C_POSITION RoiDecoder
c2hex(Color) Tools
Converts a Color to an 7 byte hex string starting with '#'.
cachedMask Roi
cal HistogramWindow
cal ImageStatistics
calculate(String, ImagePlus, ImagePlus) ImageCalculator
Deprecated.
calculateDistance(int, int, int, int) Plot
CALCULATOR MacroConstants
calibrate(ImagePlus) Calibrator
Calibrate an image with the function type defined previously.
CALIBRATE MacroConstants
calibrated() Calibration
Returns true if this image is density calibrated.
Calibration ij.measure
Calibration objects contain an image's spatial and density calibration data.
Calibration() Calibration
Constructs a new Calibration object using the default values.
Calibration(ImagePlus) Calibration
Constructs a new Calibration object using the default values.
CalibrationBar ij.plugin
This plugin implements the Analyze/Tools/Calibration Bar command.
CalibrationBar() CalibrationBar
calibrationFunction FileInfo
Calibrator ij.plugin.filter
Implements the Analyze/Calibrate command.
Calibrator() Calibrator
CALL MacroConstants
CANCELED IJ
cancelPressed() SaveChangesDialog
Returns true if the user dismissed dialog by pressing "Cancel".
cancelPressed() YesNoCancelDialog
Returns true if the user dismissed dialog by pressing "Cancel".
canEnlarge(int, int) ImageCanvas
Returns the size to which the window can be enlarged, or null if it can't be enlarged.
CanvasResizer ij.plugin
This plugin implements the Image/Adjust/Canvas Size command.
CanvasResizer() CanvasResizer
captureImage() ScreenGrabber
Captures the active image window and returns it as an ImagePlus.
captureScreen() ScreenGrabber
Captures the entire screen and returns it as an ImagePlus.
caSnapshot() ColorProcessor
Used by the ContrastAdjuster
caSnapshot(boolean) ColorProcessor
Used by the ContrastAdjuster
cChannel SyncWindows
Checkboxes for user control.
cCoords SyncWindows
Checkboxes for user control.
cCursor SyncWindows
Checkboxes for user control.
center Roi
center(Window) GUI
Positions the specified window in the center of the screen.
CENTER Plot
Text justification.
CENTER TextRoi
CENTER_JUSTIFY ImageProcessor
Center justify text.
CENTER_OF_MASS Measurements
centerDialog(boolean) GenericDialog
Display dialog centered on the primary screen.
centerNextImage() ImageWindow
Causes the next image to be opened to be centered on the screen
and displayed without informational text above the image.
CENTROID Measurements
cFrame SyncWindows
Checkboxes for user control.
CHANGE_VALUES MacroConstants
changeFont(Font) Plot
changeFont(Font) PlotWindow
Deprecated.
changes ImagePlus
True if any changes have been made to this image.
changes Editor
CHANNEL ResultsTable
ChannelArranger ij.plugin
This plugin implements the Image/Colors/Arrange Channels command,
which allows the user to change the order of channels.
ChannelArranger() ChannelArranger
channelLuts FileInfo
Channels ij.plugin.frame
Displays the ImageJ Channels window.
Channels() Channels
ChannelSplitter ij.plugin
This plugin implements the Image/Color/Split Channels command.
ChannelSplitter() ChannelSplitter
CHAPMAN CurveFitter
Constants for the built-in fit functions
CHAR_CODE_AT MacroConstants
CHECK_AVAILABLE_MEMORY NewImage
checkArguments(Object[]) ExtensionDescriptor
checkbox GenericDialog
checkForDuplicateName WindowManager
choice GenericDialog
chromaD50 ColorSpaceConverter
reference white in xyY coordinates
chromaD55 ColorSpaceConverter
chromaD65 ColorSpaceConverter
chromaD75 ColorSpaceConverter
chromaWhitePoint ColorSpaceConverter
CIRCLE Plot
Display points using a circle (5 pixels in diameter if line thickness<=1, otherwise 7).
CIRCLE PlotWindow
Display points using a circle 5 pixels in diameter.
CIRCULARITY Measurements
CIRCULARITY ResultsTable
CircularRoiMaker ij.plugin
This class implements the Process/FFT/Make Circular Selection command.
CircularRoiMaker() CircularRoiMaker
ClassChecker ij.plugin
Checks for duplicate class and JAR files in the plugins folders and deletes older duplicates.
ClassChecker() ClassChecker
clear() Overlay
Removes all the ROIs in this Overlay.
clear() TextPanel
Deletes all the lines.
clear(ImageProcessor) TextRoi
clear(ImageProcessor) Filler
CLEAR_WORKSHEET ParticleAnalyzer
Clear "Results" window before starting.
clearOutside(ImageProcessor) Filler
Deprecated.
clearSelection() TextPanel
Deletes the selected lines.
clipboard Roi
Clipboard ij.plugin
Copies/pastes images to/from the system clipboard.
Clipboard() Clipboard
clipHeight Roi
clipRectMargin() Arrow
clipRectMargin() Line
clipRectMargin() PolygonRoi
clipRectMargin() Roi
clipWidth Roi
clipX Roi
clipXMax ImageProcessor
clipXMin ImageProcessor
clipY Roi
clipYMax ImageProcessor
clipYMin ImageProcessor
clone() ImageRoi
clone() PointRoi
Returns a copy of this PointRoi.
clone() PolygonRoi
Returns a copy of this PolygonRoi.
clone() Roi
Returns a copy of this roi.
clone() ShapeRoi
Returns a deep copy of this.
clone() TextRoi
Returns a copy of this TextRoi.
clone() ImagePlus
Returns a shallow copy of this ImagePlus.
clone() FileInfo
clone() Variable
clone() Calibration
clone() ResultsTable
Duplicates this ResultsTable.
clone() ImageProcessor
Returns a shallow copy of this ImageProcessor, where this
image and the copy share pixel data.
clone() LUT
close() CompositeImage
close() ImageWindow
Removes this window from the window list and disposes of it.
close() StackWindow
close() WaitForUserDialog
close() ImagePlus
Closes this image and sets the ImageProcessor to null.
close() LogStream
close() RandomAccessStream
close() FunctionFinder
close() Channels
close() ColorPicker
close() ColorThresholder
close() ContrastAdjuster
Overrides close() in PlugInDialog.
close() Editor
Overrides close() in PlugInFrame.
close() LineWidthAdjuster
Overrides close() in PlugInFrame.
close() MemoryMonitor
close() PasteController
close() PlugInDialog
Closes this window.
close() PlugInFrame
Closes this window.
close() Recorder
close() RoiManager
Overrides PlugInFrame.close().
close() SyncWindows
close() ThresholdAdjuster
Overrides close() in PlugInFrame.
close() TextWindow
close(boolean) TextWindow
Closes this TextWindow.
CLOSE MacroConstants
CLOSE RankFilters
closeAll() Commands
Closes all image windows, or returns 'false' if the user cancels the unsaved changes dialog box.
closeAllWindows() WindowManager
Closes all windows.
closeAndRefocus() FunctionFinder
closed ImageWindow
CLOSED ImagePlus
closingAll Prefs
"Close All" command running
cm ImageProcessor
cm2 ImageProcessor
CMYK FileInfo
32-bit interleaved CMYK.
coefficients FileInfo
COLOR CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
COLOR IJ
Image display modes
COLOR_256 ImagePlus
8-bit indexed color
COLOR_MAP TiffDecoder
COLOR_PICKER_CLOSED IJEventListener
COLOR_RGB ImagePlus
32-bit RGB color
COLOR8 FileInfo
8-bit unsigned integer with color lookup table.
ColorBlitter ij.process
This class does bit blitting of RGB images.
ColorBlitter(ColorProcessor) ColorBlitter
Constructs a ColorBlitter from a ColorProcessor.
ColorChooser ij.gui
Displays a dialog that allows the user to select a color using three sliders.
ColorChooser(String, Color, boolean) ColorChooser
Constructs a ColorChooser using the specified title and initial color.
ColorChooser(String, Color, boolean, Frame) ColorChooser
ColorPicker ij.plugin.frame
Implements the Image/Color/Color Picker command.
ColorPicker() ColorPicker
ColorProcessor ij.process
This is an 32-bit RGB image and methods that operate on that image..
ColorProcessor(int, int) ColorProcessor
Creates a blank ColorProcessor of the specified dimensions.
ColorProcessor(int, int, int[]) ColorProcessor
Creates a ColorProcessor from a pixel array.
ColorProcessor(Image) ColorProcessor
Creates a ColorProcessor from an AWT Image or BufferedImage.
colors Colors
Colors ij.plugin
This plugin implements most of the Edit/Options/Colors command.
Colors() Colors
ColorSpaceConverter ij.process
ColorSpaceConverter
ColorSpaceConverter() ColorSpaceConverter
Default constructor; uses D65 for the white point
ColorSpaceConverter(String) ColorSpaceConverter
Constructor for setting a non-default white point
ColorStatistics ij.process
RGB image statistics, including histogram.
ColorStatistics(ImageProcessor) ColorStatistics
Construct an ImageStatistics object from a ColorProcessor
using the standard measurement options (area, mean,
mode, min and max).
ColorStatistics(ImageProcessor, int, Calibration) ColorStatistics
Constructs a ColorStatistics object from a ColorProcessor using
the specified measurement options.
ColorThresholder ij.plugin.frame
Selects pixels according to hsb or rgb components.
ColorThresholder() ColorThresholder
colorToString(Color) Colors
Converts a Color into a string ("red", "green", #aa55ff, etc.).
colorToString2(Color) Colors
Converts a Color into a string ("Red", "Green", #aa55ff, etc.).
COLUMN_IN_USE ResultsTable
COLUMN_NOT_FOUND ResultsTable
columnDeleted() ResultsTable
columnExists(int) ResultsTable
Returns true if the specified column exists and is not empty.
columnExists(String) ResultsTable
Returns 'true' if the specified column exists and is not emptly.
combineHorizontally(ImageStack, ImageStack) StackCombiner
combineVertically(ImageStack, ImageStack) StackCombiner
COMMAND_IN_USE Menus
COMMAND_NOT_FOUND Menus
commandExecuting(String) CommandListener
commandExecuting(String) EventListener
commandExecuting(String) Orthogonal_Views
CommandFinder ij.plugin
CommandFinder() CommandFinder
commandInUse(String) Menus
CommandListener ij
Plugins that implement this interface are notified when ImageJ
is about to run a menu command.
CommandLister ij.plugin
This class is used by the Plugins/Shortcuts/List Shortcuts
command to display a list keyboard shortcuts.
CommandLister() CommandLister
commandPrefix MacroInstaller
Commands ij.plugin
Runs miscellaneous File and Window menu commands.
Commands() Commands
Compiler ij.plugin
Compiles and runs plugins using the javac compiler.
Compiler() Compiler
COMPLETED RoiListener
COMPOSITE CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
COMPOSITE Roi
COMPOSITE IJ
Image display modes
CompositeConverter ij.plugin
This plugin implements the Image/Color/Make Composite command.
CompositeConverter() CompositeConverter
compositeImage ImagePlus
CompositeImage ij
CompositeImage(ImagePlus) CompositeImage
CompositeImage(ImagePlus, int) CompositeImage
COMPOUND_FILTER Undo
COMPOUND_FILTER_DONE Undo
compression FileInfo
COMPRESSION TiffDecoder
COMPRESSION_NONE FileInfo
COMPRESSION_UNKNOWN FileInfo
concatenate(ImagePlus[], boolean) Concatenator
Concatenates two or more images or stacks.
concatenate(ImagePlus, ImagePlus, boolean) Concatenator
Concatenate two images or stacks.
concatenateHyperstacks(ImagePlus[], String, boolean) Concatenator
Obsolete, replaced by concatenate(images,keep) and Concatenator.run(images).
Concatenator ij.plugin
This plugin, which concatenates two or more images or stacks,
implements the Image/Stacks/Tools/Concatenate command.
Concatenator() Concatenator
conjugateMultiply(FHT) FHT
Returns the image resulting from the point by point Hartley conjugate
multiplication of this image and the specified image.
CONNECTED_CIRCLES Plot
Draw black lines between the dots and a circle with the given color at each dot
constrain Roi
CONSTRUCTING Roi
contains(float, float) FloatPolygon
Returns 'true' if the point (x,y) is inside this polygon.
contains(int, int) Arrow
contains(int, int) Line
contains(int, int) OvalRoi
Tests if the specified point is inside the boundary of this OvalRoi.
contains(int, int) PointRoi
Returns true if (x,y) is one of the points in this collection.
contains(int, int) PolygonRoi
contains(int, int) Roi
contains(int, int) ShapeRoi
Checks whether the specified coordinates are inside a on this ROI's shape boundaries.
contains(Roi) Overlay
Returns 'true' if this Overlay contains the specified ROI.
CONTINUE MacroConstants
ContrastAdjuster ij.plugin.frame
This plugin implements the Brightness/Contrast, Window/level and
Color Balance commands, all in the Image/Adjust sub-menu.
ContrastAdjuster() ContrastAdjuster
ContrastEnhancer ij.plugin
Implements ImageJ's Process/Enhance Contrast command.
ContrastEnhancer() ContrastEnhancer
controlKeyDown() IJ
Returns true if the control key is down.
controlPanel() SyncWindows
Build window list display and button controls.
ControlPanel ij.plugin
ControlPanel.
ControlPanel() ControlPanel
convert(int) MedianCut
Uses Heckbert's median-cut algorithm to divide the color space defined by
"hist" into "maxcubes" cubes.
convert(ImageProcessor) ThresholdToSelection
Returns a selection created from the thresholded pixels in the
specified image, or null if there are no thresholded pixels.
convert(String) Converter
Converts the ImagePlus to the specified image type.
CONVERT_TO_FLOAT PlugInFilter
Set this flag to have the ImageProcessor that is passed to the run() method
converted to a FloatProcessor.
Converter ij.plugin
Implements the conversion commands in the Image/Type submenu.
Converter() Converter
convertGrayJpegTo8Bits(ImagePlus) Opener
Converts the specified RGB image to 8-bits if the 3 channels are identical.
convertHSBToRGB() ImageConverter
Converts a 3-slice (hue, saturation, brightness) 8-bit stack to RGB.
convertHyperstack(ImagePlus, ImagePlus) RGBStackConverter
convertImagesToStack() ImagesToStack
convertImagesToStack() StackEditor
convertIndexToPosition(int) ImagePlus
Converts the stack index 'n' (one-based) into a hyperstack position (channel, slice, frame).
convertLabToRGB() ImageConverter
Converts a Lab stack to RGB.
convertOutputType(Variable, Object) ExtensionDescriptor
convertRGBStackToRGB() ImageConverter
Converts a 2 or 3 slice 8-bit stack to RGB.
convertRGBtoIndexedColor(int) ImageConverter
Converts an RGB image to 8-bits indexed color.
convertShortcutToCode(String) Menus
convertStackToImages(ImagePlus) StackEditor
convertToByte() TypeConverter
Converts processor to a ByteProcessor.
convertToByte(boolean) ImageProcessor
Returns an 8-bit version of this image as a ByteProcessor.
convertToByte(int) MedianCut
This is a version of convert that returns a ByteProcessor.
convertToByteProcessor() ImageProcessor
Returns an 8-bit version of this image as a ByteProcessor.
convertToByteProcessor(boolean) ImageProcessor
Returns an 8-bit version of this image as a ByteProcessor.
convertToColorProcessor() ImageProcessor
Returns an RGB version of this image as a ColorProcessor.
convertToFloat() ImageStack
Creates a float version of this stack.
convertToFloat() ImageProcessor
Returns a 32-bit float version of this image as a FloatProcessor.
convertToFloat(float[]) TypeConverter
Converts processor to a FloatProcessor.
convertToFloatProcessor() ImageProcessor
Returns a 32-bit float version of this image as a FloatProcessor.
convertToGray16() ImageConverter
Converts this ImagePlus to 16-bit grayscale.
convertToGray16() StackConverter
Converts this Stack to 16-bit grayscale.
convertToGray32() ImageConverter
Converts this ImagePlus to 32-bit grayscale.
convertToGray32() StackConverter
Converts this Stack to 32-bit (float) grayscale.
convertToGray8() ImageConverter
Converts this ImagePlus to 8-bit grayscale.
convertToGray8() StackConverter
Converts this Stack to 8-bit grayscale.
convertToHSB() ImageConverter
Converts an RGB image to a HSB (hue, saturation and brightness) stack.
convertToHSBHyperstack() StackConverter
Converts the stack (which must be RGB) to a 3 channel
(hue, saturation and brightness) hyperstack.
convertToIndexedColor(int) StackConverter
Converts the stack to 8-bits indexed color.
convertToLab() ImageConverter
Converts an RGB image to a Lab stack.
convertToLabHyperstack() StackConverter
Converts the stack (which must be RGB) to a 3 channel
Lab hyperstack.
convertToMicrons Prefs
Convert tiff units to microns if pixel width is less than 0.0001 cm.
convertToRGB() ImageConverter
Converts this ImagePlus to RGB.
convertToRGB() ImageProcessor
Returns an RGB version of this image as a ColorProcessor.
convertToRGB() StackConverter
Converts the Stack to RGB.
convertToRGB() TypeConverter
Converts processor to a ColorProcessor.
convertToRGB(ImagePlus) RGBStackConverter
Converts the specified multi-channel (composite) image to RGB.
convertToRGBHyperstack() StackConverter
Converts the stack (which must be RGB) to a
3 channel (red, green and blue) hyperstack.
convertToRGBStack() ImageConverter
Converts an RGB image to an RGB (red, green and blue) stack.
convertToShort() TypeConverter
Converts processor to a ShortProcessor.
convertToShort(boolean) ImageProcessor
Returns a 16-bit version of this image as a ShortProcessor.
convertToShortProcessor() ImageProcessor
Returns a 16-bit version of this image as a ShortProcessor.
convertToShortProcessor(boolean) ImageProcessor
Returns a 16-bit version of this image as a ShortProcessor.
convertVariable(Interpreter, int, Variable) ExtensionDescriptor
convolve(float[], int, int) ByteProcessor
Performs a convolution operation using the specified kernel.
convolve(float[], int, int) ColorProcessor
Performs a convolution operation using the specified kernel.
convolve(float[], int, int) FloatProcessor
Performs a convolution operation using the specified kernel.
convolve(float[], int, int) ImageProcessor
Performs a convolution operation using the specified kernel.
convolve(float[], int, int) ShortProcessor
Performs a convolution operation using the specified kernel.
convolve(ImageProcessor, float[], int, int) Convolver
Convolves ip with a kernel of width kw and
height kh.
CONVOLVE ImageProcessor
convolve3x3(int[]) ByteProcessor
convolve3x3(int[]) ColorProcessor
3x3 convolution contributed by Glynne Casteel.
convolve3x3(int[]) FloatProcessor
Does 3x3 convolution.
convolve3x3(int[]) ImageProcessor
Convolves the image or ROI with the specified
3x3 integer convolution kernel.
convolve3x3(int[]) ShortProcessor
Does 3x3 convolution.
convolveFloat(ImageProcessor, float[], int, int) Convolver
Convolves the float image ip with a kernel of width
kw and height kh.
convolveFloat1D(FloatProcessor, float[], int, int) Convolver
Convolves the image ip with a kernel of width
kw and height kh.
convolveFloat1D(FloatProcessor, float[], int, int, double) Convolver
Convolves the image ip with a kernel of width
kw and height kh.
Convolver ij.plugin.filter
This plugin convolves images using user user defined kernels.
Convolver() Convolver
Coordinates ij.plugin
The plugin implements the Image/Adjust/Coordinates command.
Coordinates() Coordinates
COORDINATES RoiDecoder
copy HistogramWindow
copy() ImagePlus
Copies the contents of the current selection, or the entire
image if there is no selection, to the internal clipboard.
copy() Calibration
Returns a clone of this object.
copy(boolean) ImageWindow
Copies the current ROI to the clipboard.
copy(boolean) ImagePlus
Copies the contents of the current selection to the internal clipboard.
COPY Blitter
dst=src
COPY_AXIS_STYLE Plot
Flag for copying from a template: copy axis style
COPY_CONTENTS_STYLE Plot
Flag for copying from a template: copy contents style
COPY_INVERTED Blitter
dst=255-src (8-bits and RGB)
COPY_LABELS Plot
Flag for copying from a template: copy style & text of axis labels
COPY_LEGEND Plot
Flag for copying from a template: copy legend
COPY_SIZE Plot
Flag for copying from a template: copy plot size
COPY_TRANSPARENT Blitter
Copies with white pixels transparent.
COPY_ZERO_TRANSPARENT Blitter
Copies with zero pixels transparent.
copyAttributes(Roi) Roi
Copy the attributes (outline color, fill color, outline width)
of 'roi2' to the this selection.
copyAttributes(ImagePlus) ImagePlus
Copies attributes (name, ID, calibration, path, plot) of the specified image to this image.
copyBits(ImageStack, int, int, int) StackProcessor
copyBits(ImageProcessor, int, int, int) Blitter
Copies the image in 'src' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) ByteBlitter
Copies the byte image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) 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) ColorBlitter
Copies the RGB image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) 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) FloatBlitter
Copies the float image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) 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) 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) ShortBlitter
Copies the 16-bit image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) 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) StackProcessor
copyColumnHeaders Prefs
Include column headers when copying tables to clipboard.
copyFile(File, File) Functions
copyFile(String, String) Tools
Copies the contents of the file at 'path1' to 'path2', returning an error message
(as a non-empty string) if there is an error.
copyLuts(ImagePlus) CompositeImage
Copies the LUTs and display mode of 'imp' to this image.
copyScale(ImagePlus) ImagePlus
Copies the calibration of the specified image to this image.
copySelection() TextPanel
Copies the current selection to the system clipboard.
copyToClipboard() HistogramWindow
CORNER_DIAMETER Toolbar
COS MacroConstants
count HistogramWindow
COUNT MaximumFinder
Do not create an image, just count maxima and add count to Results table
COUNTERS_OFFSET RoiDecoder
create() Overlay
Returns a new Overlay that has the same properties as this one.
create(int, int, int, int) ImageStack
Creates a new ImageStack.
create(String, String) Editor
createBlankImage(int, int) GUI
Creates a white AWT Image image of the specified size.
createByteImage(String, int, int, int, int) NewImage
createColorModel(FileInfo) FileOpener
Returns an IndexColorModel for the image specified by this FileInfo.
createComposite(int, int, int, ImageStack[], boolean) RGBStackMerge
Deprecated; replaced by mergeChannels().
