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

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(Interpreter) - Static method in class ij.macro.Interpreter
Absolete, replaced by abortMacro().
abortMacro() - Method in class ij.macro.Interpreter
Aborts this macro.
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 the about.jpg in ij.jar, scaling it 400% and adding some text.
AboutBox() - Constructor for class ij.plugin.AboutBox
 
ABS - Static variable in interface ij.macro.MacroConstants
 
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
 
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
 
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.plugin.BatchConverter
 
actionPerformed(ActionEvent) - Method in class ij.plugin.BatchProcesser
 
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.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.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
 
add(Component) - Method in class ij.gui.ImageWindow
 
add(Roi) - Method in class ij.gui.Overlay
 
add(ImageProcessor, double) - Method in class ij.plugin.filter.SaltAndPepper
 
add(ImagePlus, Roi, int) - Method in class ij.plugin.frame.RoiManager
Adds the specified ROI to the list.
ADD - Static variable in interface ij.process.Blitter
dst=dst+src
add(int) - Method in class ij.process.FloatProcessor
 
add(double) - 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(double) - 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(double) - Method in class ij.process.ShortProcessor
 
ADD_TO_MANAGER - Static variable in class ij.plugin.filter.ParticleAnalyzer
Add particles to ROI Manager.
addAdjustmentListener(AdjustmentListener) - Method in class ij.gui.ScrollbarWithLabel
 
addBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
 
addChar(char) - Method in class ij.gui.TextRoi
Adds the specified character to the end of the text string.
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.
addChoice(String, String[], String) - Method in class ij.gui.GenericDialog
Adds a popup menu.
addCircle(String, String, String) - Static method in class ij.gui.ShapeRoi
 
addColumns() - Method in class ij.measure.ResultsTable
 
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.
addElement(Roi) - Method in class ij.gui.Overlay
 
addErrorBars(float[]) - Method in class ij.gui.Plot
Adds error bars to the plot.
addErrorBars(double[]) - Method in class ij.gui.Plot
Adds error bars to the plot.
addErrorBars(float[]) - Method in class ij.gui.PlotWindow
Adds error bars to the plot.
addEventListener(IJEventListener) - Static method in class ij.IJ
 
addHelp(String) - Method in class ij.gui.GenericDialog
 
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
Draws a label.
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
Adds a label to the beginning of the current row.
addLayoutComponent(String, Component) - Method in class ij.gui.ImageLayout
Not used by this class.
addMacroTool(String, MacroInstaller, int) - Method in class ij.gui.Toolbar
Used by the MacroInstaller class to install macro tools.
addMessage(String) - Method in class ij.gui.GenericDialog
Adds a message consisting of one or more lines of text.
addNotify() - Method in class ij.gui.MultiLineLabel
 
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.
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.
addPoint(int, int) - Method in class ij.gui.PointRoi
Returns a copy of this PointRoi with a point at (x,y) added.
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(double[], double[], int) - Method in class ij.gui.Plot
Adds a set of points to the plot using double arrays.
addPoints(float[], float[], int) - Method in class ij.gui.PlotWindow
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.PlotWindow
Adds a set of points to the plot using double arrays.
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.
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.
addSlice(String, Object) - Method in class ij.ImageStack
Adds an image in the forma of a pixel array to the end of the stack.
addSlice(String, ImageProcessor) - Method in class ij.ImageStack
Adds the image in 'ip' to the end of the stack.
addSlice(String, ImageProcessor, int) - Method in class ij.ImageStack
Adds the image in 'ip' to the stack following slice 'n'.
addSlice(String) - Method in class ij.VirtualStack
Adds an image to the end of the stack.
addSlice(String, Object) - Method in class ij.VirtualStack
Does nothing.
addSlice(String, ImageProcessor) - Method in class ij.VirtualStack
Does nothing..
addSlice(String, ImageProcessor, int) - Method in class ij.VirtualStack
Does noting.
addSlider(String, double, double, double) - Method in class ij.gui.GenericDialog
 
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.
addTextAreas(String, String, int, int) - Method in class ij.gui.GenericDialog
Adds one or two (side by side) text areas.
addToManager - Variable in class ij.plugin.filter.ParticleAnalyzer
 
addTool(String) - Method in class ij.gui.Toolbar
Adds a tool to the toolbar.
addUnsignedShortSlice(String, Object) - Method in class ij.ImageStack
Deprecated. Short images are always unsigned.
addValue(int, double) - Method in class ij.measure.ResultsTable
Adds a value to the end of the given column.
addValue(String, double) - Method in class ij.measure.ResultsTable
Adds a value to the end of the given column.
addWindow(Frame) - Static method in class ij.WindowManager
Adds the specified window to the Window menu.
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
 
allPoints() - Static method in class ij.gui.Wand
 
altKeyDown() - Static method in class ij.IJ
Returns true if the alt key is down.
analyze(ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
Uses ImageJ's particle analyzer to extract a set of coordinate pairs from a digitized line graph.
analyze(ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
Performs particle analysis on the specified image.
analyze(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
Performs particle analysis on the specified ImagePlus and ImageProcessor.
Analyzer - 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 results table.
analyzer - Variable in class ij.plugin.filter.ParticleAnalyzer
 
and(ShapeRoi) - Method in class ij.gui.ShapeRoi
Unary intersection operator.
AND - Static variable in interface ij.process.Blitter
dst=dst AND src
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
 
ANGLE - Static variable in class ij.gui.Roi
 
ANGLE - Static variable in class ij.gui.Toolbar
 
ANGLE - Static variable in class ij.measure.ResultsTable
 
angle - Variable in class ij.process.EllipseFitter
Angle in degrees
angle - Variable in class ij.process.ImageStatistics
Angle in degrees of fitted ellipse
angstromSymbol - Static variable in class ij.IJ
 
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.
append(String, String) - Static method in class ij.IJ
Appends a string to the end of a file.
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(ArrayList) - Method in class ij.text.TextPanel
Adds strings contained in an ArrayList to the end of this TextPanel.
append(String) - Method in class ij.text.TextWindow
Adds one or lines of text to the window.
appendLine(String) - Method in class ij.text.TextPanel
Adds a single line to the end of this TextPanel.
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
 
applyTable(int[]) - Method in class ij.process.ByteProcessor
 
applyTable(int[]) - Method in class ij.process.ColorProcessor
 
applyTable(int[], 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
 
AREA - Static variable in interface ij.measure.Measurements
 
AREA - Static variable in class ij.measure.ResultsTable
 
area - Variable in class ij.process.ImageStatistics
 
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
 
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
 
ArrowToolOptions - Class in ij.plugin
This plugin implements the Edit/Options/Arrow Tool command.
ArrowToolOptions() - Constructor for class ij.plugin.ArrowToolOptions
 
ARTEST - 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_UPDATE - Static variable in interface ij.macro.MacroConstants
 
autoClose - Static variable in class ij.gui.PlotWindow
Automatically close window after saving values.
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, 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, int, int) - Method in class ij.gui.Wand
This is a variation of legacy autoOutline that uses int threshold arguments.
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, 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.
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 from the Auto_Threshold plugin (http://pacific.mpi-cbg.de/wiki/index.php/Auto_Threshold) by G.Landini at bham dot ac dot uk.
AutoThresholder() - Constructor for class ij.process.AutoThresholder
 
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) Version 2008-07-03 by Michael Schmid, based on a plugin by Daniel Marsh and Wayne Rasband 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 compressed formats - png or jpeg-encoded individual frames.
AVI_Reader() - Constructor for class ij.plugin.AVI_Reader
 
AVI_Writer - Class in ij.plugin.filter
This plugin saves stacks in AVI format.
AVI_Writer() - Constructor for class ij.plugin.filter.AVI_Writer
 

B

BACKGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
 
backgroundColor - Static variable in class ij.ImageJ
 
BackgroundSubtracter - Class in ij.plugin.filter
Implements ImageJ's Subtract Background command.
BackgroundSubtracter() - Constructor for class ij.plugin.filter.BackgroundSubtracter
 
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/Batch/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
 
BatchProcesser - Class in ij.plugin
This plugin implements the File/Batch/Macro and File/Batch/Virtual Stack commands.
BatchProcesser() - Constructor for class ij.plugin.BatchProcesser
 
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.filter
Implements the Plugins/Utilities/Run Benchmark command.
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
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
 
BinaryProcessor - Class in ij.process
This class processes binary images.
BinaryProcessor(ByteProcessor) - Constructor for class ij.process.BinaryProcessor
Creates a BinaryProcessor from a ByteProcessor.
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
These are the three stacks created by the split(ImageStack) method.
blues - Variable in class ij.io.FileInfo
 
blur(ImageProcessor, double) - Method in class ij.plugin.filter.GaussianBlur
Gaussian Filtering of an 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.
BLUR_MORE - Static variable in class ij.process.ImageProcessor
 
blurFloat(FloatProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur
Gaussian Filtering of a FloatProcessor.
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_MARGIN - Static variable in class ij.gui.Plot
the margin width below the plot frame
BOX - Static variable in class ij.gui.Plot
Display points using an box-shaped mark.
BOX - Static variable in class ij.gui.PlotWindow
Display points using an box-shaped mark.
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
 
BUILD - Static variable in class ij.ImageJ
 
buildControlDialog(int, int) - Method in class ij.plugin.ZProjector
Builds dialog to query users for projection parameters.
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(Image) - Constructor for class ij.process.ByteProcessor
Creates a ByteProcessor from an AWT Image.
ByteProcessor(int, int) - Constructor for class ij.process.ByteProcessor
Creates a blank ByteProcessor of the specified dimensions.
ByteProcessor(int, int, byte[], ColorModel) - Constructor for class ij.process.ByteProcessor
Creates a ByteProcessor from a pixel array and IndexColorModel.
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

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)
CALCULATOR - Static variable in interface ij.macro.MacroConstants
 
CALIBRATE - Static variable in interface ij.macro.MacroConstants
 
calibrate(ImagePlus) - Method in class ij.plugin.filter.Calibrator
 
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(ImagePlus) - Constructor for class ij.measure.Calibration
Constructs a new Calibration object using the default values.
Calibration() - Constructor for class ij.measure.Calibration
Constructs a new Calibration object using the default values.
CalibrationBar - Class in ij.plugin.filter
This plugin displays a calibration bar on the active image.
CalibrationBar() - Constructor for class ij.plugin.filter.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
 
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
 
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.
center(Window) - Static method in class ij.gui.GUI
Positions the specified window in the center of the screen.
center - Variable in class ij.gui.Roi
 
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.
CENTROID - Static variable in interface ij.measure.Measurements
 
CHANGE_VALUES - Static variable in interface ij.macro.MacroConstants
 
changeFont(Font) - Method in class ij.gui.Plot
Changes the font.
changeFont(Font) - Method in class ij.gui.PlotWindow
Changes the font.
changes - Variable in class ij.ImagePlus
True if any changes have been made to this image.
CHANNEL - Static variable in class ij.measure.ResultsTable
 
channelLuts - Variable in class ij.io.FileInfo
 
Channels - Class in ij.plugin.frame
Displays the ImageJ Channels window.
Channels() - Constructor for class ij.plugin.frame.Channels
 
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
 
CIRCLE - Static variable in class ij.gui.Plot
Display points using a circle 5 pixels in diameter.
CIRCLE - Static variable in class ij.gui.PlotWindow
Display points using a circle 5 pixels in diameter.
CIRCULARITY - Static variable in interface ij.measure.Measurements
 
CIRCULARITY - Static variable in class ij.measure.ResultsTable
 
ClassChecker - Class in ij.plugin
Checks for duplicate class and JAR files in the plugins folders and deletes older duplicates.
ClassChecker() - Constructor for class ij.plugin.ClassChecker
 
clear() - Method in class ij.gui.Overlay
 
clear(ImageProcessor) - Method in class ij.plugin.filter.Filler
 
clear() - Method in class ij.text.TextPanel
Deletes all the lines.
CLEAR_WORKSHEET - Static variable in class ij.plugin.filter.ParticleAnalyzer
Clear ImageJ console 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 and pastes images to the 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.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
 
clone() - Method in class ij.io.FileInfo
 
clone() - Method in class ij.measure.Calibration
 
clone() - Method in class ij.measure.ResultsTable
Creates a copy of this ResultsTable.
clone() - Method in class ij.process.LUT
 
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.RandomAccessStream
 
CLOSE - Static variable in interface ij.macro.MacroConstants
 
close() - Method in class ij.plugin.frame.Channels
 
close() - Method in class ij.plugin.frame.ColorThresholder
 
close() - Method in class ij.plugin.frame.ContrastAdjuster
Overrides close() in PlugInFrame.
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.PasteController
 
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.ThresholdAdjuster
Overrides close() in PlugInFrame.
close() - Method in class ij.text.TextWindow
 
closeAllWindows() - Static method in class ij.WindowManager
Closes all windows.
closed - Variable in class ij.gui.ImageWindow
 
CLOSED - Static variable in class ij.ImagePlus
 
cm - Variable in class ij.process.ImageProcessor
 
cm2 - Variable in class ij.process.ImageProcessor
 
coefficients - Variable in class ij.io.FileInfo
 
COLOR - Static variable in class ij.CompositeImage
 
COLOR8 - Static variable in class ij.io.FileInfo
8-bit unsigned integer with color lookup table.
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
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(Image) - Constructor for class ij.process.ColorProcessor
Creates a ColorProcessor from an AWT 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.
Colors - Class in ij.plugin
This plugin implements most of the Edit/Options/Colors command.
Colors() - Constructor for class ij.plugin.Colors
 
colors - Static variable in class ij.plugin.Colors
 
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 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
 
columnExists(int) - Method in class ij.measure.ResultsTable
Returns true if the specified column exists and is not empty.
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.Orthogonal_Views
 
CommandFinder - Class in ij.plugin
 
CommandFinder() - Constructor for class ij.plugin.CommandFinder
 
commandInUse(String) - Static method in class ij.Menus
 
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
Lists ImageJ commands or keyboard shortcuts in a text window.
CommandLister() - Constructor for class ij.plugin.CommandLister
 
commandPrefix - Static variable in class ij.plugin.MacroInstaller
 
Commands - Class in ij.plugin
Runs File and Window menu commands.
Commands() - Constructor for class ij.plugin.Commands
 
Compiler - Class in ij.plugin
Compiles and runs plugins using the javac compiler.
Compiler() - Constructor for class ij.plugin.Compiler
 
COMPOSITE - Static variable in class ij.CompositeImage
 
COMPOSITE - Static variable in class ij.gui.Roi
 
CompositeConverter - Class in ij.plugin
This plugin imlements the Image/Color/Make Composite command.
CompositeConverter() - Constructor for class ij.plugin.CompositeConverter
 
CompositeImage - Class in ij
 
CompositeImage(ImagePlus) - Constructor for class ij.CompositeImage
 
CompositeImage(ImagePlus, int) - Constructor for class ij.CompositeImage
 
compositeImage - Variable in class ij.ImagePlus
 
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, ImagePlus, boolean) - Method in class ij.plugin.Concatenator
 
Concatenator - Class in ij.plugin
This plugin, which concatenates two images or stacks, implements the Image/Stacks/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.
constrain - Variable in class ij.gui.Roi
 
CONSTRUCTING - Static variable in class ij.gui.Roi
 
contains(int, int) - Method in class ij.gui.Line
 
contains(int, int) - Method in class ij.gui.OvalRoi
Tests if the specified point 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
 
contains(int, int) - Method in class ij.gui.Roi
 
contains(int, int) - Method in class ij.gui.ShapeRoi
Checks whether the specified coordinates are inside a on this ROI's shape boundaries.
contains(float, float) - Method in class ij.process.FloatPolygon
Returns 'true' if the point (x,y) is inside this polygon.
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 - Class in ij.plugin
ControlPanel.
ControlPanel() - Constructor for class ij.plugin.ControlPanel
 
convert(String) - Method in class ij.plugin.Converter
Converts the ImagePlus to the specified image type.
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_TO_FLOAT - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag to have the ImageProcessor that is passed to the run() method converted to a FloatProcessor.
Converter - Class in ij.plugin
Implements the conversion commands in the Image/Type submenu.
Converter() - Constructor for class ij.plugin.Converter
 
convertGrayJpegTo8Bits(ImagePlus) - Static method in class ij.io.Opener
If this image is grayscale, convert it to 8-bits.
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
 
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(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.
convertToByte() - Method in class ij.process.TypeConverter
Converts processor to a ByteProcessor.
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.
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.
convertToHSBHyperstack() - Method in class ij.process.StackConverter
Converts the stack (which must be RGB) to a 3 channel (hue, saturation and brightness) hyperstack.
convertToIndexedColor(int) - Method in class ij.process.StackConverter
Converts the stack to 8-bits indexed color.
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.
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(boolean) - Method in class ij.process.ImageProcessor
Returns a 16-bit version of this image as a ShortProcessor.
convertToShort() - Method in class ij.process.TypeConverter
Converts processor to a ShortProcessor.
convertVariable(Interpreter, int, Variable) - Static method in class ij.macro.ExtensionDescriptor
 
convolve(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
Convolves ip with a kernel of width kw and height kh.
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 - Static variable in class ij.process.ImageProcessor
 
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.
convolve3x3(int[]) - Method in class ij.process.ByteProcessor
3x3 convolution contributed by Glynne Casteel.
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.
convolveLine(float[], float[], float[][], int, int, int, int, int, int) - Method in class ij.plugin.filter.GaussianBlur
Convolve a line with a symmetric kernel and write to a separate array, possibly the pixels array of a FloatProcessor (as a row or column or part thereof)
Convolver - Class in ij.plugin.filter
This plugin convolves images using user user defined kernels.
Convolver() - Constructor for class ij.plugin.filter.Convolver
 
