScroll(int, int) - Method in class ij.gui.PlotCanvas
overrides ImageCanvas.setupScroll; if plot is not frozen, scrolling modifies the plot data range
setUseBicubic(boolean) - Static method in class ij.process.ImageProcessor
 
setUseStackHistogram(boolean) - Method in class ij.plugin.ContrastEnhancer
 
setValue(double) - Method in class ij.process.ByteProcessor
Sets the default fill/draw value, where 0<=value<=255.
setValue(double) - Method in class ij.process.ColorProcessor
Sets the default fill/draw value, where value is interpreted as an RGB int.
setValue(double) - Method in class ij.process.FloatProcessor
Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ShortProcessor
Sets the default fill/draw value, where 0<=value<=65535).
setValue(int) - Method in class ij.gui.ScrollbarWithLabel
 
setValue(int, int, double) - Method in class ij.measure.ResultsTable
Sets the value of the given column and row, where where 0<=column<=(lastRow+1 and 0<=row<=size().
setValue(int, int, String) - Method in class ij.measure.ResultsTable
Sets the string value of the given column and row, where where 0<=column<=(lastRow+1 and 0<=row<=size().
setValue(String, int, double) - Method in class ij.measure.ResultsTable
Sets the value of the given column and row, where where 0<=row<size().
setValue(String, int, String) - Method in class ij.measure.ResultsTable
Sets the string value of the given column and row, where where 0<=row<size().
setValues(String, double[]) - Method in class ij.measure.ResultsTable
Sets the values of the given column to the values in the array.
setValueUnit(String) - Method in class ij.measure.Calibration
Sets the value unit.
setVariable(String, double) - Method in class ij.macro.Interpreter
 
setVariable(String, String) - Method in class ij.macro.Interpreter
 
setVirtual(boolean) - Method in class ij.plugin.AVI_Reader
Open as virtual stack?
setVisibleAmount(int) - Method in class ij.gui.ScrollbarWithLabel
 
setVoxel(int, int, int, double) - Method in class ij.ImageStack
 
setVoxels(int, int, int, int, int, int, float[]) - Method in class ij.ImageStack
Experimental
setVoxels(int, int, int, int, int, int, float[], int) - Method in class ij.ImageStack
Experimental
setWeightingFactors(double, double, double) - Static method in class ij.process.ColorProcessor
Sets the weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
setWeights(double[]) - Method in class ij.measure.CurveFitter
Sets weights of the data points.
setWidth(double) - Static method in class ij.plugin.tool.OverlayBrushTool
 
setWidth(int) - Static method in class ij.gui.Line
Sets the default line width.
setWildcardChars(char, char) - Method in class ij.util.WildcardMatch
Sets new characters to be used as wildcard characters, overriding the the default of '?' for any single character match and '*' for any amount of characters, including 0 characters.
setWindow(ImageWindow) - Method in class ij.ImagePlus
This method should only be called from an ImageWindow.
setWindow(Frame) - Static method in class ij.WindowManager
The specified frame becomes the front window, the one returnd by getFrontWindow().
setWindow(Window) - Static method in class ij.WindowManager
The specified Window becomes the front window.
setWindowSize(int, int) - Method in class ij.gui.Plot
Sets the plot window size in pixels.
setXLabelFont(Font) - Method in class ij.gui.Plot
Sets the xLabelFont; must not be null.
setXMinorTicks(boolean) - Method in class ij.gui.Plot
Sets whether to show minor ticks on the x axis (if linear).
setXTicks(boolean) - Method in class ij.gui.Plot
Sets whether to show major ticks at the x axis.
setXUnit(String) - Method in class ij.measure.Calibration
Sets the X length unit.
setXYLabels(String, String) - Method in class ij.gui.Plot
Sets the labels of the x and y axes.
setYLabelFont(Font) - Method in class ij.gui.Plot
Sets the yLabelFont; must not be null.
setYMinorTicks(boolean) - Method in class ij.gui.Plot
Sets whether to show minor ticks on the y axis (if linear).
setYTicks(boolean) - Method in class ij.gui.Plot
Sets whether to show major ticks at the y axis.
setYUnit(String) - Method in class ij.measure.Calibration
Sets the Y length unit.
setZ(int) - Method in class ij.ImagePlus
Sets the hyperstack slice position (one based).
setZ(ImageWindow, int) - Static method in class ij.plugin.frame.SyncWindows
 
setZeroTransparent(boolean) - Method in class ij.gui.ImageRoi
 
setZUnit(String) - Method in class ij.measure.Calibration
Sets the Z length unit.
Shadows - Class in ij.plugin.filter
Implements the commands in the Process/Shadows submenu.
Shadows() - Constructor for class ij.plugin.filter.Shadows
 
Shanbhag - ij.process.AutoThresholder.Method
 
SHAPE_DESCRIPTORS - Static variable in interface ij.measure.Measurements
 
SHAPE_ROI_SIZE - Static variable in class ij.io.RoiDecoder
 
ShapeRoi - Class in ij.gui
A subclass of ij.gui.Roi (2D Regions Of Interest) implemented in terms of java.awt.Shape.
ShapeRoi(float[]) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from an array of variable length path segments.
ShapeRoi(int, int, Shape) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from a Shape.
ShapeRoi(Roi) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from an Roi.
ShapeRoi(Shape) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from a Shape.
shapeToRoi() - Method in class ij.gui.ShapeRoi
Attempts to convert this ShapeRoi into a single non-composite Roi.
sharpen() - Method in class ij.process.ImageProcessor
Sharpens the image or ROI using a 3x3 convolution kernel.
sharpenFloat(FloatProcessor, double, float) - Method in class ij.plugin.filter.UnsharpMask
Unsharp Mask filtering of a float image.
SHIFT_LEFT - Static variable in interface ij.macro.MacroConstants
 
SHIFT_RIGHT - Static variable in interface ij.macro.MacroConstants
 
shiftKeyDown() - Static method in class ij.IJ
Returns true if the shift key is down.
SHORT - Static variable in class ij.plugin.filter.EDM
Output type: new 16-bit image
ShortBlitter - Class in ij.process
This class does bit blitting of 16-bit images.
ShortBlitter(ShortProcessor) - Constructor for class ij.process.ShortBlitter
Constructs a ShortBlitter from a ShortProcessor.
SHORTCUT_IN_USE - Static variable in class ij.Menus
 
shortcutInUse(String) - Static method in class ij.Menus
Returns 'true' if this keyboard shortcut is in use.
SHORTCUTS_MENU - Static variable in class ij.Menus
 
ShortProcessor - Class in ij.process
ShortProcessors contain a 16-bit unsigned image and methods that operate on that image.
ShortProcessor(int, int) - Constructor for class ij.process.ShortProcessor
Creates a blank ShortProcessor using the default grayscale LUT that displays zero as black.
ShortProcessor(int, int, boolean) - Constructor for class ij.process.ShortProcessor
Obsolete.
ShortProcessor(int, int, short[], ColorModel) - Constructor for class ij.process.ShortProcessor
Creates a new ShortProcessor using the specified pixel array and ColorModel.
ShortProcessor(int, int, short[], ColorModel, boolean) - Constructor for class ij.process.ShortProcessor
Deprecated.
16 bit images are normally unsigned but signed images can be simulated by subtracting 32768 and using a calibration function to restore the original values.
ShortProcessor(BufferedImage) - Constructor for class ij.process.ShortProcessor
Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage.
ShortStatistics - Class in ij.process
16-bit image statistics, including histogram.
ShortStatistics(ImageProcessor) - Constructor for class ij.process.ShortStatistics
Construct an ImageStatistics object from a ShortProcessor using the standard measurement options (area, mean, mode, min and max).
ShortStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ShortStatistics
Constructs a ShortStatistics object from a ShortProcessor using the specified measurement options.
show() - Method in class ij.gui.HistogramPlot
 
show() - Method in class ij.gui.Plot
Displays the plot in a PlotWindow.
show() - Method in class ij.gui.WaitForUserDialog
 
show() - Method in class ij.ImagePlus
Opens a window to display this image and clears the status bar.
show(double) - Method in class ij.gui.ProgressBar
Updates the progress bar, where abs(progress) should run from 0 to 1.
show(double, boolean) - Method in class ij.gui.ProgressBar
Updates the progress bar, where abs(progress) should run from 0 to 1.
show(int, int) - Method in class ij.gui.ProgressBar
Updates the progress bar, where the length of the bar is set to ((abs(currentIndex)+1)/abs(finalIndex) of the maximum bar length.
show(String) - Method in class ij.ImagePlus
Opens a window to display this image and displays 'statusMessage' in the status bar.
show(String) - Method in class ij.measure.ResultsTable
Displays the contents of this ResultsTable in a window with the specified title, or updates an existing results window.
SHOW_ALL_COLOR - Static variable in class ij.Prefs
 
SHOW_LABELS - Static variable in class ij.io.RoiDecoder
 
SHOW_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display image containing binary masks of measured particles.
SHOW_MESSAGE - Static variable in interface ij.macro.MacroConstants
 
SHOW_MESSAGE_WITH_CANCEL - Static variable in interface ij.macro.MacroConstants
 
SHOW_NONE - Static variable in class ij.plugin.filter.ParticleAnalyzer
Do not display particle outline image.
SHOW_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display image containing outlines of measured particles.
SHOW_OVERLAY_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display filled particle as an overlay.
SHOW_OVERLAY_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display particle outlines as an overlay.
SHOW_PROGRESS - Static variable in interface ij.macro.MacroConstants
 
SHOW_PROGRESS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display a progress bar.
SHOW_RESULTS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display results in the ImageJ console.
SHOW_ROI_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display image containing grayscales masks that identify measured particles.
SHOW_STATUS - Static variable in interface ij.macro.MacroConstants
 