CREATED RoiListener
createEmptyStack() ImagePlus
Returns an empty image stack that has the same
width, height and color table as this image.
createFloatImage(String, int, int, int, int) NewImage
createGrayscaleColorModel(boolean) LookUpTable
createHyperStack(String, int, int, int, int) ImagePlus
This method has been replaced by IJ.createHyperStack().
createHyperStack(String, int, int, int, int, int, int) IJ
Creates a new hyperstack.
createImage() ByteProcessor
createImage() ColorProcessor
createImage() FloatProcessor
Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage() ImageProcessor
Returns a copy of this image is the form of an AWT Image.
createImage() ShortProcessor
Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage(IndexColorModel) LutLoader
Creates a 256x32 image from an IndexColorModel.
createImage(String, int, int, int, int) IJ
Creates a new image.
createImage(String, int, int, int, int, int) NewImage
createImage(String, String, int, int, int) IJ
Creates a new imagePlus.
createImage(String, String, int, int, int, int, int) IJ
Creates a new hyperstack.
createImagePlus() ImagePlus
Returns a new ImagePlus with this image's attributes
(e.g.
createInputStream(FileInfo) FileOpener
Returns an InputStream for the image described by this FileInfo.
createInvertedLut() LUT
createLut() ImagePlus
Creates a LookUpTable object that corresponds to this image.
createLutFromColor(Color) CompositeImage
createLutFromColor(Color) LUT
Creates a color LUT from a Color.
createMacro(String) NewPlugin
createMacro(String, String) Editor
createMask() ByteProcessor
Returns a binary mask, or null if a threshold is not set.
createMask() FloatProcessor
Returns a binary mask, or null if a threshold is not set.
createMask() ImageProcessor
Returns a binary mask, or null if a threshold is not set or this is an RGB image.
createMask() ShortProcessor
Returns a binary mask, or null if a threshold is not set.
createMask(ImagePlus) Thresholder
Returns an 8-bit binary (0 and 255) threshold mask
that has the same dimensions as this image.
createNewRoi(int, int) ImagePlus
Starts the process of creating a new selection, where sx and sy are the
starting screen coordinates.
createOverlay() OverlayLabels
Creates an empty Overlay that has the current label settings.
createPlugin(String, int, String) NewPlugin
createProcessor(int, int) ByteProcessor
Returns a new, blank ByteProcessor with the specified width and height.
createProcessor(int, int) ColorProcessor
Returns a new, blank ColorProcessor with the specified width and height.
createProcessor(int, int) FloatProcessor
Returns a new, blank FloatProcessor with the specified width and height.
createProcessor(int, int) ImageProcessor
Returns a new, blank processor with the specified width and height.
createProcessor(int, int) ShortProcessor
Returns a new, blank ShortProcessor with the specified width and height.
createRGBImage(String, int, int, int, int) NewImage
createRoiMask() ImagePlus
Returns an 8-bit binary (0 and 255) ROI or overlay mask
that has the same dimensions as this image.
createShortImage(String, int, int, int, int) NewImage
Creates an unsigned short image.
createSubtitle() ImageWindow
Creates the subtitle.
createSubtitle() StackWindow
createTableFromImage(ImageProcessor) ResultsTable
Creates a ResultsTable from an image or image selection.
createThreadArray() ThreadUtil
createThreadArray(int) ThreadUtil
createThresholdMask() ImagePlus
Returns an 8-bit binary (0 and 255) threshold mask
that has the same dimensions as this image.
createUnsignedShortImage(String, int, int, int, int) NewImage
Deprecated.
createWindow() ProfilePlot
Displays this profile plot in a window.
crop() ImagePlus
Returns a copy this image or stack slice, cropped if there is an ROI.
crop() ByteProcessor
crop() ColorProcessor
crop() FloatProcessor
crop() ImageProcessor
Returns a new processor containing an image
that corresponds to the current ROI.
crop() ShortProcessor
crop(int, int) Overlay
Removes ROIs having positions outside of the
interval defined by firstSlice and lastSlice.
crop(int, int, int, int) StackProcessor
Crops the stack to the specified rectangle.
crop(int, int, int, int, int, int) Overlay
Removes ROIs having a C, Z or T coordinate outside the volume
defined by firstC, lastC, firstZ, lastZ, firstT and lastT.
crop(int, int, int, int, int, int) ImageStack
Creates a new stack by cropping this one.
crop(ImagePlus) Duplicator
Returns a copy the current stack image, cropped if there is a selection.
crop(Rectangle) Overlay
cropOverlay(Overlay, Rectangle) Duplicator
CROSS Plot
Display points using an cross-shaped mark.
CROSS PlotWindow
Display points using an cross-shaped mark.
CROSSHAIR Toolbar
crosshairCursor ImageCanvas
cScaling SyncWindows
Checkboxes for user control.
cSelector StackWindow
cSlice SyncWindows
Checkboxes for user control.
cTable ImageProcessor
CTZ HyperStackConverter
cubic(double) ImageProcessor
currentMacroEditor Editor
currentMemory() IJ
Returns the amount of memory currently being used by ImageJ.
currentSlice ImagePlus
cursorOverImage() ImageCanvas
Returns 'true' if the cursor is over this image.
CurveFitter ij.measure
Curve fitting class based on the Simplex method in the Minimizer class
Notes on fitting polynomial functions:
(i) The range of x values should not be too far from 0, especially for higher-order polynomials.
CurveFitter(double[], double[]) CurveFitter
Construct a new CurveFitter.
CUSTOM Plot
Draw shape using macro code
CUSTOM Opener
CUSTOM Calibration
CUSTOM1 Toolbar
CUSTOM2 Toolbar
CUSTOM3 Toolbar
CUSTOM4 Toolbar
CUSTOM5 Toolbar
CUSTOM6 Toolbar
CUSTOM7 Toolbar
cx ImageProcessor
cy ImageProcessor
CZT HyperStackConverter
gamma(double) FloatProcessor
gamma(double) ImageProcessor
Performs gamma correction of the image or ROI.
gamma(double) ShortProcessor
GAMMA_VARIATE Calibration
GAMMA_VARIATE CurveFitter
Constants for the built-in fit functions
gapBetweenImages FileInfo
GAUSSIAN Calibration
GAUSSIAN CurveFitter
Constants for the built-in fit functions
GAUSSIAN_NOOFFSET CurveFitter
Constants for the built-in fit functions
GaussianBlur ij.plugin.filter
This plug-in filter uses convolution with a Gaussian function for smoothing.
GaussianBlur() GaussianBlur
GaussianBlur3D ij.plugin
GaussianBlur3D() GaussianBlur3D
GelAnalyzer ij.plugin
This plugin generates gel profile plots that can be analyzed using
the wand tool.
GelAnalyzer() GelAnalyzer
GenericDialog ij.gui
This class is a customizable modal dialog box.
GenericDialog(String) GenericDialog
Creates a new GenericDialog with the specified title.
GenericDialog(String, Frame) GenericDialog
Creates a new GenericDialog using the specified title and parent frame.
get(int) Overlay
Returns the ROI with the specified index or null if the index is invalid.
get(int) ByteProcessor
get(int) ColorProcessor
get(int) FloatProcessor
get(int) ImageProcessor
get(int) ShortProcessor
get(int, int) ByteProcessor
get(int, int) ColorProcessor
get(int, int) FloatProcessor
get(int, int) ImageProcessor
This is a faster version of getPixel() that does not do bounds checking.
get(int, int) ShortProcessor
get(String, boolean) Prefs
Uses the keyword key to retrieve a boolean from
the preferences file.
get(String, double) Prefs
Uses the keyword key to retrieve a number from the
preferences file.
get(String, String) Prefs
Uses the keyword key to retrieve a string from the
preferences file.
GET_ARGUMENT MacroConstants
GET_BOOLEAN MacroConstants
GET_BOUNDING_RECT MacroConstants
GET_BOUNDS MacroConstants
GET_COORDINATES MacroConstants
GET_COUNT MacroConstants
GET_CURSOR_LOC MacroConstants
GET_DATE_AND_TIME MacroConstants
GET_DIMENSIONS MacroConstants
GET_DIRECTORY MacroConstants
GET_DISPLAYED_AREA MacroConstants
GET_FILE_LIST MacroConstants
GET_FONT_LIST MacroConstants
GET_HEIGHT MacroConstants
GET_HISTOGRAM MacroConstants
GET_ID MacroConstants
GET_IMAGE_INFO MacroConstants
GET_INFO MacroConstants
GET_LINE MacroConstants
GET_LIST MacroConstants
GET_LOCATION_AND_SIZE MacroConstants
GET_LUT MacroConstants
GET_METADATA MacroConstants
GET_MIN_AND_MAX MacroConstants
GET_NUMBER MacroConstants
GET_PIXEL MacroConstants
GET_PIXEL_SIZE MacroConstants
GET_PROFILE MacroConstants
GET_RAW_STATISTICS MacroConstants
GET_RESULT MacroConstants
GET_RESULT_LABEL MacroConstants
GET_RESULT_STRING MacroConstants
GET_SLICE_NUMBER MacroConstants
GET_STATISTICS MacroConstants
GET_STRING MacroConstants
GET_STRING_WIDTH MacroConstants
GET_THRESHOLD MacroConstants
GET_TIME MacroConstants
GET_TITLE MacroConstants
GET_VALUE MacroConstants
GET_VERSION MacroConstants
GET_VOXEL_SIZE MacroConstants
GET_WIDTH MacroConstants
GET_ZOOM MacroConstants
get16BitBufferedImage() ShortProcessor
Returns a copy of this image as a TYPE_USHORT_GRAY BufferedImage.
get16bitRangeIndex() ContrastAdjuster
getActiveChannels() CompositeImage
getActiveWindow() WindowManager
Returns the front most window or null.
getAdditionalFunctions() Interpreter
getAllNonImageWindows() WindowManager
Returns an array containing a list of the non-image Frames and Dialogs.
getAllStatistics() ImagePlus
This method returns complete calibrated statistics for this image or ROI
(with "Limit to threshold"), but it is up to 70 times slower than getStatistics().
getAngle() Line
getAngle() PolygonRoi
Returns the angle in degrees between the first two segments of this polyline.
getAngle() Roi
Overridden by PolygonRoi (angle between first two points), TextRoi (text angle) and Line (line angle).
getAngle() TextRoi
getAngle(int, int, int, int) Roi
Returns the angle in degrees between the specified line and a horizontal line.
getAnimate() StackWindow
getAntialiased() TextRoi
Returns the state of the 'antialiased' instance variable.
getApplet() IJ
Returns the Applet that created this ImageJ or null if running as an application.
getArgs() ImageJ
Returns the command line arguments passed to ImageJ.
getAutoThreshold() ImageProcessor
Returns a pixel value (threshold) that can be used to divide the image into objects
and background.
getAutoThreshold(int[]) ImageProcessor
This is a version of getAutoThreshold() that uses a histogram passed as an argument.
getBackgroundColor() Toolbar
getBackgroundValue() ByteProcessor
Returns the background fill value.
getBackgroundValue() ColorProcessor
Returns the background fill value.
getBackgroundValue() FloatProcessor
Always returns 0.
getBackgroundValue() ImageProcessor
Returns the background fill value.
getBackgroundValue() ShortProcessor
Always returns 0.
getBatchModeImage(int) Interpreter
getBatchModeImageCount() Interpreter
getBatchModeImageIDs() Interpreter
getBatchModeRoiManager() Interpreter
Returns the batch mode RoiManager instance.
getBestIndex(Color) ColorProcessor
Always returns 0 since RGB images do not use LUTs.
getBestIndex(Color) ImageProcessor
Returns the LUT index that's the best match for this color.
getBicubicInterpolatedPixel(double, double, ImageProcessor) 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) 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() PlotVirtualStack
Returns either 24 (RGB) or 8 (grayscale).
getBitDepth() ImagePlus
Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth
is unknown.
getBitDepth() ImageStack
Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).
getBitDepth() ByteProcessor
getBitDepth() ColorProcessor
getBitDepth() FloatProcessor
getBitDepth() ImageProcessor
Returns the bit depth, 8, 16, 24 (RGB) or 32.
getBitDepth() ShortProcessor
getBitDepth() VirtualStack
Returns the bit depth (8, 16, 24 or 32), or 0 if the bit depth is not known.
getBits(int) BitBuffer
getBlockIncrement() ScrollbarWithLabel
getBlue(String) Colors
getBlues() LookUpTable
getBoolean(String, boolean) Prefs
Finds a boolean in IJ_Props or IJ_Prefs.txt.
getBoundingRect() Roi
Deprecated.
getBounds() Arrow
Return the bounding rectangle of this arrow.
getBounds() Line
Return the bounding rectangle of this line.
getBounds() Roi
Return this selection's bounding rectangle.
getBounds() FloatPolygon
getBrightness() ColorProcessor
Returns brightness as a FloatProcessor.
getBrushSize() Toolbar
Returns the size of the selection brush tool, or 0 if the brush tool is not enabled.
getBufferedImage() ImagePlus
Returns a copy of this image as an 8-bit or RGB BufferedImage.
getBufferedImage() ByteProcessor
Returns this image as a BufferedImage.
getBufferedImage() FloatProcessor
Returns this image as an 8-bit BufferedImage.
getBufferedImage() ImageProcessor
Returns this image as a BufferedImage.
getBufferedImage() ShortProcessor
Returns this image as an 8-bit BufferedImage .
getButton() WaitForUserDialog
Returns a reference to the 'OK' button
getButtons() GenericDialog
Returns references to the "OK" ("Yes"), "Cancel",
and if present, "No" buttons as an array.
getButtonSize() Toolbar
Returns the button width (button spacing).
getBytes() LUT
getBytesPerPixel() ImagePlus
Returns the number of bytes per pixel.
getBytesPerPixel() FileInfo
Returns the number of bytes used per pixel.
getC() ImagePlus
Returns the current hyperstack channel position.
getCalibration() ImagePlus
Returns this image's calibration.
getCalibrationTable() ImageProcessor
Returns the calibration table or null.
getCanvas() ImageWindow
getCanvas() ImagePlus
Returns the ImageCanvas being used to
display this image, or null.
getCaseSensitive() WildcardMatch
Returns the current state of case sensitivity.
getChannel() ImagePlus
getChannel(int) ColorProcessor
Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a byte array.
getChannel(int, ByteProcessor) ColorProcessor
Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a ByteProcessor.
getChannel(ImagePlus, int) ChannelSplitter
Returns, as an ImageStack, the specified channel, where 'c' must be greater
than zero and less than or equal to the number of channels in the image.
getChannelColor() CompositeImage
getChannelLut() CompositeImage
getChannelLut(int) CompositeImage
getChannelProcessor() CompositeImage
getChannelProcessor() ImagePlus
Returns a reference to the current ImageProcessor.
getCheckboxes() GenericDialog
Returns the Vector containing the Checkboxes.
getChoices() GenericDialog
Returns the Vector containing the Choices.
getClassLoader() IJ
Returns the class loader ImageJ uses to run plugins or the
system class loader if Menus.getPlugInsPath() returns null.
getClipboard() ImagePlus
Returns the internal clipboard or null if the internal clipboard is empty.
getClosestPoint(double, double, FloatPolygon) PointRoi
getClosestPoint(double, double, FloatPolygon) PolygonRoi
getCode() FileInfo
Returns JavaScript code that can be used to recreate this FileInfo.
getCode() Program
getCoefficients() Calibration
Returns the calibration function coefficients.
getColor() ColorChooser
Displays a color selection dialog and returns the color selected by the user.
getColor() Roi
Returns the default (global) color used for drawing ROI outlines.
getColor() Toolbar
Deprecated.
getColor(int, int) ColorProcessor
getColor(String, Color) Colors
getColor(String, Color) Prefs
Finds a color in IJ_Props or IJ_Prefs.txt.
getColorModel() ImageStack
Returns this stack's color model.
getColorModel() LookUpTable
getColorModel() ImageProcessor
Returns this processor's color model.
getColorModel() LUT
getColorName(Color, String) Colors
getColors(String...) Colors
getColumn(int) ResultsTable
Returns a copy of the given column as a float array,
or null if the column is empty.
getColumn(int, int, int[], int) ImageProcessor
Returns the pixel values down the column starting at (x,y).
getColumnAsDoubles(int) ResultsTable
Returns a copy of the given column as a double array,
or null if the column is empty.
getColumnAsVariables(String) ResultsTable
Implements the Table.getColumn() macro function.
getColumnAverageProfile(Rectangle, ImageProcessor) ProfilePlot
getColumnHeading(int) ResultsTable
Returns the heading of the specified column or null if the column is empty.
getColumnHeadings() ResultsTable
Returns a tab or comma delimited string containing the column headings.
getColumnHeadings() TextPanel
Returns the column headings as a tab-delimited string.
getColumnIndex(String) ResultsTable
Returns the index of the first column with the given heading.
getCommand() Executer
Returns the last command executed.
getCommand() Recorder
Returns the name of the command currently being recorded, or null.
getCommandName() ImageJ
getCommandOptions() Recorder
Used by GenericDialog to determine if any options have been recorded.
getCommands() Menus
Returns the hashtable that associates commands with plugins.
getCompletedMinimizations() Minimizer
Get number of minimizations completed (i.e.
getComplexTransform() FHT
Converts this FHT to a complex Fourier transform and returns it as a two slice stack.
getCompositeMode() ImagePlus
Returns the display mode (IJ.COMPOSITE, IJ.COLOR
or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.
getContainedFloatPoints() PointRoi
Returns the points as a FloatPolygon.
getContainedFloatPoints() Roi
Returns the coordinates of the pixels inside this ROI as a FloatPolygon.
getContainedPoints() PointRoi
Returns the points as an array of Points.
getContainedPoints() Roi
Returns the coordinates of the pixels inside this ROI as an array of Points.
getContourCentroid() Roi
getControlPanelProperties() Prefs
getConvexHull() PolygonRoi
Uses the gift wrap algorithm to find the
convex hull and returns it as a Polygon.
getConvexHull() Roi
getConvexHull() ShapeRoi
getCopy() FHT
Returns a clone of this FHT.
getCornerDiameter() Roi
Returns the rounded rectangle corner diameter (pixels).
getCount() RoiManager
Returns the ROI count.
getCount(int) PointRoi
getCounter() PointRoi
getCounter() ResultsTable
Returns the current value of the measurement counter.
getCounter() Analyzer
Returns the current measurement count.
getCounter(int) PointRoi
Returns the counter assocated with the specified point.
getCounterChoices() PointRoi
getCounterInfo() PointRoi
getCounters() PointRoi
getCPosition() Roi
Returns the channel position of this ROI, or zero
if this ROI is not associated with a particular channel.
getCrossLoc() Orthogonal_Views
getCTable() Calibration
Returns the calibration table.
getCurrentColorModel() ImageProcessor
Returns the current color model, which may have
been modified by setMinAndMax() or setThreshold().
getCurrentErrStream() LogStream
Returns the redirection stream for System.err if it exists.
getCurrentFont() TextRoi
Returns the current (instance) font.
getCurrentImage() WindowManager
Returns a reference to the active image or null if there isn't one.
getCurrentOutStream() LogStream
Returns the redirection stream for System.out if it exists.
getCurrentPasteMode() Roi
Returns the current paste transfer mode.
getCurrentSlice() ImagePlus
Returns the current stack index (one-based) or 1 if this is a single image.
getCurrentWindow() WindowManager
Returns the active ImageWindow.
getCursorLoc() ImageCanvas
Returns the current cursor location in image coordinates.
getCustomRoi() ImageCanvas
getCValue(double) Calibration
Converts a raw pixel value to a density calibrated value.
getCValue(int) Calibration
Converts a raw pixel value to a density calibrated value.
getDebugger() Interpreter
getDebugInfo() PolygonRoi
getDebugInfo() Roi
getDecimalPlaces(double) Tools
Returns the number of decimal places needed to display a
number, or -2 if exponential notation should be used.
getDecimalPlaces(double, double) Tools
Returns the number of decimal places needed to display two numbers,
or -2 if exponential notation should be used.
getDefault16bitRange() ImagePlus
Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 14, 15 or 16.
getDefaultColorModel() ImageProcessor
Returns the default grayscale IndexColorModel.
getDefaultCrossColor() PointRoi
Deprecated
getDefaultDirectory() OpenDialog
Returns the current working directory, which may be null.
getDefaultDirectory() Prefs
Returns the default directory, if any, or null.
getDefaultDoubleHeaded() Arrow
getDefaultFillColor() Roi
getDefaultFlags() Plot
The default flags, taking PlotWindow.noGridLines, PlotWindow.noTicks into account
getDefaultHeading(int) ResultsTable
getDefaultHeadSize() Arrow
getDefaultMarkerSize() PointRoi
Deprecated.
getDefaultOutline() Arrow
getDefaultSize() PointRoi
getDefaultStrokeColor() RectToolOptions
getDefaultStrokeWidth() RectToolOptions
getDefaultStyle() Arrow
getDefaultType() PointRoi
getDefaultWidth() Arrow
getDescriptionString() FileSaver
Returns a string containing information about the specified image.
getDimensions() ImagePlus
Returns the dimensions of this image (width, height, nChannels,
nSlices, nFrames) as a 5 element int array.
getDimensions(boolean) ImagePlus
getDir(String) IJ
Alias for getDirectory().
getDir(String) Opener
getDir(String) Macro
getDirectory() DirectoryChooser
Returns the directory selected by the user.
getDirectory() OpenDialog
Returns the selected directory.
getDirectory() SaveDialog
Returns the selected directory.
getDirectory() Functions
getDirectory() VirtualStack
Returns the path to the directory containing the images.
getDirectory(String) 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", "default", "image", otherwise,
displays a dialog and returns the path to the directory selected by the user.
getDisplayList() ImageCanvas
Deprecated.
getDisplayMode() ImagePlus
Returns the display mode (IJ.COMPOSITE, IJ.COLOR
or IJ.GRAYSCALE) if this is a composite color
image, or 0 if it not.
getDisplayRangeMax() CompositeImage
getDisplayRangeMax() ImagePlus
getDisplayRangeMin() CompositeImage
getDisplayRangeMin() ImagePlus
getDoScaling() ImageConverter
Returns true if scaling is enabled.
getDouble(String, double) Prefs
Looks up a real number in IJ_Props or IJ_Prefs.txt.
getDoubleFromArrayList(ArrayList) Plot
getDoubleHeaded() Arrow
getDrawBackgrounds() Overlay
getDrawingFrame() Plot
Returns the rectangle where the data are plotted.
getDrawLabels() Overlay
getDrawLabels() RoiManager
getDrawNames() Overlay
getDrawOffset() Line
getDrawOffset() PolygonRoi
getDrawOffset() Roi
Returns true if this is a PolygonRoi that supports sub-pixel
resolution and polygons are drawn on zoomed images offset
down and to the right by 0.5 pixels..
getDrawStringMode() TextRoi
getEditor() NewPlugin
Returns the Editor the newly created macro or plugin was opened in.
getErrorMessage() GenericDialog
Returns an error message if getNextNumber was unable to convert a
string into a number, otherwise, returns null.
getErrorMessage() IJ
Returns the last error message written by IJ.error() or null if there
was no error since the last time this method was called.
getErrorText() AVI_Reader
Returns a description of the error reading the file with makeStack or null if no error
getEscapeChar() WildcardMatch
Returns the character used to escape the wildcard functionality of a
wildcard character.
getExamplesMenu(ActionListener) Menus
getExtensionFunctions() MacroExtension
getf(int) ByteProcessor
getf(int) ColorProcessor
getf(int) FloatProcessor
getf(int) ImageProcessor
getf(int) ShortProcessor
getf(int, int) ByteProcessor
getf(int, int) ColorProcessor
getf(int, int) FloatProcessor
getf(int, int) ImageProcessor
Returns the value of the pixel at (x,y) as a float.
getf(int, int) ShortProcessor
getFeretsDiameter() Roi
Returns Feret's diameter, the greatest distance between
any two points along the ROI boundary.
getFeretValues() EllipseRoi
getFeretValues() Roi
Caculates "Feret" (maximum caliper width), "FeretAngle"
and "MinFeret" (minimum caliper width), "FeretX" and "FeretY".
getFeretValues() ShapeRoi
Caculates "Feret" (maximum caliper width) and "MinFeret" (minimum caliper width).