COORDINATES - Static variable in class ij.io.RoiDecoder
 
copy - Variable in class ij.gui.HistogramWindow
 
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() - Method in class ij.measure.Calibration
Returns a clone of this object.
COPY - Static variable in interface ij.process.Blitter
dst=src
COPY_INVERTED - Static variable in interface ij.process.Blitter
dst=255-src (8-bits and RGB)
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.Roi
Copy the attributes (outline color, fill color, outline width) of 'roi2' to the this selection.
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
 
copyBits(ImageStack, int, int, int) - Method in class ij.process.StackProcessor
 
copyColumnHeaders - Static variable in class ij.Prefs
Include column headers when copying tables to clipboard.
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
 
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
create(String, String) - Method in class ij.plugin.frame.Editor
 
create8BitImage() - Method in class ij.process.FloatProcessor
 
createBlankImage(int, int) - Static method in class ij.gui.GUI
Creates a white AWT Image image of the specified size.
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
 
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
Returns a new hyperstack with this image's attributes (e.g., width, height, spatial scale), but no image data.
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() - Method in class ij.process.ByteProcessor
 
createImage() - Method in class ij.process.ColorProcessor
 
createImage() - Method in class ij.process.FloatProcessor
 
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.ShortProcessor
Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
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.
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
 
createMacro(String, String) - Method in class ij.plugin.frame.Editor
 
createMacro(String) - Method in class ij.plugin.NewPlugin
 
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.
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
 
createShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
Creates an unsigned short image.
createSubtitle() - Method in class ij.gui.ImageWindow
Creates the subtitle.
createSubtitle() - Method in class ij.gui.StackWindow
 
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.process.ByteProcessor
 
crop() - Method in class ij.process.ColorProcessor
 
crop() - Method in class ij.process.FloatProcessor
 
crop() - Method in class ij.process.ImageProcessor
Creates a new processor containing an image that corresponds to the current ROI.
crop() - Method in class ij.process.ShortProcessor
 
crop(int, int, int, int) - Method in class ij.process.StackProcessor
Crops the stack to the specified rectangle.
CROSS - Static variable in class ij.gui.Plot
Display points using an cross-shaped mark.
CROSS - Static variable in class ij.gui.PlotWindow
Display points using an cross-shaped mark.
CROSSHAIR - Static variable in class ij.gui.Toolbar
 
crosshairCursor - Static variable in class ij.gui.ImageCanvas
 
cTable - Variable in class ij.process.ImageProcessor
 
currentMemory() - Static method in class ij.IJ
Returns the amount of memory currently being used by ImageJ.
currentSlice - Variable in class ij.ImagePlus
 
CurveFitter - Class in ij.measure
Curve fitting class based on the Simplex method described in the article "Fitting Curves to Data" in the May 1984 issue of Byte magazine, pages 340-362.
CurveFitter(double[], double[]) - Constructor for class ij.measure.CurveFitter
Construct a new CurveFitter.
CUSTOM - Static variable in class ij.io.Opener
 
CUSTOM - Static variable in class ij.measure.Calibration
 
cx - Variable in class ij.process.ImageProcessor
 
cy - Variable in class ij.process.ImageProcessor
 

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 - Static variable in interface ij.macro.MacroConstants
 
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.
darkBlue - Static variable in class ij.plugin.filter.Analyzer
 
DATE_TIME - Static variable in class ij.io.TiffDecoder
 
DEBUG - Static variable in interface ij.macro.MacroConstants
 
debug(Interpreter, int) - Method in class ij.plugin.frame.Editor
 
DEBUG_LOC_KEY - Static variable in class ij.text.TextWindow
 
debugInfo - Variable in class ij.io.FileInfo
 
debugMode - Static variable in class ij.IJ
 
debugMode - Variable in class ij.io.TiffDecoder
 
decimalPlaces - Variable in class ij.gui.HistogramWindow
 
decode(String, Color) - Static method in class ij.plugin.Colors
 
decodeDescriptionString(FileInfo) - Method in class ij.io.FileOpener
 
decodeToken(int) - Method in class ij.macro.Program
 
DEFAULT_FLAGS - Static variable in class ij.gui.Plot
the default flags
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
 
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
 
defaultText - Variable in class ij.gui.GenericDialog
 
defaultValues - Variable in class ij.gui.GenericDialog
 
degreeSymbol - Static variable in class ij.IJ
 
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.
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.
deleteSlice(int) - Method in class ij.ImageStack
Deletes the specified slice, were 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, were 1<=n<=nImages.
deleteSlice(int) - Method in class ij.plugin.ListVirtualStack
Deletes the specified image, were 1<=n<=nslices.
deleteSlice(int) - Method in class ij.VirtualStack
Deletes the specified slice, were 1<=n<=nslices.
description - Variable in class ij.io.FileInfo
 
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.
DIALOG - Static variable in interface ij.macro.MacroConstants
 
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.plugin.ArrowToolOptions
 
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.HyperStackReducer
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RGBStackConverter
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.SpecifyROI
 
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 implement this method.
DICOM - Static variable in class ij.io.FileInfo
 
DICOM - Static variable in class ij.io.Opener
 
DICOM - Class in ij.plugin
This plugin decodes DICOM files.
DICOM() - Constructor for class ij.plugin.DICOM
Default constructor.
DICOM(InputStream) - Constructor for class ij.plugin.DICOM
Constructs a DICOM reader that using an InputStream.
DICOM(BufferedInputStream) - Constructor for class ij.plugin.DICOM
Constructs a DICOM reader that using an BufferredInputStream.
DICOM_Sorter - Class in ij.plugin
 
DICOM_Sorter() - Constructor for class ij.plugin.DICOM_Sorter
 
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(int, int) - 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.
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.
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.
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.
displayComplex - Static variable in class ij.plugin.FFT
 
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
 
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 - Static variable in interface ij.process.Blitter
dst=dst/src
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.
divideByZeroValue - Static variable in class ij.process.FloatBlitter
 
dmode - Variable in class ij.process.ImageStatistics
 
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
 
doCommand(String) - Static method in class ij.IJ
Starts executing a menu command in a separete thread and returns immediately.
doCustomFit(String, double[], boolean) - Method in class ij.measure.CurveFitter
 
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.
doFiltering(FloatProcessor, int, int[], int, int, float) - Method in class ij.plugin.filter.RankFilters
Filter a FloatProcessor according to filterType
doFit(int) - Method in class ij.measure.CurveFitter
Perform curve fitting with the simplex method doFit(fitType) just does the fit doFit(fitType, true) pops up a dialog allowing control over simplex parameters alpha is reflection coefficient (-1) beta is contraction coefficient (0.5) gamma is expansion coefficient (2)
doFit(int, boolean) - Method in class ij.measure.CurveFitter
 
doFit(int) - Method in class ij.plugin.frame.Fitter
 
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.
doOptions() - Method in class ij.plugin.filter.Profiler
 
doProjection() - Method in class ij.plugin.ZProjector
Performs actual projection using specified method.
doProjections(ImagePlus) - Method in class ij.plugin.filter.Projector
 
doRGBProjection() - Method in class ij.plugin.ZProjector
 
doRGBProjections(ImagePlus) - Method in class ij.plugin.filter.Projector
 
DOT - Static variable in class ij.gui.Plot
Display points using a single pixel.
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
Double buffer display of selections and overlays.
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.
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
 
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(Graphics) - Method in class ij.gui.Arrow
Draws this arrow on the image.
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() - Method in class ij.gui.Plot
Draws the plot specified in the constructor.
draw() - Method in class ij.gui.PlotWindow
Displays the plot.
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.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() - 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(ImageProcessor) - Method in class ij.plugin.filter.Filler
Deprecated. replaced by ImageProcessor.draw(Roi)
draw(Roi) - Method in class ij.process.ImageProcessor
Draws an Roi.
DRAW_LINE - Static variable in interface ij.macro.MacroConstants
 
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
 
drawColorBar(Graphics, int, int, int, int) - Method in class ij.LookUpTable
 
drawColorBar(ImageProcessor, int, int) - Method in class ij.plugin.filter.CalibrationBar
 
drawColorBar(ImagePlus, int, int) - Method in class ij.plugin.filter.CalibrationBar
 
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.  
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.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
 
drawLine(double, double, double, double) - Method in class ij.gui.Plot
 
drawLine(int, int, int, int) - Method in class ij.process.ImageProcessor
Draws a line from (x1,y1) to (x2,y2).
drawOval(int, int, int, int) - Method in class ij.process.ImageProcessor
Draws an elliptical shape.
drawOverlay(Graphics) - Method in class ij.gui.Roi
 
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(ImageProcessor) - Method in class ij.gui.Arrow
 
drawPixels(ImageProcessor) - Method in class ij.gui.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() - Method in class ij.gui.Roi
Deprecated. replaced by drawPixels(ImageProcessor)
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.
drawRoiBrush(Graphics) - Method in class ij.gui.ShapeRoi
 
drawString(String) - Method in class ij.process.ImageProcessor
Draws a string at the current 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.
drawUnscaledColorBar(ImageProcessor, int, int, int, int) - Method in class ij.LookUpTable
 
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.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.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 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
 
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 interface ij.measure.Measurements
 
EllipseFitter - Class in ij.process
This class fits an ellipse to an ROI.
EllipseFitter() - Constructor for class ij.process.EllipseFitter
 
ELLIPSES - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
ELSE - Static variable in interface ij.macro.MacroConstants
 
EMBEDDED - Static variable in class ij.ImageJ
 
enableDebugging() - Method in class ij.io.TiffDecoder
 
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
 
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(Object) - Method in class ij.gui.Roi
Checks whether two rectangles are equal.
equals(Calibration) - Method in class ij.measure.Calibration
Compares two Calibration objects for equality.
erode() - Method in class ij.process.ByteProcessor
 
erode(int, int) - 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.
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.
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.
EVAL - Static variable in interface ij.macro.MacroConstants
 
evalSpline(int[], int[], int, double) - Method in class ij.measure.SplineFitter
Evalutes spline function at given point
eventOccurred(int) - Method in interface ij.IJEventListener
 
EXCLUDE_EDGE_PARTICLES - Static variable in class ij.plugin.filter.ParticleAnalyzer
Do not measure particles touching edge of image.
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 active image image.
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 - Static variable in interface ij.macro.MacroConstants
 
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_RECOVERY - Static variable in class ij.measure.CurveFitter
 
EXP_WITH_OFFSET - Static variable in class ij.measure.CurveFitter
 
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
 
EXT - Static variable in interface ij.macro.MacroConstants
 
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[], double) - Method in class ij.measure.CurveFitter
Returns formula value for parameters 'p' at 'x'
f(int, double[], double) - Static method in class ij.measure.CurveFitter
Returns 'fit' 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 class ij.macro.Interpreter
 
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_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(ImageProcessor) - Constructor for class ij.process.FHT
Constructs a FHT object from an ImageProcessor.
FILE - Static variable in interface ij.macro.MacroConstants
 
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 as a virtual stack.
FileInfoVirtualStack() - Constructor for class ij.plugin.FileInfoVirtualStack
 
FileInfoVirtualStack(FileInfo) - 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 - Static variable in interface ij.macro.MacroConstants
 
fill(ImageProcessor) - Method in class ij.plugin.filter.Filler
Deprecated. replaced by ImageProcessor.fill(Roi)
fill(ImageProcessor) - Method in class ij.process.ByteProcessor
Fills pixels that are within roi and part of the mask.
fill(ImageProcessor) - Method in class ij.process.ColorProcessor
Fills pixels that are within roi and part of the mask.
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(ImageProcessor) - Method in class ij.process.FloatProcessor
Fills pixels that are within roi and part of the mask.
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() - Method in class ij.process.ImageProcessor
Fills the image or ROI bounding rectangle with the current fill/draw value.
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(Roi) - Method in class ij.process.ImageProcessor
Fills the ROI with the current fill/draw value.
fill(ImageProcessor, Rectangle) - Method in class ij.process.PolygonFiller
Fills the polygon using the ImageProcessor's current drawing color.
fill() - Method in class ij.process.ShortProcessor
Fills the current rectangular ROI.
fill(ImageProcessor) - Method in class ij.process.ShortProcessor
Fills pixels that are within roi and part of the mask.
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().
FILL_BLACK - Static variable in class ij.gui.NewImage
 
FILL_COLOR - Static variable in class ij.io.RoiDecoder
 
FILL_OVAL - Static variable in interface ij.macro.MacroConstants
 
FILL_RAMP - 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
 
fillColor - Variable in class ij.gui.Roi
 
FILLED - Static variable in class ij.gui.Arrow
 
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.
filter(int) - Method in class ij.process.ByteProcessor
Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ColorProcessor
3x3 unweighted smoothing.
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 - Static variable in class ij.Undo
 
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
 
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(ImageProcessor, double, 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).
findMinAndMax() - Method in class ij.process.FloatProcessor
Calculates the minimum and maximum pixel value for the entire image.
findMinAndMax() - Method in class ij.process.ShortProcessor
 
findNthLowestNumber(float[], int, int) - Static method in class ij.plugin.filter.RankFilters
Find the n-th lowest number in part of an array
FIT - Static variable in interface ij.macro.MacroConstants
 
fit(ImageProcessor, ImageStatistics) - Method in class ij.process.EllipseFitter
Fits an ellipse to the current ROI.
fitList - Static variable in class ij.measure.CurveFitter
 
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(int) - Method in class ij.gui.PolygonRoi
 
fitSpline() - Method in class ij.gui.PolygonRoi
 
fitSplineForStraightening() - Method in class ij.gui.PolygonRoi
 
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
 
fixNewLines(String) - Static method in class ij.util.Tools
Converts carriage returns to line feeds.
flags - Variable in class ij.gui.ImageCanvas
 
flatten() - Method in class ij.ImagePlus
Returns a "flattened" version of this image, in RGB format.
flipHorizontal() - Method in class ij.process.ImageProcessor
Flips the image or ROI horizontally.
flipHorizontal() - Method in class ij.process.StackProcessor
 
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
 
fList - Static variable in class ij.measure.CurveFitter
 
FLOAT - Static variable in class ij.plugin.filter.EDM
Output type: new 32-bit image
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(float[], float[], int) - Constructor for class ij.process.FloatPolygon
Constructs a FloatPolygon.
FloatProcessor - Class in ij.process
This is an 32-bit floating-point image and methods that operate on that image.
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) - Constructor for class ij.process.FloatProcessor
Creates a blank FloatProcessor using the default grayscale LUT that displays zero as black.
FloatProcessor(int, int, int[]) - Constructor for class ij.process.FloatProcessor
Creates a FloatProcessor from an int array using the default grayscale LUT.
FloatProcessor(int, int, double[]) - Constructor for class ij.process.FloatProcessor
Creates a FloatProcessor from a double array using the default grayscale LUT.
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.
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.
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.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.PlugInFrame
 
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
 
fontMetrics - Variable in class ij.process.ImageProcessor
 
Fonts - Class in ij.plugin.frame
Displays a window that allows the user to set the font, size and style.
Fonts() - Constructor for class ij.plugin.frame.Fonts
 
FOR - Static variable in interface ij.macro.MacroConstants
 
FOREGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
 
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.
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
Runs the garbage collector and 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
 
FROM_CHAR_CODE - Static variable in interface ij.macro.MacroConstants
 
FUNCTION - Static variable in interface ij.macro.MacroConstants
 
FunctionFinder - Class in ij.macro
This class implements the text editor's Macros/Find Functions command.
FunctionFinder() - Constructor for class ij.macro.FunctionFinder
 
functionIDs - Static variable in interface ij.macro.MacroConstants
 
Functions - Class in ij.macro
This class implements the built-in macro functions.
functions - Static variable in interface ij.macro.MacroConstants
 

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
 
gapBetweenImages - Variable in class ij.io.FileInfo
 
GAUSSIAN - Static variable in class ij.measure.CurveFitter
 
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
Default constructor
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
 
get(String, String) - Static method in class ij.Prefs
Uses the keyword key to retrieve a string 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, boolean) - Static method in class ij.Prefs
Uses the keyword key to retrieve a boolean from the preferences file.
get(int, int) - Method in class ij.process.ByteProcessor
 
get(int) - Method in class ij.process.ByteProcessor
 
get(int, int) - Method in class ij.process.ColorProcessor
 
get(int) - Method in class ij.process.ColorProcessor
 
get(int, int) - Method in class ij.process.FloatProcessor
 
get(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) - Method in class ij.process.ImageProcessor
 
get(int, int) - Method in class ij.process.ShortProcessor
 
get(int) - Method in class ij.process.ShortProcessor
 
get16BitBufferedImage() - Method in class ij.process.ShortProcessor
Returns a copy of this image as a TYPE_USHORT_GRAY BufferedImage.
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_DIRECTORY - 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_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
 
getActiveChannels() - Method in class ij.CompositeImage
 
getAdditionalFunctions() - Static method in class ij.macro.Interpreter
 
getAngle() - Method in class ij.gui.PolygonRoi
Returns the angle in degrees between the first two segments of this polyline.
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
 
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() - 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
Always returns 0.
getBackgroundValue() - Method in class ij.process.ImageProcessor
Returns the background fill value.
getBackgroundValue() - Method in class ij.process.ShortProcessor
Always returns 0.
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.ImagePlus
Returns the bit depth, 8, 16, 24 (RGB) or 32.
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
 
getBlues() - Method in class ij.LookUpTable
 
getBoolean(String, boolean) - Static method in class ij.Prefs
Finds a boolean in IJ_Props or IJ_Prefs.txt.
getBoundingRect() - Method in class ij.gui.Roi
Deprecated. replaced by getBounds()
getBounds() - Method in class ij.gui.Line
Return the bounding rectangle of this line.
getBounds() - Method in class ij.gui.Roi
Return this selection's bounding rectangle.
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 brush tool, or 0 if the brush tool is not enabled.
getBufferedImage() - Method in class ij.ImagePlus
Returns this image as a 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.ShortProcessor
Returns this image as an 8-bit BufferedImage .
getButtons() - Method in class ij.gui.GenericDialog
Returns references to the "OK" ("Yes"), "Cancel", and if present, "No" buttons as an array.
getButtonSize() - Static method in class ij.gui.Toolbar
 
getByteRow(ImageStack, int, int, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
 