SHOW_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer
Obsolete, replaced by DISPLAY_SUMMARY
SHOW_TEXT - Static variable in interface ij.macro.MacroConstants
 
showAllPoints - Static variable in class ij.Prefs
Ignore stack positions when displaying points.
showAllSliceOnly - Static variable in class ij.Prefs
Only show ROIs associated with current slice in Roi Manager "Show All" mode.
showArrayInspector(int) - Method in class ij.macro.Interpreter
Shows array elements after clicking an array variable in Debug window N.
showCell(int, String) - Method in class ij.text.TextPanel
Updates the scroll bars so that the specified cell is visible.
showCode(String, String) - Static method in class ij.gui.Toolbar
 
showCompositeAdvisory(ImagePlus, String) - Static method in class ij.gui.GUI
 
showDialog() - Method in class ij.gui.GenericDialog
Displays this dialog box.
showDialog() - Method in class ij.gui.NonBlockingGenericDialog
 
showDialog() - Method in class ij.gui.RoiProperties
Displays the dialog box and returns 'false' if the user cancels it.
showDialog() - Method in class ij.plugin.Compiler
 
showDialog() - Method in class ij.plugin.FFTMath
 
showDialog() - Method in class ij.plugin.filter.ParticleAnalyzer
Displays a modal options dialog.
showDialog() - Method in class ij.plugin.NewPlugin
 
showDialog() - Method in class ij.plugin.OverlayLabels
 
showDialog() - Method in class ij.plugin.RoiScaler
 
showDialog(double) - Method in class ij.plugin.RoiRotator
 
showDialog(ImagePlus) - Method in class ij.plugin.filter.Calibrator
 
showDialog(ImagePlus, double) - Method in class ij.plugin.RoiEnlarger
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.BackgroundSubtracter
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Binary
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Convolver
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.EDM
Called by the PlugInFilterRunner after setup.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
This method is called after setup(arg, imp) unless the DONE flag has been set.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.GaussianBlur
Ask the user for the parameters
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.ImageMath
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.MaximumFinder
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.RankFilters
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Rotator
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.StackLabeler
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Translator
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.UnsharpMask
Ask the user for the parameters
showDialog(ImageStack) - Method in class ij.plugin.StackReducer
 
showDialog(Frame) - Method in class ij.gui.PlotContentsDialog
Shows the dialog, with a given parent Frame (may be null)
showDialog(Frame) - Method in class ij.gui.PlotDialog
Asks the user for axis scaling; then replot with new scale on the same ImageProcessor.
showHistogram(ImagePlus, int) - Method in class ij.gui.HistogramWindow
Draws the histogram using the specified title and number of bins.
showHistogram(ImagePlus, int, double, double) - Method in class ij.gui.HistogramWindow
Draws the histogram using the specified title, number of bins and histogram range.
showHistogram(ImagePlus, ImageStatistics) - Method in class ij.gui.HistogramWindow
Draws the histogram using the specified title and ImageStatistics.
showImageDialog(String) - Method in class ij.gui.RoiProperties
 
showList() - Method in class ij.gui.HistogramWindow
 
showList() - Static method in class ij.WindowManager
 
showLogWindow() - Method in class ij.plugin.frame.Editor
 
showMacroFunctions() - Method in class ij.plugin.frame.Editor
 
showMessage(String) - Static method in class ij.IJ
Displays a message in a dialog box titled "Message".
showMessage(String, String) - Static method in class ij.IJ
Displays a message in a dialog box with the specified title.
showMessageWithCancel(String, String) - Static method in class ij.IJ
Displays a message in a dialog box with the specified title.
showOptionsDialog() - Method in class ij.plugin.tool.ArrowTool
 
showOptionsDialog() - Method in class ij.plugin.tool.BrushTool
 
showOptionsDialog() - Method in class ij.plugin.tool.OverlayBrushTool
 
showOptionsDialog() - Method in class ij.plugin.tool.PixelInspectionTool
 
showOptionsDialog() - Method in class ij.plugin.tool.PlugInTool
 
showOptionsDialog() - Method in class ij.plugin.tool.RoiRotationTool
 
showOverlay - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showPopupMenu(MouseEvent, Toolbar) - Method in class ij.plugin.tool.PlugInTool
 
showProgress - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showProgress(boolean) - Method in class ij.plugin.filter.GaussianBlur
 
showProgress(double) - Static method in class ij.IJ
Updates the progress bar, where 0<=progress<=1.0.
showProgress(double) - Method in class ij.process.ImageProcessor
 
showProgress(int, int) - Static method in class ij.IJ
Updates the progress bar, where the length of the bar is set to (currentValue+1)/finalValue of the maximum bar length.
showResults - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showRow(int) - Method in class ij.text.TextPanel
Updates the vertical scroll bar so that the specified row is visible.
showRowIndexes(boolean) - Method in class ij.measure.ResultsTable
 
showRowNumbers() - Method in class ij.measure.ResultsTable
 
showRowNumbers(boolean) - Method in class ij.measure.ResultsTable
 
showSizeDistribution - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showSlice(int) - Method in class ij.gui.StackWindow
Displays the specified slice and updates the stack scrollbar.
showStatus() - Method in class ij.gui.EllipseRoi
 
showStatus() - Method in class ij.gui.Line
 
showStatus() - Method in class ij.gui.Roi
 
showStatus() - Method in class ij.gui.RotatedRectRoi
 
showStatus(boolean) - Method in class ij.plugin.filter.ThresholdToSelection
Determines whether to show status messages and a progress bar
showStatus(String) - Method in class ij.gui.PlotWindow
Shows the text in the coordinate&status readout field at the bottom.
showStatus(String) - Static method in class ij.IJ
Displays a message in the ImageJ status bar.
showStatus(String, String) - Static method in class ij.IJ
Displays a message in the status bar and flashes either the status bar or the active image.
See: http://wsr.imagej.net/macros/FlashingStatusMessages.txt
showTime(ImagePlus, long, String) - Static method in class ij.IJ
 
showTime(ImagePlus, long, String, int) - Static method in class ij.IJ
 
shrink(ImagePlus, int, int, int, int) - Method in class ij.plugin.Binner
 
shrink(ImageProcessor, int, int, int) - Method in class ij.plugin.Binner
 
shuffle(ImagePlus, int) - Method in class ij.plugin.HyperStackConverter
Changes the dimension order of a 4D or 5D stack from the specified order (CTZ, ZCT, ZTC, TCZ or TZC) to the XYCZT order used by ImageJ.
SIGNED_INT - Static variable in class ij.gui.NewImage
 
SignedShortProcessor - Class in ij.process
An extended ShortProcessor that supports signed 16-bit images (experimental).
SignedShortProcessor(int, int) - Constructor for class ij.process.SignedShortProcessor
Creates a blank SignedShortProcessor with the specified dimensions.
SignedShortProcessor(ShortProcessor) - Constructor for class ij.process.SignedShortProcessor
 
SimpleCommands - Class in ij.plugin
This plugin implements the Plugins/Utilities/Unlock, Image/Rename and Plugins/Utilities/Search commands.
SimpleCommands() - Constructor for class ij.plugin.SimpleCommands
 
SIN - Static variable in interface ij.macro.MacroConstants
 
SINGLE_POINTS - Static variable in class ij.plugin.filter.MaximumFinder
Output type single points
sixteenBitRanges - Static variable in class ij.plugin.frame.ContrastAdjuster
 
size() - Method in class ij.gui.Line
Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() - Method in class ij.gui.OvalRoi
Returns the number of corner points in the mask of this selection; equivalent to getPolygon().npoints.
size() - Method in class ij.gui.Overlay
Returns the number of ROIs in this Overlay.
size() - Method in class ij.gui.PolygonRoi
Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() - Method in class ij.gui.Roi
Returns the number of points in this selection; equivalent to getFloatPolygon().npoints.
size() - Method in class ij.gui.ShapeRoi
Retuns the number of vertices, of this shape as approximated by straight lines.
size() - Method in class ij.ImageStack
Returns the number of slices in this stack.
size() - Method in class ij.measure.ResultsTable
Returns the size of this ResultsTable.
size() - Method in class ij.plugin.FileInfoVirtualStack
Returns the number of slices in this stack.
size() - Method in class ij.util.FloatArray
Returns the number of elements in the array.
size() - Method in class ij.VirtualStack
Returns the number of slices in this stack.
SIZE - Static variable in class ij.io.RoiDecoder
 
SIZE_KEY - Static variable in class ij.gui.Arrow
 
sizes - Static variable in class ij.gui.PointRoi
 
skeletonize() - Method in class ij.process.BinaryProcessor
Converts black objects in a binary image to single pixel skeletons.
skeletonize() - Method in class ij.process.ByteProcessor
Converts black objects in a binary image to single pixel skeletons.
skeletonize(int) - Method in class ij.process.BinaryProcessor
Converts objects in a binary image with pixel values of 'forground' (255 or 0) to single pixel skeletons.
skeletonize(int) - Method in class ij.process.ByteProcessor
Converts objects with pixel values of 'forground' (255 or 0) in a binary imager to single pixel skeletons.
skewness - Variable in class ij.process.ImageStatistics
 
SKEWNESS - Static variable in interface ij.measure.Measurements
 
SKEWNESS - Static variable in class ij.measure.ResultsTable
 
skipRawDialog - Static variable in class ij.Prefs
Do not display dialog when opening .raw files
slice - Variable in class ij.gui.StackWindow
 
slice - Variable in class ij.plugin.filter.ParticleAnalyzer
 
SLICE - Static variable in interface ij.measure.Measurements
 
SLICE - Static variable in class ij.measure.ResultsTable
 
sliceLabels - Variable in class ij.io.FileInfo
 
sliceNumber - Variable in class ij.io.FileInfo
 
Slicer - Class in ij.plugin
Implements the Image/Stacks/Reslice command.
Slicer() - Constructor for class ij.plugin.Slicer
 
sliceSelector - Variable in class ij.gui.StackWindow
 
slider - Variable in class ij.gui.GenericDialog
 
smooth() - Method in class ij.process.ImageProcessor
Replaces each pixel with the 3x3 neighborhood mean.
smoothWand - Static variable in class ij.Prefs
Wand tool "Smooth if thresholded" option
snapshot() - Method in class ij.process.ByteProcessor
Make a snapshot of the current image.
snapshot() - Method in class ij.process.ColorProcessor
 
snapshot() - Method in class ij.process.FloatProcessor
 
snapshot() - Method in class ij.process.ImageProcessor
Makes a copy of this image's pixel data that can be later restored using reset() or reset(mask).
snapshot() - Method in class ij.process.ShortProcessor
 
SNAPSHOT - Static variable in interface ij.macro.MacroConstants
 
SNAPSHOT - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter requires a snapshot (copy of the pixels array).
snapshotHeight - Variable in class ij.process.ImageProcessor
 
snapshotMax - Variable in class ij.process.ShortProcessor
 
snapshotMin - Variable in class ij.process.ShortProcessor
 
snapshotPixels - Variable in class ij.process.ByteProcessor
 
snapshotPixels - Variable in class ij.process.ColorProcessor
 
snapshotWidth - Variable in class ij.process.ImageProcessor
 
SOFTWARE - Static variable in class ij.io.TiffDecoder
 
SOLIDITY - Static variable in class ij.measure.ResultsTable
 
sort() - Method in class ij.util.ArrayUtil
 
sort(ImageStack) - Static method in class ij.util.DicomTools
Sorts a DICOM stack by image number.
sort(String) - Method in class ij.measure.ResultsTable
Sorts this table on the specified column, with string support.
sort(String[]) - Static method in class ij.util.StringSorter
Sorts the array.
sortByMetaData(boolean) - Method in class ij.plugin.FolderOpener
 
sortDicom(String[], String[], int) - Method in class ij.VirtualStack
 
sortedTypes - Static variable in class ij.measure.CurveFitter
Nicer sequence of the built-in function types
sortFileList(String[]) - Method in class ij.plugin.FolderOpener
Sorts file names containing numerical components.
sortFileNames(boolean) - Method in class ij.plugin.FolderOpener
 
sortNumerically(String[]) - Static method in class ij.util.StringSorter
Sorts file names containing numerical components.
source - Variable in class ij.process.ImageProcessor
 
south(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
southeast(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
southwest(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
spaceBarDown() - Static method in class ij.IJ
Returns true if the space bar is down.
SPARE1 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE2 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE3 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE4 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE5 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE6 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE7 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE8 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SPARE9 - Static variable in class ij.gui.Toolbar
Obsolete public constants
SpecifyROI - Class in ij.plugin
This plugin implements the Edit/Selection/Specify command.
SpecifyROI() - Constructor for class ij.plugin.SpecifyROI
 