getFileFormat(String) Opener
getFileInfo() ImagePlus
Returns a FileInfo object containing information, including the
pixel array, needed to save this image.
getFileInfo() ImportDialog
Displays the dialog and returns a FileInfo object that can be used to
open the image.
getFileName() OpenDialog
Returns the selected file name.
getFileName() SaveDialog
Returns the selected file name.
getFileName() MacroInstaller
getFileName(int) VirtualStack
Returns the file name of the specified slice, were 1<=n<=nslices.
getFilePath() Macro_Runner
Returns the file path of the most recently loaded macro or script.
getFilePath(String) IJ
Displays an open file dialog and returns the path to the
choosen file, or returns null if the dialog is canceled.
getFilePointer() RandomAccessStream
getFileSeparator() Prefs
Returns the file.separator system property.
getFileType(String) Opener
Attempts to determine the image file type by looking for
'magic numbers' and the file name extension.
getFillColor() Roi
Returns the fill color used to display this ROI, or null if it is displayed transparently.
getFilteredList(String[], String, String) FolderOpener
getFit() CurveFitter
returns the code of the fit type of the fit performed
getFitCode(String) CurveFitter
Returns the code for a fit with given name as defined in fitList, or -1 if not found
getFitGoodness() CurveFitter
Get a measure of "goodness of fit" where 1.0 is best.
getFixedMax() ProfilePlot
Returns the profile plot y-axis max.
getFixedMin() ProfilePlot
Returns the profile plot y-axis min.
getFlags() Plot
Returns the flags that control the axes
getFloatAngle(double, double, double, double) Roi
Returns the angle in degrees between the specified line and a horizontal line.
getFloatArray() ImageProcessor
Returns a copy of the pixel data as a 2D float
array with dimensions [x=0..width-1][y=0..height-1].
getFloatBounds() Roi
Return this selection's bounding rectangle.
getFloatBounds() FloatPolygon
getFloatHeight() Roi
getFloatPoints() Line
Returns, as a FloatPolygon, the two points that define this line.
getFloatPolygon() Line
If the width of this line is less than or equal to one, returns the
starting and ending coordinates as a 2-point FloatPolygon, or, if
the width is greater than one, returns an outline of the line as
a 4-point FloatPolygon.
getFloatPolygon() OvalRoi
Returns this OvalRoi as a FloatPolygon.
getFloatPolygon() PolygonRoi
Returns this polygon or polyline as float arrays.
getFloatPolygon() Roi
getFloatPolygon() ShapeRoi
getFloatWidth() Roi
getFont() TextRoi
Returns the name of the global (default) font.
getFont() Menus
getFont() ImageProcessor
Returns the current font.
getFont(String, int, float) FontUtil
Returns a font with the given family name or, if not available, a similar font, e.g.
getFontMetrics() ImageProcessor
Returns the current FontMetrics.
getFontSize() Menus
Returns the size (in points) used for the fonts in ImageJ menus.
getForegroundColor() Toolbar
getFormula() CurveFitter
returns a String with the formula of the fit function used
getFrame() ImagePlus
getFrame(String) WindowManager
Obsolete; replaced by getWindow().
getFrameRate() Animator
Returns the current animation speed in frames per second.
getFreeColumn(String) ResultsTable
Sets the heading of the the first available column and
returns that column's index.
getFrontWindow() WindowManager
Obsolete; replaced by getActiveWindow.
getFullVersion() IJ
Returns the ImageJ version and build number as a String, for
example "1.46n05", or 1.46n99 if there is no build number.
getFunction() Calibration
Returns the calibration function ID.
getFunctionValue() Minimizer
Get the value of the minimum, i.e.
getGelImage() GelAnalyzer
getGlobalCalibration() ImagePlus
Returns the system-wide calibration, or null.
getGlobalJustification() TextRoi
Returns the global (default) justification (LEFT, CENTER or RIGHT).
getGlobals() Program
getGreen(String) Colors
getGreens() LookUpTable
getHashCode() Roi
Returns a hashcode for this Roi that typically changes
if it is moved, even though it is still the same object.
getHeader(ImagePlus) FITS_Writer
Extracts the original FITS header from the Properties object of the
ImagePlus image (or from the current slice label in the case of an ImageStack)
and returns it as an array of String objects representing each card.
getHeadings() ResultsTable
Returns the column headings as an array of Strings.
getHeadingsAsVariableNames() ResultsTable
Returns the column headings; headings not suitable as variable names are converted
to valid variable names by replacing non-fitting characters with underscores and
adding underscores.
getHeadSize() Arrow
getHeight() ImagePlus
getHeight() ImageStack
getHeight() AVI_Reader
Returns the image height of the virtual stack
getHeight() FileInfoVirtualStack
getHeight() ListVirtualStack
getHeight() ImageProcessor
Returns the height of this image in pixels.
getHideOverlay() ImagePlus
getHigherZoomLevel(double) ImageCanvas
getHistogram() HistogramWindow
getHistogram() ByteProcessor
getHistogram() ColorProcessor
getHistogram() FloatProcessor
Returns a 256 bin histogram of the current ROI or of the entire image if there is no ROI.
getHistogram() ImageProcessor
Returns the histogram of the image or ROI.
getHistogram() ImageStatistics
Returns the histogram as an array of longs.
getHistogram() ShortProcessor
Returns 65,536 bin histogram of the current ROI, which
can be non-rectangular.
getHistogram(int) ImageProcessor
Returns the histogram of the image or ROI, using the specified number of bins.
getHistogram(ImageProcessor) ByteProcessor
getHistogram(ImageProcessor) ColorProcessor
getHistogramMax() ImageProcessor
Returns the maximum histogram value used for histograms of float images.
getHistogramMin() ImageProcessor
Returns the minimum histogram value used for histograms of float images.
getHistogramSize() ImageProcessor
Returns the number of float image histogram bins.
getHomeDir() Prefs
Obsolete, replaced by getImageJDir(), which, unlike this method,
returns a path that ends with File.separator.
getHSB(byte[], byte[], byte[]) ColorProcessor
Returns hue, saturation and brightness in 3 byte arrays.
getHSBStack() ColorProcessor
Returns an ImageStack with three 8-bit slices,
representing hue, saturation and brightness
getID() ImagePlus
Returns this image's unique numeric ID.
getIDList() WindowManager
Returns a list of the IDs of open images.
getImage() CompositeImage
getImage() ImageCanvas
Returns the ImagePlus object that is associated with this ImageCanvas.
getImage() Roi
Returns the ImagePlus associated with this ROI, or null.
getImage() IJ
Returns a reference to the active image, or displays an error
message and aborts the plugin or macro if no images are open.
getImage() ImagePlus
Returns this image as a AWT image.
getImage() Orthogonal_Views
getImage(int) WindowManager
For IDs less than zero, returns the ImagePlus with the specified ID.
getImage(String) WindowManager
Returns the first image that has the specified title or null if it is not found.
getImageArray() ImageStack
Returns the stack as an array of 1D pixel arrays.
getImageArray() VirtualStack
Returns null.
getImageCount() WindowManager
Returns the number of open images.
getImageFromVector(int) SyncWindows
Get ImagePlus from Windows-Vector vwins.
getImageID() Roi
Returns the ID of the image associated with this ROI.
getImageID() Orthogonal_Views
getImageInfo(ImagePlus) ImageInfo
getImageInfo(ImagePlus, ImageProcessor) Info
Deprecated.
getImageJDir() Prefs
Returns the path, ending in File.separator, to the ImageJ directory.
getImageJMenu(String) Menus
Returns the specified ImageJ menu (e.g., "File>New") or null if it is not found.
getImagePlus() ImageWindow
getImagePlus() Plot
Returns the plot as an ImagePlus.
getImagePlus() AVI_Reader
Returns the ImagePlus opened by run().
getImageSize(ImagePlus) ImageWindow
getImageStack() ImagePlus
Returns the base image stack.
getImageStackSize() ImagePlus
If this is a stack, returns the actual number of images in the stack, else returns 1.
getImagesURL() Prefs
Returns the URL of the directory that contains the ImageJ sample images.
getImageTitleFromVector(int) SyncWindows
Get the title of image n from Windows-Vector vwins.
getImageTitles() WindowManager
Returns a list of the titles of all open images.
getImports() PlugInInterpreter
Returns the import statements that are added to the script.
getIndex(String) Overlay
Returns the index of the ROI with the specified name, or -1 if not found.
getIndexes() RoiManager
Returns an array of the selected indexes or all indexes if none are selected.
getIndexesAsString() RoiManager
This is a macro-callable version of getSelectedIndexes().
getIndexOfImage(ImagePlus) SyncWindows
Get index of "image" in vector of synchronized windows, if image is in vector.
getIndexSampleModel() ImageProcessor
getInfo() ImageJ
getInfo(String) DICOM
Returns the DICOM tags of the specified file as a string.
getInfoProperty() ImagePlus
Returns the "Info" property string, or null if it is not found.
getInitialMagnification() ImageWindow
getInsets() GenericDialog
getInsets() ImageWindow
Override Container getInsets() to make room for some text above the image.
getInsets() SyncWindows
getInstance() GenericDialog
getInstance() Toolbar
Returns a reference to the ImageJ toolbar.
getInstance() IJ
Returns a reference to the "ImageJ" frame.
getInstance() Interpreter
getInstance() Channels
Obsolete; always returns null.
getInstance() Editor
getInstance() Recorder
getInstance() RoiManager
Returns a reference to the ROI Manager, or null if it is not open
and a batch mode macro is not running.
getInstance() SyncWindows
getInstance() Orthogonal_Views
getInstance2() RoiManager
Returns a reference to the ROI Manager window or to the
macro batch mode RoiManager, or null if neither exists.
getInt(String, int) Prefs
Finds an int in IJ_Props or IJ_Prefs.txt.
getInt(Properties, String) OtherInstance
getIntArray() ImageProcessor
Returns a copy of the pixel data as a 2D int array with
dimensions [x=0..width-1][y=0..height-1].
getInterpolate() ImageProcessor
Returns the value of the interpolate field.
getInterpolatedPixel(double, double) ByteProcessor
Uses the current interpolation method (BILINEAR or BICUBIC)
to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) ColorProcessor
Calls getPixelValue(x,y).
getInterpolatedPixel(double, double) FloatProcessor
Uses the current interpolation method (BILINEAR or BICUBIC)
to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) ImageProcessor
Uses the current interpolation method (bilinear or bicubic)
to find the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) ShortProcessor
Uses the current interpolation method (BILINEAR or BICUBIC)
to calculate the pixel value at real coordinates (x,y).
getInterpolatedPolygon() Roi
Returns, as a FloatPolygon, an interpolated version
of this selection that has points spaced 1.0 pixel apart.
getInterpolatedPolygon(double, boolean) PolygonRoi
getInterpolatedPolygon(double, boolean) Roi
Returns, as a FloatPolygon, an interpolated version of
this selection with points spaced 'interval' pixels apart.
getInterpolatedPolygon(FloatPolygon, double, boolean) Roi
Returns, as a FloatPolygon, an interpolated version of this selection
with points spaced abs('interval') pixels apart.
getInterpolatedRGBPixel(double, double) ColorProcessor
Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedValue(double, double) ImageProcessor
Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolationMethod() ImageProcessor
Returns the current interpolation method (NONE, BILINEAR or BICUBIC).
getInterpolationMethods() ImageProcessor
getInvertY() Calibration
Returns the 'invertY' flag.
getIterations() CurveFitter
Get number of iterations performed.
getIterations() Minimizer
Get number of iterations performed (includes all restarts).
getJarFileForMenuEntry(String) Menus
getJpegQuality() FileSaver
Returns the current JPEG quality setting (0-100).
getJSPrefix(String) Editor
getJustification() TextRoi
Returns the value of the 'justification' instance variable (LEFT, CENTER or RIGHT).
getLab(ImageProcessor, byte[], byte[], byte[]) ColorThresholder
Returns Lab in 3 byte arrays.
getLabel(char) Plot
Gets the label String of the xLabel ('x'), yLabel('y') or the legend ('l').
getLabel(int) ResultsTable
Returns the label of the specified row.
getLabelColor() Overlay
getLabelFont() Overlay
getLastBatchModeImage() Interpreter
getLastColumn() ResultsTable
Returns the index of the last used column, or -1 if no columns are used.
getLastDirectory() OpenDialog
Returns the path to the directory that contains the last file
opened, or null if a file has not been opened.
getLastFileInfo() ImportDialog
Returns the FileInfo object used to import the last raw image,
or null if a raw image has not been imported.
getLastName() 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() EllipseRoi
Returns the perimeter of this ellipse.
getLength() Line
Returns the length of this line.
getLength() OvalRoi
Returns the perimeter length.
getLength() PolygonRoi
Returns the perimeter (for ROIs) or length (for lines).
getLength() Roi
Returns the perimeter length.
getLength() ShapeRoi
Returns the perimeter if this ShapeRoi can be decomposed
into simple ROIs, otherwise returns zero.
getLength(boolean) FloatPolygon
getLimits() Plot
Returns the current limits as an array xMin, xMax, yMin, yMax.
getLine(double, double, double, double) ImageProcessor
Returns an array containing the pixel values along the
line starting at (x1,y1) and ending at (x2,y2).
getLine(int) TextPanel
Returns the specified line as a string.
getLineCount() TextPanel
Returns the number of lines of text in this TextPanel.
getLineNumber() Interpreter
getLineWidth() ImageProcessor
Returns the current line width.
getList() RoiManager
Deprecated.
getListenerCount() Executer
getLoadRate(double, ImagePlus) Opener
getLocalCalibration() ImagePlus
Returns this image's local calibration, ignoring
the "Global" calibration flag.
getLocation(String) Prefs
Uses the keyword key to retrieve a location
from the preferences file.
getLocationAsString(int, int) ImagePlus
Converts the current cursor location to a string.
getLog() IJ
Returns the contents of the Log window or null if the Log window is not open.
getLongFilePointer() RandomAccessStream
getLowerZoomLevel(double) ImageCanvas
getLut() ImageProcessor
getLuts() CompositeImage
getLuts() IJ
Returns, as an array of strings, a list of the LUTs in the Image/Lookup Tables menu.
getLuts() ImagePlus
Returns an array containing the lookup tables used by this image,
one per channel, or an empty array if this is an RGB image.
getLutUpdateMode() ImageProcessor
Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT,
OVER_UNDER_LUT or NO_LUT_UPDATE.
getMacroCode(String, ImagePlus) TextRoi
Used by the Recorder for recording the text tool.
getMacroCount() Menus
getMacroCount() MacroInstaller
getMacroCount() MacroToolRunner
getMacroProgram() MacroToolRunner
getMacroProgram() PlugInTool
getMacroShortcuts() Menus
Returns the hashtable that associates keyboard shortcuts with macros.
getMacrosMenu() Menus
getMacrosPath() Menus
Returns the path to the macros directory or
null if the macros directory was not found.
getMagnification() ImageCanvas
getMagnification() Roi
getMapSize() LookUpTable
getMask() Arrow
getMask() OvalRoi
getMask() PointRoi
getMask() PolygonRoi
getMask() Roi
Always returns null for rectangular Roi's
getMask() 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() ImagePlus
For images with irregular ROIs, returns a byte mask, otherwise, returns
null.
getMask() ImageProcessor
For images with irregular ROIs, returns a mask, otherwise,
returns null.
getMask(int, int) PolygonFiller
Returns a byte mask containing a filled version of the polygon.
getMaskArray() ImageProcessor
Returns a reference to the mask pixel array, or null if there is no mask.
getMatchingCoords(ImageCanvas, ImageCanvas, int, int) SyncWindows
Get Screen Coordinates for ImageCanvas ic matching
the OffScreen Coordinates of the current ImageCanvas.
getMax() ProfilePlot
Returns the calculated maximum value.
getMax() ByteProcessor
Returns the largest displayed pixel value.
getMax() ColorProcessor
Returns the largest displayed pixel value.
getMax() FloatProcessor
Returns the largest displayed pixel value.
getMax() ImageProcessor
Returns the largest displayed pixel value.
getMax() ShortProcessor
Returns the largest displayed pixel value.
getMax(double[]) CurveFitter
Gets index of highest value in an array.
getMaxima(ImageProcessor, double, boolean) MaximumFinder
Finds the image maxima and returns them as a Polygon.
getMaximum() ScrollbarWithLabel
getMaximum() ArrayUtil
The maximum value
getMaximumBounds() ImageWindow
getMaxIterations() CurveFitter
Get maximum number of iterations allowed (sum of iteration count for all restarts)
getMaxIterations() Minimizer
Get maximum number of iterations allowed.
getMaxRestarts() Minimizer
Get maximum number of minimization restarts to do
getMaxThreshold() ImageProcessor
Returns the upper threshold level.
getMaxWindowBounds() GUI
getMean() ArrayUtil
Average value
getMeasurements() Analyzer
getMemorySetting() Memory
getMenuBar() Menus
getMenus() Program
getMessage() GenericDialog
Returns a reference to the Label or MultiLineLabel created by the
last addMessage() call, or null if addMessage() was not called.
getMethod() ThresholdAdjuster
Returns the current thresholding method ("Default", "Huang", etc).
getMethods() AutoThresholder
getMin() ProfilePlot
Returns the calculated minimum value.
getMin() ByteProcessor
Returns the smallest displayed pixel value.
getMin() ColorProcessor
Returns the smallest displayed pixel value.
getMin() FloatProcessor
Returns the smallest displayed pixel value.
getMin() ImageProcessor
Returns the smallest displayed pixel value.
getMin() ShortProcessor
Returns the smallest displayed pixel value.
getMinimizer() CurveFitter
Returns a reference to the Minimizer used, for accessing Minimizer methods directly.
getMinimum() ScrollbarWithLabel
getMinimum() ArrayUtil
The minimum value
getMinimumSize() ImagePanel
getMinimumSize() MultiLineLabel
getMinimumSize() Plot
The minimum plot size including borders, in pixels (at scale=1)
getMinimumSize() ScrollbarWithLabel
getMinimumSize() Toolbar
getMinimumSize() TrimmedButton
getMinMax(double[]) Tools
getMinMax(float[]) Tools
getMinThreshold() ImageProcessor
Returns the lower threshold level.
getMode() CompositeImage
getMode() ThresholdAdjuster
Returns the current mode ("Red","B&W" or"Over/Under").
getMode() WandToolOptions
getModeAsString() CompositeImage
getModifiers() ImageCanvas
Returns the mouse event modifiers.
getMultipleWildcardChar() WildcardMatch
Returns the character used to specify any amount of characters.
getMultiPointMode() Toolbar
Returns 'true' if the multi-point tool is enabled.
getName() Roi
Returns the name of this ROI, or null.
getName() CurveFitter
returns the name of the fit function of the fit performed
getName() PlugInInterpreter
Returns the name of this PlugInInterpreter.
getName() TextReader
Returns the file name.
getName(int) RoiManager
Returns the name of the ROI with the specified index,
or null if the index is out of range.
getName(String) Opener
getName(String) Macro
getName(String) RoiManager
Returns the name of the ROI with the specified index.
getNbCpus() ThreadUtil
getNChannels() ImagePlus
Returns the number of channels.
getNChannels() ColorProcessor
Returns the number of color channels of the image, i.e., 3.
getNChannels() ImageProcessor
Returns the number of color channels in the image.
getNCoordinates() PolygonRoi
Returns the number of points that define this PolygonRoi.
getNCounters() PointRoi
getNDimensions() ImagePlus
Returns the number of dimensions (2, 3, 4 or 5).
getNeighborhood(int, int, double[][]) ImageProcessor
Experimental
getNextBoolean() GenericDialog
Returns the state of the next checkbox.
getNextChoice() GenericDialog
Returns the selected item in the next popup menu.
getNextChoiceIndex() GenericDialog
Returns the index of the selected item in the next popup menu.
getNextNumber() GenericDialog
Returns the contents of the next numeric field,
or NaN if the field does not contain a number.
getNextRadioButton() GenericDialog
Returns the selected item in the next radio button group.
getNextString() GenericDialog
Returns the contents of the next text field.
getNextText() GenericDialog
Returns the contents of the next text area.
getNFrames() ImagePlus
Returns the number of frames (time-points).
getNonImageTitles() WindowManager
Returns an array containing the titles of non-image Frames and Dialogs.
getNonImageWindows() WindowManager
Returns an array containing a list of the non-image Frames.
getNonSplineCoordinates() PolygonRoi
getNonSplineFloatPolygon() PolygonRoi
getNScrollbars() StackWindow
getNSlices() ImagePlus
Returns the image depth (number of z-slices).
getNthImageID(int) WindowManager
Returns the ID of the Nth open image.
getNumber(String, double) IJ
Allows the user to enter a number in a dialog box.
getNumericFields() GenericDialog
Returns the Vector containing the numeric TextFields.
getNumericProperty(String) ImagePlus
Returns the numeric value from the "Info" property string
associated with 'key', or NaN if the key is not found or the
value associated with the key is not numeric.
getNumParams() CurveFitter
Get number of parameters for current fit formula
Do not use before 'doFit', because the fit function would be undefined.
getNumParams(int) CurveFitter
Returns the number of parameters for a given fit type, except for the 'custom' fit,
where the number of parameters is given by the equation: see getNumParams(String)
getNumParams(String) CurveFitter
Returns the number of parameters for a custom equation given as a macro String,
like "y = a + b*x + c*x*x" .
getNumTools() Toolbar
getOffset() FileInfo
Returns the offset as a long.
getOpacity() ImageRoi
Returns the current opacity.
getOpenAsHyperStack() ImagePlus
getOpenRecentMenu() Menus
getOpenUsingPlugins() Opener
Returns the state of the openUsingPlugins flag.
getOptions() Macro
If a command started using run(name, options) is running,
and the current thread is the same thread,
returns the options string, otherwise, returns null.
getOrCreateResultsTable() TextPanel
Returns the ResultsTable associated with this TextPanel, or
attempts to create one and returns the created table.
getOrientation() ScrollbarWithLabel
getOriginalFileInfo() ImagePlus
Returns the FileInfo object that was used to open this image.
getOutline() Arrow
getOutputImage() ParticleAnalyzer
Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image,
or null if "Nothing" is selected in the "Show:" menu.
getOutputType() EDM
Returns the current output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
getOvalToolType() Toolbar
Returns the oval tool type (OVAL_ROI, ELLIPSE_ROI or BRUSH_ROI).
getOverlay() ImageCanvas
Use ImagePlus.getOverlay().
getOverlay() ImagePlus
Returns the current overly, or null if this image does not have an overlay.
getOverlay() ImageProcessor
getOverlay(ImagePlus) FileSaver
getPaintPending() ImageCanvas
getParams() EllipseRoi
Returns x1, y1, x2, y2 and aspectRatio as a 5 element array.
getParams() RotatedRectRoi
Returns x1, y1, x2, y2 and width as a 5 element array.
getParams() CurveFitter
Get the result of fitting, i.e.
getParams() Minimizer
Get the result, i.e., the set of parameter values (i.e., variable values)
from the best corner of the simplex.
getPasteMode() Roi
Returns the current paste transfer mode, or NOT_PASTING (-1)
if no paste operation is in progress.
getPath() OpenDialog
Returns the selected file path or null if the dialog was canceled.
getPath(ImagePlus, String) SaveDialog
getPixel(int, int) ImagePlus
Returns the pixel value at (x,y) as a 4 element array.
getPixel(int, int) ByteProcessor
getPixel(int, int) ColorProcessor
getPixel(int, int) FloatProcessor
Returns a pixel value that must be converted using
Float.intBitsToFloat().