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.
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.
getChannel() - Method in class ij.ImagePlus
 
getChannelColor() - Method in class ij.CompositeImage
 
getChannelLut(int) - Method in class ij.CompositeImage
 
getChannelLut() - 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 an instance of the class loader ImageJ uses to run plugins.
getClipboard() - Static method in class ij.ImagePlus
Returns the internal clipboard or null if the internal clipboard is empty.
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(String, Color) - Static method in class ij.plugin.Colors
 
getColor(String, Color) - Static method in class ij.Prefs
Finds a color in IJ_Props or IJ_Prefs.txt.
getColor(int, int) - Method in class ij.process.ColorProcessor
 
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.
getColorName(Color, String) - Static method in class ij.plugin.Colors
 
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, int[], int) - Method in class ij.process.ImageProcessor
Returns the pixel values down the column starting at (x,y).
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.
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.
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.
getComplexTransform() - Method in class ij.process.FHT
Converts this FHT to a complex Fourier transform and returns it as a two slice stack.
getConvexHull() - Method in class ij.gui.PolygonRoi
Uses the gift wrap algorithm to find the convex hull and returns it as a Polygon.
getConvexHull() - Method in class ij.gui.Roi
 
getConvexHull() - Method in class ij.gui.ShapeRoi
Always returns null.
getCopy() - Method in class ij.process.FHT
Returns a clone of this FHT.
getCount() - Method in class ij.plugin.frame.RoiManager
Returns the ROI count.
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.
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().
getCurrentFont() - Method in class ij.gui.TextRoi
Returns the current (instance) font.
getCurrentImage() - Static method in class ij.WindowManager
Returns a reference to the active image or null if there isn't one.
getCurrentPasteMode() - Static method in class ij.gui.Roi
Returns the current paste transfer mode.
getCurrentSlice() - Method in class ij.ImagePlus
Returns the current stack slice number 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.
getCValue(int) - Method in class ij.measure.Calibration
Converts a raw pixel value to a density calibrated value.
getCValue(double) - Method in class ij.measure.Calibration
Converts a raw pixel value to a density calibrated value.
getDecimalPlaces(double, double) - Static method in class ij.util.Tools
Returns the number of decimal places need to display two numbers.
getDefaultColorModel() - Method in class ij.process.ImageProcessor
Returns the default grayscale IndexColorModel.
getDefaultDirectory() - Static method in class ij.io.OpenDialog
Returns the current working directory, which may be null.
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
 
getDefaultHeadSize() - Static method in class ij.gui.Arrow
 
getDefaultStyle() - Static method in class ij.gui.Arrow
 
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.
getDir(String) - Method in class ij.io.Opener
 
getDir(String) - Static method in class ij.Macro
 
getDirectory(String) - Static method in class ij.IJ
Returns the path to the home ("user.home"), startup, ImageJ, plugins, macros, luts, temp, current or image directory if title is "home", "startup", "imagej", "plugins", "macros", "luts", "temp", "current" or "image", otherwise, displays a dialog and returns the path to the directory selected by the user.
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.VirtualStack
Returns the path to the directory containing the images.
getDisplayList() - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.getOverlay()
getDisplayRangeMax() - Method in class ij.CompositeImage
 
getDisplayRangeMax() - Method in class ij.ImagePlus
 
getDisplayRangeMin() - Method in class ij.CompositeImage
 
getDisplayRangeMin() - Method in class ij.ImagePlus
 
getDoScaling() - Static method in class ij.process.ImageConverter
Returns true if scaling is enabled.
getDouble(String, double) - Static method in class ij.Prefs
Looks up a real number in IJ_Props or IJ_Prefs.txt.
getDoubleHeaded() - Method in class ij.gui.Arrow
 
getDrawLabels() - Method in class ij.plugin.frame.RoiManager
 
getEditor() - Method in class ij.macro.Interpreter
 
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.
getExtensionFunctions() - Method in interface ij.macro.MacroExtension
 
getf(int, int) - Method in class ij.process.ByteProcessor
 
getf(int) - Method in class ij.process.ByteProcessor
 
getf(int, int) - Method in class ij.process.ColorProcessor
 
getf(int) - Method in class ij.process.ColorProcessor
 
getf(int, int) - Method in class ij.process.FloatProcessor
 
getf(int) - Method in class ij.process.FloatProcessor
 
getf(int, int) - Method in class ij.process.ImageProcessor
 
getf(int) - Method in class ij.process.ImageProcessor
 
getf(int, int) - Method in class ij.process.ShortProcessor
 
getf(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.Roi
Caculates "Feret" (maximum caliper width), "FeretAngle" and "MinFeret" (minimum caliper width), "FeretX" and "FeretY".
getFeretValues() - Method in class ij.gui.ShapeRoi
Caculates "Feret" (maximum caliper width) and "MinFeret" (minimum caliper width).
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.VirtualStack
Returns the file name of the specified slice, were 1<=n<=nslices.
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 the color used to fill this ROI when it is in a display, or null.
getFit() - Method in class ij.measure.CurveFitter
 
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.
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].
getFloatPolygon() - Method in class ij.gui.PolygonRoi
Returns this polygon or polyline as float arrays.
getFloatPolygon() - Method in class ij.gui.Roi
 
getFont() - Static method in class ij.gui.TextRoi
Returns the name of the global font.
getFont() - Static method in class ij.Menus
 
getFont() - Method in class ij.process.ImageProcessor
Returns the current font.
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.
getForegroundColor() - Static method in class ij.gui.Toolbar
 
getFormula() - Method in class ij.measure.CurveFitter
 
getFrame() - Method in class ij.ImagePlus
 
getFrame(String) - Static method in class ij.WindowManager
Returns the frame with the specified title or null if a frame with that title is not found.
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
Returns the front most window or null.
getFunction() - Method in class ij.measure.Calibration
Returns the calibration function ID.
getGlobalCalibration() - Method in class ij.ImagePlus
Returns the system-wide calibration, or null.
getGlobals() - Method in class ij.macro.Program
 
getGreens() - Method in class ij.LookUpTable
 
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.
getHeadSize() - Method in class ij.gui.Arrow
 
getHeight() - Method in class ij.ImagePlus
 
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.
getHigherZoomLevel(double) - Static method in class ij.gui.ImageCanvas
 
getHistogram() - Method in class ij.gui.HistogramWindow
 
getHistogram() - Method in class ij.process.ByteProcessor
 
getHistogram(ImageProcessor) - Method in class ij.process.ByteProcessor
 
getHistogram() - Method in class ij.process.ColorProcessor
 
getHistogram(ImageProcessor) - Method in class ij.process.ColorProcessor
 
getHistogram() - Method in class ij.process.FloatProcessor
Not implemented.
getHistogram() - Method in class ij.process.ImageProcessor
Returns the histogram of the image or ROI.
getHistogram() - Method in class ij.process.ShortProcessor
Returns 65536 bin histogram of the current ROI, which can be non-rectangular.
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
Returns the path to the ImageJ directory.
getHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Returns hue, saturation and brightness in 3 byte arrays.
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() - Static method in class ij.IJ
Returns a reference to the active image.
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(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.
getImageID() - Method in class ij.gui.Roi
Returns the ID of the image associated with this ROI.
getImageInfo(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.Info
 
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().
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.
getIndexSampleModel() - Method in class ij.process.ImageProcessor
 
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.
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
 
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.
getInt(String, int) - Static method in class ij.Prefs
Finds an int in IJ_Props or IJ_Prefs.txt.
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).
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).
getInterpolationMethods() - Static method in class ij.process.ImageProcessor
 
getIterations() - Method in class ij.measure.CurveFitter
Get number of iterations performed
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
 
getLab(ImageProcessor, byte[], byte[], byte[]) - Method in class ij.plugin.frame.ColorThresholder
 
getLabel(int) - Method in class ij.measure.ResultsTable
Returns the label of the specified row.
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.
getLastDirectory() - Static method in class ij.io.OpenDialog
Returns the path to the last directory opened by the user using a file open or file save dialog, or using drag and drop.
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.Line
Returns the length of this line.
getLength() - Method in class ij.gui.OvalRoi
Returns the perimeter length.
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 length of this shape (perimeter, if shape is closed).
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
Returns the selection list.
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.
getLongFilePointer() - Method in class ij.io.RandomAccessStream
 
getLowerZoomLevel(double) - Static method in class ij.gui.ImageCanvas
 
getLuts() - Method in class ij.CompositeImage
 
getLuts() - Method in class ij.ImagePlus
 
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(ImageProcessor) - Method in class ij.gui.TextRoi
 
getMacroCount() - Method in class ij.Menus
 
getMacroCount() - Method in class ij.plugin.MacroInstaller
 
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
 
getMapSize() - Method in class ij.LookUpTable
 
getMask() - Method in class ij.gui.OvalRoi
 
getMask() - Method in class ij.gui.PointRoi
 
getMask() - Method in class ij.gui.PolygonRoi
Override Roi.nudge() to support splines.
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 the mask byte array, or null if there is no mask.
getMax() - Method in class ij.gui.ProfilePlot
Returns the calculated maximum value.
getMax(double[]) - Static method in class ij.measure.CurveFitter
Gets index of highest value in an array.
getMax() - Method in class ij.process.ByteProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ColorProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.FloatProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ImageProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ShortProcessor
Returns the largest displayed pixel value.
getMaximum() - Method in class ij.gui.ScrollbarWithLabel
 
getMaximumBounds() - Method in class ij.gui.ImageWindow
 
getMaxIterations() - Method in class ij.measure.CurveFitter
Get maximum number of iterations allowed
getMaxThreshold() - Method in class ij.process.ImageProcessor
Returns the upper threshold level.
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, or null if addMessage() was not called.
getMethods() - Static method in class ij.process.AutoThresholder
 
getMin() - Method in class ij.gui.ProfilePlot
Returns the calculated minimum value.
getMin() - Method in class ij.process.ByteProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ColorProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.FloatProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ImageProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ShortProcessor
Returns the smallest displayed pixel value.
getMinimum() - Method in class ij.gui.ScrollbarWithLabel
 
getMinimumSize() - Method in class ij.gui.MultiLineLabel
 
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
 
getMinMax(float[]) - Static method in class ij.util.Tools
 
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.WandToolOptions
 
getModeAsString() - Method in class ij.CompositeImage
 
getModifiers() - Method in class ij.gui.ImageCanvas
Returns the mouse event modifiers.
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(String) - Method in class ij.io.Opener
 
getName(String) - Static method in class ij.Macro
 
getName() - Method in class ij.measure.CurveFitter
 
getName(String) - Static method in class ij.plugin.frame.RoiManager
Returns the name of the ROI with the specified index.
getName() - Method in class ij.plugin.TextReader
Returns the file name.
getNChannels() - Method in class ij.ImagePlus
Returns the number of channels.
getNChannels() - Method in class ij.process.ColorProcessor
Returns the number of color channels of the image, i.e., 3.
getNChannels() - Method in class ij.process.ImageProcessor
Returns the number of color channels in the image.
getNCoordinates() - Method in class ij.gui.PolygonRoi
Returns the number of XY coordinates.
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.
getNextNumber() - Method in class ij.gui.GenericDialog
Returns the contents of the next numeric field.
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 textarea.
getNFrames() - Method in class ij.ImagePlus
Returns the number of frames (time-points).
getNonImageWindows() - Static method in class ij.WindowManager
Returns an array containing a list of the non-image windows.
getNonSplineCoordinates() - Method in class ij.gui.PolygonRoi
 
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.
getNumericFields() - Method in class ij.gui.GenericDialog
Returns the Vector containing the numeric TextFields.
getNumParams() - Method in class ij.measure.CurveFitter
Get number of parameters for current fit formula
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
 
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.
getOrientation() - Method in class ij.gui.ScrollbarWithLabel
 
getOriginalFileInfo() - Method in class ij.ImagePlus
Returns the FileInfo object that was used to open this image.
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)
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.
getParams() - Method in class ij.measure.CurveFitter
Get the set of parameter 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.
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, 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) - Method in class ij.process.FloatProcessor
Returns a pixel value that must be converted using Float.intBitsToFloat().
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) - Method in class ij.process.ImageProcessor
Returns the value of the pixel at (x,y).
getPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
Returns the samples for the pixel at (x,y) in an int array.
getPixel(int, int) - Method in class ij.process.ShortProcessor
 
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(int) - Method in class ij.ImageStack
Returns the pixel array for the specified slice, were 1<=n<=nslices.
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.VirtualStack
Returns the pixel array for the specified slice, were 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.ShortProcessor
Returns the value of the pixel at (x,y) as a float.
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.
getPlugInsPath() - Static method in class ij.Menus
Returns the path to the user plugins directory or null if the plugins directory was not found.
getPolygon() - Method in class ij.gui.Line
 
getPolygon() - Method in class ij.gui.OvalRoi
Returns this OvalRoi as a polygon.
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, or null if this is a straight line selection.
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.
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.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
Gets the path to the directory where the preferences file (IJPrefs.txt) is saved.
getPreviewCheckbox() - Method in class ij.gui.GenericDialog
Returns a reference to the Preview Checkbox.
getProcessor(int) - Method in class ij.CompositeImage
 
getProcessor() - Method in class ij.gui.Plot
Returns the plot as an ImageProcessor.
getProcessor() - Method in class ij.ImagePlus
Returns a reference to the current ImageProcessor.
getProcessor(int) - Method in class ij.ImageStack
Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
getProcessor(int) - Method in class ij.plugin.AVI_Reader
Returns an ImageProcessor for the specified frame 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, were 1<=n<=nImages.
getProcessor(int) - Method in class ij.plugin.ListVirtualStack
Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
getProcessor(int) - Method in class ij.VirtualStack
Returns an ImageProcessor for the specified slice, were 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
 
getProjection() - Method in class ij.plugin.ZProjector
Retrieve results of most recent projection operation.
getProperties() - Method in class ij.ImagePlus
Returns this image's Properties.
getProperty(String) - Method in class ij.ImagePlus
Returns the property associated with 'key'.
getQuality() - Static method in class ij.plugin.JpegWriter
Deprecated. replaced by FileSaver.getJpegQuality()
getRawLength() - Method in class ij.gui.Line
Returns the length of this line in pixels.
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.
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
 
getResiduals() - Method in class ij.measure.CurveFitter
Returns residuals array ie.
getRestarts() - Method in class ij.measure.CurveFitter
Get number of simplex restarts to do
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.
getResultString() - Method in class ij.measure.CurveFitter
Get a string description of the curve fitting results for easy output.
getRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Returns the red, green and blue planes as 3 byte arrays.
getRGBRow(ImageStack, int, int, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
 
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.
getRois() - Method in class ij.gui.ShapeRoi
Converts a Shape into Roi object(s).
getROIs() - Method in class ij.plugin.frame.RoiManager
Returns the ROI Hashtable.
getRoisAsArray() - Method in class ij.plugin.frame.RoiManager
Returns the ROIs as an array.
getRoot() - Method in class ij.plugin.ControlPanel
 
getRoundRectArcSize() - Method in class ij.gui.Roi
 
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, 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<=counter-1.
getRSquared() - Method in class ij.measure.CurveFitter
Returns R^2, where 1.0 is best.
getSaveAsMenu() - Static method in class ij.Menus
 
getScaledStroke() - Method in class ij.gui.Roi
 
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.
getSelectedRoisAsArray() - Method in class ij.plugin.frame.RoiManager
Returns the selected ROIs as an array, or all the ROIs if none are selected.
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.
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.
getShortSliceLabel(int) - Method in class ij.ImageStack
Returns a shortened version (up to the first 60 characters or first newline and suffix removed) of the label of the specified slice.
getShortTitle() - Method in class ij.ImagePlus
Returns a shortened version of image name that does not include spaces or a file name extension.
getShowAllColor() - Static method in class ij.gui.ImageCanvas
Returns the color used for "Show All" mode.
getShowAllList() - Method in class ij.gui.ImageCanvas
 
getShowAllROIs() - Method in class ij.gui.ImageCanvas
Returns the state of the ROI Manager "Show All" flag.
getSize() - Static method in class ij.gui.TextRoi
Returns the global font size.
getSize() - Method in class ij.ImageStack
Returns the number of slices in this stack.
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
Returns the number of images in this stack.
getSize() - Method in class ij.plugin.ListVirtualStack
Returns the number of images in this stack.
getSize() - Method in class ij.VirtualStack
Returns the number of slices in this stack.
getSlice() - Method in class ij.ImagePlus
 
getSliceLabel(int) - Method in class ij.ImageStack
Returns the label of the specified slice, were 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(String) - Method in class ij.gui.ImageCanvas
 
getSliceNumber() - Method in class ij.plugin.filter.PlugInFilterRunner
Return the slice number currently processed by the calling thread.
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.
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
 
getSrcRect() - Method in class ij.gui.ImageCanvas
 
getStack() - Method in class ij.ImagePlus
Returns the image stack.
getStackIndex(int, int, int) - Method in class ij.ImagePlus
Returns that stack index (1-based) corresponding to the specified position.
getStackSize() - Method in class ij.ImagePlus
If this is a stack, returns the number of slices, else returns 1.
getStartTime() - Method in class ij.ImagePlus
Returns the time in milliseconds when startTiming() was last called.
getState() - Method in class ij.gui.Roi
 
getStatistics() - Method in class ij.ImagePlus
Returns an ImageStatistics object generated using the standard measurement options (area, mean, mode, min and max).
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() - Method in class ij.process.ImageProcessor
 
getStatistics(ImageProcessor, int, Calibration) - Static method in class ij.process.ImageStatistics
 
getStatusBar() - Method in class ij.ImageJ
 
getString(String, String) - Static method in class ij.IJ
Allows the user to enter a string in a dialog box.
getString(String) - Static method in class ij.Prefs
Finds an string in IJ_Props or IJ_Prefs.txt.
getString(String, String) - Static method in class ij.Prefs
Finds an string in IJ_Props or IJ_Prefs.txt.
getStringFields() - Method in class ij.gui.GenericDialog
Returns the Vector containing the string TextFields.
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.
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 lineWidth.
getStyle() - Method in class ij.gui.Arrow
 
getStyle() - Static method in class ij.gui.TextRoi
Returns the global font style.
getSumResidualsSqr() - Method in class ij.measure.CurveFitter
 
getSymbolTable() - Method in class ij.macro.Program
 
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.
getThreads() - Static method in class ij.Prefs
Returns the number of threads used by PlugInFilters to process stacks.
getThreshold(String, int[]) - Method in class ij.process.AutoThresholder
 