SPLINE_FIT - Static variable in class ij.io.RoiDecoder
 
splineFitLines - Static variable in class ij.Prefs
Automatically spline fit line selections
SplineFitter - Class in ij.measure
This class interpolates a set of points using natural cubic splines (assuming zero second derivatives at end points).
SplineFitter(float[], float[], int) - Constructor for class ij.measure.SplineFitter
 
SplineFitter(float[], float[], int, boolean) - Constructor for class ij.measure.SplineFitter
For closed curves: the first and last y value should be identical; internally, a periodic continuation with a few will be used at both ends
SplineFitter(int[], int[], int) - Constructor for class ij.measure.SplineFitter
 
splinePoints - Variable in class ij.gui.PolygonRoi
 
split(ImagePlus) - Static method in class ij.plugin.ChannelSplitter
Splits the specified image into separate channels.
split(ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
Deprecated; replaced by ij.plugin.ChannelSplitter.
split(ImageStack, boolean) - Method in class ij.plugin.filter.RGBStackSplitter
Deprecated; replaced by ChannelSplitter.splitRGB().
split(String) - Static method in class ij.util.Tools
Splits a string into substrings using the default delimiter set, which is " \t\n\r" (space, tab, newline and carriage-return).
split(String, String) - Static method in class ij.util.Tools
Splits a string into substring using the characters contained in the second argument as the delimiter set.
SPLIT - Static variable in interface ij.macro.MacroConstants
 
splitRGB(ImageStack, boolean) - Static method in class ij.plugin.ChannelSplitter
Splits the specified RGB stack into three 8-bit grayscale stacks.
sqr() - Method in class ij.process.FloatProcessor
 
sqr() - Method in class ij.process.ImageProcessor
Performs a square transform on the image or ROI.
sqr() - Method in class ij.process.ShortProcessor
 
sqrt() - Method in class ij.process.FloatProcessor
 
sqrt() - Method in class ij.process.ImageProcessor
Performs a square root transform on the image or ROI.
sqrt() - Method in class ij.process.ShortProcessor
 
SQRT - Static variable in interface ij.macro.MacroConstants
 
SQRT2 - Static variable in class ij.plugin.filter.EDM
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(2)
SQRT5 - Static variable in class ij.plugin.filter.EDM
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(5)
srcEnd - Variable in class ij.process.DownsizeTable
index of the last point of the source data that should be accessed
srcRect - Variable in class ij.gui.ImageCanvas
 
srcStart - Variable in class ij.process.DownsizeTable
index of the first point of the source data that should be accessed
STACK - Static variable in interface ij.macro.MacroConstants
 
STACK_POSITION - Static variable in interface ij.measure.Measurements
 
STACK_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter requires a stack.
Stack_Statistics - Class in ij.plugin
This plugin implements the Image/Stacks/Statistics command.
Stack_Statistics() - Constructor for class ij.plugin.Stack_Statistics
 
StackCombiner - Class in ij.plugin
This plugin implements the Image/Stacks/Combine command.
StackCombiner() - Constructor for class ij.plugin.StackCombiner
 
StackConverter - Class in ij.process
This class does stack type conversions.
StackConverter(ImagePlus) - Constructor for class ij.process.StackConverter
 
StackEditor - Class in ij.plugin
Implements the AddSlice, DeleteSlice and "Stack to Images" commands.
StackEditor() - Constructor for class ij.plugin.StackEditor
 
StackInserter - Class in ij.plugin
This plugin, which implements the Image/Stacks/Tools/Insert command, inserts an image or stack into another image or stack.
StackInserter() - Constructor for class ij.plugin.StackInserter
 
StackLabeler - Class in ij.plugin.filter
This plugin implements the Image/Stacks/Label command.
StackLabeler() - Constructor for class ij.plugin.filter.StackLabeler
 
StackMaker - Class in ij.plugin
The plugin implements the Image/Stacks/Tools/Montage to Stack command.
StackMaker() - Constructor for class ij.plugin.StackMaker
 
StackPlotter - Class in ij.plugin
 
StackPlotter() - Constructor for class ij.plugin.StackPlotter
 
StackProcessor - Class in ij.process
This class processes stacks.
StackProcessor(ImageStack) - Constructor for class ij.process.StackProcessor
Constructs a StackProcessor from a stack.
StackProcessor(ImageStack, ImageProcessor) - Constructor for class ij.process.StackProcessor
Constructs a StackProcessor from a stack.
StackReducer - Class in ij.plugin
This plugin implements the Image/Stacks/Tools/Reduce command.
StackReducer() - Constructor for class ij.plugin.StackReducer
 
StackReverser - Class in ij.plugin
This plugin implements the Image/Transform/Flip Z and Image/Stacks/Tools/Reverse commands.
StackReverser() - Constructor for class ij.plugin.StackReverser
 
stackStatistics - Variable in class ij.process.ImageStatistics
Used by HistogramWindow
StackStatistics - Class in ij.process
Statistics, including the histogram, of a stack.
StackStatistics(ImagePlus) - Constructor for class ij.process.StackStatistics
Creates a StackStatistics object from a stack, using 256 histogram bins and the entire stack pixel value range.
StackStatistics(ImagePlus, int, double, double) - Constructor for class ij.process.StackStatistics
Creates a StackStatistics object from a stack, using the specified histogram bin count and x-axis range (pixel value tange).
StackWindow - Class in ij.gui
This class is an extended ImageWindow that displays stacks and hyperstacks.
StackWindow(ImagePlus) - Constructor for class ij.gui.StackWindow
 
StackWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.StackWindow
 
StackWriter - Class in ij.plugin
This plugin, which saves the images in a stack as separate files, implements the File/Save As/Image Sequence command.
StackWriter() - Constructor for class ij.plugin.StackWriter
 
STANDALONE - Static variable in class ij.ImageJ
Run as normal application.
start(Callable[]) - Static method in class ij.util.ThreadUtil
Starts all callables for parallel execution (using a ThreadPoolExecutor) without waiting for the results.
startAndJoin(Thread[]) - Static method in class ij.util.ThreadUtil
Start all given threads and wait on each of them until all are done.
startAndJoin(Callable[]) - Static method in class ij.util.ThreadUtil
Starts all callables for parallel execution (using a ThreadPoolExecutor) and waits until each of them has finished.
startPaste(ImagePlus) - Method in class ij.gui.Roi
 
STARTS_WITH - Static variable in interface ij.macro.MacroConstants
 
startServer() - Static method in class ij.OtherInstance
 
startTiming() - Method in class ij.ImagePlus
Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation.
Startup - Class in ij.plugin
This plugin implements the Edit/Options/Startup command.
Startup() - Constructor for class ij.plugin.Startup
 
StartupRunner - Class in ij.macro
Runs the RunAtStartup (created by Edit/Options/Startup) and AutoRun (in StartupMacros) macros.
StartupRunner() - Constructor for class ij.macro.StartupRunner
 
startxd - Variable in class ij.gui.Line
 
startyd - Variable in class ij.gui.Line
 
staticShowChoice - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
stats - Variable in class ij.gui.HistogramWindow
 
STATUS_STRING - Static variable in class ij.measure.Minimizer
Strings describing the status codes
statusBarProtected() - Static method in class ij.IJ
 
STD_DEV - Static variable in interface ij.measure.Measurements
 
STD_DEV - Static variable in class ij.measure.ResultsTable
 
stdDev - Variable in class ij.process.ImageStatistics
 
STEP - Static variable in interface ij.macro.Debugger
 
stop() - Static method in class ij.plugin.Orthogonal_Views
 
str - Variable in class ij.macro.Symbol
 
STRAIGHT_LINE - Static variable in class ij.measure.Calibration
 
STRAIGHT_LINE - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
straighten(ImagePlus, Roi, int) - Method in class ij.plugin.Straightener
 
Straightener - Class in ij.plugin
This plugin implements the Edit/Selection/Straighten command.
Straightener() - Constructor for class ij.plugin.Straightener
 
straightenLine(ImagePlus, int) - Method in class ij.plugin.Straightener
 
straightenLine(ImagePlus, Line, int) - Method in class ij.plugin.Straightener
 
straightenStack(ImagePlus, Roi, int) - Method in class ij.plugin.Straightener
 
stretchHistogram(ImagePlus, double) - Method in class ij.plugin.ContrastEnhancer
 
stretchHistogram(ImageProcessor, double) - Method in class ij.plugin.ContrastEnhancer
 
stretchHistogram(ImageProcessor, double, ImageStatistics) - Method in class ij.plugin.ContrastEnhancer
 
STRING - Static variable in interface ij.macro.MacroConstants
 
STRING_CONSTANT - Static variable in interface ij.macro.MacroConstants
 
STRING_FUNCTION - Static variable in interface ij.macro.MacroConstants
 
stringField - Variable in class ij.gui.GenericDialog
 
stringFunctionIDs - Static variable in interface ij.macro.MacroConstants
 
stringFunctions - Static variable in interface ij.macro.MacroConstants
 
StringSorter - Class in ij.util
A simple QuickSort for String arrays.
StringSorter() - Constructor for class ij.util.StringSorter
 
stringToPasteMode(String) - Static method in class ij.IJ
 
STRIP_BYTE_COUNT - Static variable in class ij.io.TiffDecoder
 
STRIP_OFFSETS - Static variable in class ij.io.TiffDecoder
 
stripLengths - Variable in class ij.io.FileInfo
 
stripOffsets - Variable in class ij.io.FileInfo
 
stroke - Variable in class ij.gui.Roi
 
STROKE_COLOR - Static variable in class ij.io.RoiDecoder
 
STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
 
STROKE_WIDTH - Static variable in class ij.plugin.CalibrationBar
 
strokeColor - Variable in class ij.gui.Roi
 
STYLE - Static variable in class ij.gui.PlotContentsDialog
Types of dialog (ERROR suppresses the dialog after an invalid call of a constructor)
STYLE_KEY - Static variable in class ij.gui.Arrow
 
styles - Static variable in class ij.gui.Arrow
 
SUB_PIXEL_RESOLUTION - Static variable in class ij.io.RoiDecoder
 
SubHyperstackMaker - Class in ij.plugin
This plugin is used by the Image/Stacks/Tools/Make Substack command to create substacks of hyperstacks.
SubHyperstackMaker() - Constructor for class ij.plugin.SubHyperstackMaker
 
subPixelResolution - Static variable in class ij.Prefs
Use sub-pixel resolution with line selections
subPixelResolution() - Method in class ij.gui.EllipseRoi
Always returns true.
subPixelResolution() - Method in class ij.gui.Line
Always returns true.
subPixelResolution() - Method in class ij.gui.PointRoi
Always returns true.
subPixelResolution() - Method in class ij.gui.Roi
Returns true if this is a slection that supports sub-pixel resolution.
subPixelResolution() - Method in class ij.gui.RotatedRectRoi
Always returns true.
SubstackMaker - Class in ij.plugin
This plugin implements the Image/Stacks/Tools/Make Substack command.
SubstackMaker() - Constructor for class ij.plugin.SubstackMaker
 
SUBSTRING - Static variable in interface ij.macro.MacroConstants
 
subtract(double) - Method in class ij.process.ImageProcessor
Subtracts 'value' from each pixel in the image or ROI.
SUBTRACT - Static variable in interface ij.process.Blitter
dst=dst-src
subtractBackround(ImageProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
Depracated.
subtractPoints(Roi) - Method in class ij.gui.PointRoi
Returns the points of this Roi that are not contained in the specified area ROI.
subtractRGBBackround(ColorProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
Depracated.
SUBTYPE - Static variable in class ij.io.RoiDecoder
 