getPixel(int, int) ImageProcessor
Returns the value of the pixel at (x,y).
getPixel(int, int) ShortProcessor
getPixel(int, int, int[]) ColorProcessor
Returns the 3 samples for the pixel at (x,y) in an array of int.
getPixel(int, int, int[]) FloatProcessor
Returns the value of the pixel at (x,y) in a
one element int array.
getPixel(int, int, int[]) ImageProcessor
Returns the samples for the pixel at (x,y) in an int array.
getPixelCount() ImageProcessor
getPixelInterpolated(double, double) ByteProcessor
getPixelInterpolated(double, double) ColorProcessor
getPixelInterpolated(double, double) FloatProcessor
getPixelInterpolated(double, double) ImageProcessor
Uses the current interpolation method to find the pixel value at real coordinates (x,y).
getPixelInterpolated(double, double) ShortProcessor
getPixels() Line
Returns the pixel values along this line.
getPixels() ByteProcessor
Returns a reference to the byte array containing this image's
pixel data.
getPixels() ColorProcessor
Returns a reference to the int array containing
this image's pixel data.
getPixels() FloatProcessor
Returns a reference to the float array containing
this image's pixel data.
getPixels() ImageProcessor
Returns a reference to this image's pixel array.
getPixels() ShortProcessor
Returns a reference to the short array containing this image's
pixel data.
getPixels(int) PlotVirtualStack
Returns the pixel array for the specified slice, were 1<=n<=nslices.
getPixels(int) ImageStack
Returns the pixel array for the specified slice, were 1<=n<=nslices.
getPixels(int) VirtualStack
Returns the pixel array for the specified slice, were 1<=n<=nslices.
getPixelsCopy() ByteProcessor
Returns a copy of the pixel data.
getPixelsCopy() ColorProcessor
Returns a copy of the pixel data.
getPixelsCopy() FloatProcessor
Returns a copy of the pixel data.
getPixelsCopy() ImageProcessor
Returns a copy of the pixel data.
getPixelsCopy() ShortProcessor
Returns a copy of the pixel data.
getPixelValue(int, int) ByteProcessor
getPixelValue(int, int) ColorProcessor
Converts the specified pixel to grayscale using the
formula g=(r+g+b)/3 and returns it as a float.
getPixelValue(int, int) FloatProcessor
Returns the value of the pixel at (x,y) as a float.
getPixelValue(int, int) ImageProcessor
Returns the value of the pixel at (x,y).
getPixelValue(int, int) ShortProcessor
Returns the value of the pixel at (x,y) as a float.
getPlot() PlotCanvas
Returns the Plot displayed in this canvas
getPlot() PlotMaker
Returns a profile plot.
getPlot() PlotWindow
Returns the Plot associated with this PlotWindow.
getPlot() ProfilePlot
getPlot() Profiler
getPlot() ZAxisProfiler
getPlot(ImagePlus) ZAxisProfiler
Returns a Plot of the selection mean gray value versus slice number.
getPlot(ImagePlus, String) ZAxisProfiler
Returns a Plot of the selection mean versus slice number for the
specified hyperstack, where 'options' can be "time" or "z-axis".
getPlotObjectDesignations() Plot
Get an array with human-readable designations of the PlotObjects (curves, labels, ...)
in the sequence they are plotted (i.e., foreground last).
getPlotObjectStyles(int) Plot
Get the style of the i-th PlotObject (curve, label, ...) in the sequence
they are plotted (i.e., foreground last), as String with comma delimiters:
Main Color, Secondary Color (or "none"), Line Width [, Symbol shape for XY_DATA] [,hidden]
getPlotSize() ProfilePlot
Returns the size of the plot that createWindow() creates.
getPluginCount() Menus
getPlugins() Menus
Returns a list of the plugins in the plugins menu.
getPlugInsPath() Menus
Returns the path to the user plugins directory or
null if the plugins directory was not found.
getPlugInTool() Toolbar
getPointPosition(int) PointRoi
getPoints() Line
Returns, as a Polygon, the two points that define this line.
getPointType() PointRoi
Returns the point type (0=hybrid, 1=crosshair, 2=dot, 3=circle).
getPolygon() Line
If the width of this line is less than or equal to one, returns the
starting and ending coordinates as a 2-point Polygon, or, if
the width is greater than one, returns an outline of the line as
a 4-point Polygon.
getPolygon() OvalRoi
Returns this OvalRoi as a Polygon.
getPolygon() PolygonRoi
Returns this PolygonRoi as a Polygon.
getPolygon() Roi
Returns the outline of this selection as a Polygon, or
null if this is a straight line selection.
getPolygon() ShapeRoi
getPopupMenu() Menus
getPort() ImageJ
Returns the port that ImageJ checks on startup to see if another instance is running.
getPosition() Roi
Returns the stack position (image number) of this ROI, or
zero if the ROI is not associated with a particular stack image.
getPowerSpectrum() FHT
Returns an 8-bit power spectrum, log-scaled to 1-254.
getPrecision() Analyzer
Returns the number of digits displayed to the right of decimal point.
getPreferredLocation() ImageJ
getPreferredSize() ImageCanvas
getPreferredSize() ImagePanel
getPreferredSize() MultiLineLabel
getPreferredSize() ProgressBar
getPreferredSize() ScrollbarWithLabel
getPreferredSize() Toolbar
getPreferredSize() TrimmedButton
getPrefsDir() Prefs
Returns the path to the directory where the
preferences file (IJPrefs.txt) is saved.
getPrefsDirectory() OtherInstance
getPreviewCheckbox() GenericDialog
Returns a reference to the Preview checkbox.
getProcessor() ImageRoi
getProcessor() Plot
Draws the plot (if not done before) in an ImageProcessor and returns the ImageProcessor with the plot.
getProcessor() IJ
Returns the active image or stack slice as an ImageProcessor, or displays
an error message and aborts the plugin or macro if no images are open.
getProcessor() ImagePlus
Returns a reference to the current ImageProcessor.
getProcessor(int) CompositeImage
getProcessor(int) PlotVirtualStack
Returns an ImageProcessor for the specified slice,
were 1<=n<=nslices.
getProcessor(int) ImageStack
Returns an ImageProcessor for the specified slice,
were 1<=n<=nslices.
getProcessor(int) AVI_Reader
Returns an ImageProcessor for the specified slice of this virtual stack (if it is one)
where 1<=n<=nslices.
getProcessor(int) FileInfoVirtualStack
Returns an ImageProcessor for the specified image,
were 1<=n<=nImages.
getProcessor(int) ListVirtualStack
Returns an ImageProcessor for the specified slice,
were 1<=n<=nslices.
getProcessor(int) VirtualStack
Returns an ImageProcessor for the specified slice,
were 1<=n<=nslices.
getProfile() ProfilePlot
Returns the profile plot data.
getProgram() MacroInstaller
getProgressBar() ImageJ
getProgressIncrement(int, int) ImageProcessor
getProjection() ZProjector
Retrieve results of most recent projection operation.
getProp(String) ImagePlus
Deprecated.
getProperties() Roi
getProperties() ImagePlus
Returns this image's Properties.
getProperties() VirtualStack
Returns the ImagePlus Properties assoctated with the current slice, or null.
getProperty(String) Roi
getProperty(String) IJ
Returns the object in IJ.properties associated
with 'key', or null if 'key' is not found.
getProperty(String) ImagePlus
Returns the property associated with 'key', or null if it is not found.
getPropertyCount() Roi
getPrototypeOverlay() Roi
getQuality() JpegWriter
Deprecated.
getRadioButtonGroups() GenericDialog
Returns the Vector that contains the RadioButtonGroups.
getRawInstance() RoiManager
getRawLength() Line
Returns the length of this line in pixels.
getRawStatistics() ImagePlus
getRawType(int) ExtensionDescriptor
getRawValue(double) Calibration
Converts a density calibrated value into a raw pixel value.
getRawX(double) Calibration
Converts a x-coordinate in physical units to pixels.
getRawY(double) Calibration
Converts a y-coodinate in physical units to pixels.
getRawY(double, int) Calibration
Converts a y-coodinate in physical units to pixels,
taking into account the 'invertY' flag.
getRawZ(double) Calibration
Converts a z-coodinate in physical units to pixels.
getRectToolType() Toolbar
Returns the rectangle tool type (RECT_ROI, ROUNDED_RECT_ROI or ROTATED_RECT_ROI).
getRed(String) Colors
getRedirectImage(ImagePlus) 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() LookUpTable
getResiduals() CurveFitter
Returns residuals array, i.e., differences between data and curve.
getRestarts() CurveFitter
Get maximum number of simplex restarts to do.
getResultsTable() HistogramWindow
Returns the histogram values as a ResultsTable.
getResultsTable() Plot
Creates a ResultsTable with the plot data.
getResultsTable() PlotWindow
Returns the plot values as a ResultsTable.
getResultsTable() ResultsTable
Returns the ResultsTable used by the Measure command.
getResultsTable() Analyzer
Returns the default results table.
getResultsTable() TextPanel
Returns the ResultsTable associated with this TextPanel, or null.
getResultsTable() TextWindow
Returns the ResultsTable associated with this TextWindow, or null.
getResultsTable(boolean) Plot
Creates a ResultsTable with the data of the plot.
getResultString() CurveFitter
Get a string with detailed description of the curve fitting results (several lines,
including the fit parameters).
getResultsWindow() ResultsTable
Returns the "Results" TextWindow.
getReturnValue() PlugInInterpreter
Returns the value returned by the script, if any, or null.
getRGB(byte[], byte[], byte[]) ColorProcessor
Returns the red, green and blue planes as 3 byte arrays.
getRGBWeights() ColorProcessor
Returns the values set by setRGBWeights(), or null if setRGBWeights() has not been called.
getRoi() ImagePlus
Returns the current selection, or null if there is no selection.
getRoi() ImageStack
getRoi() RoiDecoder
Returns the ROI.
getRoi() ImageProcessor
Returns a Rectangle that represents the current
region of interest.
getRoi(int) RoiManager
Returns a reference to the ROI at the specified index.
getRoiIndex(Roi) RoiManager
Returns the index of the specified Roi, or -1 if it is not found.
getRoiManager() RoiManager
Returns a reference to the ROI Manager and opens
the "ROI Manager" window if it is not already open.
getRois() ShapeRoi
Converts a Shape into Roi object(s).
getROIs() RoiManager
Deprecated.
getRoisAsArray() RoiManager
Returns the ROIs as an array.
getRoot() ControlPanel
getRotationCenter() Line
getRotationCenter() Roi
getRoundRectArcSize() Roi
Obsolete; replaced by getCornerDiameter().
getRoundRectArcSize() Toolbar
Returns the rounded rectangle arc size, or 0 if the rounded rectangle tool is not enabled.
getRow(int, int, float[], int) ImageProcessor
Returns the pixel values along the horizontal line starting at (x,y).
getRow(int, int, int[], int) ImageProcessor
Returns the pixel values along the horizontal line starting at (x,y).
getRowAsString(int) ResultsTable
Returns a tab or comma delimited string representing the
given row, where 0<=row<=size()-1.
getRSquared() CurveFitter
Returns R^2, where 1.0 is best.
getSampleImageNames() URLOpener
getSaveAsMenu() Menus
getScale(float[]) Convolver
getScaledStroke() Roi
getScaleToFit() ImageCanvas
getScreenSize() IJ
Returns the size, in pixels, of the primary display.
getSD() CurveFitter
Returns the standard deviation of the residuals.
getSD() Filters
Returns the default standard deviation used by Process/Noise/Add Specified Noise.
getSelectedIndex() RoiManager
Returns the index of the first selected ROI or -1 if no ROI is selected.
getSelectedIndexes() RoiManager
Returns an array of the selected indexes.
getSelectedRoisAsArray() RoiManager
Returns the selected ROIs as an array, or
all the ROIs if none are selected.
getSelectionEnd() TextPanel
Returns the index of the last selected line, or -1
if there is no slection.
getSelectionStart() TextPanel
Returns the index of the first selected line, or -1
if there is no slection.
getSerializedImage() ImageRoi
Returns a serialized version of the image.
getShape() ShapeRoi
Returns a reference to the Shape object encapsulated by this ShapeRoi.
getShapeAsArray() ShapeRoi
Retrieves the end points and control points of the path as a float array.
getShapeRoi() RoiDecoder
getShortcuts() Menus
Returns the hashtable that associates shortcuts with commands.
getShortcuts() CommandLister
getShortSliceLabel(int) 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() ImagePlus
Returns a shortened version of image name that does not
include spaces or a file name extension.
getShowAllColor() ImageCanvas
Obsolete
getShowAllList() ImageCanvas
getShowAllROIs() ImageCanvas
Obsolete
getShowLabels() PointRoi
getSimilarFontsList(String) FontUtil
For a few basic font types, gets a list of replacement font families
Note that java's 'SansSerif' has wider characters (significantly different metrics) than the other
sans-serif fonts in the list; thus it should be considered a fallback option only.
getSingleWildcardChar() WildcardMatch
Returns the character used to specify exactly one character.
getSixteenBitRanges() ContrastAdjuster
getSize() Plot
The size of the plot including borders with axis labels etc., in pixels
getSize() PlotVirtualStack
Returns the number of slices in this stack.
getSize() PointRoi
Returns the point size (0-4).
getSize() TextRoi
Returns the global (default) font size.
getSize() ImageStack
Returns the number of slices in this stack.
getSize() Program
getSize() AVI_Reader
Returns the number of images in this virtual stack (if it is one)
getSize() FileInfoVirtualStack
Returns the number of images in this stack.
getSize() ListVirtualStack
Returns the number of images in this stack.
getSize() VirtualStack
Returns the number of slices in this stack.
getSlice() ImagePlus
getSliceLabel(int) PlotVirtualStack
getSliceLabel(int) ImageStack
Returns the label of the specified slice, were 1<=n<=nslices.
getSliceLabel(int) AVI_Reader
Returns the label of the specified slice in this virtual stack (if it is one).
getSliceLabel(int) FileInfoVirtualStack
Returns the label of the Nth image.
getSliceLabel(int) ListVirtualStack
Returns the name of the specified image.
getSliceLabel(int) VirtualStack
Returns the label of the Nth image.
getSliceLabels() ImageStack
Returns the slice labels as an array of Strings.
getSliceNumber() PlugInFilterRunner
Return the slice number currently processed by the calling thread.
getSliceNumber() ImageProcessor
getSliceNumber(String) ImageCanvas
getSliceNumber(String) RoiManager
Returns the slice number associated with the specified name,
or -1 if the name does not include a slice number.
getSliderHeight() ImageWindow
getSliders() GenericDialog
Returns the Vector containing the sliders (Scrollbars).
getSnapshotPixels() ByteProcessor
getSnapshotPixels() ColorProcessor
Returns a reference to the snapshot pixel array.
getSnapshotPixels() FloatProcessor
getSnapshotPixels() ImageProcessor
Returns a reference to the snapshot (undo) buffer, or null.
getSnapshotPixels() ShortProcessor
getSortedFitList() CurveFitter
Returns an array of fit names with nicer sorting
getSourceImage() PlotMaker
Returns the ImagePlus used to generate the profile plots.
getSourceImage() Profiler
getSourceImage() ZAxisProfiler
getSrcRect() ImageCanvas
getStack() Plot
Returns the virtual stack created by addToStack().
getStack() ImagePlus
Returns the image stack.
getStackIndex(int, int, int) ImagePlus
Returns that stack index (one-based) corresponding to the specified position.
getStackSize() ImagePlus
If this is a stack, returns the number of slices, else returns 1.
getStartTime() ImagePlus
Returns the time in milliseconds when
startTiming() was last called.
getStartupMacro() Startup
getState() Roi
getStaticGlobalCalibration() ImagePlus
This is a version of getGlobalCalibration() that can be called from a static context.
getStatistics() Roi
getStatistics() ImagePlus
Get calibrated statistics for this image or ROI, including
histogram, area, mean, min and max, standard
deviation and mode.
getStatistics() ImageProcessor
This method calculates and returns complete uncalibrated statistics for
this image or ROI but it is up to 70 times slower than getStats().
getStatistics(double[]) Tools
getStatistics(int) ImagePlus
Returns an ImageStatistics object generated using the
specified measurement options.
getStatistics(int, int) ImagePlus
Returns an ImageStatistics object generated using the
specified measurement options and histogram bin count.
getStatistics(int, int, double, double) ImagePlus
Returns an ImageStatistics object generated using the
specified measurement options, histogram bin count and histogram range.
getStatistics(ImageProcessor) ImageStatistics
getStatistics(ImageProcessor, int, Calibration) ImageStatistics
getStats() ImageProcessor
Calculates and returns uncalibrated statistics for this image or ROI,
including histogram, area, mean, min and max, standard deviation,
and mode.
getStatus() CurveFitter
getStatusBar() ImageJ
getStatusString() CurveFitter
Get a short text with a short description of the status.
getString() Variable
getString(String) Prefs
Finds an string in IJ_Props or IJ_Prefs.txt.
getString(String, String) IJ
Allows the user to enter a string in a dialog box.
getString(String, String) Prefs
Finds an string in IJ_Props or IJ_Prefs.txt.
getStringBounds(String) ImageProcessor
Returns a rectangle enclosing the pixels affected by drawString
assuming it is drawn at (x=0, y=0).
getStringFields() GenericDialog
Returns the Vector containing the string TextFields.
getStringProperty(String) ImagePlus
Returns the string value from the "Info" property string
associated with 'key', or null if the key is not found.
getStringValue(int, int) ResultsTable
Returns the string value of the given column and row, where
column must be less than or equal the value returned by
getLastColumn() and row must be greater than or equal
zero and less than the value returned by size().
getStringValue(String, int) ResultsTable
Returns the string value of the given column and row,
where row must be greater than or equal zero
and less than the value returned by size().
getStringVariable(String) Interpreter
getStringWidth(String) ImageProcessor
Returns the width in pixels of the specified string, including any background
space (whitespace) between the x drawing coordinate and the string, not necessarily
including all whitespace at the right.
getStringWidth(String, FontMetrics, Graphics) Java2
getStroke() Roi
Returns the Stroke used to draw this ROI, or null if no Stroke is used.
getStrokeColor() Roi
Returns the the color used to draw the ROI outline or null if the default color is being used.
getStrokeWidth() Roi
Returns the lineWidth.
getStubPath() OtherInstance
getStyle() Arrow
getStyle() TextRoi
Returns the global (default) font style.
getSumResidualsSqr() CurveFitter
getSymbolTable() Program
getT() ImagePlus
Returns the current hyperstack frame position.
getTableAsImage() ResultsTable
Returns the contents of this ResultsTable as a FloatProcessor.
getTag(ImagePlus, String) DicomTools
Returns the value (as a string) of the specified DICOM tag id (in the form "0018,0050")
of the specified image or stack slice.
getTagName(String) DICOM
Returns the name of the specified DICOM tag id.
getTagName(String) DicomTools
Returns the name of the specified DICOM tag id.
getTempCurrentImage() WindowManager
Returns the temporary current image for this thread, or null.
getText() TextRoi
getText() Editor
getText() Recorder
getText() TextPanel
Returns all the text as a string.
getTextArea() Editor
getTextArea1() GenericDialog
Returns a reference to textArea1.
getTextArea2() GenericDialog
Returns a reference to textArea2.
getTextPanel() IJ
Returns a reference to the "Results" window TextPanel.
getTextPanel() TextWindow
Returns a reference to this TextWindow's TextPanel.
getThread() MacroRunner
getThreads() Prefs
Returns the number of threads used by PlugInFilters to process images and stacks.
getThreshold(AutoThresholder.Method, int[]) AutoThresholder
Calculates and returns a threshold using the specified
method and 256 bin histogram.
getThreshold(String, int[]) AutoThresholder
getThresholdColorModel() ImageProcessor
getTiffFileInfo(String) Opener
Returns the FileInfo of the specified TIFF file.
getTiffInfo() TiffDecoder
getTimeUnit() Calibration
Returns the distance unit (e.g.
getTitle() Plot
Returns the title of the image showing the plot (if any) or title of the plot
getTitle() ImagePlus
Returns the image name.
getTitle() ResultsTable
getTolerance() WandToolOptions
getToolIcon() ArrowTool
getToolIcon() BrushTool
getToolIcon() OverlayBrushTool
getToolIcon() PixelInspectionTool
getToolIcon() PlugInTool
Return the string encoding of the tool icon.
getToolIcon() RoiRotationTool
getToolId() Toolbar
Returns the ID of the current tool (Toolbar.RECTANGLE, Toolbar.OVAL, etc.).
getToolId(String) 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() Toolbar
Returns the name of the current tool.
getToolName() IJ
Returns the name of the current tool.
getToolName() ArrowTool
getToolName() BrushTool
getToolName() OverlayBrushTool
getToolName() PixelInspectionTool
getToolName() PlugInTool
Return the tool name.
getToolName() RoiRotationTool
getTPosition() Roi
Returns the frame position of this ROI, or zero
if this ROI is not associated with a particular frame.
getTransferData(DataFlavor) Clipboard
getTransferDataFlavors() Clipboard
getTransparentIndex() Prefs
Returns the transparent index (0-255), or -1 if transparency is disabled.
getType() Roi
getType() ImagePlus
Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16,
ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
getTypeAsString() Roi
Convenience method that converts Roi type to a human-readable form.
getTypeName(int) ExtensionDescriptor
getUMeans() Analyzer
Returns an array containing the first 20 uncalibrated means.
getUncalibratedLength() PolygonRoi
getUnionOfBounds() GUI
getUniqueName(String) WindowManager
Returns a unique name by adding, before the extension, -1, -2, etc.
getUnit() Calibration
Returns the default length unit (e.g.
getUnitIncrement() ScrollbarWithLabel
getUnits() Calibration
Returns the plural form of the length unit (e.g.
getValue() ScrollbarWithLabel
getValue() Variable
getValue(int, int) ResultsTable
Deprecated.
getValue(String) GenericDialog
getValue(String, int) ResultsTable
Returns the value of the specified column and row, where
column is the column heading and row is a number greater
than or equal zero and less than value returned by size().
getValue(String, String, String) Macro
getValueAsDouble(int, int) ResultsTable
Returns the value of the given column and row, where
column must be less than or equal the value returned by
getLastColumn() and row must be greater than or equal
zero and less than the value returned by size().
getValueUnit() Calibration
Returns the value unit.
getVariable(String) Interpreter
getVariable2(String) Interpreter
getVariableAsString(String) Interpreter
getVariableNames() Interpreter
Returns the names of all variables, without any annotation
getVariables() Interpreter
Returns the names of all variables and functions with human-readable annotations
getVariance() ArrayUtil
Variance value
getVersion() IJ
Returns the ImageJ version number as a string.
getVersion() PlugInInterpreter
Returns the version of ImageJ at the time this plugin was created.
getVisibleAmount() ScrollbarWithLabel
getVoxel(int, int, int) ImageStack
Returns, as a double, the specified voxel.
getVoxelDepth(ImageStack) DicomTools
Calculates the voxel depth of the specified DICOM stack based
on the distance between the first and last slices.
getVoxels(int, int, int, int, int, int, float[]) ImageStack
getVoxels(int, int, int, int, int, int, float[], int) ImageStack
getWeightingFactors() ColorProcessor
Returns the three weighting factors used by getPixelValue(),
getHistogram() and convertToByte() to do color conversions.
getWidth() Line
getWidth() ImagePlus
getWidth() ImageStack
getWidth() AVI_Reader
Returns the image width of the virtual stack
getWidth() FileInfoVirtualStack
getWidth() ListVirtualStack
getWidth() ImageProcessor
Returns the width of this image in pixels.
getWindow() ImagePlus
Returns the ImageWindow that is being used to display
this image.
getWindow(String) WindowManager
Returns the window (a Frame or a Dialog) with the specified
title, or null if a window with that title is not found.
getWindowCount() WindowManager
Returns the number of open image windows.
getX(double) Calibration
Converts a x-coodinate in pixels to physical units (e.g.
getXBase() Roi
getXCoordinates() PolygonRoi
Obsolete; replaced by either getPolygon() or getFloatPolygon().
getXPoints() CurveFitter
returns the array with the x data
getXUnit() Calibration
Returns the X length unit.
getXValues() HistogramWindow
getXValues() Plot
Get the x coordinates of the data set passed with the constructor (if not null)
or otherwise of the data set of the first 'addPoints'.
getXValues() PlotWindow
getXZImage() Orthogonal_Views
getY(double) Calibration
Converts a y-coordinate in pixels to physical units (e.g.
getY(double, int) Calibration
Converts a y-coordinate in pixels to physical units (e.g.
getYBase() Roi
getYCoordinates() PolygonRoi
Obsolete; replaced by either getPolygon() or getFloatPolygon().
getYPoints() CurveFitter
returns the array with the y data
getYUnit() Calibration
Returns the Y length unit, or the default unit if 'yunit' is null.
getYUV(ImageProcessor, byte[], byte[], byte[]) ColorThresholder
getYValues() Plot
Get the y coordinates of the data set passed with the constructor (if not null)
or otherwise of the data set of the first 'addPoints'.
getYValues() PlotWindow
getYZImage() Orthogonal_Views
getZ() ImagePlus
Returns the current hyperstack slice position.
getZ(double) Calibration
Converts a z-coordinate in pixels to physical units (e.g.
getZeroBasedMaxBounds() GUI
getZeroTransparent() ImageRoi
getZPosition() Roi
Returns the slice position of this ROI, or zero
if this ROI is not associated with a particular slice.
getZUnit() Calibration
Returns the Z length unit, or the default unit if 'zunit' is null.