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.ImagePlus
Returns the image name.
getTolerance() - Static method in class ij.plugin.WandToolOptions
 
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.
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
 
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
 
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(String) - Method in class ij.gui.GenericDialog
 
getValue() - Method in class ij.gui.ScrollbarWithLabel
 
getValue(String, String, String) - Static method in class ij.Macro
 
getValue(int, int) - Method in class ij.measure.ResultsTable
Deprecated. replaced by getValueAsDouble
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 getCounter().
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 getCounter().
getValueUnit() - Method in class ij.measure.Calibration
Returns the value unit.
getVariable(String) - Method in class ij.macro.Interpreter
 
getVariables() - Method in class ij.macro.Interpreter
 
getVersion() - Static method in class ij.IJ
Returns the ImageJ version number as a string.
getVersion() - Method in class ij.plugin.ControlPanel
 
getVisibleAmount() - Method in class ij.gui.ScrollbarWithLabel
 
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
 
getWidth() - Method in class ij.ImagePlus
 
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.
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.
getXCoordinates() - Method in class ij.gui.PolygonRoi
Returns this ROI's X-coordinates, which are relative to origin of the bounding box.
getXPoints() - Method in class ij.measure.CurveFitter
 
getXUnit() - Method in class ij.measure.Calibration
Returns the X length unit.
getXValues() - Method in class ij.gui.HistogramWindow
 
getXValues() - Method in class ij.gui.PlotWindow
 
getY(double) - Method in class ij.measure.Calibration
Converts a y-coodinate in pixels to physical units (e.g.
getY(double, int) - Method in class ij.measure.Calibration
Converts a y-coodinate in pixels to physical units (e.g.
getYCoordinates() - Method in class ij.gui.PolygonRoi
Returns this ROI's Y-coordinates, which are relative to origin of the bounding box.
getYPoints() - Method in class ij.measure.CurveFitter
 
getYUnit() - Method in class ij.measure.Calibration
Returns the Y length unit, or the default unit if 'yunit' is null.
getYUV(ImageProcessor, byte[], byte[], byte[]) - Method in class ij.plugin.frame.ColorThresholder
 
getYValues() - Method in class ij.gui.PlotWindow
 
getZ(double) - Method in class ij.measure.Calibration
Converts a z-coodinate in pixels to physical units (e.g.
getZUnit() - Method in class ij.measure.Calibration
Returns the Z length unit, or the default unit if 'zunit' is null.
GIF - Static variable in class ij.io.Opener
 
GIF_OR_JPG - Static variable in class ij.io.FileInfo
 
GifWriter - Class in ij.plugin
Writes a stack as an animated Gif
GifWriter() - Constructor for class ij.plugin.GifWriter
 
gLUT1 - Variable in class ij.process.ImageProcessor
 
gLUT2 - Variable in class ij.process.ImageProcessor
 
GRAY12_UNSIGNED - Static variable in class ij.io.FileInfo
12-bit unsigned integer (0-4095).
GRAY16 - Static variable in class ij.gui.NewImage
 
GRAY16 - Static variable in class ij.ImagePlus
16-bit grayscale (unsigned)
GRAY16_SIGNED - Static variable in class ij.io.FileInfo
16-bit signed integer (-32768-32767).
GRAY16_UNSIGNED - Static variable in class ij.io.FileInfo
16-bit unsigned integer (0-65535).
GRAY24_UNSIGNED - Static variable in class ij.io.FileInfo
24-bit unsigned integer.
GRAY32 - Static variable in class ij.gui.NewImage
 
GRAY32 - Static variable in class ij.ImagePlus
32-bit floating-point grayscale
GRAY32_FLOAT - Static variable in class ij.io.FileInfo
32-bit floating-point.
GRAY32_INT - Static variable in class ij.io.FileInfo
32-bit signed integer.
GRAY32_UNSIGNED - Static variable in class ij.io.FileInfo
32-bit unsigned integer.
GRAY64_FLOAT - Static variable in class ij.io.FileInfo
64-bit floating-point.
GRAY8 - Static variable in class ij.gui.NewImage
 
GRAY8 - Static variable in class ij.ImagePlus
8-bit grayscale (unsigned)
GRAY8 - Static variable in class ij.io.FileInfo
8-bit unsigned integer (0-255).
GRAYSCALE - Static variable in class ij.CompositeImage
 
green - Variable in class ij.plugin.filter.RGBStackSplitter
These are the three stacks created by the split(ImageStack) method.
greens - Variable in class ij.io.FileInfo
 
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
 
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
 

H

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_SIZE - Static variable in class ij.gui.Roi
 
handleColor - Variable in class ij.gui.Roi
 
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.Roi
 
handleMouseDrag(int, int, int) - Method in class ij.gui.Roi
 
handleMouseUp(int, int) - Method in class ij.gui.FreehandRoi
 
handleMouseUp(int, int) - Method in class ij.gui.PointRoi
 
handleMouseUp(int, int) - Method in class ij.gui.PolygonRoi
 
handleMouseUp(int, int) - Method in class ij.gui.Roi
 
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
 
hasCustomLuts() - Method in class ij.CompositeImage
 
hasVars() - Method in class ij.macro.Program
 
hasWord(String) - Method in class ij.macro.Program
 
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_KEY - Static variable in class ij.text.TextWindow
 
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.
hide() - Method in class ij.ImagePlus
Closes the window, if any, that is displaying this image.
hideCancelButton() - Method in class ij.gui.GenericDialog
No 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.  
histMax - Variable in class ij.process.ImageStatistics
 
histMin - Variable in class ij.process.ImageStatistics
 
histogram - Variable in class ij.gui.HistogramWindow
 
Histogram - Class in ij.plugin
This plugin implements the Analyze/Histogram command.
Histogram() - Constructor for class ij.plugin.Histogram
 
histogram - Variable in class ij.process.ImageStatistics
 
histogram16 - Variable in class ij.process.ImageStatistics
65536 element histogram (16-bit images only)
histogramMax - Variable in class ij.process.ImageProcessor
 
histogramMin - Variable in class ij.process.ImageProcessor
 
histogramSize - Variable in class ij.process.ImageProcessor
 
HistogramWindow - Class in ij.gui
This class is an extended ImageWindow that displays histograms.
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/Install and Remove commands.
Hotkeys() - Constructor for class ij.plugin.Hotkeys
 
HTMLDialog - Class in ij.gui
This is modal dialog box that displays HTML formated text.
HTMLDialog(String, String) - Constructor for 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
 
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
 
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.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.process - package ij.process
 
ij.text - package ij.text
 
ij.util - package ij.util
 
IJ_CALL - Static variable in interface ij.macro.MacroConstants
 
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.
image - Variable in class ij.process.ImageProcessor
 
IMAGE_DESCRIPTION - Static variable in class ij.io.TiffDecoder
 
IMAGE_LENGTH - Static variable in class ij.io.TiffDecoder
 
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 interface ij.ImageListener
 
imageClosed(ImagePlus) - Method in class ij.plugin.frame.Recorder
 
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
 
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(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_Updater - Class in ij.plugin
This plugin implements the Help/Update ImageJ command.
ImageJ_Updater() - Constructor for class ij.plugin.ImageJ_Updater
 
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 and 5 pixel horizontal and vertical gaps.
ImageListener - Interface in ij
Plugins that implement this interface are notified when an image window 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 interface ij.ImageListener
 
imageOpened(ImagePlus) - Method in class ij.plugin.frame.Recorder
 
imageOpened(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
 
ImagePlus - Class in ij
This is an extended image class that supports 8-bit, 16-bit, 32-bit (real) and RGB images.
ImagePlus() - Constructor for class ij.ImagePlus
Constructs an uninitialized ImagePlus.
ImagePlus(String, Image) - Constructor for class ij.ImagePlus
Constructs an ImagePlus from an Image or BufferedImage.
ImagePlus(String, ImageProcessor) - Constructor for class ij.ImagePlus
Constructs an ImagePlus from an ImageProcessor.
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.
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 displays an image as an overlay.
ImageRoi(int, int, BufferedImage) - Constructor for class ij.gui.ImageRoi
Creates a new ImageRoi from a BufferedImage.
ImageRoi(int, int, ImageProcessor) - Constructor for class ij.gui.ImageRoi
Creates a new ImageRoi from a ImageProcessor.
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 image stack with a capacity of 'size'.
ImageStack(int, int, ColorModel) - Constructor for class ij.ImageStack
Creates a new, empty image stack.
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 interface ij.ImageListener
 
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.Recorder
 
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(String) - Constructor for class ij.gui.ImageWindow
 
ImageWindow(ImagePlus) - Constructor for class ij.gui.ImageWindow
 
ImageWindow(ImagePlus, ImageCanvas) - 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
 
ImportDialog - Class in ij.io
This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.
ImportDialog(String, String) - Constructor for class ij.io.ImportDialog
 
ImportDialog() - Constructor for class ij.io.ImportDialog
 
in - Variable in class ij.io.TiffDecoder
 
IN_PLACE - Static variable in class ij.plugin.Resizer
 
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
Increments the measurement counter by one.
INDEX_OF - Static variable in interface ij.macro.MacroConstants
 
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
This plugin implements the Image/Show Info command.
Info() - Constructor for class ij.plugin.filter.Info
 
init() - Method in class ij.ImageJApplet
Starts ImageJ if it's not already running.
inputStream - Variable in class ij.io.FileInfo
 
insert(ImageProcessor, int, int) - Method in class ij.process.ImageProcessor
Inserts the image contained in 'ip' at (xloc, yloc).
install(String) - Method in class ij.plugin.MacroInstaller
 
install(String, Menu) - Method in class ij.plugin.MacroInstaller
 
Installer - Class in ij.plugin
Implements the Plugins/Shortcuts/Install...
Installer() - Constructor for class ij.plugin.Installer
 
installFile(String) - Method in class ij.plugin.MacroInstaller
 
installFromIJJar(String) - 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.
installUserPlugin(String, boolean) - Method in class ij.Menus
 
instanceColor - Variable in class ij.gui.Roi
 
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 Raw using little-endian byte order.
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
 
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.
inverseTransform() - Method in class ij.process.FHT
Performs an inverse transform, converting this image into the space domain.
inversionTested - Variable in class ij.process.ImageProcessor
 
INVERT - Static variable in interface ij.macro.MacroConstants
 
invert() - Method in class ij.process.FloatProcessor
 
invert() - Method in class ij.process.ImageProcessor
Inverts the image or ROI.
invert() - Method in class ij.process.ShortProcessor
 
invert() - Method in class ij.process.StackProcessor
 
INVERT_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
 
is64Bit() - Static method in class ij.IJ
Returns true if ImageJ is running a 64-bit version of Java.
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
 
isAntialiased() - Static method in class ij.gui.TextRoi
 
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).
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.
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.
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., Rounded Rectangle, TextRoi or Arrow).
isDrawingTool() - Method in class ij.gui.TextRoi
 
isGrayscale() - Method in class ij.LookUpTable
Returns true if this is a 256 entry grayscale LUT.
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.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.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.
isHyperStack() - Method in class ij.gui.StackWindow
 
isHyperStack() - Method in class ij.ImagePlus
Returns 'true' if this image is a hyperstack.
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
Returns true if ImageJ is running on a Java 1.4 or greater JVM.
isJava15() - Static method in class ij.IJ
Returns true if ImageJ is running on a Java 1.5 or greater JVM.
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.
isJava2() - Static method in class ij.IJ
Always returns true.
isKillable() - Method in class ij.process.ImageProcessor
Deprecated.  
isLine() - Method in class ij.gui.Roi
Returns 'true' if this is a line 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.
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() - Static method in class ij.IJ
Returns true if a macro is running, or if the run(), open() or newImage() method is executing.
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
 
isOutputArg(int) - Static method in class ij.macro.ExtensionDescriptor
 
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.
isResultsWindow() - Static method in class ij.IJ
Returns true if the "Results" window is open.
isRGB() - Method in class ij.ImageStack
Returns true if this is a 3-slice RGB stack.
isSigned16Bit() - Method in class ij.measure.Calibration
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.
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
Returns true if ImageJ is running on Windows Vista.
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.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.BatchProcesser
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Colors
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.CommandFinder
 
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.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.Fonts
 
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.ThresholdAdjuster
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Resizer
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Slicer
 
itemStateChanged(ItemEvent) - Method in class ij.text.TextWindow
 
IterFactor - Static variable in class ij.measure.CurveFitter
 

J

Java2 - Class in ij.util
This class contains static methods that use the Java 2 API.
Java2() - Constructor for class ij.util.Java2
 
JAVA_OR_TEXT - Static variable in class ij.io.Opener
 
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
 
JavaScriptIncludes - Static variable in class ij.plugin.frame.Editor
ImportPackage statements added in front of scripts.
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
 
JS_NOT_FOUND - Static variable in class ij.plugin.frame.Editor
 
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.
KEY_PREFIX - Static variable in class ij.Prefs
 
keyPressed(KeyEvent) - Method in class ij.gui.GenericDialog
 
keyPressed(KeyEvent) - Method in class ij.gui.MessageDialog
 
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.plugin.CommandFinder
 
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.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.plugin.CommandFinder
 
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.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.plugin.CommandFinder
 
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
 
killRoi() - Method in class ij.ImagePlus
Deletes the current region of interest.
killStack() - Method in class ij.ImagePlus
 
kNPoints - Variable in class ij.plugin.filter.RankFilters
 
kRadius - Variable in class ij.plugin.filter.RankFilters
 
KURTOSIS - Static variable in interface ij.measure.Measurements
 
KURTOSIS - Static variable in class ij.measure.ResultsTable
 
kurtosis - Variable in class ij.process.ImageStatistics
 

L

label - Variable in class ij.gui.MessageDialog
 
label - Variable in class ij.gui.WaitForUserDialog
 
label(ImageProcessor) - Method in class ij.plugin.filter.Filler
 
LABELS - Static variable in interface ij.measure.Measurements
 
LAST_HEADING - Static variable in class ij.measure.ResultsTable
 
LAST_INDEX_OF - Static variable in interface ij.macro.MacroConstants
 
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.io.RoiDecoder
 
LEFT_JUSTIFY - Static variable in class ij.process.ImageProcessor
Left justify text.
LEFT_MARGIN - Static variable in class ij.gui.Plot
the margin width left of the plot frame (enough for 5-digit numbers such as unscaled 16-bit data
LEGACY_MODE - Static variable in class ij.gui.Wand
Wand operation type similar to that of ImageJ 1.42p and before; for backwards compatibility.
LENGTH_OF - Static variable in interface ij.macro.MacroConstants
 
LIMIT - Static variable in interface ij.measure.Measurements
 
Line - Class in ij.gui
This class represents a straight line selection.
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(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, ImagePlus) - Constructor for class ij.gui.Line
Starts the process of creating a new user-generated straight line selection.
Line(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Line
Deprecated.  
LINE - Static variable in class ij.gui.Plot
Connect points with solid lines.
LINE - Static variable in class ij.gui.PlotWindow
Connect points with solid lines.
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
 
LineGraphAnalyzer - Class in ij.plugin.filter
Implements ImageJ's Analyze/Tools/Analyze Line Graph command.
LineGraphAnalyzer() - Constructor for class ij.plugin.filter.LineGraphAnalyzer
 
lineRadius - Variable in class ij.plugin.filter.RankFilters
 
lineTo(int, int) - Method in class ij.process.ImageProcessor
Draws a line from the current drawing location to (x2,y2).
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
 
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
 
load(Object, Applet) - Static method in class ij.Prefs
Finds and loads the ImageJ configuration file, "IJ_Props.txt".
load(BufferedReader) - Method in class ij.text.TextWindow
Appends the text in the specified file to the end of this TextWindow.
LOC_KEY - Static variable in class ij.plugin.frame.ContrastAdjuster
 
LOC_KEY - Static variable in class ij.plugin.frame.Fonts
 
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(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
 
log() - Method in class ij.process.FloatProcessor
 
log() - Method in class ij.process.ImageProcessor
Performs a log transform on the image or ROI.
log() - Method in class ij.process.ShortProcessor
 
LOG2 - Static variable in class ij.measure.Calibration
 
LOG2 - Static variable in class ij.measure.CurveFitter
 
LOG_LOC_KEY - Static variable in class ij.text.TextWindow
 
LOG_WINDOW_CLOSED - Static variable in interface ij.IJEventListener
 
LOGICAL_AND - Static variable in interface ij.macro.MacroConstants
 
LOGICAL_OR - Static variable in interface ij.macro.MacroConstants
 
logScale - Variable in class ij.gui.HistogramWindow
 
longOffset - Variable in class ij.io.FileInfo
 
longPixelCount - Variable in class ij.process.ImageStatistics
 
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
Loop back and forth when animating stack
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.text.TextPanel
 