SUCCESS - Static variable in class ij.measure.Minimizer
Status returned: successful completion
SUM - Static variable in class ij.plugin.Binner
 
SUM_METHOD - Static variable in class ij.plugin.ZProjector
 
SUM_PROJECTION - Static variable in class ij.process.ImageProcessor
Composite image projection modes.
summarize() - Method in class ij.plugin.filter.Analyzer
 
supportMacroUndo - Static variable in class ij.Prefs
Support TRANSFORM Undo in macros
SUPPORTS_MASKING - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter wants ImageJ, for non-rectangular ROIs, to restore that part of the image that's inside the bounding rectangle but outside of the ROI.
suppressPluginNotFoundError() - Static method in class ij.IJ
Temporarily suppress "plugin not found" errors.
SurfacePlotter - Class in ij.plugin
 
SurfacePlotter() - Constructor for class ij.plugin.SurfacePlotter
 
swapPixelArrays() - Method in class ij.process.ByteProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.ColorProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.FloatProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.ImageProcessor
Swaps the pixel and snapshot (undo) buffers.
swapPixelArrays() - Method in class ij.process.ShortProcessor
Swaps the pixel and snapshot (undo) arrays.
swapQuadrants() - Method in class ij.process.FHT
Swap quadrants 1 and 3 and 2 and 4 of the image contained in this FHT.
swapQuadrants(ImageProcessor) - Static method in class ij.plugin.FFT
 
swapQuadrants(ImageProcessor) - Method in class ij.process.FHT
Swap quadrants 1 and 3 and 2 and 4 of the specified ImageProcessor so the power spectrum origin is at the center of the image.
Symbol - Class in ij.macro
Objects of this class are used as entries in the macro language symbol table.
SyncWindows - Class in ij.plugin.frame
This class "synchronizes" mouse input in multiple windows.
SyncWindows() - Constructor for class ij.plugin.frame.SyncWindows
Create window sync frame.
SyncWindows(String) - Constructor for class ij.plugin.frame.SyncWindows
 

T

T_POSITION - Static variable in class ij.io.RoiDecoder
 
TABLE - Static variable in class ij.io.Opener
 
TABLE - Static variable in interface ij.macro.MacroConstants
 
TABLE - Static variable in class ij.plugin.NewPlugin
 
TABLE_FULL - Static variable in class ij.measure.ResultsTable
 
TableListener - Interface in ij.text
Plugins that implement this interface are notified when a table is opened, closed or updated.
TableUpdated(TextPanel, String, int) - Method in interface ij.text.TableListener
 
tableWindowExists() - Static method in class ij.gui.PlotContentsDialog
Returns whether there is at least one table that can be used for "Add from Table"
TAN - Static variable in interface ij.macro.MacroConstants
 
TCZ - Static variable in class ij.plugin.HyperStackConverter
 
TEMPLATE - Static variable in class ij.gui.PlotDialog
Types of dialog.
TEMPLATE - Static variable in class ij.plugin.NewPlugin
 
temporarilyHide() - Method in class ij.gui.Roi
Deprecated
tempOverlay() - Method in class ij.ImagePlus
 
Text - Class in ij.plugin
This plugin implements the Edit/Options/Fonts command and the dialog displayed when you double click on the text tool.
Text() - Constructor for class ij.plugin.Text
 
TEXT - Static variable in class ij.gui.Toolbar
 
TEXT - Static variable in class ij.io.Opener
 
TEXT - Static variable in class ij.io.RoiDecoder
 
TEXT_FILE - Static variable in class ij.plugin.NewPlugin
 
textArea1 - Variable in class ij.gui.GenericDialog
 
textArea2 - Variable in class ij.gui.GenericDialog
 
TextEncoder - Class in ij.io
Saves an image described by an ImageProcessor object as a tab-delimited text file.
TextEncoder(ImageProcessor, Calibration, int) - Constructor for class ij.io.TextEncoder
Constructs a TextEncoder from an ImageProcessor and optional Calibration.
TextFileReader - Class in ij.plugin
This plugin displays the contents of a text file in a window.
TextFileReader() - Constructor for class ij.plugin.TextFileReader
 
TextPanel - Class in ij.text
This is an unlimited size text panel with tab-delimited, labeled and resizable columns.
TextPanel() - Constructor for class ij.text.TextPanel
Constructs a new TextPanel.
TextPanel(String) - Constructor for class ij.text.TextPanel
Constructs a new TextPanel.
TextReader - Class in ij.plugin
This plugin opens a tab or comma delimeted text file as an image.
TextReader() - Constructor for class ij.plugin.TextReader
 
TextRoi - Class in ij.gui
This class is a rectangular ROI containing text.
TextRoi(double, double, double, double, String, Font) - Constructor for class ij.gui.TextRoi
Creates a TextRoi using the specified sub-pixel location, size and Font.
TextRoi(double, double, String) - Constructor for class ij.gui.TextRoi
Creates a TextRoi using sub-pixel coordinates.
TextRoi(double, double, String, Font) - Constructor for class ij.gui.TextRoi
Creates a TextRoi using the specified sub-pixel location and Font.
TextRoi(int, int, ImagePlus) - Constructor for class ij.gui.TextRoi
 
TextRoi(int, int, String) - Constructor for class ij.gui.TextRoi
Creates a TextRoi using the defaultFont.
TextRoi(int, int, String, Font) - Constructor for class ij.gui.TextRoi
Creates a TextRoi using the specified location and Font.
TextRoi(int, int, String, Font, Color) - Constructor for class ij.gui.TextRoi
Deprecated. 
TextRoi(String, double, double, Font) - Constructor for class ij.gui.TextRoi
Use this constructor as a drop-in replacement for ImageProcessor.drawString().
textValueChanged(TextEvent) - Method in class ij.gui.ColorChooser
 
textValueChanged(TextEvent) - Method in class ij.gui.GenericDialog
 
textValueChanged(TextEvent) - Method in class ij.gui.RoiProperties
 
textValueChanged(TextEvent) - Method in class ij.macro.FunctionFinder
 
textValueChanged(TextEvent) - Method in class ij.plugin.ChannelArranger
 
textValueChanged(TextEvent) - Method in class ij.plugin.Distribution
 
textValueChanged(TextEvent) - Method in class ij.plugin.Duplicator
 
textValueChanged(TextEvent) - Method in class ij.plugin.filter.ImageProperties
 
textValueChanged(TextEvent) - Method in class ij.plugin.FolderOpener
 
textValueChanged(TextEvent) - Method in class ij.plugin.frame.Editor
 
textValueChanged(TextEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
 
textValueChanged(TextEvent) - Method in class ij.plugin.Histogram
 
textValueChanged(TextEvent) - Method in class ij.plugin.Resizer
 
textValueChanged(TextEvent) - Method in class ij.plugin.Scaler
 
textValueChanged(TextEvent) - Method in class ij.plugin.Slicer
 
TextWindow - Class in ij.text
Uses a TextPanel to displays text in a window.
TextWindow(String, int, int) - Constructor for class ij.text.TextWindow
Opens a new text window containing the contents of a text file.
TextWindow(String, String, int, int) - Constructor for class ij.text.TextWindow
Opens a new single-column text window.
TextWindow(String, String, String, int, int) - Constructor for class ij.text.TextWindow
Opens a new multi-column text window.
TextWindow(String, String, ArrayList, int, int) - Constructor for class ij.text.TextWindow
Opens a new multi-column text window.
TextWriter - Class in ij.plugin
This plugin implements the File/Save As/Text command, which saves the contents of Editor windows and TextWindows (e.g., "Log" and "Results").
TextWriter() - Constructor for class ij.plugin.TextWriter
 
theLabel - Variable in class ij.gui.GenericDialog
 
theta - Variable in class ij.process.EllipseFitter
Angle in radians
thread - Variable in class ij.gui.StackWindow
 
ThreadLister - Class in ij.plugin
Displays thread information in a text window.
ThreadLister() - Constructor for class ij.plugin.ThreadLister
 
threadPoolExecutor - Static variable in class ij.util.ThreadUtil
The threadPoolExecutor holds at least as many threads for parallel execution as the number of processors; additional threads are added as required.
THREADS - Static variable in class ij.Prefs
 
ThreadUtil - Class in ij.util
 
ThreadUtil() - Constructor for class ij.util.ThreadUtil
 
threshold(int) - Method in class ij.process.ByteProcessor
Sets pixels less than or equal to 'level' to 0 and all other pixels to 255.
threshold(int) - Method in class ij.process.ColorProcessor
Not implemented.
threshold(int) - Method in class ij.process.FloatProcessor
Not implemented.
threshold(int) - Method in class ij.process.ImageProcessor
Sets pixels less than or equal to level to 0 and all other pixels to 255.
threshold(int) - Method in class ij.process.ShortProcessor
 
threshold(int, int) - Method in class ij.process.ByteProcessor
Sets pixels less than 'level1' or greater than 'level2' to 0 and all other pixels to 255.
threshold(int, int) - Method in class ij.process.ImageProcessor
Sets pixels less than 'level1' or greater than 'level2' to 0 and all other pixels to 255.
ThresholdAdjuster - Class in ij.plugin.frame
Adjusts the lower and upper threshold levels of the active image.
ThresholdAdjuster() - Constructor for class ij.plugin.frame.ThresholdAdjuster
 
Thresholder - Class in ij.plugin
This plugin implements the Process/Binary/Make Binary and Convert to Mask commands.
Thresholder() - Constructor for class ij.plugin.Thresholder
 
ThresholdToSelection - Class in ij.plugin.filter
 
ThresholdToSelection() - Constructor for class ij.plugin.filter.ThresholdToSelection
 
TIFF - Static variable in class ij.io.FileInfo
 
TIFF - Static variable in class ij.io.Opener
 
TIFF_AND_DICOM - Static variable in class ij.io.Opener
 
TiffDecoder - Class in ij.io
Decodes single and multi-image TIFF files.
TiffDecoder(InputStream, String) - Constructor for class ij.io.TiffDecoder
 
TiffDecoder(String, String) - Constructor for class ij.io.TiffDecoder
 
TiffEncoder - Class in ij.io
Saves an image described by a FileInfo object as an uncompressed TIFF file.
TiffEncoder(FileInfo) - Constructor for class ij.io.TiffEncoder
 
TILE_WIDTH - Static variable in class ij.io.TiffDecoder
 
tileMirror(ImageProcessor, int, int, int, int) - Method in class ij.plugin.filter.FFTFilter
Puts ImageProcessor (ROI) into a new ImageProcessor of size width x height y at position (x,y).
time(ImagePlus, long) - Static method in class ij.IJ
Experimental
TO_BINARY - Static variable in interface ij.macro.MacroConstants
 