GIF Opener
GIF_OR_JPG FileInfo
GIF_Reader ij.plugin
This plugin opens GIFs and Animated GIFs.
GIF_Reader() GIF_Reader
GifWriter ij.plugin
Saves the active image in GIF format, or as an animated GIF if the image is a stack.
GifWriter() GifWriter
gLUT1 ImageProcessor
gLUT2 ImageProcessor
GRAY12_UNSIGNED FileInfo
12-bit unsigned integer (0-4095).
GRAY16 NewImage
GRAY16 ImagePlus
16-bit grayscale (unsigned)
GRAY16_SIGNED FileInfo
16-bit signed integer (-32768-32767).
GRAY16_UNSIGNED FileInfo
16-bit unsigned integer (0-65535).
GRAY24_UNSIGNED FileInfo
24-bit unsigned integer.
GRAY32 NewImage
GRAY32 ImagePlus
32-bit floating-point grayscale
GRAY32_FLOAT FileInfo
32-bit floating-point.
GRAY32_INT FileInfo
32-bit signed integer.
GRAY32_UNSIGNED FileInfo
32-bit unsigned integer.
GRAY64_FLOAT FileInfo
64-bit floating-point.
GRAY8 NewImage
GRAY8 ImagePlus
8-bit grayscale (unsigned)
GRAY8 FileInfo
8-bit unsigned integer (0-255).
GRAYSCALE CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
GRAYSCALE IJ
Image display modes
green RGBStackSplitter
greens FileInfo
Grid ij.plugin
This class implements the Analyze/Tools/Grid command.
Grid() Grid
GroupedZProjector ij.plugin
This plugin implements the Image/Stacks/Tools/Grouped Z Project command.
GroupedZProjector() GroupedZProjector
groupZProject(ImagePlus, int, int) GroupedZProjector
grow(int, int) EllipseRoi
grow(int, int) FreehandRoi
grow(int, int) Line
grow(int, int) PolygonRoi
grow(int, int) Roi
grow(int, int) RotatedRectRoi
GT MacroConstants
GTE MacroConstants
GUI ij.gui
This class consists of static GUI utility methods.
GUI() GUI
ic ImageWindow
ic Roi
IF MacroConstants
ignoreClipRect Roi
ignoreNonImageWidths(boolean) ImageLayout
Determines whether to ignore the width of non-image components when calculating
the preferred width (default false, i.e.
ij - package ij
ij ImageCanvas
ij ImageWindow
IJ ij
This class consists of static utility methods.
IJ() IJ
IJ_CALL MacroConstants
IJ_IsoData AutoThresholder.Method
IJ.ExceptionHandler ij
ij.gui - package ij.gui
ij.io - package ij.io
ij.macro - package ij.macro
ij.measure - package ij.measure
ij.plugin - package ij.plugin
ij.plugin.filter - package ij.plugin.filter
ij.plugin.frame - package ij.plugin.frame
ij.plugin.tool - package ij.plugin.tool
ij.process - package ij.process
ij.text - package ij.text
ij.util - package ij.util
IJEventListener ij
Plugins that implement this interface are notified when the user
changes the foreground color, changes the background color,
closes the color picker, closes the Log window or switches to
another tool.
ijInstance SyncWindows
reference to current instance of ImageJ (to avoid repeated IJ.getInstance() s)
IJMath ij.util
IJMath() IJMath
image ImageProcessor
IMAGE RoiDecoder
IMAGE_DESCRIPTION TiffDecoder
IMAGE_LENGTH TiffDecoder
IMAGE_OPACITY RoiDecoder
IMAGE_SIZE RoiDecoder
IMAGE_WIDTH TiffDecoder
ImageCalculator ij.plugin
This plugin implements the Process/Image Calculator command.
ImageCalculator() ImageCalculator
ImageCanvas ij.gui
This is a Canvas used to display images in a Window.
ImageCanvas(ImagePlus) ImageCanvas
imageClosed(ImagePlus) HistogramWindow
imageClosed(ImagePlus) PlotWindow
For live plots, if either the source image or this image are closed, exit live mode
imageClosed(ImagePlus) ImageListener
imageClosed(ImagePlus) EventListener
imageClosed(ImagePlus) Recorder
imageClosed(ImagePlus) SyncWindows
Implementation of ImageListener interface: update window list, if image is opened or closed
imageClosed(ImagePlus) ThresholdAdjuster
imageClosed(ImagePlus) Orthogonal_Views
ImageConverter ij.process
This class converts an ImagePlus object to a different type.
ImageConverter(ImagePlus) ImageConverter
Constructs an ImageConverter based on an ImagePlus object.
imageHeight ImageCanvas
ImageInfo ij.plugin
This plugin implements the Image/Show Info command.
ImageInfo() ImageInfo
IMAGEIO FileInfo
ImageJ ij
This frame is the main ImageJ class.
ImageJ() ImageJ
Creates a new ImageJ frame that runs as an application.
ImageJ(int) ImageJ
Creates a new ImageJ frame that runs as an application in the specified mode.
ImageJ(Applet) ImageJ
Creates a new ImageJ frame that runs as an applet.
ImageJ(Applet, int) ImageJ
If 'applet' is not null, creates a new ImageJ frame that runs as an applet.
ImageJ_Updater ij.plugin
This plugin implements the Help/Update ImageJ command.
ImageJ_Updater() ImageJ_Updater
ImageJApplet ij
Runs ImageJ as an applet and optionally opens up to
nine images using URLs passed as a parameters.
ImageJApplet() ImageJApplet
ImageLayout ij.gui
This is a custom layout manager that supports resizing of zoomed
images.
ImageLayout(ImageCanvas) ImageLayout
Creates a new ImageLayout with center alignment.
ImageListener ij
Plugins that implement this interface are notified when
an image is opened, closed or updated.
ImageMath ij.plugin.filter
This plugin implements ImageJ's Process/Math submenu.
ImageMath() ImageMath
imageOpened(ImagePlus) HistogramWindow
imageOpened(ImagePlus) PlotWindow
imageOpened(ImagePlus) ImageListener
imageOpened(ImagePlus) EventListener
imageOpened(ImagePlus) Recorder
imageOpened(ImagePlus) SyncWindows
Implementation of ImageListener interface: update window list, if image is opened or closed
imageOpened(ImagePlus) ThresholdAdjuster
imageOpened(ImagePlus) Orthogonal_Views
ImagePanel ij.gui
This class is used by GenericDialog to add images to dialogs.
ImagePlus ij
An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image).
ImagePlus() ImagePlus
Constructs an uninitialized ImagePlus.
ImagePlus(String) 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) ImagePlus
Constructs an ImagePlus from a stack.
ImagePlus(String, ImageProcessor) ImagePlus
Constructs an ImagePlus from an ImageProcessor.
ImagePlus(String, Image) ImagePlus
Constructs an ImagePlus from an Image or BufferedImage.
ImageProcessor 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() ImageProcessor
ImageProperties ij.plugin.filter
ImageProperties() ImageProperties
ImageReader ij.io
Reads raw 8-bit, 16-bit or 32-bit (float or RGB)
images from a stream or URL.
ImageReader(FileInfo) ImageReader
Constructs a new ImageReader using a FileInfo object to describe the file to be read.
ImageRoi ij.gui
An ImageRoi is an Roi that overlays an image.
ImageRoi(int, int, ImageProcessor) ImageRoi
Creates a new ImageRoi from a ImageProcessor.
ImageRoi(int, int, BufferedImage) ImageRoi
Creates a new ImageRoi from a BufferedImage.
ImageStack ij
This class represents an expandable array of images.
ImageStack() ImageStack
Default constructor.
ImageStack(int, int) ImageStack
Creates a new, empty image stack.
ImageStack(int, int, int) ImageStack
Creates a new, empty image stack with a capacity of 'size'.
ImageStack(int, int, ColorModel) ImageStack
Creates a new, empty image stack using the specified color model.
ImageStatistics ij.process
Statistics, including the histogram, of an image or selection.
ImageStatistics() ImageStatistics
ImagesToStack ij.plugin
Implements the Image/Stacks/Images to Stack" command.
ImagesToStack() ImagesToStack
imageUpdate(Image, int, int, int, int, int) ImagePlus
Used by ImagePlus to monitor loading of images.
imageUpdated ImageCanvas
imageUpdated(ImagePlus) HistogramWindow
imageUpdated(ImagePlus) PlotWindow
For live plots, this method is called if the source image content is changed.
imageUpdated(ImagePlus) ImageListener
imageUpdated(ImagePlus) EventListener
imageUpdated(ImagePlus) Recorder
imageUpdated(ImagePlus) SyncWindows
imageUpdated(ImagePlus) ThresholdAdjuster
imageUpdated(ImagePlus) Orthogonal_Views
imageWidth ImageCanvas
ImageWindow ij.gui
A frame for displaying images.
ImageWindow(ImagePlus) ImageWindow
ImageWindow(ImagePlus, ImageCanvas) ImageWindow
ImageWindow(String) ImageWindow
ImageWriter ij.io
Writes a raw image described by a FileInfo object to an OutputStream.
ImageWriter(FileInfo) ImageWriter
img ImagePlus
img ImageProcessor
imp ImageCanvas
imp ImageWindow
imp ProfilePlot
imp Roi
imp ParticleAnalyzer
IMPORT_MENU Menus
ImportDialog ij.io
This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.
ImportDialog() ImportDialog
ImportDialog(String, String) ImportDialog
in TiffDecoder
IN_PLACE Resizer
IN_SITU_SHOW ParticleAnalyzer
Replace original image with masks.
IN_TOLERANCE MaximumFinder
Output type all points around the maximum within the tolerance
INCLUDE_HOLES ParticleAnalyzer
Flood fill to ignore interior holes.
incrementCounter() ResultsTable
Increments the measurement counter by one.
INDEX_OF MacroConstants
indices DownsizeTable
For each source point between srcStart and srcEnd, indices of destination
points where the data should be added.
info FileInfo
info Calibration
Plugin writers can use this string to store information about the
image.
Info ij.plugin.filter
Deprecated.
Info() Info
Deprecated.
init() ImageJApplet
Starts ImageJ if it's not already running.
INITIALIZATION_FAILURE Minimizer
Status returned: Could not initialize the simplex because either the initialParams
resulted in the target function returning NaN or all attempts to find starting
parameters for the other simplex points resulted in the target function returning NaN.
inputStream FileInfo
insert(ImagePlus, ImagePlus, int, int) StackInserter
insert(ImageProcessor, int, int) ImageProcessor
Inserts the image contained in 'ip' at (xloc, yloc).
inSituShow ParticleAnalyzer
install(String) MacroInstaller
install(String) PluginInstaller
install(String, Menu) MacroInstaller
installFile(String) MacroInstaller
installFromIJJar(String) MacroInstaller
Installs a macro set contained in ij.jar.
installLibrary(String) MacroInstaller
installPlugin(String, char, String, String, ImageJ) Menus
Adds a plugin based command to the end of a specified menu.
installSingleTool(String) MacroInstaller
installStartupMacros(String) MacroInstaller
Installs startup macros and runs AutoRun macro on current thread.
installStartupMacrosTools() Toolbar
installStartupTools() Toolbar
installTool(String) MacroInstaller
installUserPlugin(String, boolean) Menus
instanceColor Roi
int2hex(int, int) Tools
Converts an int to a zero-padded hex string of fixed length 'digits'.
INTEGRATED_DENSITY Measurements
INTEGRATED_DENSITY ResultsTable
intelByteOrder FileInfo
intelByteOrder Prefs
Export TIFF and Raw using little-endian byte order.
Intermodes AutoThresholder.Method
interpolate PlotWindow
Interpolate line profiles.
interpolate ImageProcessor
interpolateScaledImages Prefs
Display images scaled <100% using bilinear interpolation
interpolationMethod ImageProcessor
Interpreter ij.macro
This is the recursive descent parser/interpreter for the ImageJ macro language.
Interpreter() Interpreter
INV_RODBARD CurveFitter
Constants for the built-in fit functions
INVALID_SHORTCUT Menus
invalidNumber() GenericDialog
Returns true if one or more of the numeric fields contained an
invalid number.
inverse(ImagePlus) FFT
Performs an inverse FHT transform.
inverseTransform() FHT
Performs an inverse transform, converting this image into the space domain.
inverseTransform1D(float[]) FHT
Performs an inverse 1D Fast Hartley Transform (FHT) of an array
inversionTested ImageProcessor
invert() FloatProcessor
Each pixel in the image is inverted using p=max-(p-min), where 'min'
and 'max' are the display range limits set using setMinAndMax().
invert() ImageProcessor
Inverts the image or ROI.
invert() ShortProcessor
invert() StackProcessor
INVERT MacroConstants
INVERT_Y Measurements
invertedLut ImageProcessor
invertLut() ColorProcessor
Does nothing since RGB images do not use LUTs.
invertLut() ImageProcessor
Inverts the values in this image's LUT (indexed color model).
ip ImagePlus
IPLAB TiffDecoder
IS MacroConstants
IS_ACTIVE MacroConstants
IS_KEY_DOWN MacroConstants
IS_NAN MacroConstants
IS_OPEN MacroConstants
is64Bit() IJ
Returns true if ImageJ is running a 64-bit version of Java.
isActiveOverlayRoi() Roi
Returns 'true' if this ROI is displayed and is also in an overlay.
isAntialiased() TextRoi
Returns the state of the global 'antialiasedText' variable, which is used by the "Fonts" widget.
isArea() Roi
Returns 'true' if this is an area selection.
isAutoRunAndHide() MacroInstaller
Returns true if an "AutoRunAndHide" macro was run/installed.
isBatchMode() Interpreter
isBatchModeRoiManager() Interpreter
Returns true if there is an internal batch mode RoiManager.
isBinary() ByteProcessor
Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isBinary() ImageProcessor
Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isCalibrationBar() Overlay
isClosed() ImageWindow
Has this window been closed?
isColorLut() ImageProcessor
Returns true if this image uses a color LUT.
isComposite() ImagePlus
Returns true if this is a CompositeImage.
isCursor() Roi
isDataFlavorSupported(DataFlavor) Clipboard
isDefaultLut() ImageProcessor
Returns true if the image is using the default grayscale LUT.
isDisplayedHyperStack() ImagePlus
Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.
isDrawingTool() Arrow
isDrawingTool() Roi
Returns 'true' if this is an ROI primarily used from drawing
(e.g., TextRoi or Arrow).
isDrawingTool() TextRoi
isFrozen() Plot
isFrozen() PlotCanvas
Whether the plot is frozen, i.e.
isGrayscale() LookUpTable
Returns true if this is a 256 entry grayscale LUT.
isGrayscale() ColorProcessor
Returns 'true' if this is a grayscale image.
isGrayscale() ImageProcessor
Returns 'true' if this is an image with a grayscale LUT or an
RGB image with identical red, green and blue channels.
isHandle(int, int) EllipseRoi
isHandle(int, int) Line
Returns a handle number if the specified screen coordinates are
inside or near a handle, otherwise returns -1.
isHandle(int, int) OvalRoi
Returns a handle number if the specified screen coordinates are
inside or near a handle, otherwise returns -1.
isHandle(int, int) PointRoi
Returns a point index if it has been at least one second since
the last point was added and the specified screen coordinates are
inside or near a point, otherwise returns -1.
isHandle(int, int) PolygonRoi
Returns a handle number if the specified screen coordinates are
inside or near a handle, otherwise returns -1.
isHandle(int, int) Roi
Returns a handle number if the specified screen coordinates are
inside or near a handle, otherwise returns -1.
isHandle(int, int) RotatedRectRoi
isHandle(int, int) ShapeRoi
Always returns -1 since ShapeRois do not have handles.
isHSB() ImageStack
Returns true if this is a 3-slice HSB stack.
isHyperStack() StackWindow
isHyperStack() ImagePlus
Returns 'true' if this image is a hyperstack.
isInvertedLut() ImagePlus
Returns true is this image uses an inverting LUT that
displays zero as white and 255 as black.
isInvertedLut() ColorProcessor
Always returns false since RGB images do not use LUTs.
isInvertedLut() ImageProcessor
Returns true if this image uses an inverting LUT
that displays zero as white and 255 as black.
isJava14() IJ
Always returns true.
isJava15() IJ
Always returns true.
isJava16() IJ
Returns true if ImageJ is running on a Java 1.6 or greater JVM.
isJava17() IJ
Returns true if ImageJ is running on a Java 1.7 or greater JVM.
isJava18() IJ
Returns true if ImageJ is running on a Java 1.8 or greater JVM.
isJava19() IJ
Returns true if ImageJ is running on a Java 1.9 or greater JVM.
isJava2() IJ
Always returns true.
isKillable() ImageProcessor
Deprecated.
isLab() ImageStack
Returns true if this is a Lab stack.
isLine() Roi
Returns 'true' if this is a line selection.
isLinux() IJ
Returns true if ImageJ is running on Linux.
isLocked() ImagePlus
Returns 'true' if the image is locked.
isMacintosh() IJ
Returns true if this machine is a Macintosh.
isMacOSX() IJ
Returns true if this machine is a Macintosh running OS X.
isMacro() GenericDialog
isMacro() IJ
Returns true if a macro is running, or if the run(), open()
or newImage() method is executing.
isMaximum(double) ArrayUtil
IsoData AutoThresholder.Method
ISODATA ImageProcessor
Isodata thresholding method
ISODATA2 ImageProcessor
Modified isodata method used in Image/Adjust/Threshold tool
isOptionalArg(int) ExtensionDescriptor
isOrthoViewsImage(ImagePlus) Orthogonal_Views
isOutputArg(int) ExtensionDescriptor
isPowerOf2(int) FHT
isPreviewActive() GenericDialog
Returns 'true' if this dialog has a "Preview" checkbox and it is enabled.
isProcessor() ImagePlus
isPseudoColorLut() ImageProcessor
Returns true if this image uses a pseudocolor or grayscale LUT,
in other words, is this an image that can be filtered.
isRedirectImage() Analyzer
Returns true if an image is selected in the "Redirect To:"
popup menu of the Analyze/Set Measurements dialog box.
isResultsWindow() IJ
Returns true if the "Results" window is open.
isRGB() ImageStack
Returns true if this is a 3-slice, 8-bit RGB stack.
isRMIEnabled() OtherInstance
isSelectable() Overlay
Returns 'true' if ROIs in this overlay can be activated
by clicking on their labels or by a long press.
isSelected(int) RoiManager
Returns 'true' if the index is valid and the indexed ROI is selected.
isSigned16Bit() Calibration
Returns true if this is a signed 16-bit image.
isSigned16Bit() ImageProcessor
Returns 'true' if this is a signed 16-bit image.
isSigned16Bit() ShortProcessor
Returns 'true' if this is a signed 16-bit image.
isSplineFit() PolygonRoi
Returns 'true' if this selection has been fitted with a spline.
isStack() ImagePlus
isThreshold() ImagePlus
Returns 'true' if this image is thresholded.
isVirtual() ImageStack
Returns true if this is a virtual (disk resident) stack.
isVirtual() VirtualStack
Always return true.
isVisible() Roi
Returns true if this ROI is currently displayed on an image.
isVisible() ImagePlus
Returns true if this image is currently being displayed in a window.
isVista() IJ
Obsolete; always returns false.
isWindows() IJ
Returns true if this machine is running Windows.
itemStateChanged(ItemEvent) GenericDialog
itemStateChanged(ItemEvent) PlotWindow
Called if the user activates/deactivates a CheckboxMenuItem
itemStateChanged(ItemEvent) Toolbar
itemStateChanged(ItemEvent) ImageJ
Handles CheckboxMenuItem state changes.
itemStateChanged(ItemEvent) FunctionFinder
itemStateChanged(ItemEvent) BatchProcessor
itemStateChanged(ItemEvent) Colors
itemStateChanged(ItemEvent) CommandFinder
itemStateChanged(ItemEvent) Concatenator
itemStateChanged(ItemEvent) Duplicator
itemStateChanged(ItemEvent) Channels
itemStateChanged(ItemEvent) ColorThresholder
itemStateChanged(ItemEvent) ContrastAdjuster
itemStateChanged(ItemEvent) Editor
itemStateChanged(ItemEvent) Fitter
itemStateChanged(ItemEvent) LineWidthAdjuster
itemStateChanged(ItemEvent) PasteController
itemStateChanged(ItemEvent) Recorder
itemStateChanged(ItemEvent) RoiManager
itemStateChanged(ItemEvent) SyncWindows
Item Listener method
itemStateChanged(ItemEvent) ThresholdAdjuster
itemStateChanged(ItemEvent) Resizer
itemStateChanged(ItemEvent) Slicer
itemStateChanged(ItemEvent) Startup
itemStateChanged(ItemEvent) Thresholder
itemStateChanged(ItemEvent) TextWindow
iterator() Line
iterator() PointRoi
Custom iterator for points contained in a
PointRoi.
iterator() Roi
IterFactor CurveFitter
Deprecated.
radioButtonGroups GenericDialog
rand(int, int) SaltAndPepper
RANDOM MacroConstants
RandomAccessStream ij.io
This class uses a memory cache to allow seeking within
an InputStream.
RandomAccessStream(InputStream) RandomAccessStream
Constructs a RandomAccessStream from an InputStream.