LT - Static variable in interface ij.macro.MacroConstants
 
LTE - Static variable in interface ij.macro.MacroConstants
 
lut - Variable in class ij.gui.HistogramWindow
 
LUT - Static variable in class ij.io.Opener
 
LUT - Class in ij.process
 
LUT(byte[], byte[], byte[]) - Constructor for class ij.process.LUT
 
LUT(int, int, byte[], byte[], byte[]) - Constructor for class ij.process.LUT
 
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

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_CANCELED - Static variable in class ij.Macro
 
MACRO_KEY - Static variable in class ij.plugin.filter.ImageMath
 
Macro_Runner - Class in ij.plugin
Opens and runs a macro file.
Macro_Runner() - Constructor for class ij.plugin.Macro_Runner
 
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 MacrRunner.
MacroRunner(String) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets macro source in a separate thread.
MacroRunner(String, Editor) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets macro source in debug mode if 'editor' is not null.
MacroRunner(String, String) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets macro source in a separate thread, and also passing a string argument.
MacroRunner(File) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets a macro file using a separate thread.
MacroRunner(Program, int, String) - Constructor for class ij.macro.MacroRunner
Create a new object that runs a tokenized macro in a separate thread.
MacroRunner(Program, int, String, String) - Constructor for class ij.macro.MacroRunner
Create a new object that runs a tokenized macro in a separate thread, passing a string argument.
MacroRunner(Program, int, String, Editor) - Constructor for class ij.macro.MacroRunner
Create a new object that runs a tokenized macro in debug mode if 'editor' is not null.
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
 
mag - Variable in class ij.gui.Roi
 
magnification - Variable in class ij.gui.ImageCanvas
 
magnification - Variable in class ij.gui.ProfilePlot
 
MAGNIFIER - Static variable in class ij.gui.Toolbar
 
main(String[]) - Static method in class ij.ImageJ
 
MAJOR - Static variable in class ij.measure.ResultsTable
 
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
make16bitEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM
Calculates a 16-bit grayscale Euclidean Distance Map for a binary 8-bit image.
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_SELECTION - Static variable in interface ij.macro.MacroConstants
 
MAKE_TEXT - Static variable in interface ij.macro.MacroConstants
 
makeDefaultColorModel() - Method in class ij.process.ImageProcessor
 
makeFloatEDM(ImageProcessor, int, boolean) - Method in class ij.plugin.filter.EDM
Creates the Euclidian Distance Map of a (binary) byte image.
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.
makeKernel(double) - Method in class ij.plugin.filter.RankFilters
Create a circular kernel of a given radius.
makeLine(int, int, int, int) - Static method in class ij.IJ
Creates a straight line selection.
makeLine(double, double, double, double) - Static method in class ij.IJ
Creates a straight line selection using double coordinates.
makeListLabel(String, CommandFinder.CommandAction, boolean) - Method in class ij.plugin.CommandFinder
 
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(int, int, int, int) - Static method in class ij.IJ
Creates an elliptical selection.
makePoint(int, int) - Static method in class ij.IJ
Creates a point 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.
makeStack(String, int, int, boolean, boolean, boolean) - Method in class ij.plugin.AVI_Reader
Create an ImageStack from an avi file with given path.
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 scaled 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
 
MATCHES - Static variable in interface ij.macro.MacroConstants
 
max - Variable in class ij.io.ImageReader
 
MAX - Static variable in class ij.measure.ResultsTable
 
MAX - Static variable in class ij.plugin.filter.RankFilters
 
MAX - Static variable in interface ij.process.Blitter
dst=max(dst,src)
max(double) - Method in class ij.process.FloatProcessor
 
MAX - Static variable in class ij.process.ImageProcessor
 
max(double) - Method in class ij.process.ImageProcessor
Pixels greater than 'value' are set to 'value'.
max - Variable in class ij.process.ImageStatistics
 
max - Variable in class ij.process.LUT
 
max(double) - Method in class ij.process.ShortProcessor
 
MAX_CHANNELS - Static variable in class ij.CompositeImage
 
MAX_COLUMNS - Static variable in class ij.measure.ResultsTable
Obsolete; use getLastColumn().
MAX_MACROS - Static variable in class ij.plugin.MacroInstaller
 
MAX_METHOD - Static variable in class ij.plugin.ZProjector
 
MAX_OF - Static variable in interface ij.macro.MacroConstants
 
MAX_OPEN_RECENT_ITEMS - Static variable in class ij.Menus
 
MAX_SIZE - Static variable in class ij.plugin.frame.Editor
 
MAX_SIZE - Static variable in class ij.plugin.MacroInstaller
 
MAX_SLIDERS - Static variable in class ij.gui.GenericDialog
 
MAX_STANDARDS - Static variable in interface ij.measure.Measurements
Maximum number of calibration standard (20)
maxCount - Variable in class ij.process.ImageStatistics
 
maximize() - Method in class ij.gui.ImageWindow
 
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
 
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 - 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 - Variable in class ij.process.ImageStatistics
 
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.
Measurements - Interface in ij.measure
 
MeasurementsWriter - Class in ij.plugin
Writes measurements to a tab-delimited text file.
MeasurementsWriter() - Constructor for class ij.plugin.MeasurementsWriter
 
MEDIAN - Static variable in interface ij.measure.Measurements
 
MEDIAN - Static variable in class ij.measure.ResultsTable
 
MEDIAN - Static variable in class ij.plugin.filter.RankFilters
 
median - Variable in class ij.process.ImageStatistics
 
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.
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
This plugin continuously plots ImageJ's memory utilization.
MemoryMonitor() - Constructor for class ij.plugin.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.
mergeHyperstacks(ImagePlus[], boolean) - Method in class ij.plugin.RGBStackMerge
 
mergeStacks() - Method in class ij.plugin.RGBStackMerge
Combines three grayscale stacks into one RGB stack.
mergeStacks(int, int, int, ImageStack, ImageStack, ImageStack, boolean) - 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.ZProjector
 
micronSymbol - Static variable in class ij.IJ
 
min - Variable in class ij.io.ImageReader
 
MIN - Static variable in class ij.measure.ResultsTable
 
MIN - Static variable in class ij.plugin.filter.RankFilters
 
MIN - Static variable in interface ij.process.Blitter
dst=min(dst,src)
min(double) - Method in class ij.process.FloatProcessor
 
MIN - Static variable in class ij.process.ImageProcessor
 
min(double) - Method in class ij.process.ImageProcessor
Pixels less than 'value' are set to 'value'.
min - Variable in class ij.process.ImageStatistics
 
min - Variable in class ij.process.LUT
 
min(double) - Method in class ij.process.ShortProcessor
 
MIN_FERET - Static variable in class ij.measure.ResultsTable
 
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_WIDTH - Static variable in class ij.gui.ImageWindow
 
minimize() - Method in class ij.gui.ImageWindow
 
minimumLayoutSize(Container) - Method in class ij.gui.ImageLayout
Returns the minimum dimensions for this layout.
minMaxSet - Variable in class ij.process.ImageProcessor
 
MINOR - Static variable in class ij.measure.ResultsTable
 
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
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 - Static variable in interface ij.measure.Measurements
 
MODE - Static variable in class ij.measure.ResultsTable
 
mode - Variable in class ij.process.ImageStatistics
 
MODE_KEY - Static variable in class ij.plugin.frame.ThresholdAdjuster
 
modifiers(int) - Static method in class ij.ImageJ
Return the current list of modifier keys.
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(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.RoiManager
 
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(MouseEvent) - Method in class ij.gui.ImageCanvas
 
mouseDragged(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseDragged(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseDragged(MouseEvent) - Method in class ij.text.TextPanel
 
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.RoiManager
 
mouseEntered(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseEntered(MouseEvent) - Method in class ij.text.TextPanel
 
mouseExited(MouseEvent) - Method in class ij.gui.ImageCanvas
 
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.RoiManager
 
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(MouseEvent) - Method in class ij.gui.ImageCanvas
 
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 graph X and Y values when the mouse is moved.
mouseMoved(MouseEvent) - Method in class ij.gui.Toolbar
 
mouseMoved(int, int) - Method in class ij.ImagePlus
Displays the cursor coordinates and pixel value in the status bar.
mouseMoved(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mouseMoved(MouseEvent) - Method in class ij.text.TextPanel
 
mousePressed(MouseEvent) - Method in class ij.gui.ImageCanvas
 
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.RoiManager
 
mousePressed(MouseEvent) - Method in class ij.plugin.Orthogonal_Views
 
mousePressed(MouseEvent) - Method in class ij.text.TextPanel
 
mouseReleased(MouseEvent) - Method in class ij.gui.ImageCanvas
 
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.RoiManager
 
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.StackWindow
 
mouseWheelMoved(MouseWheelEvent) - Method in class ij.plugin.frame.RoiManager
 
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
 
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
 
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
 
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
 
MULTIPLY - Static variable in interface ij.process.Blitter
dst=src*src
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(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
 
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.gui.Roi
 
name - Variable in class ij.macro.ExtensionDescriptor
 
NaN - Static variable in interface ij.macro.MacroConstants
 
nBins - Static variable in class ij.gui.HistogramWindow
 
nBins - Variable in class ij.process.ImageStatistics
 
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, int[]) - Static method in class ij.macro.ExtensionDescriptor
 
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, 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
 
NewImage - Class in ij.gui
New image dialog box plus several static utility methods for creating images.
NewImage() - Constructor for class ij.gui.NewImage
 
newImage(String, String, int, int, int) - Static method in class ij.IJ
Opens a new image.
newMaxCount - Variable in class ij.gui.HistogramWindow
 
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
NextImageOpener - Class in ij.plugin
 
NextImageOpener() - Constructor for class ij.plugin.NextImageOpener
 
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_THRESHOLD - Static variable in class ij.process.ImageProcessor
Value returned by getMinThreshold() when thresholding is not enabled.
NO_UNDO - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter does not require undo.
noBorder - Static variable in class ij.Prefs
Do not draw black border around image.
noGridLines - Static variable in class ij.gui.PlotWindow
Add grid lines to plots
noImage() - Static method in class ij.IJ
Displays a "no images are open" dialog box.
noise(double) - Method in class ij.process.ByteProcessor
 
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 random noise to the image or ROI.
noise(double) - Method in class ij.process.ShortProcessor
 
NOISE_SD - Static variable in class ij.Prefs
 
NonBlockingGenericDialog - Class in ij.gui
This is an xtension of GenericDialog that is non-model.
NonBlockingGenericDialog(String) - Constructor for class ij.gui.NonBlockingGenericDialog
 
NONE - Static variable in class ij.macro.Interpreter
 
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_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
 
notifyEventListeners(int) - Static method in class ij.IJ
 
notifyListeners(int) - Method in class ij.ImagePlus
 
nPoints - Variable in class ij.gui.PolygonRoi
 
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.
NRESULTS - Static variable in interface ij.macro.MacroConstants
 
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.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.
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.
offScreenXD(int) - Method in class ij.gui.ImageCanvas
Converts a screen x-coordinate to a floating-point offscreen x-coordinate.
offScreenY(int) - Method in class ij.gui.ImageCanvas
Converts a screen y-coordinate to an offscreen y-coordinate.
offScreenYD(int) - Method in class ij.gui.ImageCanvas
Converts a screen y-coordinate to a floating-point offscreen y-coordinate.
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.
oldHeight - Variable in class ij.gui.Roi
 
oldWidth - Variable in class ij.gui.Roi
 
oldX - Variable in class ij.gui.Roi
 
oldY - Variable in class ij.gui.Roi
 
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 variable in class ij.gui.Arrow
 
open(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
 
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(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, int) - Static method in class ij.IJ
Opens and displays the nth image in the specified tiff stack.
open() - Method in class ij.io.FileOpener
Opens the image and displays it.
open(boolean) - Method in class ij.io.FileOpener
Opens the image.
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(String) - Method in class ij.io.Opener
Opens and displays a tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file.
OPEN - Static variable in interface ij.macro.MacroConstants
 
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 as a ResultsTable.
open(String) - Method in class ij.plugin.DICOM
Opens the specified file as a DICOM.
open(String, String) - Method in class ij.plugin.frame.Editor
 
open() - Method in class ij.plugin.TextReader
Displays a file open dialog and opens the specified text file as a float image.
open(String) - Method in class ij.plugin.TextReader
Opens the specified text file as a float image.
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
 
openAndAddToRecent(String) - Method in class ij.io.Opener
Opens the specified file and adds it to the File/Open Recent menu.
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.
OpenDialog - Class in ij.io
This class displays a dialog window from which the user can select an input file.
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.
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
 
openFile(File) - Method in class ij.plugin.DragAndDrop
Open a file.
openFile(String) - Method in class ij.plugin.PGM_Reader
 
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.
openHeader(StreamTokenizer) - Method in class ij.plugin.PGM_Reader
 
openImage(String) - Static method in class ij.IJ
Opens the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg image and returns an ImagePlus object if successful.
openImage(String, int) - Static method in class ij.IJ
Opens the nth image of the specified tiff stack.
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.ImportDialog
Displays the dialog and opens the specified image or images.
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.
openImage(String) - Method in class ij.io.Opener
Attempts to open the specified file as a tiff, bmp, dicom, fits, pgm, gif or jpeg.
openImage(String, int) - Method in class ij.io.Opener
Open the nth image of the specified tiff stack.
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.
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
 
openTiff(String, String) - Method in class ij.io.Opener
Attempts to open the specified file as a tiff.
openTiff(String, int) - Method in class ij.io.Opener
Opens the nth image of the specified TIFF stack.
openTiff(InputStream, String) - Method in class ij.io.Opener
Attempts to open the specified inputStream as a TIFF, returning an ImagePlus object if successful.
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.
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 - Static variable in class ij.io.RoiDecoder
 
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.Prefs
 
or(ShapeRoi) - Method in class ij.gui.ShapeRoi
Unary union operator.
OR - Static variable in interface ij.process.Blitter
dst=dst OR src
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
 
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
 
Orthogonal_Views() - Constructor for class ij.plugin.Orthogonal_Views
 
OUTLIERS - Static variable in class ij.plugin.filter.RankFilters
 
outline() - Method in class ij.process.BinaryProcessor
 
outline() - Method in class ij.process.ByteProcessor
 
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
 
OvalRoi - Class in ij.gui
Oval region of interest
OvalRoi(int, int, int, int) - Constructor for class ij.gui.OvalRoi
Creates a new OvalRoi.
OvalRoi(int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
Starts the process of creating a user-defined OvalRoi.
OvalRoi(int, int, int, int, ImagePlus) - Constructor for class ij.gui.OvalRoi
Deprecated.  
OVER_UNDER_LUT - Static variable in class ij.process.ImageProcessor
 
Overlay - Class in ij.gui
 
Overlay() - Constructor for class ij.gui.Overlay
 
Overlay(Roi) - Constructor for class ij.gui.Overlay
 
overlay - Variable in class ij.gui.Roi
 
overlay - Variable in class ij.io.FileInfo
 
OVERLAY - Static variable in interface ij.macro.MacroConstants
 
OVERLAY_ADDITION - Static variable in class ij.Undo
 
OverlayCommands - Class in ij.plugin
This plugin implements the commands in the Image/Overlay menu.
OverlayCommands() - Constructor for class ij.plugin.OverlayCommands
 

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.
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.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
 
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, double) - Static method in class ij.util.Tools
Returns a double containg the value represented by the specified String.
parseDouble(String) - 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(int, int, ResultsTable, double, double, double, double) - Constructor for class ij.plugin.filter.ParticleAnalyzer
Constructs a ParticleAnalyzer.
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() - Constructor for class ij.plugin.filter.ParticleAnalyzer
Default constructor
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 the active image.
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
 
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
 
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
pixels - Variable in class ij.io.FileInfo
 
pixels - Variable in class ij.process.ByteProcessor
 
pixels - Variable in class ij.process.ColorProcessor
 
pixels8 - Variable in class ij.process.FloatProcessor
 
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 - Class in ij.gui
This class is an image that line graphs can be drawn on.
Plot(String, String, String, float[], float[], int) - Constructor for class ij.gui.Plot
Construct a new PlotWindow.
Plot(String, String, String, float[], float[]) - Constructor for class ij.gui.Plot
This version of the constructor uses the default flags.
Plot(String, String, String, double[], double[], int) - Constructor for class ij.gui.Plot
This version of the constructor accepts double arrays.
Plot(String, String, String, double[], double[]) - Constructor for class ij.gui.Plot
This version of the constructor accepts double arrays and uses the default flags
PLOT - Static variable in interface ij.macro.MacroConstants
 
plot(CurveFitter) - Static method in class ij.plugin.frame.Fitter
 
plotHeight - Static variable in class ij.gui.PlotWindow
The height of the plot in pixels.
plotScale - Variable in class ij.gui.HistogramWindow
 
plotWidth - Static variable in class ij.gui.PlotWindow
The width of the plot in pixels.
PlotWindow - Class in ij.gui
Obsolete; mostly replaced by the Plot class.
PlotWindow(String, String, String, float[], float[]) - Constructor for class ij.gui.PlotWindow
Deprecated. replaced by the Plot class.
PlotWindow(String, String, String, double[], double[]) - Constructor for class ij.gui.PlotWindow
Deprecated. replaced by the Plot class.
PLUGIN - Static variable in class ij.plugin.NewPlugin
 
PlugIn - Interface in ij.plugin
Plugins that acquire images or display windows should implement this interface.
PLUGIN_FILTER - Static variable in class ij.plugin.NewPlugin
 
PLUGIN_FRAME - 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.
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
 
PLUGINS_MENU - Static variable in class ij.Menus
 
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
pointAddToManager - Static variable in class ij.Prefs
Add points to ROI Manager.
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).
PointRoi - Class in ij.gui
This class represents a collection of points.
PointRoi(int[], int[], int) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified arrays of offscreen coordinates.
PointRoi(Polygon) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi from a Polygon.
PointRoi(int, int) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified offscreen coordinates.
PointRoi(int, int, ImagePlus) - Constructor for class ij.gui.PointRoi
Creates a new PointRoi using the specified screen coordinates.
POLY2 - Static variable in class ij.measure.Calibration
 
POLY2 - Static variable in class ij.measure.CurveFitter
 
POLY3 - Static variable in class ij.measure.Calibration
 
POLY3 - Static variable in class ij.measure.CurveFitter
 
POLY4 - Static variable in class ij.measure.Calibration
 
POLY4 - Static variable in class ij.measure.CurveFitter
 
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(int[], int[], int) - Constructor for class ij.process.PolygonFiller
Constructs a PolygonFiller using the specified polygon.
PolygonRoi - Class in ij.gui
This class represents a polygon region of interest or polyline of interest.
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(Polygon, int) - Constructor for class ij.gui.PolygonRoi
Creates a new polygon or polyline ROI from a Polygon.
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.
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
 
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
 
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.
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
 
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
 
PRINT - Static variable in interface ij.macro.MacroConstants
 
print(Graphics, PageFormat, int) - Method in class ij.plugin.filter.Printer
 
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
 
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.filter
Implements the Process/Plot Profile and Edit/Options/Profile Plot Options commands.
Profiler() - Constructor for class ij.plugin.filter.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.filter
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.filter.Projector
 
PROPS_NAME - Static variable in class ij.Prefs
 
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.
putByteRow(ImageStack, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
 
putColumn(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
 
putColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
Inserts the pixels contained in 'data' into a column starting at (x,y).
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
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.ColorProcessor
Stores the specified value at (x,y).
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.FloatProcessor
Stores the specified value at (x,y).
putPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
Sets a pixel in the image using an int array of samples.
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).
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).
putRGBRow(ImageStack, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
 
putRow(ImageProcessor, int, int, float[], int) - Method in class ij.plugin.Slicer
 
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).
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.