TO_HEX - Static variable in interface ij.macro.MacroConstants
 
TO_LOWER_CASE - Static variable in interface ij.macro.MacroConstants
 
TO_SCALED - Static variable in interface ij.macro.MacroConstants
 
TO_STRING - Static variable in interface ij.macro.MacroConstants
 
TO_UNSCALED - Static variable in interface ij.macro.MacroConstants
 
TO_UPPER_CASE - Static variable in interface ij.macro.MacroConstants
 
toArray() - Method in class ij.gui.Overlay
Returns on array containing the ROIs in this Overlay.
toArray() - Method in class ij.util.FloatArray
Returns a float array containing all elements of this FloatArray.
toArray(int[]) - Method in class ij.gui.Overlay
Returns on array containing the ROIs with the specified indexes.
toByteArray() - Method in class ij.gui.Plot
Writes this plot into a byte array containing (1) the serialized PlotProperties and (2) the serialized Vector of all 'added' PlotObjects.
toColor(int, int, int) - Static method in class ij.plugin.Colors
Returns an opaque color with the specified red, green, and blue values.
toDouble(float[]) - Static method in class ij.util.Tools
Converts the float array 'a' to a double array.
toEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM
Converts a binary image into a 8-bit grayscale Euclidean Distance Map (EDM).
toFloat(double[]) - Static method in class ij.util.Tools
Converts the double array 'a' to a float array.
toFloat(int[]) - Static method in class ij.gui.Roi
Converts an int array to a float array.
toFloat(int, FloatProcessor) - Method in class ij.process.ByteProcessor
Returns a FloatProcessor with the same image, no scaling or calibration (pixel values 0 to 255).
toFloat(int, FloatProcessor) - Method in class ij.process.ColorProcessor
Returns a FloatProcessor with one color channel of the image.
toFloat(int, FloatProcessor) - Method in class ij.process.FloatProcessor
Returns this FloatProcessor.
toFloat(int, FloatProcessor) - Method in class ij.process.ImageProcessor
Returns a FloatProcessor with the image or one color channel thereof.
toFloat(int, FloatProcessor) - Method in class ij.process.ShortProcessor
Returns a FloatProcessor with the same image, no scaling or calibration (pixel values 0 to 65535).
toFloatArrays() - Method in class ij.process.ByteProcessor
 
toFloatProcessors() - Method in class ij.process.ByteProcessor
 
toFront(Frame) - Static method in class ij.WindowManager
 
toFront(Window) - Static method in class ij.WindowManager
 
toggleOverlay() - Method in class ij.ImagePlus
 
toHyperStack(ImagePlus, int, int, int) - Static method in class ij.plugin.HyperStackConverter
Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and 't' frames using the default ordering ("xyczt") and display mode ("Composite").
toHyperStack(ImagePlus, int, int, int, String) - Static method in class ij.plugin.HyperStackConverter
Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and 't' frames using the default ordering ("xyczt") and the specified display mode ("composite", "color" or "grayscale").
toHyperStack(ImagePlus, int, int, int, String, String) - Static method in class ij.plugin.HyperStackConverter
Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and 't' frames.
toInt(float[]) - Static method in class ij.gui.Roi
Converts a float array to an int array using truncation.
toInt(float[], int[], int) - Static method in class ij.gui.Roi
 
toIntR(float[]) - Static method in class ij.gui.Roi
Converts a float array to an int array using rounding.
TOK_MASK - Static variable in interface ij.macro.MacroConstants
 
TOK_SHIFT - Static variable in interface ij.macro.MacroConstants
 
tokenize(String) - Method in class ij.macro.Tokenizer
Uses a StreamTokenizer to convert an ImageJ macro file into a token stream.
Tokenizer - Class in ij.macro
This class converts an imageJ macro file file into a token stream.
Tokenizer() - Constructor for class ij.macro.Tokenizer
 
TOOL_CHANGED - Static variable in interface ij.IJEventListener
 
TOOL_ID - Static variable in interface ij.macro.MacroConstants
 
TOOL_KEY - Static variable in class ij.gui.Toolbar
 
Toolbar - Class in ij.gui
The ImageJ toolbar.
Toolbar() - Constructor for class ij.gui.Toolbar
 
Tools - Class in ij.util
This class contains static utility methods.
Tools() - Constructor for class ij.util.Tools
 
TOOLS_MENU - Static variable in class ij.Menus
 
TOP - Static variable in class ij.io.RoiDecoder
 
TOP_HAT - Static variable in class ij.plugin.filter.RankFilters
 
TOP_LEFT - Static variable in class ij.gui.Plot
Legend positions
TOP_MARGIN - Static variable in class ij.gui.Plot
Deprecated.
Not a fixed value any more, use getDrawingFrame() to get the drawing area
TOP_RIGHT - Static variable in class ij.gui.Plot
Legend positions
toSelection(ImagePlus) - Static method in class ij.plugin.Zoom
 
toShape(String) - Static method in class ij.gui.Plot
Returns the number for a given plot symbol shape, -1 for xError and -2 for yError (all case-insensitive)
toStack(ImagePlus) - Static method in class ij.plugin.HyperStackConverter
Converts the specified hyperstack into a stack.
toString() - Method in class ij.gui.ImageWindow
 
toString() - Method in class ij.gui.Overlay
 
toString() - Method in class ij.gui.PointRoi
 
toString() - Method in class ij.gui.Roi
 
toString() - Method in class ij.ImagePlus
 
toString() - Method in class ij.ImageStack
 
toString() - Method in class ij.io.FileInfo
 
toString() - Method in class ij.macro.Program
 
toString() - Method in class ij.macro.Symbol
 
toString() - Method in class ij.macro.Variable
 
toString() - Method in class ij.measure.Calibration
 
toString() - Method in class ij.measure.ResultsTable
 
toString() - Method in class ij.plugin.frame.RoiManager
 
toString() - Method in class ij.plugin.JavaScriptEvaluator
 
toString() - Method in class ij.plugin.MacroInstaller
 
toString() - Method in class ij.process.FHT
Returns a string containing information about this FHT.
toString() - Method in class ij.process.FloatPolygon
 
toString() - Method in class ij.process.ImageProcessor
Returns a string containing information about this ImageProcessor.
toString() - Method in class ij.process.ImageStatistics
 
toString() - Method in class ij.process.LUT
 
toString() - Method in class ij.util.ArrayUtil
information to be displayed
toWatershed(ImageProcessor) - Method in class ij.plugin.filter.EDM
Do watershed segmentation based on the EDM of the foreground objects (nonzero pixels) in an 8-bit image.
TRACE - Static variable in interface ij.macro.Debugger
 
TRACED_ROI - Static variable in class ij.gui.Roi
 
transform() - Method in class ij.process.FHT
Performs a forward transform, converting this image into the frequency domain.
TRANSFORM - Static variable in class ij.Undo
Undo using a single image, or composite color stack, copy (limited to 200MB).
transform1D(float[]) - Method in class ij.process.FHT
Performs an optimized 1D Fast Hartley Transform (FHT) of an array.
Transformer - Class in ij.plugin.filter
Implements the Flip and Rotate commands in the Image/Transform submenu.
Transformer() - Constructor for class ij.plugin.filter.Transformer
 
translate(double, double) - Method in class ij.gui.Overlay
Moves all the ROIs in this overlay.
translate(double, double) - Method in class ij.gui.Roi
 
translate(double, double) - Method in class ij.plugin.frame.RoiManager
Moves the selected ROIs or all the ROIs if none are selected.
translate(double, double) - Method in class ij.process.FloatPolygon
 
translate(double, double) - Method in class ij.process.ImageProcessor
Moves the image or selection vertically or horizontally by a specified number of pixels.
translate(int) - Method in class ij.VirtualStack
Translates slice numbers of hyperstacks not in default CZT order.
translate(int, int) - Method in class ij.gui.Overlay
Moves all the ROIs in this overlay.
translate(int, int, boolean) - Method in class ij.process.ImageProcessor
Deprecated.
replaced by translate(x,y)
Translator - Class in ij.plugin.filter
This plugin implements the Image/Translate command.
Translator() - Constructor for class ij.plugin.filter.Translator
 
TRANSPARENT - Static variable in class ij.CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
Triangle - ij.process.AutoThresholder.Method
 
TRIANGLE - Static variable in class ij.gui.Plot
Display points using an tiangular mark.
TRIANGLE - Static variable in class ij.gui.PlotWindow
Deprecated. 
triggerPopupMenu(int, MouseEvent, boolean, boolean) - Method in class ij.gui.Toolbar
 
trim() - Method in class ij.ImageStack
Frees memory by deleting a few slices from the end of the stack.
trim() - Method in class ij.VirtualStack
Does nothing.
TRIM - Static variable in interface ij.macro.MacroConstants
 
trimFileList(String[]) - Method in class ij.plugin.FolderOpener
Removes names that start with "." or end with ".db", ".txt", ".lut", "roi", ".pty", ".hdr", ".py", etc.
trimKey(String) - Static method in class ij.Macro
 
TrimmedButton - Class in ij.gui
This is an extended Button class used to reduce the width of the HUGE buttons on Mac OS X.
TrimmedButton(String, int) - Constructor for class ij.gui.TrimmedButton
 
trimProcessor() - Method in class ij.ImagePlus
Frees RAM by setting the snapshot (undo) buffer in the current ImageProcessor to null.
trimToSize() - Method in class ij.util.FloatArray
Trims the capacity of this FloatArray instance to be its current size, minimizing the storage of the FloatArray instance.
TRUE - Static variable in interface ij.macro.MacroConstants
 
trySimplify() - Method in class ij.gui.ShapeRoi
Attempts to convert this ShapeRoi into a single non-composite Roi.
tSelector - Variable in class ij.gui.StackWindow
 
type - Variable in class ij.gui.Roi
 
type - Variable in class ij.macro.Symbol
 
TYPE - Static variable in class ij.io.RoiDecoder
 
TYPE_CONVERSION - Static variable in class ij.Undo
Undo using an ImageProcessor copy.
TypeConverter - Class in ij.process
This class converts an ImageProcessor to another data type.
TypeConverter(ImageProcessor, boolean) - Constructor for class ij.process.TypeConverter
 
types - Static variable in class ij.gui.PointRoi
 
types - Static variable in class ij.io.Opener
 
TZC - Static variable in class ij.plugin.HyperStackConverter
 

U

umean - Variable in class ij.process.ImageStatistics
Uncalibrated mean
UNCALIBRATED_OD - Static variable in class ij.measure.Calibration
 
uncaughtException(Thread, Throwable) - Method in class ij.ImageJ.ExceptionHandler
 
undo() - Static method in class ij.Undo
 
Undo - Class in ij
This class consists of static methods and fields that implement ImageJ's Undo command.
Undo() - Constructor for class ij.Undo
 
uninstallPlugin(String) - Static method in class ij.Menus
Deletes a command installed by Plugins/Shortcuts/Add Shortcut.
unit - Variable in class ij.io.FileInfo
 
units - Variable in class ij.gui.ProfilePlot
 
UNKNOWN - Static variable in class ij.io.FileInfo
 
UNKNOWN - Static variable in class ij.io.Opener
 
unlock() - Method in class ij.ImagePlus
Unlocks the image.
UnsharpMask - Class in ij.plugin.filter
This plugin-filter implements ImageJ's Unsharp Mask command.
UnsharpMask() - Constructor for class ij.plugin.filter.UnsharpMask
 