RandomAccessStream(RandomAccessFile) RandomAccessStream
Constructs a RandomAccessStream from an RandomAccessFile.
rank(double[]) Tools
Returns a sorted list of indices of the specified double array.
rank(ImageProcessor, double, int) RankFilters
Filters an image by any method except 'despecle' or 'remove outliers'.
rank(ImageProcessor, double, int, int, float) RankFilters
Filters an image by any method except 'despecle' (for 'despeckle', use 'median' and radius=1)
rank(String[]) Tools
Returns a sorted list of indices of the specified String array.
RankFilters ij.plugin.filter
This plugin implements the Mean, Minimum, Maximum, Variance, Median, Open Maxima, Close Maxima,
Remove Outliers, Remove NaNs and Despeckle commands.
RankFilters() RankFilters
raster ImageProcessor
Raw ij.plugin
This plugin implements the File/Import/Raw command.
Raw() Raw
RAW FileInfo
RAW Opener
RAW_INTEGRATED_DENSITY ResultsTable
rc2DFHT(float[], boolean, int) FHT
Performs a 2D FHT (Fast Hartley Transform).
read() RandomAccessStream
read(byte[], int, int) RandomAccessStream
readDouble() RandomAccessStream
readFloat() RandomAccessStream
readFully(byte[]) RandomAccessStream
readFully(byte[], int) RandomAccessStream
readInt() RandomAccessStream
readLong() RandomAccessStream
readPixels(InputStream) ImageReader
Reads the image from the InputStream and returns the pixel
array (byte, short, int or float).
readPixels(InputStream, long) ImageReader
Skips the specified number of bytes, then reads an image and
returns the pixel array (byte, short, int or float).
readPixels(String) ImageReader
Reads the image from a URL and returns the pixel array (byte,
short, int or float).
readShort() RandomAccessStream
RecentOpener ij
Opens, in a separate thread, files selected from the File/Open Recent submenu.
record Recorder
This variable is true if the recorder is running.
record(String) Recorder
record(String, double, double) Recorder
record(String, int) Recorder
record(String, int, int) Recorder
record(String, int, int, int) Recorder
record(String, int, int, int, int) Recorder
record(String, int, int, int, int, double) Recorder
record(String, int, int, int, int, int) Recorder
record(String, int, int, String) Recorder
record(String, String) Recorder
record(String, String, int) Recorder
record(String, String, int, int) Recorder
record(String, String, String) Recorder
record(String, String, String, int, int, int, int, int) Recorder
record(String, String, String, String) Recorder
RECORD_STARTS ParticleAnalyzer
Record starting coordinates so outline can be recreated later using doWand(x,y).
recordCall(String) Recorder
recordCall(String, String) Recorder
Recorder ij.plugin.frame
This is ImageJ's macro recorder.
Recorder() Recorder
Recorder(boolean) Recorder
recordInMacros Recorder
Set this variable true to allow recording within IJ.run() calls.
recordOption(String) Recorder
recordOption(String, String) Recorder
recordPath(String, String) Recorder
recordRoi(Roi) Recorder
recordRoi(Polygon, int) Recorder
recordScriptRoi(Polygon, int) Recorder
recordSetMinAndMax(double, double) ContrastAdjuster
recordStarts ParticleAnalyzer
recordString(String) Recorder
RECT Measurements
RECT_ROI Toolbar
RECTANGLE Roi
RECTANGLE Toolbar
RectToolOptions ij.plugin
This plugin implements the rounded rectangle tool dialog box.
RectToolOptions() RectToolOptions
red RGBStackSplitter
RED_LUT ImageProcessor
redirectErrorMessages() IJ
Causes IJ.error() output to be temporarily redirected to the "Log" window.
redirectErrorMessages(boolean) IJ
Set 'true' and IJ.error() output will be temporarily redirected to the "Log" window.
redirectingErrorMessages() IJ
Returns the state of the 'redirectErrorMessages' flag, which is set by File/Import/Image Sequence.
redirectSystem() LogStream
Redirects all output sent to System.out and System.err to ImageJ's log console
using the default prefixes.
redirectSystem(boolean) LogStream
Redirects all output sent to System.out and System.err to ImageJ's log console
using the default prefixes.
redirectSystemErr(String) LogStream
Redirects all output sent to System.err to ImageJ's log console.
redirectSystemOut(String) LogStream
Redirects all output sent to System.out to ImageJ's log console.
redrawGrid() Plot
reds FileInfo
reduce(ImagePlus) HyperStackReducer
reduceHyperstack(ImagePlus, int, boolean) StackReducer
reduceStack(ImagePlus, int) StackReducer
reflexAngle Prefs
Angle tool measures reflex angle
register(Class) 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) ImageJ
Adds the specified class to a Vector to keep it from being
garbage collected, causing static fields to be reset.
registerExtensions(MacroExtension) Functions
REINITIALIZATION_FAILURE Minimizer
Status returned: Could not reinitialize the simplex because all attempts to find restarting
parameters resulted in the target function returning NaN.
remove() Line.PointIterator
remove(int) Overlay
Removes the ROI with the specified index from this Overlay.
remove(Roi) Overlay
Removes the specified ROI from this Overlay.
remove(String) Overlay
Removes all ROIs that have the specified name.
REMOVE_NAN RankFilters
removeAdjustmentListener(AdjustmentListener) ScrollbarWithLabel
removeBatchModeImage(ImagePlus) Interpreter
removeCommandListener(CommandListener) Executer
Removes the specified command listener.
removeEventListener(IJEventListener) IJ
removeImageListener(ImageListener) ImagePlus
removeKeyListener(KeyListener) ScrollbarWithLabel
removeLayoutComponent(Component) ImageLayout
Not used by this class.
removeMacroTools() Toolbar
removeRoiListener(RoiListener) Roi
removeSplineFit() PolygonRoi
removeWindow(Frame) WindowManager
Removes the specified Frame from the Window menu.
removeWindow(Window) WindowManager
Removes the specified window from the Window menu.
rename(int, String) RoiManager
rename(String) TextWindow
RENAME MacroConstants
renameColumn(String, String) ResultsTable
Changes the name of a column.
renameResults(String) IJ
Renames a results window.
renameResults(String, String) IJ
Changes the name of a table window from 'oldTitle' to 'newTitle'.
RenyiEntropy AutoThresholder.Method
repaint() GenericDialog
repaintImageWindows() WindowManager
Repaints all open image windows.
repaintWindow() 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 MacroConstants
requireControlKey Prefs
Require control or command key for keybaord shortcuts.
REQUIRES MacroConstants
resampleArray(double[], int) Tools
Returns an array linearly resampled to a different length.
reset() CompositeImage
reset() ResultsTable
reset() RoiManager
Clears this RoiManager so that it contains no ROIs.
reset() ByteProcessor
Reset the image from snapshot.
reset() ColorProcessor
reset() FloatProcessor
reset() ImageProcessor
Restores the pixel data from the snapshot (undo) buffer.
reset() ShortProcessor
reset() Undo
reset(ImageProcessor) ByteProcessor
Restore pixels that are within roi but not part of mask.
reset(ImageProcessor) ColorProcessor
reset(ImageProcessor) FloatProcessor
reset(ImageProcessor) ImageProcessor
Restores pixels from the snapshot buffer that are
within the rectangular roi but not part of the mask.
reset(ImageProcessor) ShortProcessor
RESET MacroConstants
RESET_MIN_MAX MacroConstants
RESET_THRESHOLD MacroConstants
resetBinaryThreshold() ImageProcessor
Resets the threshold if minThreshold=maxThreshold and lutUpdateMode=NO_LUT_UPDATE.
resetBoundingRect() PolygonRoi
resetClassLoader() IJ
resetClipboard() ImagePlus
Clears the internal clipboard.
resetCounter ParticleAnalyzer
resetCounter() Analyzer
Sets the measurement counter to zero.
resetCounters() PointRoi
resetDisplayRange() CompositeImage
resetDisplayRange() ImagePlus
resetDisplayRanges() CompositeImage
resetDoubleBuffer() ImageCanvas
resetEscape() IJ
This method sets the Esc key to the "up" position.
resetMinAndMax() IJ
Resets the minimum and maximum displayed pixel values of the
current image to be the same as the min and max pixel values.
resetMinAndMax() ByteProcessor
Resets this image's LUT.
resetMinAndMax() FloatProcessor
Recalculates the min and max values used to scale pixel
values to 0-255 for display.
resetMinAndMax() ImageProcessor
For short and float images, recalculates the min and max
image values needed to correctly display the image.
resetMinAndMax() ShortProcessor
Recalculates the min and max values used to scale pixel
values to 0-255 for display.
resetMinAndMax(ImagePlus) IJ
Resets the minimum and maximum displayed pixel values of the
specified image to be the same as the min and max pixel values.
resetMultiMeasureResults() RoiManager
resetOutOfRoi(ImageProcessor, int) GaussianBlur
Set the processed pixels above and below the roi rectangle back to their
previous value (i.e., snapshot buffer).
resetPreferences() Prefs
Delete the preferences file when ImageJ quits.
resetRoi() ImageProcessor
Sets the ROI (Region of Interest) and clipping rectangle to the entire image.
resetSelection() TextPanel
Clears the selection, if any.
resetStack() ImagePlus
resetThreshold() IJ
Disables thresholding on the current image.
resetThreshold() ImageProcessor
Disables thresholding.
resetThreshold(ImagePlus) IJ
Disables thresholding on the specified image.
resize(int) ImageProcessor
Returns a new ImageProcessor containing a scaled copy
of this image or ROI, with the aspect ratio maintained.
resize(int, int) ByteProcessor
Creates a new ByteProcessor containing a scaled copy of this image or selection.
resize(int, int) ColorProcessor
Creates a new ColorProcessor containing a scaled copy of this image or selection.
resize(int, int) FloatProcessor
Creates a new FloatProcessor containing a scaled copy of this image or selection.
resize(int, int) ImageProcessor
Returns a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int, int) ShortProcessor
Creates a new ShortProcessor containing a scaled copy of this image or selection.
resize(int, int) StackProcessor
Creates a new stack with dimensions 'newWidth' x 'newHeight'.
resize(int, int, boolean) ImageProcessor
Returns a new ImageProcessor containing a scaled copy of this image or ROI.
resize(int, int, boolean) StackProcessor
resizeLinearly(int, int) ImageProcessor
Use linear interpolation to resize images that have a width or height of one.
Resizer ij.plugin
This plugin implements the Edit/Crop and Image/Adjust/Size commands.
Resizer() Resizer
RESIZING Roi
reslice(ImagePlus) Slicer
RESOLUTION_UNIT TiffDecoder
RESTORE_PREVIOUS_TOOL MacroConstants
RESTORE_SETTINGS MacroConstants
restorePreviousTool() Toolbar
restoreRoi() ImagePlus
restoreTools() Toolbar
ResultsSorter ij.plugin
This plugin implements the Results Table's Sort command.
ResultsSorter() ResultsSorter
ResultsTable ij.measure
This is a table for storing measurement results and strings as columns of values.
ResultsTable() ResultsTable
Constructs an empty ResultsTable with the counter=0, no columns
and the precision set to 3 or the "Decimal places" value in
Analyze/Set Measurements if that value is higher than 3.
ResultsTable(Integer) ResultsTable
Constructs a ResultsTable with 'nRows' rows.
ResultsTableMacros ij.measure
This class implements the Apply Macro command in tables.
ResultsTableMacros(ResultsTable) ResultsTableMacros
RETURN MacroConstants
reverseNextPreviousOrder Prefs
Reverse channel-slice-frame priority used by Next Slice and Previous Slice commands.
revert() ImagePlus
Implements the File/Revert command.
revert() Editor
revertSystem() LogStream
Use this method to revert both System.out and System.err
to their original output streams.
revertSystemErr() LogStream
Use this method to revertSystem.err
to the original output stream.
revertSystemOut() LogStream
Use this method to revertSystem.out
to the original output stream.
revertToSaved(ImagePlus) FileOpener
Restores the original version of the specified image.
rgb HistogramWindow
rgb FHT
Used by the FFT class.
RGB NewImage
RGB FileInfo
24-bit interleaved RGB.
RGB_DILATE ColorProcessor
RGB_ERODE ColorProcessor
RGB_FIND_EDGES ColorProcessor
RGB_MAX ColorProcessor
RGB_MEDIAN ColorProcessor
RGB_MIN ColorProcessor
RGB_NOISE ColorProcessor
RGB_PLANAR FileInfo
24-bit planer RGB.
RGB_RESIZE ColorProcessor
RGB_ROTATE ColorProcessor
RGB_SCALE ColorProcessor
RGB_THRESHOLD ColorProcessor
RGB_TRANSLATE ColorProcessor
RGB48 FileInfo
48-bit interleaved RGB.
RGB48_PLANAR FileInfo
48-bit planar RGB.
RGBStackConverter ij.plugin
Converts a 2 or 3 slice stack, or a hyperstack, to RGB.
RGBStackConverter() RGBStackConverter
RGBStackMerge ij.plugin
This plugin implements the Image/Color/Merge Channels command.
RGBStackMerge() RGBStackMerge
RGBStackSplitter ij.plugin.filter
Deprecated; replaced by ij.plugin.ChannelSplitter.
RGBStackSplitter() RGBStackSplitter
RGBtoHSB(int[]) ColorSpaceConverter
RGBtoHSB(int, int, int) ColorSpaceConverter
RGBtoLab() ColorThresholder
Converts the current image from RGB to CIE L*a*b* and stores the results
in the same RGB image R=L*, G=a*, B=b*.
RGBtoLAB(int) ColorSpaceConverter
RGBtoLAB(int[]) ColorSpaceConverter
RGBToLab(ImagePlus) ColorSpaceConverter
Converts an RGB image into a Lab stack.
RGBtoXYZ(int[]) ColorSpaceConverter
Convert RGB to XYZ
RGBtoXYZ(int, int, int) ColorSpaceConverter
Convert RGB to XYZ
RGBtoYUV() ColorThresholder
Converts the current image from RGB to YUV and stores
the results in the same RGB image R=Y, G=U, B=V.
rh ImageStatistics
RIGHT Plot
Text justification.
RIGHT TextRoi
RIGHT RoiDecoder
RIGHT_JUSTIFY ImageProcessor
Right justify text.
RIGHT_MARGIN Plot
Deprecated.
rLUT1 ImageProcessor
rLUT2 ImageProcessor
rnd ImageProcessor
RODBARD Calibration
RODBARD CurveFitter
Constants for the built-in fit functions
RODBARD2 Calibration
RODBARD2 CurveFitter
Constants for the built-in fit functions
roi ImagePlus
roi FileInfo
Roi ij.gui
A rectangular region of interest and superclass for the other ROI classes.
Roi(double, double, double, double) Roi
Creates a rectangular ROI using double arguments.
Roi(double, double, double, double, int) Roi
Creates a rounded rectangular ROI using double arguments.
Roi(int, int, int, int) Roi
Creates a rectangular ROI.
Roi(int, int, int, int, int) Roi
Creates a new rounded rectangular ROI.
Roi(int, int, int, int, ImagePlus) Roi
Deprecated.
Roi(int, int, ImagePlus) 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) Roi
Starts the process of creating a user-defined rectangular Roi,
where sx and sy are the starting screen coordinates.
Roi(Rectangle) Roi
Creates a new rectangular Roi.
Roi(double, double, double, double) IJ
Creates an Roi.
ROI Opener
ROI MacroConstants
ROI Undo
ROI_HEIGHT ResultsTable
ROI_MANAGER MacroConstants
ROI_MASKS ParticleAnalyzer
ROI_PROPS_LENGTH RoiDecoder
ROI_PROPS_OFFSET RoiDecoder
ROI_REQUIRED PlugInFilter
Set this flag if the filter requires an ROI.
ROI_WIDTH ResultsTable
ROI_X ResultsTable
ROI_Y ResultsTable
ROIColor Roi
ROICOLOR Prefs
RoiDecoder ij.io
Decodes an ImageJ, NIH Image or Scion Image ROI file.
RoiDecoder(byte[], String) RoiDecoder
Constructs an RoiDecoder using a byte array.
RoiDecoder(String) RoiDecoder
Constructs an RoiDecoder using a file path.
RoiEncoder ij.io
Saves an ROI to a file or stream.
RoiEncoder(OutputStream) RoiEncoder
Creates an RoiEncoder using the specified OutputStream.
RoiEncoder(String) RoiEncoder
Creates an RoiEncoder using the specified path.
RoiEnlarger ij.plugin
This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command.
RoiEnlarger() RoiEnlarger
roiHeight ImageProcessor
roiHeight ImageStatistics
RoiInterpolator ij.plugin
This class interpolates between ROIs in the ROI Manager.
RoiInterpolator() RoiInterpolator
RoiListener ij.gui
Plugins that implement this interface are notified when
an ROI is created, modified or deleted.
RoiManager ij.plugin.frame
This plugin implements the Analyze/Tools/ROI Manager command.
RoiManager() RoiManager
Opens the "ROI Manager" window, or activates it if it is already open.
RoiManager(boolean) RoiManager
Constructs an ROIManager without displaying it.
roiManagerSelect(Roi, boolean) ImageCanvas
roiModified(ImagePlus, int) HistogramWindow
roiModified(ImagePlus, int) PlotWindow
For live plots, update the plot if the ROI of the source image changes
roiModified(ImagePlus, int) RoiListener
roiModified(ImagePlus, int) EventListener
RoiProperties ij.gui
Displays a dialog that allows the user to specify ROI properties such as color and line width.
RoiProperties(String, Roi) RoiProperties
Constructs a ColorChooser using the specified title and initial color.
RoiReader ij.plugin
Opens ImageJ, NIH Image and Scion Image for windows ROI outlines.
RoiReader() RoiReader
RoiRotationTool ij.plugin.tool
RoiRotationTool() RoiRotationTool
RoiRotator ij.plugin
This plugin implements the Edit/Selection/Rotate command.
RoiRotator() RoiRotator
RoiScaler ij.plugin
This plugin implements the Edit/Selection/Scale command.
RoiScaler() RoiScaler
roiWidth ImageProcessor
roiWidth ImageStatistics
RoiWriter ij.plugin.filter
Saves the current ROI outline to a file.
RoiWriter() RoiWriter
roiX ImageProcessor
roiX ImageStatistics
roiY ImageProcessor
roiY ImageStatistics
rollingBallBackground(ImageProcessor, double, boolean, boolean, boolean, boolean, boolean) BackgroundSubtracter
Create or subtract a background, works for all image types.
rollingBallBrightnessBackground(ColorProcessor, double, boolean, boolean, boolean, boolean, boolean) BackgroundSubtracter
Create or subtract a background, based on the brightness of an RGB image (keeping
the hue of each pixel unchanged)
rotate(double) ImageRoi
rotate(double) ByteProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) ColorProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) FloatProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(double) ImageProcessor
Rotates the image or selection 'angle' degrees clockwise.
rotate(double) ShortProcessor
Rotates the image or ROI 'angle' degrees clockwise.
rotate(Roi, double) RoiRotator
rotate(Roi, double, double, double) RoiRotator
ROTATED_RECT RoiDecoder
ROTATED_RECT_ROI Toolbar
RotatedRectRoi ij.gui
This class implements the rotated rectangle selection tool.
RotatedRectRoi(double, double, double, double, double) RotatedRectRoi
RotatedRectRoi(int, int, ImagePlus) RotatedRectRoi
rotateLeft() ImageProcessor
Rotates the entire image 90 degrees counter-clockwise.
rotateLeft() StackProcessor
rotateLine(ImagePlus, int) Straightener
rotateRight() ImageProcessor
Rotates the entire image 90 degrees clockwise.
rotateRight() StackProcessor
rotateYZ Prefs
Rotate YZ orthogonal views 90 degrees
Rotator ij.plugin.filter
This plugin implements the Image/Rotate/Arbitrarily command.
Rotator() Rotator
ROUND MacroConstants
ROUNDED_RECT_ARC_SIZE RoiDecoder
ROUNDED_RECT_ROI Toolbar
ROUNDNESS ResultsTable
rowIndex(int) TextPanel
Converts a y coordinate in pixels into a row index.