R

rand(int, int) - Method in class ij.plugin.filter.SaltAndPepper
 
RANDOM - Static variable in interface ij.macro.MacroConstants
 
RandomAccessStream - Class in ij.io
This is a class that 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(ImageProcessor, double, int) - Method in class ij.plugin.filter.RankFilters
Filters an image
RankFilters - Class in ij.plugin.filter
This plugin implements the Mean, Minimum, Maximum, Variance, Median, Remove Outliers and Despeckle commands.
RankFilters() - Constructor for class ij.plugin.filter.RankFilters
 
raster - Variable in class ij.process.ImageProcessor
 
RAW - Static variable in class ij.io.FileInfo
 
Raw - Class in ij.plugin
This plugin implements the File/Import/Raw command.
Raw() - Constructor for class ij.plugin.Raw
 
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(String) - Static method in class ij.plugin.frame.Recorder
 
record(String, String) - Static method in class ij.plugin.frame.Recorder
 
record(String, String, String) - Static method in class ij.plugin.frame.Recorder
 
record(String, String, String, String) - 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, double, double) - Static method in class ij.plugin.frame.Recorder
 
record(String, int, int, int) - 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, int, int, int, int) - 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, String, String, int, int, int, int, int) - 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
 
Recorder - Class in ij.plugin.frame
This is ImageJ's macro recorder.
Recorder() - 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.
recordOption(String, String) - Static method in class ij.plugin.frame.Recorder
 
recordOption(String) - Static method in class ij.plugin.frame.Recorder
 
recordPath(String, String) - 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
 
recordSetFont() - Static method in class ij.gui.TextRoi
 
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
 
RECTANGLE - Static variable in class ij.gui.Roi
 
RECTANGLE - Static variable in class ij.gui.Toolbar
 
red - Variable in class ij.plugin.filter.RGBStackSplitter
These are the three stacks created by the split(ImageStack) method.
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 redirected to the "Log" window.
redirectingErrorMessages() - Static method in class ij.IJ
Returns the state of the 'redirectErrorMessages' flag.
reds - Variable in class ij.io.FileInfo
 
reduce(ImagePlus) - Method in class ij.plugin.HyperStackReducer
 
register(Class) - Static method in class ij.IJ
Adds the specified class to a Vector to keep it from being garbage collected, which would cause the classes static fields to be reset.
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
 
remove(int) - Method in class ij.gui.Overlay
 
remove(Roi) - Method in class ij.gui.Overlay
 
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
 
removeLayoutComponent(Component) - Method in class ij.gui.ImageLayout
Not used by this class.
removeSplineFit() - Method in class ij.gui.PolygonRoi
 
removeWindow(Frame) - Static method in class ij.WindowManager
Removes the specified window from the Window menu.
RENAME - Static variable in interface ij.macro.MacroConstants
 
repaintImageWindows() - Static method in class ij.WindowManager
Repaints all open image windows.
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 - 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
 
reset() - Method in class ij.CompositeImage
 
RESET - Static variable in interface ij.macro.MacroConstants
 
reset() - Method in class ij.measure.ResultsTable
Clears all the columns and sets the counter to zero.
reset() - Method in class ij.process.ByteProcessor
Reset the image from snapshot.
reset(ImageProcessor) - Method in class ij.process.ByteProcessor
Restore pixels that are within roi but not part of mask.
reset() - Method in class ij.process.ColorProcessor
 
reset(ImageProcessor) - Method in class ij.process.ColorProcessor
 
reset() - Method in class ij.process.FloatProcessor
 
reset(ImageProcessor) - Method in class ij.process.FloatProcessor
 
reset() - Method in class ij.process.ImageProcessor
Restores the pixel data from the snapshot (undo) buffer.
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() - Method in class ij.process.ShortProcessor
 
reset(ImageProcessor) - Method in class ij.process.ShortProcessor
 
reset() - Static method in class ij.Undo
 
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.
resetClipboard() - Static method in class ij.ImagePlus
Clears the internal clipboard.
resetCounter() - Static method in class ij.plugin.filter.Analyzer
Sets the measurement counter to zero.
resetCounter - Variable in class ij.plugin.filter.ParticleAnalyzer
 
resetDisplayRange() - Method in class ij.CompositeImage
 
resetDisplayRange() - Method in class ij.ImagePlus
 
resetDisplayRanges() - Method in class ij.CompositeImage
 
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 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.ShortProcessor
Recalculates the min and max values used to scale pixel values to 0-255 for display.
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).
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.
resetThreshold() - Method in class ij.process.ImageProcessor
Disables thresholding.
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
Creates a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int) - Method in class ij.process.ImageProcessor
Creates 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.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'.
Resizer - Class in ij.plugin.filter
Deprecated. replaced by ij.plugin.Resizer
Resizer() - Constructor for class ij.plugin.filter.Resizer
Deprecated.  
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
 
restorePreviousTool() - Method in class ij.gui.Toolbar
 
restoreRoi() - Method in class ij.ImagePlus
 
ResultsTable - Class in ij.measure
This is a table for storing measurement results as columns of numeric values.
ResultsTable() - Constructor for class ij.measure.ResultsTable
Constructs an empty ResultsTable with the counter=0 and no columns.
RETURN - Static variable in interface ij.macro.MacroConstants
 
revert() - Method in class ij.ImagePlus
Implements the File/Revert command.
revertToSaved(ImagePlus) - Method in class ij.io.FileOpener
Restores original disk or network version of image.
RGB - Static variable in class ij.gui.NewImage
 
RGB - Static variable in class ij.io.FileInfo
24-bit interleaved RGB.
rgb - Variable in class ij.process.FHT
Used by the FFT class.
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.
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_MEDIAN - 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
 
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
 
RGBStackMerge() - Constructor for class ij.plugin.RGBStackMerge
 
RGBStackSplitter - Class in ij.plugin.filter
Splits an RGB image or stack into three 8-bit grayscale images or stacks.
RGBStackSplitter() - Constructor for class ij.plugin.filter.RGBStackSplitter
 
rh - Variable in class ij.process.ImageStatistics
 
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
the margin width right of the plot frame
rLUT1 - Variable in class ij.process.ImageProcessor
 
rLUT2 - Variable in class ij.process.ImageProcessor
 
RODBARD - Static variable in class ij.measure.Calibration
 
RODBARD - Static variable in class ij.measure.CurveFitter
 
RODBARD2 - Static variable in class ij.measure.Calibration
 
RODBARD2 - Static variable in class ij.measure.CurveFitter
 
Roi - Class in ij.gui
A rectangular region of interest and superclass for the other ROI classes.
Roi(int, int, int, int) - Constructor for class ij.gui.Roi
Creates a new rectangular Roi.
Roi(int, int, int, int, int) - Constructor for class ij.gui.Roi
Creates a new rounded rectangular Roi.
Roi(Rectangle) - Constructor for class ij.gui.Roi
Creates a new rectangular Roi.
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(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Roi
Deprecated.  
roi - Variable in class ij.ImagePlus
 
roi - Variable in class ij.io.FileInfo
 
ROI - Static variable in class ij.io.Opener
 
ROI_HEIGHT - Static variable in class ij.measure.ResultsTable
 
ROI_MANAGER - Static variable in interface ij.macro.MacroConstants
 
ROI_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
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
Decodes an ImageJ, NIH Image or Scion Image ROI file.
RoiDecoder(String) - Constructor for class ij.io.RoiDecoder
Constructs an RoiDecoder using a file path.
RoiDecoder(byte[], String) - Constructor for class ij.io.RoiDecoder
Constructs an RoiDecoder using a byte array.
RoiEncoder - Class in ij.io
Saves an ROI to a file or stream.
RoiEncoder(String) - Constructor for class ij.io.RoiEncoder
Creates an RoiEncoder using the specified path.
RoiEncoder(OutputStream) - Constructor for class ij.io.RoiEncoder
Creates an RoiEncoder using the specified OutputStream.
roiHeight - Variable in class ij.process.ImageProcessor
 
roiHeight - Variable in class ij.process.ImageStatistics
 
RoiManager - Class in ij.plugin.frame
This plugin implements the Analyze/Tools/ROI Manager command.
RoiManager() - Constructor for class ij.plugin.frame.RoiManager
 
RoiManager(boolean) - Constructor for class ij.plugin.frame.RoiManager
 
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
 
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.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.
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
 
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
 
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.StackWindow
 
run(String) - Static method in class ij.IJ
Runs an ImageJ command.
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(ImagePlus, String, String) - Static method in class ij.IJ
Runs an ImageJ command using the specified image and options.
run() - Method in class ij.ImageJ
Quit using a separate thread, hopefully avoiding thread deadlocks.
RUN - Static variable in class ij.macro.Interpreter
 
run(String) - Method in class ij.macro.Interpreter
Interprets the specified string.
run(String, String) - Method in class ij.macro.Interpreter
Runs the specified macro, passing it a string argument and returning a string value.
run(Program) - Method in class ij.macro.Interpreter
Interprets the specified tokenized macro file starting at location 0.
run(int) - Method in class ij.macro.Interpreter
Runs an existing macro starting at the specified program counter location.
RUN - Static variable in interface ij.macro.MacroConstants
 
run() - Method in class ij.macro.MacroRunner
 
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.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.BatchProcesser
 
run() - Method in class ij.plugin.BatchProcesser
 
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.CanvasResizer
 
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
 
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
 
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 (some of the) ImageJ's commands according to the structure of the String argument (see below).
run(String) - Method in class ij.plugin.Converter
 
run(String) - Method in class ij.plugin.DICOM
 
run(String) - Method in class ij.plugin.DICOM_Sorter
 
run(String) - Method in class ij.plugin.Distribution
 
run(String) - Method in class ij.plugin.DragAndDrop
 
run() - Method in class ij.plugin.DragAndDrop
 
run(String) - Method in class ij.plugin.Duplicator
 
run(ImagePlus) - Method in class ij.plugin.Duplicator
Returns a copy of the image, stack or hyperstack contained in the specified ImagePlus.
run(ImagePlus, int, int) - Method in class ij.plugin.Duplicator
Returns a new stack containing a subrange of the specified stack.
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(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.CalibrationBar
 
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
 
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() - Method in class ij.plugin.filter.PlugInFilterRunner
The dispatcher for the background threads
run(ImageProcessor) - Method in class ij.plugin.filter.Printer
 
run(ImageProcessor) - Method in class ij.plugin.filter.Profiler
 
run(ImageProcessor) - Method in class ij.plugin.filter.Projector
 
run(ImageProcessor) - Method in class ij.plugin.filter.RankFilters
 
run(ImageProcessor) - Method in class ij.plugin.filter.Resizer
Deprecated.  
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
 
run(ImageProcessor) - Method in class ij.plugin.filter.XYWriter
 
run(ImageProcessor) - Method in class ij.plugin.filter.ZAxisProfiler
 
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() - Method in class ij.plugin.frame.ColorThresholder
 
run(String) - Method in class ij.plugin.frame.ContrastAdjuster
 
run() - Method in class ij.plugin.frame.ContrastAdjuster
 
run() - Method in class ij.plugin.frame.LineWidthAdjuster
 
run(String) - Method in class ij.plugin.frame.PlugInFrame
 
run() - Method in class ij.plugin.frame.ThresholdAdjuster
 
run(String) - Method in class ij.plugin.GelAnalyzer
 
run(String) - Method in class ij.plugin.GifWriter
 
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.HyperStackReducer
 
run(String) - Method in class ij.plugin.ImageCalculator
 
run(String, ImagePlus, ImagePlus) - Method in class ij.plugin.ImageCalculator
 
run(String) - Method in class ij.plugin.ImageJ_Updater
 
run(String) - Method in class ij.plugin.ImagesToStack
 
run(String) - Method in class ij.plugin.Installer
 
run(String) - Method in class ij.plugin.JavaProperties
 
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 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.MemoryMonitor
 
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.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.PNG_Writer
 
run(String) - Method in class ij.plugin.PNM_Writer
 
run(String) - Method in class ij.plugin.ProxySettings
 
run(String) - Method in class ij.plugin.Raw
 
run(String) - Method in class ij.plugin.Resizer
 
run(String) - Method in class ij.plugin.RGBStackConverter
 
run(String) - Method in class ij.plugin.RGBStackMerge
Merges one, two or three 8-bit or RGB stacks into a single RGB stack.
run(String) - Method in class ij.plugin.RoiReader
 
run(String) - Method in class ij.plugin.ScaleBar
 
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.StackCombiner
 
run(String) - Method in class ij.plugin.StackEditor
 
run(String) - Method in class ij.plugin.StackReverser
 
run(String) - Method in class ij.plugin.StackWriter
 
run(String) - Method in class ij.plugin.Straightener
 
run(String) - Method in class ij.plugin.SurfacePlotter
 
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.Timer
 
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.XYCoordinates
 
run(String) - Method in class ij.plugin.Zoom
'arg' must be "in", "out", "100%" or "orig".
run(String) - Method in class ij.plugin.ZProjector
 
run() - Method in class ij.RecentOpener
Open the file and move the path to top of the submenu.
run() - Method in class ij.SocketListener
 
run() - Method in class ij.text.TextPanel
For better performance, open double-clicked files on separate thread instead of on event dispatch thread.
RUN_MACRO - Static variable in interface ij.macro.MacroConstants
 
RUN_TO_CARET - Static variable in class ij.macro.Interpreter
 
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", "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
 
runFromLabel(String) - Method in class ij.plugin.CommandFinder
 
runJavaScript(String, String) - Method in class ij.plugin.Macro_Runner
Runs a script on the current thread, passing 'arg', which the script can retrieve using the getArgument() function.
runMacro(String) - Static method in class ij.IJ
Runs the macro contained in the string macro.
runMacro(String, String) - Static method in class ij.IJ
Runs the macro contained in the string macro.
runMacro(Program, int, String) - Method in class ij.macro.Interpreter
Interprets the specified tokenized macro starting at the specified location.
runMacro(String, String) - Method in class ij.plugin.Macro_Runner
Opens and runs the specified macro on the current thread.
runMacro(String) - Method in class ij.plugin.MacroInstaller
 
runMacro(String, Editor) - Method in class ij.plugin.MacroInstaller
 
runMacroCommand(String) - Static method in class ij.plugin.MacroInstaller
 
runMacroFile(String, String) - Static method in class ij.IJ
Runs the specified macro or script file in the current thread.
runMacroFile(String) - Static method in class ij.IJ
Runs the specified macro file.
runMacroFile(String, String) - Method in class ij.plugin.Macro_Runner
Opens and runs the specified macro file on the current thread.
runMacroFromIJJar(String, String) - Method in class ij.plugin.Macro_Runner
 
runMacroShortcut(String) - Static method in class ij.plugin.MacroInstaller
 
runMacroTool(String) - Method in class ij.plugin.MacroInstaller
 
runMenuTool(String, String) - Method in class ij.plugin.MacroInstaller
 
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.
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.
save - Variable in class ij.gui.HistogramWindow
 
save(String) - Static method in class ij.IJ
Saves the current image, lookup table, selection or text window to the specified file path.
save(ImagePlus, String) - Static method in class ij.IJ
Saves the specified image, lookup table or selection to the specified file path.
save() - Method in class ij.io.FileSaver
Resaves the image.
SAVE - Static variable in interface ij.macro.MacroConstants
 
save(ImagePlus, String, int) - Static method in class ij.plugin.JpegWriter
Thread-safe method.
save(String) - Method in class ij.plugin.MeasurementsWriter
 
save(PrintWriter) - Method in class ij.text.TextPanel
Writes all the text in this TextPanel to a file.
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
 
saveAs(String, String) - Static method in class ij.IJ
 
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
Saves this ResultsTable as a tab or comma delimited text file.
saveAs() - Method in class ij.plugin.frame.Editor
 
saveAs(String) - Method in class ij.text.TextPanel
Saves all the text in this TextPanel to a file.
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
Save the image or stack in TIFF format using a save file dialog.
saveAsTiff(String) - Method in class ij.io.FileSaver
Save the image in TIFF format using the specified path.
saveAsTiffStack(String) - Method in class ij.io.FileSaver
Save 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
 
saveCommand() - Static method in class ij.plugin.frame.Recorder
Writes the current command and options to the Recorder window.
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.
saveGlobals(Program) - Method in class ij.macro.Interpreter
Saves global variables.
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
 