UNUSED - Static variable in class ij.gui.Toolbar
 
unzoom() - Method in class ij.gui.ImageCanvas
Implements the Image/Zoom/Original Scale command.
unzoom() - Method in class ij.gui.PlotCanvas
Implements the Image/Zoom/Original Scale command.
unzoom(ImagePlus) - Static method in class ij.plugin.Zoom
 
update() - Method in class ij.gui.Plot
Draws the plot again, ignored if the plot has not been drawn before or the plot is frozen.
update() - Method in class ij.plugin.frame.Channels
 
update() - Static method in class ij.plugin.frame.ColorPicker
 
update() - Static method in class ij.plugin.frame.ContrastAdjuster
Updates the ContrastAdjuster.
update() - Static method in class ij.plugin.frame.LineWidthAdjuster
 
update() - Static method in class ij.plugin.frame.ThresholdAdjuster
Notifies the ThresholdAdjuster that the image has changed.
update() - Static method in class ij.plugin.PointToolOptions
 
update(boolean, boolean) - Method in class ij.gui.Roi
If 'add' is true, adds this selection to the previous one.
update(int, ImagePlus, Roi) - Method in class ij.measure.ResultsTable
 
update(ImageProcessor) - Method in class ij.ImageStack
Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.
update(Graphics) - Method in class ij.gui.ImageCanvas
 
update(Graphics) - Method in class ij.gui.ProgressBar
 
UPDATE_BLUE - Static variable in class ij.process.ImageProcessor
Composite image projection modes.
UPDATE_DISPLAY - Static variable in interface ij.macro.MacroConstants
 
UPDATE_GREEN - Static variable in class ij.process.ImageProcessor
Composite image projection modes.
UPDATE_RED - Static variable in class ij.process.ImageProcessor
Composite image projection modes.
UPDATE_RESULTS - Static variable in interface ij.macro.MacroConstants
 
updateAllChannelsAndDraw() - Method in class ij.CompositeImage
 
updateAndDraw() - Method in class ij.CompositeImage
 
updateAndDraw() - Method in class ij.ImagePlus
Updates this image from the pixel data in its associated ImageProcessor, then displays it.
updateAndDraw() - Method in class ij.plugin.frame.ContrastAdjuster
Resets this ContrastAdjuster and brings it to the front.
updateAndRepaintWindow() - Method in class ij.ImagePlus
Calls updateAndDraw to update from the pixel data and draw the image, and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.
updateArrayInspector() - Method in class ij.macro.Interpreter
Updates Array inspector if variable exists, otherwise closes ArrayInspector
updateChannelAndDraw() - Method in class ij.CompositeImage
 
updateChannelAndDraw() - Method in class ij.ImagePlus
Updates this image from the pixel data in its associated ImageProcessor, then displays it.
updateChannels() - Static method in class ij.plugin.frame.Channels
 
updateClassName(String, String) - Method in class ij.plugin.frame.Editor
Changes a plugins class name to reflect a new file name.
updateClipRect() - Method in class ij.gui.Roi
 
updateColumnHeadings(String) - Method in class ij.text.TextPanel
 
updateComposite(int[], int) - Method in class ij.process.ColorProcessor
 
updateComposite(int[], int) - Method in class ij.process.ImageProcessor
This method is used by CompositeImage.updateImage() to create RGB images (for display) of a multi-channel composite images.
updateCounts() - Method in class ij.gui.PointRoi
Updates the counts for each category in 'counters'
UPDATED - Static variable in class ij.ImagePlus
 
updateDebugWindow(String[], TextWindow) - Method in class ij.macro.Interpreter
 
updateDisplay() - Method in class ij.text.TextPanel
 
updateFont() - Static method in class ij.Menus
 
updateFullWindow - Variable in class ij.gui.Roi
 
updateHeadings() - Method in class ij.plugin.filter.Analyzer
Redisplays the results table.
updateImage() - Method in class ij.CompositeImage
 
updateImage() - Method in class ij.gui.Plot
Draws the plot again, ignored if the plot has not been drawn before or the plot is frozen.
updateImage() - Method in class ij.ImagePlus
ImageCanvas.paint() calls this method when the ImageProcessor has generated a new image.
updateImage(ImagePlus) - Method in class ij.gui.ImageWindow
 
updateImageJMenus() - Static method in class ij.Menus
 
updateImagePlus(String, int) - Method in class ij.io.FileSaver
 
updateMenus() - Static method in class ij.Menus
Updates the Image/Type and Window menus.
updatePlayPauseIcon() - Method in class ij.gui.ScrollbarWithLabel
 
updatePolygon() - Method in class ij.gui.PolygonRoi
 
updatePosition(int, int, int) - Method in class ij.ImagePlus
 
updateResults() - Method in class ij.measure.ResultsTable
Updates the Results window.
updateSliceSelector() - Method in class ij.gui.StackWindow
Updates the stack scrollbar.
updateStatusbarValue() - Method in class ij.ImagePlus
Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar.
updateTableOverlay(ImagePlus, int, int, int) - Static method in class ij.gui.Overlay
Updates overlays created by the particle analyzer after rows are deleted from the Results table.
updateUrl(String) - Static method in class ij.io.Opener
Can't open imagej.nih.gov URLs due to encryption so redirect to imagej.net mirror.
updateVirtualSlice() - Method in class ij.ImagePlus
Use to update the image when the underlying virtual stack changes.
updateWideLine(float) - Method in class ij.gui.Roi
 
updateWindowList() - Method in class ij.plugin.frame.SyncWindows
 
updateWindowMenuItem(ImagePlus, String, String) - Static method in class ij.Menus
Changes the name of an item in the Window menu.
updateWindowMenuItem(String, String) - Static method in class ij.Menus
Changes the name of an item in the Window menu.
updateY(double, int) - Static method in class ij.plugin.filter.Analyzer
Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
updateY(int, int) - Static method in class ij.plugin.filter.Analyzer
Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
upperThreshold - Variable in class ij.process.ImageStatistics
Maximum threshold when "Limit to threshold" enabled
url - Variable in class ij.io.FileInfo
 
URL - Static variable in class ij.IJ
Deprecated. 
URL2 - Static variable in class ij.IJ
ImageJ website
URLOpener - Class in ij.plugin
Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.
URLOpener() - Constructor for class ij.plugin.URLOpener
 
useFileChooser - Static variable in class ij.Prefs
Use the file chooser to import and export image sequences on Windows and Linux
useInfo(String) - Static method in class ij.plugin.FolderOpener
 
useInvertingLut - Static variable in class ij.Prefs
Open 8-bit images with inverting LUT so 0 is white and 255 is black.
useJFileChooser - Static variable in class ij.Prefs
Use JFileChooser instead of FileDialog to open and save files.
useLineSubpixelConvention() - Method in class ij.gui.Roi
Returns 'true' if this ROI uses for drawing the convention for line and point ROIs, where the coordinates are with respect to the pixel center.
useNamesAsLabels - Static variable in class ij.Prefs
Use ROI names as "show all" labels in the ROI Manager
usePointer - Static variable in class ij.gui.ImageCanvas
 
usePointerCursor - Static variable in class ij.Prefs
Use pointer cursor instead of cross
USER_FUNCTION - Static variable in interface ij.macro.MacroConstants
 
userFunction(double[], double) - Method in class ij.measure.CurveFitter
This function is called by the Minimizer and calculates the sum of squared residuals for given parameters.
userFunction(double[], double) - Method in interface ij.measure.UserFunction
A user-supplied function
UserFunction - Interface in ij.measure
A plugin should implement this interface for minimizing a single-valued function or fitting a curve with a custom fit function.
useSystemProxies - Static variable in class ij.Prefs
Set the "java.net.useSystemProxies" property
useTemplate(Plot) - Method in class ij.gui.Plot
Adjusts the format with another plot as a template, using the current (usually default) templateFlags of this plot.
useTemplate(Plot, int) - Method in class ij.gui.Plot
Adjusts the format (style) with another plot as a template.
UTILITIES_MENU - Static variable in class ij.Menus
 

V

validDimensions() - Method in class ij.gui.StackWindow
 
validExtensions - Static variable in class ij.plugin.PluginInstaller
 
value - Variable in class ij.gui.HistogramWindow
 
value - Variable in class ij.macro.Symbol
 
valueChanged(ListSelectionEvent) - Method in class ij.plugin.frame.RoiManager
 
valueOf(String) - Static method in enum ij.process.AutoThresholder.Method
Returns the enum constant of this type with the specified name.
values() - Static method in enum ij.process.AutoThresholder.Method
Returns an array containing the constants of this enum type, in the order they are declared.
valueUnit - Variable in class ij.io.FileInfo
 
VAR - Static variable in interface ij.macro.MacroConstants
 
VAR - Static variable in class ij.plugin.Filters3D
 
Variable - Class in ij.macro
 
Variable() - Constructor for class ij.macro.Variable
 
Variable(double) - Constructor for class ij.macro.Variable
 
Variable(Variable[]) - Constructor for class ij.macro.Variable
 
Variable(String) - Constructor for class ij.macro.Variable
 
VARIABLE_FUNCTION - Static variable in interface ij.macro.MacroConstants
 
variableFunctionIDs - Static variable in interface ij.macro.MacroConstants
 
variableFunctions - Static variable in interface ij.macro.MacroConstants
 
VARIANCE - Static variable in class ij.plugin.filter.RankFilters
 
VERSION - Static variable in class ij.ImageJ
Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string.
VERSION_OFFSET - Static variable in class ij.io.RoiDecoder
 
versionLessThan(String) - Static method in class ij.IJ
Displays an error message and returns true if the ImageJ version is less than the one specified.
verticalProfile - Static variable in class ij.Prefs
Plot rectangular selectons vertically
VGAP - Static variable in class ij.gui.ImageWindow
 
virtualStack - Variable in class ij.io.FileInfo
 
VirtualStack - Class in ij
This class represents an array of disk-resident images.
VirtualStack() - Constructor for class ij.VirtualStack
Default constructor.
VirtualStack(int, int) - Constructor for class ij.VirtualStack
 
VirtualStack(int, int, int) - Constructor for class ij.VirtualStack
Creates a virtual stack with no backing storage.
See: Help>Examples>JavaScript>Terabyte VirtualStack
VirtualStack(int, int, int, String) - Constructor for class ij.VirtualStack
Creates a virtual stack with no backing storage.
See: Help>Examples>JavaScript>Terabyte VirtualStack
VirtualStack(int, int, ColorModel, String) - Constructor for class ij.VirtualStack
Creates an empty virtual stack.
vistaHint - Static variable in class ij.Prefs
 
vListMap - Variable in class ij.plugin.frame.SyncWindows
Hashtable to map list ids to image window ids.
vwins - Variable in class ij.plugin.frame.SyncWindows
Indices of synchronized image windows are maintained in this Vector.