ROWS_PER_STRIP TiffDecoder
rowsPerStrip FileInfo
rt ParticleAnalyzer
run() Executer
run() HistogramWindow
run() PlotWindow
run() StackWindow
run() ImageJ
Quit using a separate thread, hopefully avoiding thread deadlocks.
run() MacroRunner
run() StartupRunner
run() ResultsTableMacros
run() BatchProcessor
run() Concatenator
Displays a dialog requiring user to choose images and
returns ImagePlus of concatenated images.
run() DragAndDrop
run() PlugInFilterRunner
The dispatcher for the background threads
run() ColorThresholder
run() ContrastAdjuster
run() Editor
Downloads BeanShell or Jython interpreter using a separate thread.
run() LineWidthAdjuster
run() ThresholdAdjuster
run() JavaScriptEvaluator
run() Orthogonal_Views
run() BrushTool
run() OverlayBrushTool
run() RecentOpener
Open the file and move the path to top of the submenu.
run() TextPanel
For better performance, open double-clicked files on
separate thread instead of on event dispatch thread.
run(boolean) StartupRunner
Runs the RunAtStartup and AutoRun macros, on the current thread
if 'batchMode' true, otherwise on a separate thread.
run(int) Interpreter
Runs an existing macro starting at the specified program counter location.
run(ImagePlus) Duplicator
Returns a copy of the image, stack or hyperstack contained in the specified ImagePlus.
run(ImagePlus) ThresholdToSelection
Returns a selection created from the thresholded pixels in the
specified image, or null if there are no thresholded pixels.
run(ImagePlus[]) Concatenator
Concatenates two or more images, stacks or hyperstacks.
run(ImagePlus[]) ImagesToStack
Converts the images in 'images' to a stack, using the
default settings ("copy center" and "titles as labels").
run(ImagePlus, int[]) ChannelArranger
Changes the order of the channels in a hyperstack.
run(ImagePlus, int, int) Duplicator
Returns a new stack containing a subrange of the specified stack.
run(ImagePlus, int, int, int, int, int, int) Duplicator
Returns a new hyperstack containing a possibly reduced version of the input image.
run(ImagePlus, Roi[]) BinaryInterpolator
run(ImagePlus, ImagePlus) Concatenator
Concatenates two images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus) Concatenator
Concatenates three images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus, ImagePlus) Concatenator
Concatenates four images, stacks or hyperstacks.
run(ImagePlus, ImagePlus, ImagePlus, ImagePlus, ImagePlus) Concatenator
Concatenates five images, stacks or hyperstacks.
run(ImagePlus, String) ZProjector
Performs projection on the entire stack using the specified method and returns
the result, where 'method' is "avg", "min", "max", "sum", "sd" or "median".
run(ImagePlus, String, int, int) ZProjector
Performs projection using the specified method and stack range, and returns
the result, where 'method' is "avg", "min", "max", "sum", "sd" or "median".
run(ImagePlus, String, String) IJ
Runs an ImageJ command using the specified image and options.
run(ImageStack) BinaryInterpolator
run(Program) Interpreter
Interprets the specified tokenized macro file starting at location 0.
run(Program, int, String) MacroRunner
Runs a tokenized macro on the current thread.
run(ImageProcessor) Analyzer
run(ImageProcessor) AVI_Writer
Asks for the compression type and filename; then saves as AVI file
run(ImageProcessor) BackgroundSubtracter
Background for any image type
run(ImageProcessor) Benchmark
run(ImageProcessor) Binary
run(ImageProcessor) Calibrator
run(ImageProcessor) Convolver
run(ImageProcessor) Duplicater
Deprecated.
run(ImageProcessor) EDM
Called by the PlugInFilterRunner to process the image or one frame of a stack
run(ImageProcessor) FFTCustomFilter
run(ImageProcessor) FFTFilter
run(ImageProcessor) Filler
run(ImageProcessor) Filters
run(ImageProcessor) FractalBoxCounter
run(ImageProcessor) GaussianBlur
This method is invoked for each slice during execution
run(ImageProcessor) ImageMath
run(ImageProcessor) ImageProperties
run(ImageProcessor) Info
Deprecated.
run(ImageProcessor) LineGraphAnalyzer
run(ImageProcessor) LutApplier
run(ImageProcessor) LutViewer
run(ImageProcessor) MaximumFinder
The plugin is inferred from ImageJ by this method
run(ImageProcessor) ParticleAnalyzer
run(ImageProcessor) PlugInFilter
Filters use this method to process the image.
run(ImageProcessor) Printer
run(ImageProcessor) RankFilters
run(ImageProcessor) RGBStackSplitter
run(ImageProcessor) RoiWriter
run(ImageProcessor) Rotator
run(ImageProcessor) SaltAndPepper
run(ImageProcessor) ScaleDialog
run(ImageProcessor) Shadows
run(ImageProcessor) StackLabeler
run(ImageProcessor) ThresholdToSelection
run(ImageProcessor) Transformer
run(ImageProcessor) Translator
run(ImageProcessor) UnsharpMask
This method is invoked for each slice or color channel.
run(ImageProcessor) Writer
Deprecated.
run(ImageProcessor) XYWriter
run(String) IJ
Runs an ImageJ command.
run(String) Interpreter
Interprets the specified string.
run(String) AboutBox
run(String) Animator
Set 'arg' to "set" to display a dialog that allows the user to specify the
animation speed.
run(String) AppearanceOptions
run(String) ArrowToolOptions
run(String) AVI_Reader
The plugin is invoked by ImageJ using this method.
run(String) BatchConverter
run(String) BatchMeasure
run(String) BatchProcessor
run(String) Binner
run(String) BMP_Reader
run(String) BMP_Writer
run(String) BrowserLauncher
Opens the specified URL (default is the ImageJ home page).
run(String) CalibrationBar
run(String) CanvasResizer
run(String) ChannelArranger
run(String) ChannelSplitter
run(String) CircularRoiMaker
run(String) ClassChecker
run(String) Clipboard
run(String) Colors
run(String) CommandFinder
Displays the Command Finder dialog.
run(String) CommandLister
run(String) Commands
run(String) Compiler
run(String) CompositeConverter
run(String) Concatenator
Optional string argument sets the name dialog boxes if called from another plugin.
run(String) ContrastEnhancer
run(String) ControlPanel
Creates a panel with the hierarchical tree structure of ImageJ's commands.
run(String) Converter
run(String) Coordinates
run(String) DICOM
run(String) Distribution
run(String) DragAndDrop
run(String) Duplicator
run(String) EventListener
run(String) FFT
run(String) FFTMath
run(String) FileInfoVirtualStack
run(String) Filters3D
run(String) FITS_Reader
run(String) FITS_Writer
run(String) FolderOpener
run(String) ContrastAdjuster
run(String) PlugInDialog
run(String) PlugInFrame
run(String) GaussianBlur3D
run(String) GelAnalyzer
run(String) GIF_Reader
run(String) GifWriter
run(String) Grid
run(String) GroupedZProjector
run(String) Histogram
run(String) Hotkeys
run(String) HyperStackConverter
run(String) HyperStackMaker
run(String) HyperStackReducer
run(String) ImageCalculator
run(String) ImageInfo
run(String) ImageJ_Updater
run(String) ImagesToStack
run(String) JavaProperties
run(String) JavaScriptEvaluator
run(String) JpegWriter
run(String) ListVirtualStack
run(String) LUT_Editor
run(String) LutLoader
If 'arg'="", displays a file open dialog and opens the specified
LUT.
run(String) Macro_Runner
Opens and runs the specified macro file (.txt or .ijm) or script file (.js, .bsh or .py)
on the current thread.
run(String) MacroInstaller
run(String) MeasurementsWriter
run(String) Memory
run(String) MontageMaker
run(String) NewPlugin
run(String) NextImageOpener
run(String) Options
run(String) Orthogonal_Views
run(String) OverlayCommands
run(String) OverlayLabels
run(String) PGM_Reader
run(String) PlugIn
This method is called when the plugin is loaded.
run(String) PluginInstaller
run(String) PlugInInterpreter
Run script on separate thread.
run(String) PNG_Writer
run(String) PNM_Writer
run(String) PointToolOptions
run(String) Profiler
run(String) Projector
run(String) ProxySettings
run(String) Raw
run(String) RectToolOptions
run(String) Resizer
run(String) ResultsSorter
run(String) RGBStackConverter
run(String) RGBStackMerge
run(String) RoiEnlarger
run(String) RoiInterpolator
run(String) RoiReader
run(String) RoiRotator
run(String) RoiScaler
run(String) ScaleBar
run(String) Scaler
run(String) ScreenGrabber
run(String) Selection
run(String) SimpleCommands
run(String) Slicer
run(String) SpecifyROI
run(String) Stack_Statistics
run(String) StackCombiner
run(String) StackEditor
run(String) StackInserter
run(String) StackMaker
run(String) StackPlotter
run(String) StackReducer
run(String) StackReverser
run(String) StackWriter
run(String) Startup
run(String) Straightener
run(String) SubHyperstackMaker
run(String) SubstackMaker
run(String) SurfacePlotter
run(String) Text
run(String) TextFileReader
run(String) TextReader
run(String) TextWriter
run(String) ThreadLister
run(String) Thresholder
run(String) BrushTool
run(String) PlugInTool
run(String) URLOpener
If 'urlOrName' is a URL, opens the image at that URL.
run(String) WandToolOptions
run(String) WindowOrganizer
run(String) XY_Reader
run(String) XYCoordinates
run(String) ZAxisProfiler
run(String) Zoom
run(String) ZProjector
run(String, ImagePlus, ImagePlus) ImageCalculator
run(String, String) IJ
Runs an ImageJ command, with options that are passed to the
GenericDialog and OpenDialog classes.
run(String, String) Interpreter
Runs the specified macro, passing it a string
argument and returning a string value.
run(String, String) JavaScriptEvaluator
run(String, String) PlugInInterpreter
Run script on current thread.
RUN MacroConstants
RUN_MACRO MacroConstants
RUN_TO_CARET Debugger
RUN_TO_COMPLETION Debugger
runBatchMacro(String, ImagePlus) Interpreter
Runs Process/Batch/ macros.
runBeanShell(String, String) Macro_Runner
Runs a BeanShell script on the current thread, passing a string argument,
which the script can retrieve using the getArgument() function.
runCommand(ImagePlus, String) RoiManager
Using the specified image, runs the ROI Manager "Add", "Add & Draw", "Update",
"Delete", "Measure", "Draw", "Show All", "Show None", "Fill", "Deselect", "Select All",
"Combine", "AND", "XOR", "Split", "Sort" or "Multi Measure" command.
runCommand(String) CommandFinder
runCommand(String) RoiManager
Executes the ROI Manager "Add", "Add & Draw", "Update", "Delete", "Measure", "Draw",
"Show All", "Show None", "Fill", "Deselect", "Select All", "Combine", "AND", "XOR", "Split",
"Sort" or "Multi Measure" command.
runCommand(String, String) RoiManager
Executes the ROI Manager "Open", "Save" or "Rename" command.
runCommand(String, String, double) 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) ImageJ
runFromLabel(String) FunctionFinder
runJavaScript(String, String) Macro_Runner
Runs a JavaScript script on the current thread, passing a string argument,
which the script can retrieve using the getArgument() function.
runMacro(Program, int, String) Interpreter
Interprets the specified tokenized macro starting at the specified location.
runMacro(String) IJ
Runs the macro contained in the string macro.
runMacro(String) MacroInstaller
runMacro(String, Editor) MacroInstaller
runMacro(String, String) IJ
Runs the macro contained in the string macro.
runMacro(String, String) Macro_Runner
Runs the specified macro on the current thread.
runMacroCommand(String) MacroInstaller
Runs a command in the Plugins/Macros submenu on the current thread.
runMacroFile(String) IJ
Runs the specified macro file.
runMacroFile(String, String) IJ
Runs the specified macro or script file in the current thread.
runMacroFile(String, String) Macro_Runner
Opens and runs the specified macro or script on the current
thread.
runMacroFromIJJar(String, String) Macro_Runner
runMacroFromJar(String, String) Macro_Runner
Runs the specified macro from a JAR file in the plugins folder,
passing it the specified argument.
runMacroShortcut(String) MacroInstaller
runMacroTool(String) MacroInstaller
runMacroTool(String) MacroToolRunner
runMacroTool(String) PlugInTool
These methods are overridden by MacroToolRunner.
runMenuTool(String, String) MacroInstaller
runMenuTool(String, String) MacroToolRunner
runMenuTool(String, String) PlugInTool
running ImageWindow
This variable is set false if the user presses the escape key or closes the window.
running2 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) IJ
Runs the specified plugin using the specified image.
runPlugIn(String, String) IJ
Runs the specified plugin and returns a reference to it.
runPlugIn(String, String, String) IJ
Runs the specified plugin and returns a reference to it.
runPython(String, String) Macro_Runner
Runs a Python script on the current thread, passing a string argument,
which the script can retrieve using the getArgument() function.
runShortcut(Program, int, String) MacroRunner
Runs tokenized macro on current thread if pgm.queueCommands is true.
runSocketListener Prefs
Run the SocketListener.
runUserPlugIn(String, String, String, boolean) ImageJ
rw ImageStatistics
rx ImageStatistics
ry ImageStatistics
s2ints(String) ControlPanel
Breaks the specified string into an array
of ints.
s2ints(String) FractalBoxCounter
Breaks the specified string into an array
of ints.
SaltAndPepper ij.plugin.filter
Implements ImageJ's Process/Noise/Salt and Pepper command.
SaltAndPepper() SaltAndPepper
SAMPLE_FORMAT TiffDecoder
sampleModel ImageProcessor
SAMPLES_PER_PIXEL TiffDecoder
samplesPerPixel FileInfo
SansSerif12 ImageJ
SansSerif, 12-point, plain font.
save HistogramWindow
save() FileSaver
Resaves the image.
save(Roi, String) RoiEncoder
Saves the specified ROI as a file, returning 'true' if successful.
save(ImagePlus, String) IJ
Saves the specified image, lookup table or selection to the specified file path.
save(ImagePlus, String) GifWriter
Saves the specified image in GIF format or as an animated GIF if the image is a stack.
save(ImagePlus, String, int) JpegWriter
Thread-safe method.
save(PrintWriter) TextPanel
Writes all the text in this TextPanel to a file.
save(String) IJ
Saves the current image, lookup table, selection or text window to the specified file path.
save(String) ResultsTable
Saves this ResultsTable as a tab or comma delimited text file.
save(String) MeasurementsWriter
SAVE MacroConstants
SAVE_AS MacroConstants
SAVE_AS_MENU Menus
SAVE_SETTINGS MacroConstants
saveAs() Editor
saveAs(ImagePlus, String, String) IJ
saveAs(String) Macro
saveAs(String) ResultsTable
saveAs(String) TextPanel
Saves all the text in this TextPanel to a file.
saveAs(String, String) IJ
saveAsBmp() FileSaver
Save the image in BMP format using a save file dialog.
saveAsBmp(String) FileSaver
Save the image in BMP format using the specified path.
saveAsByteArray(Roi) RoiEncoder
Saves the specified ROI as a byte array.
saveAsFits() FileSaver
Save the image in FITS format using a save file dialog.
saveAsFits(String) FileSaver
Save the image in FITS format using the specified path.
saveAsGif() FileSaver
Save the image in GIF format using a save file
dialog.
saveAsGif(String) FileSaver
Save the image in Gif format using the specified path.
saveAsJpeg() FileSaver
Save the image in JPEG format using a save file
dialog.
saveAsJpeg(String) FileSaver
Save the image in JPEG format using the specified path.
saveAsLut() FileSaver
Save the current LUT using a save file
dialog.
saveAsLut(String) FileSaver
Save the current LUT using the specified path.
saveAsPgm() FileSaver
Saves grayscale images in PGM (portable graymap) format
and RGB images in PPM (portable pixmap) format,
using a save file dialog.
saveAsPgm(String) FileSaver
Saves grayscale images in PGM (portable graymap) format
and RGB images in PPM (portable pixmap) format,
using the specified path.
saveAsPng() FileSaver
Save the image in PNG format using a save file dialog.
saveAsPng(String) FileSaver
Save the image in PNG format using the specified path.
saveAsRaw() FileSaver
Save the image or stack as raw data using a save file
dialog.
saveAsRaw(String) FileSaver
Save the image as raw data using the specified path.
saveAsRawStack(String) FileSaver
Save the stack as raw data using the specified path.
saveAsText() FileSaver
Save the image as tab-delimited text using a save file
dialog.
saveAsText(String) FileSaver
Save the image as tab-delimited text using the specified path.
saveAsTiff() FileSaver
Saves the image or stack in TIFF format using a save file
dialog.
saveAsTiff(ImagePlus, String) IJ
Saves the specified image in TIFF format.
saveAsTiff(String) FileSaver
Saves the image in TIFF format using the specified path.
saveAsTiffStack(String) FileSaver
Saves the stack as a multi-image TIFF using the specified path.
saveAsZip() FileSaver
Uses a save file dialog to save the image or stack as a TIFF
in a ZIP archive.
saveAsZip(String) FileSaver
Save the image or stack in TIFF/ZIP format using the specified path.
saveBitmap(String, Image, int, int) BMP_Writer
saveChanges(int) VirtualStack
Currently not implemented
SaveChangesDialog ij.gui
A modal dialog box with a one line message and
"Don't Save", "Cancel" and "Save" buttons.
SaveChangesDialog(Frame, String) SaveChangesDialog
saveCommand() Recorder
Writes the current command and options to the Recorder window.
SaveDialog ij.io
This class displays a dialog window from
which the user can save a file.
SaveDialog(String, String, String) 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) SaveDialog
Displays a file save dialog, using the specified
default directory and file name and extension.
saveDisplayRangesAndLuts(ImagePlus, FileInfo) FileSaver
saveGlobals(Program) Interpreter
Saves global variables.
saveImageDescription(byte[], FileInfo) TiffDecoder
Save the image description in the specified FileInfo.
saveLocation(String, Point) Prefs
Saves the Point loc in the preferences
file as a string using the keyword key.
saveMetadata(String, String) TiffDecoder
saveOutput(boolean) BatchProcessor
savePreferences() Prefs
Saves user preferences in the IJ_Prefs.txt properties file.
savePreferences(Properties) NewImage
Called when ImageJ quits.
savePreferences(Properties) PlotWindow
Called once when ImageJ quits.
savePreferences(Properties) ImageJ
Called once when ImageJ quits.
savePreferences(Properties) ImportDialog
Called once when ImageJ quits.
savePreferences(Properties) Menus
Called once when ImageJ quits.
savePreferences(Properties) Analyzer
Called once when ImageJ quits.
savePreferences(Properties) ParticleAnalyzer
Called once when ImageJ quits.
savePrefs(Properties, String) Prefs
savePressed() SaveChangesDialog
Returns true if the user dismissed dialog by pressing "Save".
saveResults(ImageStatistics, Roi) Analyzer
Saves the measurements specified in the "Set Measurements" dialog,
or by calling setMeasurements(), in the default results table.
saveResults(ImageStatistics, Roi) ParticleAnalyzer
Saves statistics for one particle in a results table.
saveRoi() ImagePlus
saveRoi(ImagePlus) RoiWriter
saveString(String, String) IJ
Saves a string as a file.
saveThreshold(double, double, Calibration) ImageStatistics
saveXValues PlotWindow
Write first X column when listing or saving.
saveXYCoordinates(ImagePlus) XYWriter
scalableLabels() Overlay
scale(double, double) ByteProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) ColorProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) FloatProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) ImageProcessor
Scales the image by the specified factors.
scale(double, double) ShortProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) StackProcessor
scale(double, double, double) StackProcessor
scale(Roi, double, double, boolean) RoiScaler
SCALE_T Resizer
scaleAndSetThreshold(double, double, int) ImageProcessor
Set the threshold using a 0-255 range.
ScaleBar ij.plugin
This plugin implements the Analyze/Tools/Draw Scale Bar command.
ScaleBar() ScaleBar
scaled() Calibration
Returns true if this image is spatially calibrated.
ScaleDialog ij.plugin.filter
Implements the Analyze/Set Scale command.
ScaleDialog() ScaleDialog
Scaler ij.plugin
This plugin implements the Image/Scale command.
Scaler() Scaler
scaleXtoPxl(double) Plot
Converts calibrated coordinates to pixel coordinates.
scaleYtoPxl(double) Plot
Converts calibrated coordinates to pixel coordinates.
SCIENTIFIC_NOTATION Measurements
SCREEN_HEIGHT MacroConstants
SCREEN_WIDTH MacroConstants
ScreenGrabber ij.plugin
This plugin implements the Plugins/Utilities/Capture Screen
and Plugins/Utilities/Capture Image commands.
ScreenGrabber() ScreenGrabber
screenX(int) ImageCanvas
Converts an offscreen x-coordinate to a screen x-coordinate.
screenX(int) Roi
screenXD(double) ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenXD(double) Roi
screenY(int) ImageCanvas
Converts an offscreen y-coordinate to a screen y-coordinate.
screenY(int) Roi
screenYD(double) ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenYD(double) Roi
scriptMode() Recorder
scroll(int, int) ImageCanvas
scroll(int, int) PlotCanvas
overrides ImageCanvas.scroll; if plot is not frozen, scrolling modifies the plot data range
ScrollbarWithLabel 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() ScrollbarWithLabel
ScrollbarWithLabel(StackWindow, int, int, int, int, char) ScrollbarWithLabel
scrollToTop() TextPanel
SD_METHOD ZProjector
seed ImageProcessor
seek(int) RandomAccessStream
seek(long) RandomAccessStream
SEGMENTED MaximumFinder
Output type watershed-segmented image
select(int) RoiManager
Assigns the ROI at the specified index to the current image.
select(int, boolean, boolean) RoiManager
select(ImagePlus, int) RoiManager
Assigns the ROI at the specified index to 'imp'.
SELECT MacroConstants
SELECT_IMAGE MacroConstants
selectable(boolean) Overlay
Set 'false' to prevent ROIs in this overlay from being activated
by clicking on their labels or by a long clicking.
selectAll() TextPanel
Selects all the lines in this TextPanel.
selectAndMakeVisible(ImagePlus, int) RoiManager
Selection ij.plugin
This plugin implements the commands in the Edit/Selection submenu.
Selection() Selection
SELECTION_CONTAINS MacroConstants
SELECTION_NAME MacroConstants
SELECTION_TYPE MacroConstants
selectRow(Roi) ResultsTable
Selects the row in the "Results" table assocuiated with the specified Roi.
selectWindow(int) IJ
For IDs less than zero, activates the image with the specified ID.
selectWindow(String) IJ
Activates the window with the specified title.
sendArguments(String[]) OtherInstance
separator Prefs
file.separator system property
serialize() FileSaver
Converts this image to a TIFF encoded array of bytes,
which can be decoded using Opener.deserialize().
set(double) FloatProcessor
set(double) ImageProcessor
Assigns 'value' to each pixel in the image or ROI.
set(double) ShortProcessor
set(int, int) ByteProcessor
set(int, int) ColorProcessor
set(int, int) FloatProcessor
set(int, int) ImageProcessor
set(int, int) ShortProcessor
set(int, int, int) ByteProcessor
set(int, int, int) ColorProcessor
set(int, int, int) FloatProcessor
set(int, int, int) ImageProcessor
This is a faster version of putPixel() that does not clip
out of range values and does not do bounds checking.
set(int, int, int) ShortProcessor
set(Roi, int) Overlay
Replaces the ROI at the specified index.
set(String, boolean) Prefs
Saves the boolean variable value in the preferences
file using the keyword key.
set(String, double) Prefs
Saves value in the preferences file using
the keyword key.
set(String, int) Prefs
Saves value in the preferences file using
the keyword key.
set(String, String) Prefs
Saves the value of the string text in the preferences
file using the keyword key.