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.
savePreferences(Properties) - Static method in class ij.plugin.GelAnalyzer
Called once when ImageJ quits.
savePreferences() - Static method in class ij.Prefs
Saves user preferences in the IJ_Prefs.txt properties file.
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.
saveXValues - Static variable in class ij.gui.PlotWindow
Save x-values only.
saveXYCoordinates(ImagePlus) - Method in class ij.plugin.filter.XYWriter
 
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, double) - Method in class ij.process.StackProcessor
 
SCALE_T - Static variable in class ij.plugin.Resizer
 
ScaleBar - Class in ij.plugin
This plugin implements the Analyze/Tools/Draw 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
 
Scaler - Class in ij.plugin
This plugin implements the Image/Scale command.
Scaler() - Constructor for class ij.plugin.Scaler
 
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 Image/Flatten, 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.
screenXD(double) - Method in class ij.gui.ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenY(int) - Method in class ij.gui.ImageCanvas
Converts an offscreen y-coordinate to a screen y-coordinate.
screenYD(double) - Method in class ij.gui.ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
scriptMode() - Static method in class ij.plugin.frame.Recorder
 
scroll(int, int) - Method in class ij.gui.ImageCanvas
 
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, String) - Constructor for class ij.gui.ScrollbarWithLabel
 
scrollToTop() - Method in class ij.text.TextPanel
 
SD_METHOD - Static variable in class ij.plugin.ZProjector
 
seek(long) - Method in class ij.io.RandomAccessStream
 
seek(int) - Method in class ij.io.RandomAccessStream
 
SEGMENTED - Static variable in class ij.plugin.filter.MaximumFinder
Output type watershed-segmented image
SELECT - Static variable in interface ij.macro.MacroConstants
 
select(int) - Method in class ij.plugin.frame.RoiManager
Assigns the ROI at the specified index to the current image.
select(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager
Assigns the ROI at the specified index to 'imp'.
select(int, boolean, boolean) - Method in class ij.plugin.frame.RoiManager
 
SELECT_IMAGE - Static variable in interface ij.macro.MacroConstants
 
selectAll() - Method in class ij.text.TextPanel
Selects all the lines in this TextPanel.
Selection - Class in ij.plugin
This plugin implements the commands in the Edit/Section submenu.
Selection() - Constructor for class ij.plugin.Selection
 
SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
 
SELECTION_TYPE - Static variable in interface ij.macro.MacroConstants
 
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.
separator - Static variable in class ij.Prefs
file.separator system property
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(String, int) - Static method in class ij.Prefs
Saves value in the preferences file using the keyword key.
set(String, double) - Static method in class ij.Prefs
Saves value in the preferences file using the keyword key.
set(String, boolean) - Static method in class ij.Prefs
Saves the boolean variable value in the preferences file using the keyword key.
set(int, int, int) - Method in class ij.process.ByteProcessor
 
set(int, int) - Method in class ij.process.ByteProcessor
 
set(int, int, int) - Method in class ij.process.ColorProcessor
 
set(int, int) - Method in class ij.process.ColorProcessor
 
set(int, int, int) - Method in class ij.process.FloatProcessor
 
set(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) - Method in class ij.process.ImageProcessor
 
set(int, int, int) - Method in class ij.process.ShortProcessor
 
set(int, int) - Method in class ij.process.ShortProcessor
 
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_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_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
 
setActivated() - Method in class ij.ImagePlus
Called by ImageWindow.windowActivated().
setAdditionalFunctions(String) - Static method in class ij.macro.Interpreter
The specified string, if not null, is added to strings passed to the run() method.
setAllPoints(boolean) - Static method in class ij.gui.Wand
 
setAnimate(boolean) - Method in class ij.gui.StackWindow
 
setAntialiased(Graphics, boolean) - Static method in class ij.util.Java2
 
setAntialiasedText(boolean) - Method in class ij.process.ImageProcessor
Specifies whether or not text is drawn using antialiasing.
setAntialiasedText(Graphics, boolean) - Static method in class ij.util.Java2
 
setAutoThreshold(String) - Method in class ij.process.ImageProcessor
 
setAutoThreshold(String, boolean, int) - Method in class ij.process.ImageProcessor
 
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.
setBackgroundColor(Color) - Static method in class ij.gui.Toolbar
 
setBackgroundColor(int, int, int) - Static method in class ij.IJ
Sets the background color.
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
Does nothing.
setBackgroundValue(double) - Method in class ij.process.ImageProcessor
Sets the background fill value used by the rotate(), scale() and translate() methods.
setBackgroundValue(double) - Method in class ij.process.ShortProcessor
Does nothing.
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.VirtualStack
Sets the bit depth (8, 16, 24 or 32).
setBlockIncrement(int) - Method in class ij.gui.ScrollbarWithLabel
 
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 brush tool, which must be greater than 4.
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.
setChannelColorModel(IndexColorModel) - Method in class ij.CompositeImage
 
setChannelLut(LUT) - Method in class ij.CompositeImage
 
setChannelLut(LUT, int) - Method in class ij.CompositeImage
 
setClipRect(Rectangle) - Method in class ij.process.ImageProcessor
Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
setColor(Color) - Method in class ij.gui.Plot
Changes the drawing color.
setColor(Color) - Method in class ij.gui.PlotWindow
Changes the drawing color.
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(int) - Method in class ij.process.ColorProcessor
Sets the fill/draw color, where color is an RGB int.
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(int) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value.
setColor(Color) - Method in class ij.process.ShortProcessor
Sets the foreground fill/draw color.
setColorModel(ColorModel) - Method in class ij.ImageStack
Assigns a new color model to this stack.
setColorModel(ColorModel) - Method in class ij.process.ImageProcessor
Sets the color model.
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.
setComposite(Composite) - Method in class ij.gui.ImageRoi
Sets the composite mode.
setCTable(float[], String) - Method in class ij.measure.Calibration
Sets the calibration table.
setCurrentFont(Font) - Method in class ij.gui.TextRoi
Set the current (instance) 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.
setCustomRoi(boolean) - Method in class ij.gui.ImageCanvas
Allows plugins (e.g., Orthogonal_Views) to create a custom ROI using a display list.
setDebugMode(int) - Method in class ij.macro.Interpreter
 
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 current working directory.
setDefaultDirectory(String) - Static method in class ij.plugin.frame.Editor
 
setDefaultDoubleHeaded(boolean) - Static method in class ij.gui.Arrow
 
setDefaultFillColor(Color) - Static method in class ij.gui.Roi
 
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
 
setDefaultStyle(int) - Static method in class ij.gui.Arrow
 
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.
setDisplayList(Vector) - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.setOverlay(ij.gui.Overlay)
setDisplayList(Shape, Color, BasicStroke) - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.setOverlay(Shape, Color, BasicStroke)
setDisplayList(Roi, Color) - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.setOverlay(Roi, Color, int, Color)
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
 
setDrawingColor(int, int, boolean) - Method in class ij.gui.ImageCanvas
 
setDrawingSize(int, int) - Method in class ij.gui.ImageCanvas
 
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.Interpreter
 
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
 
setf(int, int, float) - Method in class ij.process.ByteProcessor
 
setf(int, float) - Method in class ij.process.ByteProcessor
 
setf(int, int, float) - Method in class ij.process.ColorProcessor
 
setf(int, float) - Method in class ij.process.ColorProcessor
 
setf(int, int, float) - Method in class ij.process.FloatProcessor
 
setf(int, float) - Method in class ij.process.FloatProcessor
 
setf(int, int, float) - Method in class ij.process.ImageProcessor
 
setf(int, float) - Method in class ij.process.ImageProcessor
 
setf(int, int, float) - Method in class ij.process.ShortProcessor
 
setf(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
 
setFillColor(Color) - Method in class ij.gui.Roi
Sets the color used to fill ROIs when they are in an overlay.
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(Font) - Method in class ij.gui.MultiLineLabel
 
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, 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.
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
 
setFontSize(int) - Static method in class ij.Menus
Set the size (in points) used for the fonts in ImageJ menus.
setForegroundColor(Color) - Static method in class ij.gui.Toolbar
 
setForegroundColor(int, int, int) - Static method in class ij.IJ
Sets the foreground color.
setFromFloatArrays(float[][]) - Method in class ij.process.ByteProcessor
 
setFromFloatProcessors(FloatProcessor[]) - Method in class ij.process.ByteProcessor
 
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
 
setGlobalCalibration(Calibration) - Method in class ij.ImagePlus
Sets the system-wide calibration.
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
 
setHideOutputImage(boolean) - Method in class ij.plugin.filter.ParticleAnalyzer
Set 'hideOutputImage' true to not display the "Show:" image.
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).
setIgnoreFlush(boolean) - Method in class ij.ImagePlus
 
setImage(ImagePlus) - Method in class ij.gui.Roi
 
setImage(Image) - Method in class ij.ImagePlus
Replaces the image, if any, with the one specified.
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.
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 get paint to update the image from the ImageProcessor.
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.
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.
setIsMacroWindow(boolean) - Method in class ij.plugin.frame.Editor
 
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 ImageProcessor.LEFT, ImageProcessor.CENTER or ImageProcessor.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(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<=rowsetLastDirectory(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.
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
Sets the x-axis and y-axis range.
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(int) - Method in class ij.gui.Plot
Changes the line width.
setLineWidth(int) - Method in class ij.gui.PlotWindow
Changes the line width.
setLineWidth(int) - Method in class ij.gui.Roi
Deprecated. replaced by setStrokeWidth(int)
setLineWidth(int) - Method in class ij.process.ImageProcessor
Sets the line width used by lineTo() and drawDot().
setLocation(int, int) - Method in class ij.gui.Roi
Set the location of the ROI in image coordinates.
setLocationAndSize(int, int, int, int) - Method in class ij.gui.ImageWindow
Moves and resizes this window.
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.
setLuts(LUT[]) - Method in class ij.CompositeImage
 
setMagnification(double) - Method in class ij.gui.ImageCanvas
 
setMask(ImageProcessor) - Method in class ij.process.ImageProcessor
Defines a byte mask that limits processing to an irregular ROI.
setMaximum(int) - Method in class ij.gui.ScrollbarWithLabel
 
setMaxIterations(int) - Method in class ij.measure.CurveFitter
Set maximum number of iterations allowed
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.
setMethod(int) - Method in class ij.plugin.ZProjector
 
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 minimum and maximum displayed pixel 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) - 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, int) - Method in class ij.process.ColorProcessor
 
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.
setMinimum(int) - Method in class ij.gui.ScrollbarWithLabel
 
setMode(int) - Method in class ij.CompositeImage
 
setName(String) - Method in class ij.gui.Roi
Sets the name of this ROI.
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.filter.Convolver
 
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.
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) - 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.
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(Shape, Color, BasicStroke) - Method in class ij.ImagePlus
Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image.
setOverlay(Roi, Color, int, Color) - Method in class ij.ImagePlus
Creates an Overlay from the specified ROI, and assigns it to this image.
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(Object, int) - Method in class ij.ImageStack
Assigns a pixel array to the specified slice, were 1<=n<=nslices.
setPixels(Object) - Method in class ij.process.ByteProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.ByteProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object) - Method in class ij.process.ColorProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.ColorProcessor
Sets the pixels of one color channel from a FloatProcessor.
setPixels(Object) - Method in class ij.process.FloatProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.FloatProcessor
Sets the pixels, and min&max values from a FloatProcessor.
setPixels(Object) - Method in class ij.process.ImageProcessor
Sets a new pixel array for the image.
setPixels(int, FloatProcessor) - Method in class ij.process.ImageProcessor
Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
setPixels(Object) - Method in class ij.process.ShortProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.ShortProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object, int) - Method in class ij.VirtualStack
Assigns a pixel array to the specified slice, were 1<=n<=nslices.
setPolygon(int[], int[], int) - Method in class ij.process.PolygonFiller
Specifies the polygon to be filled.
setPosition(int, int, int) - Method in class ij.gui.StackWindow
 
setPosition(int, int, int) - Method in class ij.ImagePlus
 
setPosition(int) - Method in class ij.ImagePlus
 
setPositionWithoutUpdate(int, int, int) - Method in class ij.ImagePlus
 
setPrecision(int) - Method in class ij.measure.ResultsTable
Sets the number of digits to the right of decimal point.
setPrecision(int) - Static method in class ij.plugin.filter.Analyzer
Sets the number of digits displayed to the right of decimal point.
setProcessor(ImageProcessor) - Method in class ij.ImagePlus
Replaces the ImageProcessor with the one specified and updates the display.
setProcessor(String, ImageProcessor) - Method in class ij.ImagePlus
Replaces the ImageProcessor with the one specified and updates the display.
setProgressBar(ProgressBar) - Method in class ij.process.ImageProcessor
Assigns a progress bar to this processor.
setProperty(String, Object) - Method in class ij.ImagePlus
Adds a key-value pair to this image's properties.
setQuality(int) - Static method in class ij.plugin.JpegWriter
Deprecated. replaced by FileSaver.setJpegQuality()
setRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer
Set the "Redirect To" image.
setRestarts(int) - Method in class ij.measure.CurveFitter
Set number of simplex restarts to do
setResultsTable(ResultsTable) - Static method in class ij.plugin.filter.Analyzer
 
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).
setRoi(Roi) - Method in class ij.ImagePlus
Assigns the specified ROI to this image and displays it.
setRoi(Roi, boolean) - Method in class ij.ImagePlus
Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.
setRoi(int, int, int, int) - Method in class ij.ImagePlus
Creates a rectangular selection.
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.
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.process.ImageProcessor
Defines a non-rectangular region of interest that will consist of a rectangular ROI and a mask.
setRoi(Polygon) - Method in class ij.process.ImageProcessor
Defines a polygonal region of interest that will consist of a rectangular ROI and a mask.
setRoundRectArcSize(int) - Method in class ij.gui.Roi
Sets the rounded rectangle arc size (pixels).
setRoundRectArcSize(int) - Static method in class ij.gui.Toolbar
Sets the rounded rectangle arc size (pixels).
setSelection(int, int) - Method in class ij.text.TextPanel
Creates a selection.
setShowAllColor(Color) - Static method in class ij.gui.ImageCanvas
Sets the color used used for "Show All" mode.
setShowAllROIs(boolean) - Method in class ij.gui.ImageCanvas
Enables/disables the ROI Manager "Show All" mode.
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.
setShowProgress(boolean) - Method in class ij.process.FHT
Enables/disables display of the progress bar during transforms.
setSilentMode(boolean) - Method in class ij.io.Opener
The "Opening: path" status message is not displayed in silent mode.
setSize(int, int) - Method in class ij.gui.Plot
Sets the canvas size (i.e., size of the resulting ImageProcessor).
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, were 1<=n<=nslices.
setSliceLabel(String, int) - Method in class ij.VirtualStack
Does nothing.
setSliceWithoutUpdate(int) - Method in class ij.ImagePlus
Displays the specified stack image (1<=n<=stackSize) without updating the display.
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
 
setStack(ImageStack) - Method in class ij.ImagePlus
Replaces the image with the specified stack and updates the display.
setStack(String, 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
 
setStartSlice(int) - Method in class ij.plugin.ZProjector
 
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.Roi
Sets the color used by this ROI to draw its outline.
setStrokeWidth(float) - Method in class ij.gui.Line
 
setStrokeWidth(float) - Method in class ij.gui.Roi
Sets the width of the lines used to draw this ROI when it is part of an Overlay list or ROI Manager "Show All" list.
setStyle(int) - Method in class ij.gui.Arrow
 
setSystemLookAndFeel() - Static method in class ij.util.Java2
Sets the Swing look and feel to the system look and feel.
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.
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, 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(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
 
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(String) - Method in class ij.gui.Toolbar
 
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) - 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
 
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
 
setup() - Method in class ij.gui.GenericDialog
 
setup() - Method in class ij.gui.HistogramWindow
 
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.CalibrationBar
 
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
 
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.Profiler
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Projector
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.RankFilters
Setup of the PlugInFilter.
setup(String, ImagePlus) - Method in class ij.plugin.filter.Resizer
Deprecated.  
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
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.XYWriter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ZAxisProfiler
 
setup(int, ImagePlus) - Static method in class ij.Undo
 
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
 
setUseBicubic(boolean) - Static method in class ij.process.ImageProcessor
 
setValue(int) - Method in class ij.gui.ScrollbarWithLabel
 
setValue(String, int, double) - Method in class ij.measure.ResultsTable
Sets the value of the given column and row, where where 0<=row<counter.
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<counter.
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).
setValueUnit(String) - Method in class ij.measure.Calibration
Sets the value unit.
setVariable(String, double) - Method in class ij.macro.Interpreter
 
setVisibleAmount(int) - Method in class ij.gui.ScrollbarWithLabel
 
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.
setWidth(int) - Static method in class ij.gui.Line
 
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().
setXUnit(String) - Method in class ij.measure.Calibration
Sets the X length unit.
setYUnit(String) - Method in class ij.measure.Calibration
Sets the Y length unit.
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
 
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(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.
ShapeRoi(int, int, Shape) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from a Shape.
ShapeRoi(float[]) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from an array of variable length path segments.
shapeToRoi() - Method in class ij.gui.ShapeRoi
Attempts to convert this ShapeRoi into a 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
 