W

wait(int) - Static method in class ij.IJ
Delays 'msecs' milliseconds.
WAIT - Static variable in interface ij.macro.MacroConstants
 
WAIT_FOR_USER - Static variable in interface ij.macro.MacroConstants
 
WaitForUserDialog - Class in ij.gui
This is a non-modal dialog box used to ask the user to perform some task while a macro or plugin is running.
WaitForUserDialog(String) - Constructor for class ij.gui.WaitForUserDialog
 
WaitForUserDialog(String, String) - Constructor for class ij.gui.WaitForUserDialog
 
waitTillActivated() - Method in class ij.ImagePlus
Waits until the image window becomes activated.
Wand - Class in ij.gui
This class implements ImageJ's wand (tracing) tool.
Wand(ImageProcessor) - Constructor for class ij.gui.Wand
Constructs a Wand object from an ImageProcessor.
WAND - Static variable in class ij.gui.Toolbar
 
WandToolOptions - Class in ij.plugin
This plugin implements the Edit/Options/Wand Tool command.
WandToolOptions() - Constructor for class ij.plugin.WandToolOptions
 
wasCanceled() - Method in class ij.gui.GenericDialog
Returns true if the user clicked on "Cancel".
wasError() - Method in class ij.macro.Interpreter
 
wasOKed() - Method in class ij.gui.GenericDialog
Returns true if the user has clicked on "OK" or a macro is running.
wavelengthToColor(double) - Static method in class ij.plugin.Colors
Converts a wavelength (380-750 nm) to color.
weightedColor - Static variable in class ij.Prefs
Color to grayscale conversion is weighted (0.299, 0.587, 0.114) if the variable is true.
weightedHistogram() - Method in class ij.process.ColorProcessor
 
weights - Variable in class ij.process.DownsizeTable
For each source point, weights for adding it to the destination point given in the corresponding element of 'indices'
west(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
WHILE - Static variable in interface ij.macro.MacroConstants
 
whiteIsZero - Variable in class ij.io.FileInfo
 
whitePoint - Variable in class ij.process.ColorSpaceConverter
 
wideLine - Variable in class ij.gui.Roi
 
width - Variable in class ij.ImagePlus
 
width - Variable in class ij.io.FileInfo
 
width - Variable in class ij.process.ImageProcessor
 
width - Variable in class ij.process.ImageStatistics
 
WIDTH - Static variable in class ij.gui.ProgressBar
 
WIDTH_KEY - Static variable in class ij.gui.Arrow
 
WIDTH_KEY - Static variable in class ij.text.TextWindow
 
WIDTHD - Static variable in class ij.io.RoiDecoder
 
WildcardMatch - Class in ij.util
This class allows for simple wildcard pattern matching.
WildcardMatch() - Constructor for class ij.util.WildcardMatch
 
WildcardMatch(char, char) - Constructor for class ij.util.WildcardMatch
 
win - Variable in class ij.ImagePlus
 
WINDOW_MENU_ITEMS - Static variable in class ij.Menus
 
windowActivated() - Method in class ij.ImagePlus
 
windowActivated(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowActivated(WindowEvent) - Method in class ij.gui.HTMLDialog
 
windowActivated(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowActivated(WindowEvent) - Method in class ij.gui.MessageDialog
 
windowActivated(WindowEvent) - Method in class ij.gui.NonBlockingGenericDialog
Put the dialog into the foreground when the image we work on gets into the foreground
windowActivated(WindowEvent) - Method in class ij.gui.PlotWindow
Called when the window is activated (WindowListener) Window layout is finished at latest a few millisec after windowActivated, then the 'wasActivated' boolean is set to tell the ImageCanvas that resize events should lead to resizing the canvas (before, creating the layout can lead to resize events)
windowActivated(WindowEvent) - Method in class ij.gui.RoiProperties
 
windowActivated(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
 
windowActivated(WindowEvent) - Method in class ij.ImageJ
 
windowActivated(WindowEvent) - Method in class ij.macro.FunctionFinder
 
windowActivated(WindowEvent) - Method in class ij.plugin.CommandFinder
 
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ColorThresholder
 
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ContrastAdjuster
 
windowActivated(WindowEvent) - Method in class ij.plugin.frame.Editor
Override windowActivated in PlugInFrame to prevent Mac menu bar from being installed.
windowActivated(WindowEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
 
windowActivated(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
 
windowActivated(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowActivated(WindowEvent) - Method in class ij.plugin.frame.Recorder
Override windowActivated in PlugInFrame.
windowActivated(WindowEvent) - Method in class ij.plugin.frame.RoiManager
 
windowActivated(WindowEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
 
windowActivated(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
windowClosed(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowClosed(WindowEvent) - Method in class ij.gui.HTMLDialog
 
windowClosed(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowClosed(WindowEvent) - Method in class ij.gui.MessageDialog
 
windowClosed(WindowEvent) - Method in class ij.gui.RoiProperties
 
windowClosed(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
 
windowClosed(WindowEvent) - Method in class ij.ImageJ
 
windowClosed(WindowEvent) - Method in class ij.macro.FunctionFinder
 
windowClosed(WindowEvent) - Method in class ij.plugin.CommandFinder
 
windowClosed(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
 
windowClosed(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowClosed(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
windowClosing(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowClosing(WindowEvent) - Method in class ij.gui.HTMLDialog
 
windowClosing(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowClosing(WindowEvent) - Method in class ij.gui.MessageDialog
 
windowClosing(WindowEvent) - Method in class ij.gui.NonBlockingGenericDialog
 
windowClosing(WindowEvent) - Method in class ij.gui.RoiProperties
 
windowClosing(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
 
windowClosing(WindowEvent) - Method in class ij.ImageJ
 
windowClosing(WindowEvent) - Method in class ij.macro.FunctionFinder
 
windowClosing(WindowEvent) - Method in class ij.plugin.CommandFinder
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.SyncWindows
Override parent windowClosing method to clean up synchronized resources on exit.
windowClosing(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
windowDeactivated(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowDeactivated(WindowEvent) - Method in class ij.gui.HTMLDialog
 
windowDeactivated(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowDeactivated(WindowEvent) - Method in class ij.gui.MessageDialog
 
windowDeactivated(WindowEvent) - Method in class ij.gui.RoiProperties
 
windowDeactivated(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
 
windowDeactivated(WindowEvent) - Method in class ij.ImageJ
 
windowDeactivated(WindowEvent) - Method in class ij.macro.FunctionFinder
 
windowDeactivated(WindowEvent) - Method in class ij.plugin.CommandFinder
 
windowDeactivated(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
 
windowDeactivated(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowDeactivated(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
windowDeiconified(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowDeiconified(WindowEvent) - Method in class ij.gui.HTMLDialog
 
windowDeiconified(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowDeiconified(WindowEvent) - Method in class ij.gui.MessageDialog
 
windowDeiconified(WindowEvent) - Method in class ij.gui.RoiProperties
 
windowDeiconified(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
 
windowDeiconified(WindowEvent) - Method in class ij.ImageJ
 
windowDeiconified(WindowEvent) - Method in class ij.macro.FunctionFinder
 
windowDeiconified(WindowEvent) - Method in class ij.plugin.CommandFinder
 
windowDeiconified(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
 
windowDeiconified(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowDeiconified(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
windowIconified(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowIconified(WindowEvent) - Method in class ij.gui.HTMLDialog
 
windowIconified(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowIconified(WindowEvent) - Method in class ij.gui.MessageDialog
 
windowIconified(WindowEvent) - Method in class ij.gui.RoiProperties
 
windowIconified(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
 
windowIconified(WindowEvent) - Method in class ij.ImageJ
 
windowIconified(WindowEvent) - Method in class ij.macro.FunctionFinder
 
windowIconified(WindowEvent) - Method in class ij.plugin.CommandFinder
 
windowIconified(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
 
windowIconified(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowIconified(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
WindowManager - Class in ij
This class consists of static methods used to manage ImageJ's windows.
windowOpened(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowOpened(WindowEvent) - Method in class ij.gui.HTMLDialog
 
windowOpened(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowOpened(WindowEvent) - Method in class ij.gui.MessageDialog
 
windowOpened(WindowEvent) - Method in class ij.gui.RoiProperties
 
windowOpened(WindowEvent) - Method in class ij.gui.YesNoCancelDialog
 
windowOpened(WindowEvent) - Method in class ij.ImageJ
 
windowOpened(WindowEvent) - Method in class ij.macro.FunctionFinder
 
windowOpened(WindowEvent) - Method in class ij.plugin.CommandFinder
 
windowOpened(WindowEvent) - Method in class ij.plugin.frame.PlugInDialog
 
windowOpened(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowOpened(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
WindowOrganizer - Class in ij.plugin
This class implements the Window menu's "Show All", "Main Window", "Cascade" and "Tile" commands.
WindowOrganizer() - Constructor for class ij.plugin.WindowOrganizer
 
windowStateChanged(WindowEvent) - Method in class ij.gui.ImageWindow
 
wipeBack() - Method in class ij.gui.PolygonRoi
 
wList - Variable in class ij.plugin.frame.SyncWindows
List of currently displayed windows retrieved from ImageJ window manager.
WORD - Static variable in interface ij.macro.MacroConstants
 
write(byte[]) - Method in class ij.io.LogStream
 
write(byte[], int, int) - Method in class ij.io.LogStream
 
write(int) - Method in class ij.io.LogStream
 
write(Roi) - Method in class ij.io.RoiEncoder
Save the Roi to the file of stream.
write(DataOutputStream) - Method in class ij.io.TextEncoder
Saves the image as a tab-delimited text file.
write(DataOutputStream) - Method in class ij.io.TiffEncoder
 
write(OutputStream) - Method in class ij.io.ImageWriter
Writes the image to the specified OutputStream.
write(OutputStream) - Method in class ij.io.TiffEncoder
Saves the image as a TIFF file.
write(String) - Static method in class ij.IJ
Deprecated.
replaced by IJ.log(), ResultsTable.setResult() and TextWindow.append(). There are examples at http://imagej.nih.gov/ij/plugins/sine-cosine.html
WRITE - Static variable in interface ij.macro.MacroConstants
 
writeImage(ImagePlus, String, int) - Method in class ij.plugin.PNG_Writer
 
writeImage(ImagePlus, String, int, int) - Method in class ij.plugin.filter.AVI_Writer
Writes an ImagePlus (stack) as AVI file.
Writer - Class in ij.plugin.filter
Deprecated. 
Writer() - Constructor for class ij.plugin.filter.Writer
Deprecated.
 

X

x - Variable in class ij.plugin.frame.SyncWindows
 
X - Static variable in class ij.gui.Plot
Display points using an X-shaped mark.
X - Static variable in class ij.gui.PlotWindow
Deprecated. 
X_AXIS - Static variable in class ij.gui.PlotDialog
Types of dialog.
X_CENTER_OF_MASS - Static variable in class ij.measure.ResultsTable
 
X_CENTROID - Static variable in class ij.measure.ResultsTable
 
X_FORCE2GRID - Static variable in class ij.gui.Plot
flag for forcing frame to coincide with the grid/ticks in x direction (results in unused space)
X_GRID - Static variable in class ij.gui.Plot
flag for drawing vertical grid lines for x axis
X_LEFT - Static variable in class ij.gui.PlotDialog
Types of dialog.
X_LOG_NUMBERS - Static variable in class ij.gui.Plot
flag for logarithmic x-axis
X_LOG_TICKS - Static variable in class ij.gui.Plot
flag for ticks (major and minor, if space) on logarithmic x axis
X_MINOR_TICKS - Static variable in class ij.gui.Plot
flag for drawing minor ticks on linear (non-logarithmic) x axis
X_NUMBERS - Static variable in class ij.gui.Plot
flag for numeric labels of x-axis ticks
X_RANGE - Static variable in class ij.gui.Plot
Flag for addressing the x axis, for copying from a template: copy/write x axis range.
X_RESOLUTION - Static variable in class ij.io.TiffDecoder
 
X_RIGHT - Static variable in class ij.gui.PlotDialog
Types of dialog.
X_TICKS - Static variable in class ij.gui.Plot
flag for drawing major ticks on linear (non-logarithmic) x axis
x1 - Variable in class ij.gui.Line
 
X1 - Static variable in class ij.io.RoiDecoder
 
x1d - Variable in class ij.gui.Line
 
x1R - Variable in class ij.gui.Line
 
x2 - Variable in class ij.gui.Line
 
X2 - Static variable in class ij.io.RoiDecoder
 
x2d - Variable in class ij.gui.Line
 
x2R - Variable in class ij.gui.Line
 
xCenter - Variable in class ij.process.EllipseFitter
X centroid
xCenterOfMass - Variable in class ij.process.ImageStatistics
 
xCentroid - Variable in class ij.process.ImageStatistics
 
xCoordinates - Variable in class ij.process.EllipseFitter
Initialized by makeRoi()
XD - Static variable in class ij.io.RoiDecoder
 
xInc - Variable in class ij.gui.ProfilePlot
 
XINC - Static variable in class ij.plugin.frame.Editor
 
XINC - Static variable in class ij.plugin.MacroInstaller
 
xloc - Static variable in class ij.gui.WaitForUserDialog
 
xMax - Variable in class ij.gui.Roi
 
xMax - Variable in class ij.process.ImageProcessor
 
xMin - Variable in class ij.process.ImageProcessor
 
xMouse - Variable in class ij.gui.ImageCanvas
 
xMouseStart - Variable in class ij.gui.ImageCanvas
 
xor(int) - Method in class ij.process.FloatProcessor
 
xor(int) - Method in class ij.process.ImageProcessor
Binary exclusive OR of each pixel in the image or ROI with 'value'.
xor(int) - Method in class ij.process.ShortProcessor
 
xor(int[]) - Method in class ij.gui.Overlay
Returns the bounds of this overlay.
xor(Roi[]) - Static method in class ij.gui.Roi
 
xor(ShapeRoi) - Method in class ij.gui.ShapeRoi
Unary exclusive or operator.
XOR - Static variable in interface ij.process.Blitter
dst=dst XOR src
xOrigin - Variable in class ij.measure.Calibration
X origin in pixels.
xp - Variable in class ij.gui.PolygonRoi
 
xp2 - Variable in class ij.gui.PolygonRoi
 
xpf - Variable in class ij.gui.PolygonRoi
 
xpoints - Variable in class ij.gui.Wand
The x-coordinates of the points in the outline.
xpoints - Variable in class ij.process.FloatPolygon
 
xSpline - Variable in class ij.gui.PolygonRoi
 
xSrcStart - Variable in class ij.gui.ImageCanvas
 
xstart - Variable in class ij.process.ImageStatistics
Used internally by AnalyzeParticles
xValues - Variable in class ij.gui.ProfilePlot
 
XY_Reader - Class in ij.plugin
This plugin implements the File/Import/XY Coordinates command.
XY_Reader() - Constructor for class ij.plugin.XY_Reader
 
XYCoordinates - Class in ij.plugin
Writes the XY coordinates and pixel values of all non-background pixels to a tab-delimited text file.
XYCoordinates() - Constructor for class ij.plugin.XYCoordinates
 
XYWriter - Class in ij.plugin.filter
Saves the XY coordinates of the current ROI boundary.
XYWriter() - Constructor for class ij.plugin.filter.XYWriter
 
xyYtoXYZ(double[]) - Method in class ij.process.ColorSpaceConverter
 
xyYtoXYZ(double, double, double) - Method in class ij.process.ColorSpaceConverter
 
XYZtoLAB(double[]) - Method in class ij.process.ColorSpaceConverter
Convert XYZ to LAB.
XYZtoLAB(double, double, double) - Method in class ij.process.ColorSpaceConverter
Convert XYZ to LAB.
XYZtoRGB(double[]) - Method in class ij.process.ColorSpaceConverter
Convert XYZ to RGB
XYZtoRGB(double, double, double) - Method in class ij.process.ColorSpaceConverter
Convert XYZ to RGB.
XYZtoxyY(double[]) - Method in class ij.process.ColorSpaceConverter
 
XYZtoxyY(double, double, double) - Method in class ij.process.ColorSpaceConverter
 

Y

y - Variable in class ij.plugin.frame.SyncWindows
 
Y_AXIS - Static variable in class ij.gui.PlotDialog
Types of dialog.
Y_BOTTOM - Static variable in class ij.gui.PlotDialog
Types of dialog.
Y_CENTER_OF_MASS - Static variable in class ij.measure.ResultsTable
 
Y_CENTROID - Static variable in class ij.measure.ResultsTable
 
Y_FORCE2GRID - Static variable in class ij.gui.Plot
flag for forcing frame to coincide with the grid/ticks in y direction (results in unused space)
Y_GRID - Static variable in class ij.gui.Plot
flag for drawing horizontal grid lines for y axis
Y_LOG_NUMBERS - Static variable in class ij.gui.Plot
flag for logarithmic y axis
Y_LOG_TICKS - Static variable in class ij.gui.Plot
flag for ticks (major and minor, if space) on logarithmic y axis
Y_MINOR_TICKS - Static variable in class ij.gui.Plot
flag for drawing minor ticks on linear (non-logarithmic) y axis
Y_NUMBERS - Static variable in class ij.gui.Plot
flag for numeric labels of x-axis ticks
Y_RANGE - Static variable in class ij.gui.Plot
Flag for addressing the y axis, for copying from a template: copy/write y axis range
Y_RESOLUTION - Static variable in class ij.io.TiffDecoder
 
Y_TICKS - Static variable in class ij.gui.Plot
flag for drawing major ticks on linear (non-logarithmic) y axis
Y_TOP - Static variable in class ij.gui.PlotDialog
Types of dialog.
y1 - Variable in class ij.gui.Line
 
Y1 - Static variable in class ij.io.RoiDecoder
 
y1d - Variable in class ij.gui.Line
 
y1R - Variable in class ij.gui.Line
 
y2 - Variable in class ij.gui.Line
 
Y2 - Static variable in class ij.io.RoiDecoder
 
y2d - Variable in class ij.gui.Line
 
y2R - Variable in class ij.gui.Line
 
ybase - Static variable in class ij.plugin.frame.ColorPicker
 
yCenter - Variable in class ij.process.EllipseFitter
X centroid
yCenterOfMass - Variable in class ij.process.ImageStatistics
 
yCentroid - Variable in class ij.process.ImageStatistics
 
yCoordinates - Variable in class ij.process.EllipseFitter
Initialized by makeRoi()
YD - Static variable in class ij.io.RoiDecoder
 
Yen - ij.process.AutoThresholder.Method
 
YesNoCancelDialog - Class in ij.gui
A modal dialog box with a one line message and "Yes", "No" and "Cancel" buttons.
YesNoCancelDialog(Frame, String, String) - Constructor for class ij.gui.YesNoCancelDialog
 
YesNoCancelDialog(Frame, String, String, String, String) - Constructor for class ij.gui.YesNoCancelDialog
 
yesPressed() - Method in class ij.gui.YesNoCancelDialog
Returns true if the user dismissed dialog by pressing "Yes".
YINC - Static variable in class ij.plugin.frame.Editor
 
YINC - Static variable in class ij.plugin.MacroInstaller
 
yLabel - Variable in class ij.gui.ProfilePlot
 
yloc - Static variable in class ij.gui.WaitForUserDialog
 
yMax - Variable in class ij.gui.HistogramWindow
 
yMax - Variable in class ij.gui.Roi
 
yMax - Variable in class ij.process.ImageProcessor
 
yMin - Variable in class ij.process.ImageProcessor
 
yMouse - Variable in class ij.gui.ImageCanvas
 
yMouseStart - Variable in class ij.gui.ImageCanvas
 
yOrigin - Variable in class ij.measure.Calibration
Y origin in pixels.
yp - Variable in class ij.gui.PolygonRoi
 
yp2 - Variable in class ij.gui.PolygonRoi
 
ypf - Variable in class ij.gui.PolygonRoi
 
ypoints - Variable in class ij.gui.Wand
The y-coordinates of the points in the outline.
ypoints - Variable in class ij.process.FloatPolygon
 
ySpline - Variable in class ij.gui.PolygonRoi
 
ySrcStart - Variable in class ij.gui.ImageCanvas
 
ystart - Variable in class ij.process.ImageStatistics
Used internally by AnalyzeParticles

Z

Z_POSITION - Static variable in class ij.io.RoiDecoder
 
ZAxisProfiler - Class in ij.plugin
Implements the Image/Stacks/Plot Z-axis Profile command, which plots the selection mean gray value versus slice number.
ZAxisProfiler() - Constructor for class ij.plugin.ZAxisProfiler
 
ZCT - Static variable in class ij.plugin.HyperStackConverter
 
ZERO_TRANSPARENT - Static variable in class ij.io.RoiDecoder
 
zeroClip() - Method in class ij.measure.Calibration
Returns true if zero clipping is enabled.
ZIP - Static variable in class ij.io.FileInfo
 
ZIP - Static variable in class ij.io.Opener
 
ZIP_ARCHIVE - Static variable in class ij.io.FileInfo
 
ZIP_WITH_DIFFERENCING - Static variable in class ij.io.FileInfo
 
zipUncompress(byte[]) - Method in class ij.io.ImageReader
TIFF Adobe ZIP support contributed by Jason Newton.
zoom(String) - Method in class ij.gui.PlotCanvas
Zoom operations that are handled by ij.plugin.Zoom
Zoom - Class in ij.plugin
This plugin implements the commands in the Image/Zoom submenu.
Zoom() - Constructor for class ij.plugin.Zoom
 
zoom100Percent() - Method in class ij.gui.ImageCanvas
Implements the Image/Zoom/View 100% command.
zoom100Percent() - Method in class ij.gui.PlotCanvas
Implements the Image/Zoom/View 100% command: Sets the original frame size as specified in Edit/Options/Plots (unless the plot is frozen)
zoomIn(int, int) - Method in class ij.gui.ImageCanvas
Zooms in by making the window bigger.
zoomIn(int, int) - Method in class ij.gui.PlotCanvas
Zooms in by modifying the plot range; sx and sy are screen coordinates
zoomOut(int, int) - Method in class ij.gui.ImageCanvas
Zooms out by making the source rectangle (srcRect) larger and centering it on (x,y).
zoomOut(int, int) - Method in class ij.gui.PlotCanvas
Zooms out by modifying the plot range; sx and sy are screen coordinates
zoomTargetOX - Variable in class ij.gui.ImageCanvas
Image (=offscreen) coordinates where the cursor was moved to for zooming
zoomTargetOY - Variable in class ij.gui.ImageCanvas
 
zOrigin - Variable in class ij.measure.Calibration
Z origin in pixels.
ZProjector - Class in ij.plugin
This plugin performs a z-projection of the input stack.
ZProjector() - Constructor for class ij.plugin.ZProjector
 
ZProjector(ImagePlus) - Constructor for class ij.plugin.ZProjector
Construction of ZProjector with image to be projected.
zScale(ImagePlus, int, int) - Method in class ij.plugin.Resizer
 
zSelector - Variable in class ij.gui.StackWindow
 
ZTC - Static variable in class ij.plugin.HyperStackConverter
 
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