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, short[], ColorModel) - Constructor for class ij.process.ShortProcessor
Creates a new ShortProcessor using the specified pixel array and ColorModel.
ShortProcessor(int, int) - Constructor for class ij.process.ShortProcessor
Creates a blank ShortProcessor using the default grayscale LUT that displays zero as black.
ShortProcessor(BufferedImage) - Constructor for class ij.process.ShortProcessor
Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage.
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(int, int, boolean) - Constructor for class ij.process.ShortProcessor
Obsolete.
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.Plot
Displays the plot in a PlotWindow and returns a reference to the PlotWindow.
show(double) - Method in class ij.gui.ProgressBar
Updates the progress bar, where percent should run from 0 to 1.
show(double, boolean) - Method in class ij.gui.ProgressBar
Updates the progress bar, where percent 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 (currentValue+1)/finalValue of the maximum bar length.
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(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.
SHOW_ALL_COLOR - Static variable in class ij.Prefs
 
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_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
SHOW_TEXT - Static variable in interface ij.macro.MacroConstants
 
showAllSliceOnly - Static variable in class ij.Prefs
Only show ROIs associated with current slice in Roi Manager "Show All" mode.
showChoice - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
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 the dialog.
showDialog() - Method in class ij.plugin.Compiler
 
showDialog() - Method in class ij.plugin.FFTMath
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.BackgroundSubtracter
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Binary
 
showDialog(ImagePlus) - Method in class ij.plugin.filter.Calibrator
 
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() - Method in class ij.plugin.filter.ParticleAnalyzer
Displays a modal options dialog.
showDialog() - Method in class ij.plugin.filter.Projector
 
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() - Method in class ij.plugin.NewPlugin
 
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
 
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.
showProgress(double) - Static method in class ij.IJ
Updates the progress bar, where 0<=progress<=1.0.
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.
showProgress - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showProgress(double) - Method in class ij.process.ImageProcessor
 
showResults - Variable in class ij.plugin.filter.ParticleAnalyzer
 
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.Roi
 
showStatus(String) - Static method in class ij.IJ
Displays a message in the ImageJ status bar.
showTime(ImagePlus, long, String) - Static method in class ij.IJ
 
showTime(ImagePlus, long, String, int) - Static method in class ij.IJ
 
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.
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
size() - Method in class ij.gui.Overlay
 
SIZE_KEY - Static variable in class ij.gui.Arrow
 
skeletonize() - Method in class ij.process.BinaryProcessor
Uses a lookup table to repeatably removes pixels from the edges of objects in a binary image, reducing them to single pixel wide skeletons.
skeletonize() - Method in class ij.process.ByteProcessor
 
SKEWNESS - Static variable in interface ij.measure.Measurements
 
SKEWNESS - Static variable in class ij.measure.ResultsTable
 
skewness - Variable in class ij.process.ImageStatistics
 
slice - Variable in class ij.gui.StackWindow
 
SLICE - Static variable in interface ij.measure.Measurements
 
SLICE - Static variable in class ij.measure.ResultsTable
 
slice - Variable in class ij.plugin.filter.ParticleAnalyzer
 
sliceLabels - 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.
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).
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
 
snapshotHeight - Variable in class ij.process.ImageProcessor
 
snapshotPixels - Variable in class ij.process.ByteProcessor
 
snapshotPixels - Variable in class ij.process.ColorProcessor
 
snapshotWidth - Variable in class ij.process.ImageProcessor
 
SocketListener - Class in ij
Runs commands sent to the port returned by ImageJ.getPort().
SocketListener() - Constructor for class ij.SocketListener
 
SOFTWARE - Static variable in class ij.io.TiffDecoder
 
SOLIDITY - Static variable in class ij.measure.ResultsTable
 
sort(ImageStack) - Method in class ij.plugin.DICOM_Sorter
 
sort(String[]) - Static method in class ij.util.StringSorter
Sorts the array.
sortFileList(String[]) - Method in class ij.plugin.FolderOpener
Sorts the file names into numeric order.
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
 
SPARE2 - Static variable in class ij.gui.Toolbar
 
SPARE3 - Static variable in class ij.gui.Toolbar
 
SPARE4 - Static variable in class ij.gui.Toolbar
 
SPARE5 - Static variable in class ij.gui.Toolbar
 
SPARE6 - Static variable in class ij.gui.Toolbar
 
SPARE7 - Static variable in class ij.gui.Toolbar
 
SPARE8 - Static variable in class ij.gui.Toolbar
 
SPARE9 - Static variable in class ij.gui.Toolbar
 
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
 
SplineFitter - Class in ij.measure
This class fits a spline function to a set of points.
SplineFitter(int[], int[], int) - Constructor for class ij.measure.SplineFitter
 
splinePoints - Variable in class ij.gui.PolygonRoi
 
SPLIT - Static variable in interface ij.macro.MacroConstants
 
split(ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
Splits the specified RGB image or stack into three 8-bit grayscale images or stacks.
split(ImageStack, boolean) - Method in class ij.plugin.filter.RGBStackSplitter
Splits the specified RGB stack into three 8-bit grayscale stacks.
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.
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 - Static variable in interface ij.macro.MacroConstants
 
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
 
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)
srcRect - Variable in class ij.gui.ImageCanvas
 
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.
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
 
StackLabeler - Class in ij.plugin.filter
This plugin implements the Image/Stacks/Label command.
StackLabeler() - Constructor for class ij.plugin.filter.StackLabeler
 
StackProcessor - Class in ij.process
This class processes stacks.
StackProcessor(ImageStack, ImageProcessor) - Constructor for class ij.process.StackProcessor
Constructs a StackProcessor from a stack.
StackReverser - Class in ij.plugin
Implements the Image/Transform/Flip Z command.
StackReverser() - Constructor for class ij.plugin.StackReverser
 
StackStatistics - Class in ij.process
Statistics, including the histogram, of a stack.
StackStatistics(ImagePlus) - Constructor for class ij.process.StackStatistics
 
StackStatistics(ImagePlus, int, double, double) - Constructor for class ij.process.StackStatistics
 
StackWindow - Class in ij.gui
This class is an extended ImageWindow used to display image stacks.
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
 
startPaste(ImagePlus) - Method in class ij.gui.Roi
 
STARTS_WITH - Static variable in interface ij.macro.MacroConstants
 
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.
stats - Variable in class ij.gui.HistogramWindow
 
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 class ij.macro.Interpreter
 
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
 
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
 
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
 
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
 
strokeColor - Variable in class ij.gui.Roi
 
STYLE_KEY - Static variable in class ij.gui.Arrow
 
styles - Static variable in class ij.gui.Arrow
 
SUBSTRING - Static variable in interface ij.macro.MacroConstants
 
SUBTRACT - Static variable in interface ij.process.Blitter
dst=dst-src
subtractBackround(ImageProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
Depracated.
subtractCircle(String, String, String) - Static method in class ij.gui.ShapeRoi
 
subtractPoints(Roi) - Method in class ij.gui.PointRoi
Subtract the points that intersect the specified ROI and return the result.
subtractRGBBackround(ColorProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
Depracated.
SUBTYPE - Static variable in class ij.io.RoiDecoder
 
SUM_METHOD - Static variable in class ij.plugin.ZProjector
 
summarize() - Method in class ij.plugin.filter.Analyzer
 
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
 
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.
swapQuadrants() - Method in class ij.process.FHT
Swap quadrants 1 and 3 and 2 and 4 of the image contained in this FHT.
Symbol - Class in ij.macro
Objects of this class are used as entries in the macro language symbol table.

T

TABLE - Static variable in class ij.io.Opener
 
TABLE - Static variable in class ij.plugin.NewPlugin
 
TABLE_FULL - Static variable in class ij.measure.ResultsTable
 
TAN - Static variable in interface ij.macro.MacroConstants
 
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(int, int, String) - Constructor for class ij.gui.TextRoi
Creates a new TextRoi.
TextRoi(int, int, String, Font) - Constructor for class ij.gui.TextRoi
Creates a new TextRoi with the specified location and Font.
TextRoi(int, int, String, Font, Color) - Constructor for class ij.gui.TextRoi
Deprecated.  
TextRoi(int, int, ImagePlus) - Constructor for class ij.gui.TextRoi
 
textValueChanged(TextEvent) - Method in class ij.gui.ColorChooser
 
textValueChanged(TextEvent) - Method in class ij.gui.GenericDialog
 
textValueChanged(TextEvent) - Method in class ij.macro.FunctionFinder
 
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.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, 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, int, int) - Constructor for class ij.text.TextWindow
Opens a new text window containing the contents of a text file.
TextWriter - Class in ij.plugin
This plugin implements the File/Save As/Text command.
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
 
THREADS - Static variable in class ij.Prefs
 
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
 
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(String, String) - Constructor for class ij.io.TiffDecoder
 
TiffDecoder(InputStream, String) - Constructor for class ij.io.TiffDecoder
 
TiffEncoder - Class in ij.io
Saves an image described by a FileInfo object as an uncompressed, big-endian TIFF file.
TiffEncoder(FileInfo) - Constructor for class ij.io.TiffEncoder
 
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).
Timer - Class in ij.plugin
ImageJ plugin for measuring the speed of various Java operations.
Timer() - Constructor for class ij.plugin.Timer
 
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_STRING - Static variable in interface ij.macro.MacroConstants
 
TO_UPPER_CASE - Static variable in interface ij.macro.MacroConstants
 
toArray() - Method in class ij.gui.Overlay
 
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(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).
toFloat(double[]) - Static method in class ij.util.Tools
Converts the double array 'a' to a float array.
toFloatArrays() - Method in class ij.process.ByteProcessor
 
toFloatProcessors() - Method in class ij.process.ByteProcessor
 
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
 
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_MARGIN - Static variable in class ij.gui.Plot
the margin width above the plot frame
toString() - Method in class ij.gui.ImageWindow
 
toString() - Method in class ij.gui.Overlay
 
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.Symbol
 
toString() - Method in class ij.measure.Calibration
 
toString() - Method in class ij.measure.ResultsTable
 
toString() - Method in class ij.process.FHT
Returns a string containing information about this FHT.
toString() - Method in class ij.process.ImageProcessor
Returns a string containing information about this ImageProcessor.
toString() - Method in class ij.process.ImageStatistics
 
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 class ij.macro.Interpreter
 
TRACED_ROI - Static variable in class ij.gui.Roi
 
transform() - Method in class ij.process.FHT
Performs a foreward transform, converting this image into the frequency domain.
TRANSFORM - Static variable in class ij.Undo
 
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.process.ImageProcessor
Moves the image or selection vertically or horizontally by a specified number of pixels.
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
 
TRIANGLE - Static variable in class ij.gui.Plot
Display points using an tiangular mark.
TRIANGLE - Static variable in class ij.gui.PlotWindow
Display points using an tiangular mark.
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.
trimFileList(String[]) - Method in class ij.plugin.FolderOpener
Removes names that start with "." or end with ".db".
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.
TRUE - Static variable in interface ij.macro.MacroConstants
 
type - Variable in class ij.gui.Roi
 
TYPE - Static variable in class ij.io.RoiDecoder
 
type - Variable in class ij.macro.Symbol
 
TYPE_CONVERSION - Static variable in class ij.Undo
 
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.io.Opener
 

U

umean - Variable in class ij.process.ImageStatistics
Uncalibrated mean
UNCALIBRATED_OD - Static variable in class ij.measure.Calibration
 
Undo - Class in ij
This class consists of static methods and fields that implement ImageJ's Undo command.
Undo() - Constructor for class ij.Undo
 
undo() - Static method in class ij.Undo
 
uninstallPlugin(String) - Static method in class ij.Menus
Deletes a command installed by installPlugin.
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
 
unzoom() - Method in class ij.gui.ImageCanvas
Implements the Image/Zoom/Original Scale command.
update(Graphics) - Method in class ij.gui.ImageCanvas
 
update(Graphics) - Method in class ij.gui.ProgressBar
 
update(boolean, boolean) - Method in class ij.gui.Roi
If 'add' is true, adds this selection to the previous one.
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(int, ImagePlus, Roi) - Method in class ij.measure.ResultsTable
 
update() - Method in class ij.plugin.frame.Channels
 
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
Updates the ThresholdAdjuster when it is in B&W mode.
UPDATE_DISPLAY - Static variable in interface ij.macro.MacroConstants
 
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.
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.
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
CompositeImage calls this method to generate an updated color image.
UPDATED - Static variable in class ij.ImagePlus
 
updateDebugWindow(String[], TextWindow) - Method in class ij.macro.Interpreter
 
updateDisplay() - Method in class ij.text.TextPanel
 
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(ImagePlus) - Method in class ij.gui.ImageWindow
 
updateImage() - Method in class ij.ImagePlus
ImageCanvas.paint() calls this method when the ImageProcessor has generated new image.
updateImageJMenus() - Static method in class ij.Menus
 
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.
updateWideLine(float) - Method in class ij.gui.Roi
 
updateWindowMenuItem(String, String) - Static method in class ij.Menus
Changes the name of an item in the Window menu.
updateY(int, int) - Static method in class ij.plugin.filter.Analyzer
Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
updateY(double, int) - Static method in class ij.plugin.filter.Analyzer
Returns an updated Y coordinate based on the current "Invert Y Coordinates" flag.
URL - Static variable in class ij.IJ
 
url - Variable in class ij.io.FileInfo
 
URLOpener - Class in ij.plugin
Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.
URLOpener() - Constructor for class ij.plugin.URLOpener
 
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.
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
 
UTILITIES_MENU - Static variable in class ij.Menus
 

V

validDimensions() - Method in class ij.gui.StackWindow
 
value - Variable in class ij.gui.HistogramWindow
 
value - Variable in class ij.macro.Symbol
 
valueUnit - Variable in class ij.io.FileInfo
 
VAR - 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() 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 false if the ImageJ version is less than the one specified.
verticalColorBar(ImageProcessor, int, int, int, int) - Method in class ij.plugin.filter.CalibrationBar
 
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, ColorModel, String) - Constructor for class ij.VirtualStack
Creates a new, empty virtual stack.
vistaHint - Static variable in class ij.Prefs
 

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, String) - Constructor for class ij.gui.WaitForUserDialog
 
WaitForUserDialog(String) - Constructor for class ij.gui.WaitForUserDialog
 
WAND - Static variable in class ij.gui.Toolbar
 
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.
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.
weightedColor - Static variable in class ij.Prefs
Color to grayscale conversion is weighted (0.299, 0.587, 0.114) if the variable is true.
west(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
WHILE - Static variable in interface ij.macro.MacroConstants
 
whiteIsZero - Variable in class ij.io.FileInfo
 
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_KEY - Static variable in class ij.gui.Arrow
 
WIDTH_KEY - Static variable in class ij.text.TextWindow
 
win - Variable in class ij.ImagePlus
 
WINDOW_MENU_ITEMS - Static variable in class ij.Menus
 
windowActivated(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowActivated(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowActivated(WindowEvent) - Method in class ij.gui.MessageDialog
 
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.PlugInFrame
 
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.ImageWindow
 
windowClosed(WindowEvent) - Method in class ij.gui.MessageDialog
 
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.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.ImageWindow
 
windowClosing(WindowEvent) - Method in class ij.gui.MessageDialog
 
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.Channels
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.ColorPicker
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.ColorThresholder
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.ContrastAdjuster
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.Editor
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.Fonts
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PasteController
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.PlugInFrame
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.Recorder
 
windowClosing(WindowEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
 
windowClosing(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
windowDeactivated(WindowEvent) - Method in class ij.gui.GenericDialog
 
windowDeactivated(WindowEvent) - Method in class ij.gui.ImageWindow
 
windowDeactivated(WindowEvent) - Method in class ij.gui.MessageDialog
 
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.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.ImageWindow
 
windowDeiconified(WindowEvent) - Method in class ij.gui.MessageDialog
 
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.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.ImageWindow
 
windowIconified(WindowEvent) - Method in class ij.gui.MessageDialog
 
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.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.ImageWindow
 
windowOpened(WindowEvent) - Method in class ij.gui.MessageDialog
 
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.PlugInFrame
 
windowOpened(WindowEvent) - Method in class ij.plugin.Orthogonal_Views
 
WindowOrganizer - Class in ij.plugin
 
WindowOrganizer() - Constructor for class ij.plugin.WindowOrganizer
 
windowStateChanged(WindowEvent) - Method in class ij.gui.ImageWindow
 
WORD - Static variable in interface ij.macro.MacroConstants
 
write(String) - Static method in class ij.IJ
Deprecated. replaced by IJ.log()
write(OutputStream) - Method in class ij.io.ImageWriter
Writes the image to the specified OutputStream.
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(OutputStream) - Method in class ij.io.TiffEncoder
Saves the image as a TIFF file.
write(DataOutputStream) - Method in class ij.io.TiffEncoder
 
WRITE - Static variable in interface ij.macro.MacroConstants
 
writeImage(ImagePlus, String, int, int) - Method in class ij.plugin.filter.AVI_Writer
Writes an ImagePlus (stack) as AVI file.
writeImage(ImagePlus, String, int) - Method in class ij.plugin.PNG_Writer
 
Writer - Class in ij.plugin.filter
This plugin saves an image in tiff, gif, jpeg, bmp, png, text or raw format.
Writer() - Constructor for class ij.plugin.filter.Writer
 

X

X - Static variable in class ij.gui.Plot
Display points using an X-shaped mark.
X - Static variable in class ij.gui.PlotWindow
Display points using an X-shaped mark.
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
 
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 ticks
X_NUMBERS - Static variable in class ij.gui.Plot
flag for numeric labels of x-axis ticks
X_RESOLUTION - Static variable in class ij.io.TiffDecoder
 
X_TICKS - Static variable in class ij.gui.Plot
flag for drawing x-axis ticks
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()
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(ShapeRoi) - Method in class ij.gui.ShapeRoi
Unary exclusive or operator.
XOR - Static variable in interface ij.process.Blitter
dst=dst XOR src
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
 
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
 
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
 
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
 

Y

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
 
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 ticks
Y_NUMBERS - Static variable in class ij.gui.Plot
flag for numeric labels of x-axis ticks
Y_RESOLUTION - Static variable in class ij.io.TiffDecoder
 
Y_TICKS - Static variable in class ij.gui.Plot
flag for drawing x-axis ticks
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()
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
 
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.