SET_AUTO_THRESHOLD MacroConstants
SET_BACKGROUND MacroConstants
SET_BATCH_MODE MacroConstants
SET_COLOR MacroConstants
SET_FONT MacroConstants
SET_FOREGROUND MacroConstants
SET_JUSTIFICATION MacroConstants
SET_KEY_DOWN MacroConstants
SET_LINE_WIDTH MacroConstants
SET_LOCATION MacroConstants
SET_LUT MacroConstants
SET_METADATA MacroConstants
SET_MIN_MAX MacroConstants
SET_OPTION MacroConstants
SET_PASTE_MODE MacroConstants
SET_PIXEL MacroConstants
SET_RANGE PlotDialog
types of dialog
SET_RESULT MacroConstants
SET_RGB_WEIGHTS MacroConstants
SET_SELECTION_LOC MacroConstants
SET_SELECTION_NAME MacroConstants
SET_SLICE MacroConstants
SET_THRESHOLD MacroConstants
SET_TOOL MacroConstants
SET_VOXEL_SIZE MacroConstants
SET_Z_COORDINATE MacroConstants
set16bitRange(int) ContrastAdjuster
setActivated() ImagePlus
Called by ImageWindow.windowActivated().
setActiveChannels(String) ImagePlus
Controls which channels in a composite color image are displayed,
where 'channels' is a list of ones and zeros that specify the channels to
display.
setAdditionalFunctions(String) Interpreter
The specified string, if not null, is added to strings passed to the run() method.
setAllPoints(boolean) Wand
Set 'true' and output will contain intermediate points for straight lines longer than one pixel.
setAngle(double) ImageRoi
setAngle(double) TextRoi
setAnimate(boolean) StackWindow
setAntialiased(boolean) TextRoi
Sets the 'antialiased' instance variable.
setAntialiased(Graphics, boolean) Java2
setAntialiasedText(boolean) Plot
Determines whether to use antialiased text (default true)
setAntialiasedText(boolean) TextRoi
Sets the state of the global 'antialiasedText' variable.
setAntialiasedText(boolean) ImageProcessor
Specifies whether or not text is drawn using antialiasing.
setAntialiasedText(Graphics, boolean) Java2
setAntialiasRendering(boolean) ImagePlus
Enable/disable use of antialiasing by the flatten() method.
setApplyMacroTable(ResultsTable) Interpreter
setAutoThreshold(int, int) ImageProcessor
Automatically sets the lower and upper threshold levels, where 'method'
must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT,
BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
setAutoThreshold(ImagePlus, String) IJ
setAutoThreshold(AutoThresholder.Method, boolean) ImageProcessor
setAutoThreshold(AutoThresholder.Method, boolean, int) ImageProcessor
setAutoThreshold(String) ImageProcessor
Automatically sets the lower and upper threshold levels, where 'method'
must be "Default", "Huang", "Intermodes", "IsoData", "IJ_IsoData", "Li",
"MaxEntropy", "Mean", "MinError", "Minimum", "Moments", "Otsu",
"Percentile", "RenyiEntropy", "Shanbhag", "Triangle" or "Yen".
setAutoThreshold(String, boolean, int) ImageProcessor
setAverageWhenDownsizing(boolean) Resizer
setAxes(boolean, boolean, boolean, boolean, boolean, boolean, int, int) Plot
Sets the properties of the axes.
setAxisLabelFont(int, float) Plot
Sets the size of the x and y label font size and style.
setAxisXLog(boolean) Plot
Sets the X Axis format to Log or Linear.
setAxisYLog(boolean) Plot
Sets the Y Axis format to Log or Linear.
setBackground(String) Thresholder
setBackgroundColor(int, int, int) IJ
Sets the background color.
setBackgroundColor(Color) Plot
Set the plot frame background color.
setBackgroundColor(Color) Toolbar
setBackgroundColor(Color) Recorder
setBackgroundColor(String) Plot
Set the plot frame background color.
setBackgroundValue(double) ByteProcessor
Sets the background fill value, where 0<=value<=255.
setBackgroundValue(double) ColorProcessor
Sets the background fill value, where value is interpreted as an RGB int.
setBackgroundValue(double) FloatProcessor
Does nothing.
setBackgroundValue(double) ImageProcessor
Sets the background fill value used by the rotate() and scale() methods.
setBackgroundValue(double) ShortProcessor
Does nothing.
setBatchMode(boolean) ProgressBar
setBilinearInterpolation(Graphics, boolean) Java2
setBinaryThreshold() ImageProcessor
setBitDepth(int) PlotVirtualStack
setBitDepth(int) VirtualStack
Sets the bit depth (8, 16, 24 or 32).
setBlackBackground() Recorder
setBlockIncrement(int) ScrollbarWithLabel
setBrightness(FloatProcessor) ColorProcessor
Updates the brightness using the pixels in the specified FloatProcessor).
setBrushSize(int) Toolbar
Set the size of the selection brush tool, in pixels.
setBrushWidth(int) BrushTool
setC(int) ImagePlus
Sets the hyperstack channel position (one based).
setC(ImageWindow, int) SyncWindows
setCalibration(Calibration) ImagePlus
Sets this image's calibration.
setCalibrationTable(float[]) ImageProcessor
Set a lookup table used by getPixelValue(), getLine() and
convertToFloat() to calibrate pixel values.
setCancelLabel(String) GenericDialog
Sets a replacement label for the "Cancel" button.
setCaseSensitive(boolean) WildcardMatch
Makes pattern matching case insensitive.
setChannel(int, ByteProcessor) ColorProcessor
Sets the pixels of one color channel from a ByteProcessor.
setChannelColorModel(IndexColorModel) CompositeImage
setChannelLut(LUT) CompositeImage
setChannelLut(LUT, int) CompositeImage
setChannelsUpdated() CompositeImage
Deprecated
setClipRect(Rectangle) ImageProcessor
Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
setColor(double) ImageProcessor
Sets the default fill/draw value.
setColor(int) ColorProcessor
Sets the fill/draw color, where color is an RGB int.
setColor(int) ImageProcessor
Sets the default fill/draw value.
setColor(Color) Plot
Changes the drawing color for the next objects that will be added to the plot.
setColor(Color) PlotWindow
Deprecated.
setColor(Color) Roi
Sets the default (global) color used for ROI outlines.
setColor(Color) Toolbar
Deprecated.
setColor(Color) ImagePlus
Sets current foreground color.
setColor(Color) ByteProcessor
Sets the foreground drawing color.
setColor(Color) ColorProcessor
Sets the foreground color.
setColor(Color) FloatProcessor
Sets the foreground fill/draw color.
setColor(Color) ImageProcessor
Sets the default fill/draw value to the pixel
value closest to the specified color.
setColor(Color) ShortProcessor
Sets the foreground fill/draw color.
setColor(Color, Color) Plot
Changes the drawing color for the next objects that will be added to the plot.
setColor(String) Plot
setColor(String, String) Plot
Sets the drawing color for the next objects that will be added to the plot.
setColorModel(ColorModel) ImageStack
Assigns a new color model to this stack.
setColorModel(ColorModel) ColorProcessor
setColorModel(ColorModel) ImageProcessor
Sets the color model.
setColumn(String, Variable[]) ResultsTable
Implements the Table.setColumn() macro function.
setColumnHeadings(String) IJ
Clears the "Results" window and sets the column headings to
those in the tab-delimited 'headings' String.
setColumnHeadings(String) TextPanel
Clears this TextPanel and sets the column headings to
those in the tab-delimited 'headings' String.
setCommand(String) Recorder
Starts recording a command.
setCommandName(String) ImageJ
setComposite(Composite) ImageRoi
Sets the composite mode.
setCornerDiameter(int) Roi
Sets the rounded rectangle corner diameter (pixels).
setCounter(int) PointRoi
setCounterInfo(int[]) PointRoi
setCounters(int[]) PointRoi
setCrossLoc(int, int, int) Orthogonal_Views
setCTable(float[], String) Calibration
Sets the calibration table.
setCurrentFont(Font) TextRoi
Set the current (instance) font.
setCurrentWindow(ImageWindow) WindowManager
Makes the image contained in the specified window the active image.
setCursor(int, int, int, int) ImageCanvas
Sets the cursor based on the current tool and cursor location.
setCursor(ImagePlus, Roi) SyncWindows
setCursor(Cursor, int) ImageCanvas
Experimental
setCustomRoi(boolean) ImageCanvas
Allows plugins (e.g., Orthogonal_Views) to create a custom ROI using a display list.
setDebugger(Debugger) Interpreter
setDebugMode(boolean) IJ
Enable/disable debug mode.
setDebugMode(int) Interpreter
setDecimalPlaces(int, int) ResultsTable
setDefault16bitRange(int) ImagePlus
Set the default 16-bit display range, where 'bitDepth' must be 0 (auto-scaling),
8 (0-255), 10 (0-1023), 12 (0-4095, 14 (0-16383), 15 (0-32767) or 16 (0-65535).
setDefaultAngle(double) TextRoi
Sets the default angle.
setDefaultCounter(int) PointRoi
setDefaultCrossColor(Color) PointRoi
Deprecated
setDefaultDirectory(String) DirectoryChooser
Sets the default directory presented in the dialog.
setDefaultDirectory(String) OpenDialog
Sets the current working directory.
setDefaultDirectory(String) Editor
setDefaultDoubleHeaded(boolean) Arrow
setDefaultFillColor(Color) Roi
setDefaultFillColor(Color) TextRoi
Sets the default fill (background) color.
setDefaultHeadings() ResultsTable
Sets the headings used by the Measure command ("Area", "Mean", etc.).
setDefaultHeadings() Analyzer
Sets the default headings ("Area", "Mean", etc.).
setDefaultHeadSize(double) Arrow
setDefaultMarkerSize(String) PointRoi
Deprecated.
setDefaultOutline(boolean) Arrow
setDefaultSize(int) PointRoi
setDefaultString(int, String) GenericDialog
setDefaultStyle(int) Arrow
setDefaultType(int) PointRoi
setDefaultWidth(double) Arrow
setDialog(GenericDialog) PlugInFilterRunner
setDimensions(int, int, int) ImagePlus
Sets the 3rd, 4th and 5th dimensions, where
nChannels*nSlices*nFrames
must be equal to the stack size.
setDisplayList(Roi, Color) ImageCanvas
Deprecated.
setDisplayList(Shape, Color, BasicStroke) ImageCanvas
Deprecated.
setDisplayList(Vector) ImageCanvas
Deprecated.
setDisplayMode(int) ImagePlus
Sets the display mode of composite color images, where 'mode'
should be IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE.
setDisplayRange(double, double) CompositeImage
setDisplayRange(double, double) ImagePlus
Sets the display range of the current channel.
setDisplayRange(double, double, int) 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) 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) Arrow
setDrawingColor(int, int, boolean) ImageCanvas
Sets the foreground drawing color (or background color if
'setBackground' is true) to the color of the pixel at (ox,oy).
setDrawingSize(int, int) ImageCanvas
Obsolete; replaced by setSize()
setDrawOffset(boolean) Line
setDrawOffset(boolean) PolygonRoi
setDrawOffset(boolean) Roi
setDrawStringMode(boolean) TextRoi
setEchoChar(char) GenericDialog
Sets the echo character for the next string field.
setEditMode(ImagePlus, boolean) RoiManager
setEscapeChar(char) WildcardMatch
Sets the new character to be used as an escape character, overriding the
the default of '\'.
setExceptionHandler(IJ.ExceptionHandler) IJ
Installs a custom exception handler that
overrides the handleException() method.
setExtension(String, String) SaveDialog
setExtraArrayElements(int) Minimizer
Add a given number of extra elements to array of parameters (independent vaiables)
for private use in the user function.
setf(int, float) ByteProcessor
setf(int, float) ColorProcessor
setf(int, float) FloatProcessor
setf(int, float) ImageProcessor
setf(int, float) ShortProcessor
setf(int, int, float) ByteProcessor
setf(int, int, float) ColorProcessor
setf(int, int, float) FloatProcessor
setf(int, int, float) ImageProcessor
Sets the value of the pixel at (x,y) to 'value'.
setf(int, int, float) ShortProcessor
setFileInfo(FileInfo) ImagePlus
Saves this image's FileInfo so it can be later
retieved using getOriginalFileInfo().
setFileName(String) MacroInstaller
setFilePath(String) Macro_Runner
setFillColor(Color) Overlay
Sets the fill color of all the ROIs in this overlay.
setFillColor(Color) Roi
Sets the fill color used to display this ROI, or set to null to display it transparently.
setFlattenScale(double) Roi
setFloatArray(float[][]) ImageProcessor
Replaces the pixel data with contents of the specified 2D float array.
setFocusable(boolean) ScrollbarWithLabel
setFont(int, float) Plot
Sets the font size and style for all following drawLabel etc.
setFont(Font) MultiLineLabel
setFont(Font) Plot
Sets the font for all following drawLabel etc.
setFont(Font) Editor
setFont(Font) ImageProcessor
Sets the font used by drawString().
setFont(Font, boolean) TextPanel
setFont(String, int, int) 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) TextRoi
Sets the font face, size, style and antialiasing mode that will
be used by TextROIs interactively created using the text tool.
setFontColor(String) ParticleAnalyzer
Sets the color ("blue", "black", etc.) of the font used to label outlines in the next particle analyzer instance.
setFontSize(int) Menus
Set the size (in points) used for the fonts in ImageJ menus.
setFontSize(int) ParticleAnalyzer
Sets the size of the font used to label outlines in the next particle analyzer instance.
setFontSize(int) MontageMaker
setForegroundColor(int, int, int) IJ
Sets the foreground color.
setForegroundColor(Color) Toolbar
setForegroundColor(Color) Recorder
setFormatFlags(int) Plot
Sets the flags that control the axes format.
setFrameSize(int, int) Plot
Sets the plot frame size in (unscaled) pixels.
setFromFloatArrays(float[][]) ByteProcessor
setFromFloatProcessors(FloatProcessor[]) ByteProcessor
setFrozen(boolean) Plot
Freezes or unfreezes the plot.
setFunction(int, double[], String) Calibration
Sets the calibration function, coefficient table and unit (e.g.
setFunction(int, double[], String, boolean) Calibration
setFunction(UserFunction, int) Minimizer
Set the the target function, i.e.
setGlobalCalibration(Calibration) ImagePlus
Sets the system-wide calibration.
setGlobalJustification(int) TextRoi
Sets the 'justification' instance variable (must be LEFT, CENTER or RIGHT)
setHeading(int, String) ResultsTable
Deprecated.
setHeadSize(double) Arrow
setHelpLabel(String) GenericDialog
Sets a replacement label for the "Help" button.
setHideLabels(boolean) PointRoi
Deprecated.
setHideOutputImage(boolean) ParticleAnalyzer
Set 'hideOutputImage' true to not display the "Show:" image.
setHideOverlay(boolean) ImagePlus
setHistogramRange(double, double) ImageProcessor
Set the range used for histograms of float images.
setHistogramSize(int) ImageProcessor
Set the number of bins to be used for histograms of float images.
setHSB(byte[], byte[], byte[]) ColorProcessor
Sets the current pixels from 3 byte arrays (hue, saturation and brightness).
setIgnoreClipRect(boolean) Roi
setIgnoreFlush(boolean) ImagePlus
setIgnoreGlobalCalibration(boolean) ImagePlus
setIJMenuBar ImagePlus
setIJMenuBar Prefs
Set MenuBar on Macs running Java 8.
setIJMenuBar() ImagePlus
setIJMenuBar(boolean) ImagePlus
setIm5D(boolean) Concatenator
setImage(ImagePlus) ImageWindow
setImage(ImagePlus) Roi
setImage(ImagePlus) ImagePlus
Replaces this image with the specified ImagePlus.
setImage(ImagePlus) Calibration
Disables the density calibation if the specified image has a differenent bit depth.
setImage(ImagePlus) ZProjector
Explicitly set image to be projected.
setImage(Image) ImagePlus
Replaces the image, if any, with the one specified.
setImageJMenuBar(ImageWindow) ImageWindow
setImagePlus(ImagePlus) Plot
Sets the ImagePlus where the plot will be displayed.
setImagesURL(String) Prefs
Sets the URL of the directory that contains the ImageJ sample images.
setImageUpdated() ImageCanvas
ImagePlus.updateAndDraw calls this method to force the paint()
method to update the image from the ImageProcessor.
setInitialParameters(double[]) CurveFitter
Sets the initial parameters, which override the default initial parameters.
setInputEvent(InputEvent) IJ
setInsets(int, int, int) GenericDialog
Set the insets (margins), in pixels, that will be
used for the next component added to the dialog
(except components added to the same row with addToSameRow)
setInstanceColor(Color) Roi
Deprecated.
setIntArray(int[][]) ImageProcessor
Replaces the pixel data with contents of the specified 2D int array.
setInterpolate(boolean) ImageProcessor
This method has been replaced by setInterpolationMethod().
setInterpolationMethod(int) ImageProcessor
Use this method to set the interpolation method (NONE,
BILINEAR or BICUBIC) used by scale(), resize() and rotate().
setInvertY(boolean) Calibration
Sets the 'invertY' flag.
setIsCalibrationBar(boolean) Overlay
setIsCursor(boolean) Roi
setIsMacroWindow(boolean) Editor
setJpegQuality(int) FileSaver
Specifies the image quality (0-100).
setJustification(int) Plot
Sets the justification used by addLabel(), where justification
is Plot.LEFT, Plot.CENTER or Plot.RIGHT.
setJustification(int) TextRoi
Sets the 'justification' instance variable (must be LEFT, CENTER or RIGHT)
setJustification(int) ImageProcessor
Sets the justification used by drawString(), where justification
is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY.
setKeyDown(int) IJ
setKeyUp(int) IJ
setLabel(String, int) ResultsTable
Adds a label to the beginning of the specified row,
or updates an existing lable, where 0<=row
setLabelColor(Color) Overlay
setLabelFont(Font) Overlay
setLabelFont(Font, boolean) Overlay
setLastDirectory(String) OpenDialog
Sets the path to the directory containing the last file opened by the user.
setLastName(String) OpenDialog
Sets the name of the last file opened by the user.
setLegend(String, int) Plot
Adds a legend.
setLimits(double, double, double, double) Plot
Sets the x-axis and y-axis range.
setLimits(double, double, double, double) PlotWindow
Deprecated.
setLimitsToDefaults(boolean) Plot
Sets the plot range to the initial value determined from minima&maxima or given by setLimits.
setLimitsToFit(boolean) Plot
Sets the plot range to encompass all data.
setLine(int, String) TextPanel
Replaces the contents of the specified line, where 'index'
must be greater than or equal to zero and less than
the value returned by getLineCount().
setLineWidth(float) Plot
Changes the line width for the next objects that will be added to the plot.
setLineWidth(int) Plot
Changes the line width for the next objects that will be added to the plot.
setLineWidth(int) PlotWindow
Deprecated.
setLineWidth(int) Roi
Deprecated.
setLineWidth(int) ParticleAnalyzer
Sets the outline line width for the next ParticleAnalyzer instance.
setLineWidth(int) ImageProcessor
Sets the line width used by lineTo() and drawDot().
setLocation(double, double) PolygonRoi
setLocation(double, double) Roi
Set the location of the ROI in image coordinates.
setLocation(int, int) GenericDialog
setLocation(int, int) Line
setLocation(int, int) Roi
Set the location of the ROI in image coordinates.
setLocationAndSize(int, int, int, int) ImageWindow
Moves and resizes this window.
setLogScaleX() Plot
Sets log scale in x.
setLogScaleY() Plot
setLoopBackAndForth(boolean) Calibration
Set the default state of the animation "Loop back and forth" flag
setLut(LUT) ImagePlus
Assigns a LUT (lookup table) to this image.
setLut(LUT) ImageProcessor
setLutAnimation(boolean) FloatProcessor
setLutAnimation(boolean) ImageProcessor
For 16 and 32 bit processors, set 'lutAnimation' true
to have createImage() use the cached 8-bit version
of the image.
setLutAnimation(boolean) ShortProcessor
setLuts(LUT[]) CompositeImage
setMagnification(double) ImageCanvas
setMagnification(double) PlotCanvas
The image of a PlotCanvas is always shown at 100% magnification unless the plot is frozen
setMask(ImageProcessor) ImageProcessor
Defines a byte mask that limits processing to an
irregular ROI.
setMaxError(double) CurveFitter
Set the maximum error.
setMaxError(double) Minimizer
Sets the accuracy of convergence.
setMaxError(double, double) Minimizer
Sets the accuracy of convergence.
setMaximum(int) ScrollbarWithLabel
setMaximumThreads(int) Minimizer
Call setMaximuThreads(1) to avoid multi-threaded execution (in case the user-provided
target function does not allow moultithreading).
setMaxIntervals(int) Plot
Sets the maximum number of intervals in a plot.
setMaxIterations(int) CurveFitter
Set maximum number of iterations allowed (sum of iteration count for all restarts)
setMaxIterations(int) Minimizer
Set maximum number of iterations allowed (including all restarts and all threads).
setMaxRestarts(int) Minimizer
Set maximum number of minimization restarts to do.
setMeasurement(int, boolean) Analyzer
Sets the specified system-wide measurement option.
setMeasurements(int) Analyzer
Sets the system-wide measurement options.
setMenuBarCount Menus
setMenuBarTime ImageWindow
setMethod(int) ZProjector
setMethod(String) ThresholdAdjuster
Sets the thresholding method ("Default", "Huang", etc).
setMethod(String) Thresholder
setMinAndMax(double, double) ProfilePlot
Sets the y-axis min and max.
setMinAndMax(double, double) IJ
Sets the display range (minimum and maximum displayed pixel values) of the current image.
setMinAndMax(double, double) ByteProcessor
Maps the entries in this image's LUT from min-max to 0-255.
setMinAndMax(double, double) ColorProcessor
Uses a table look-up to map the pixels in this image from min-max to 0-255.
setMinAndMax(double, double) FloatProcessor
Sets the min and max variables that control how real
pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double) 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) ShortProcessor
Sets the min and max variables that control how real
pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double, int) IJ
Sets the minimum and maximum displayed pixel values on the specified RGB
channels, where 4=red, 2=green and 1=blue.
setMinAndMax(double, double, int) ColorProcessor
setMinAndMax(ImagePlus, double, double) IJ
Sets the display range (minimum and maximum displayed pixel values) of the specified image.
setMinimum(int) ScrollbarWithLabel
setMinorTickLength(int) Plot
Sets the length of the minor tick in pixels.
setMode(int) CompositeImage
setMode(String) ThresholdAdjuster
Sets the current mode ("Red","B&W" or"Over/Under").
setName(String) Roi
Sets the name of this ROI.
setNaNEmptyCells(boolean) ResultsTable
Set 'true' to initially fill data arrays with NaNs instead of zeros.
setNextLocation(int, int) ImageWindow
Causes the next image to be displayed at the specified location.
setNextLocation(int, int) WaitForUserDialog
Display the next WaitForUser dialog at the specified location.
setNextLocation(Point) ImageWindow
Causes the next image to be displayed at the specified location.
setNonScalable(boolean) Roi
Set 'nonScalable' true to have TextRois in a display
list drawn at a fixed location and size.
setNormalize(boolean) ContrastEnhancer
setNormalize(boolean) Convolver
If 'normalize' is true (the default), the convolve(), convolveFloat() and
convolveFloat1D() (4 argument version) methods divide each kernel
coefficient by the sum of the coefficients, preserving image brightness.
setNPasses(int) PlotContentsStyleDialog
setNPasses(int) BackgroundSubtracter
setNPasses(int) Binary
setNPasses(int) Convolver
setNPasses(int) EDM
Prepare the progress bar.
setNPasses(int) ExtendedPlugInFilter
This method is called by ImageJ to inform the plugin-filter
about the passes to its run method.
setNPasses(int) GaussianBlur
Set the number of passes of the blur1Direction method.
setNPasses(int) ImageMath
setNPasses(int) MaximumFinder
Set his to the number of images to process (for the watershed progress bar only).
setNPasses(int) 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) Rotator
setNPasses(int) StackLabeler
setNPasses(int) Translator
setNPasses(int) UnsharpMask
Since most computing time is spent in GaussianBlur, forward the
information about the number of passes to Gaussian Blur.
setOffsetMultiplySlopeParams(int, int, int) CurveFitter
For improved fitting performance when using a custom fit formula, one may
specify parameters that can be calculated directly by linear regression.
setOKLabel(String) GenericDialog
Sets a replacement label for the "OK" button.
setOpacity(double) 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) ImagePlus
setOpenUsingPlugins(boolean) Opener
Open all images using HandleExtraFileTypes.
setOption(String, boolean) Analyzer
setOptions(String) Macro
Define a set of Macro options for the current Thread.
setOptions(Thread, String) Macro
Define a set of Macro options for a Thread.
setOutline(boolean) Arrow
setOutputType(int) EDM
Sets the output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
setOverColor(int, int, int) ImageProcessor
Sets the upper Over/Under threshold color.
setOverlay(Overlay) ImageCanvas
Use ImagePlus.setOverlay(ij.gui.Overlay).
setOverlay(Overlay) ImagePlus
Installs a list of ROIs that will be drawn on this image as a non-destructive overlay.
setOverlay(Overlay) ImageProcessor
This method is used to display virtual stack overlays.
setOverlay(Roi, Color, int, Color) ImagePlus
Creates an Overlay from the specified ROI, and assigns it to this image.
setOverlay(Shape, Color, BasicStroke) ImagePlus
Creates an Overlay from the specified Shape, Color
and BasicStroke, and assigns it to this image.
setPaintPending(boolean) ImageCanvas
setParamResolutions(double[]) Minimizer
Set the resolution of the parameters, for problems where the target function is not smooth
but suffers from numerical noise.
setPasteMode(int) Roi
Sets the Paste transfer mode.
setPasteMode(String) IJ
Sets the transfer mode used by the Edit/Paste command, where mode is "Copy", "Blend", "Average", "Difference",
"Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide".
setPixels(int, FloatProcessor) ByteProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(int, FloatProcessor) ColorProcessor
Sets the pixels of one color channel from a FloatProcessor.
setPixels(int, FloatProcessor) FloatProcessor
Sets the pixels, and min&max values from a FloatProcessor.
setPixels(int, FloatProcessor) ImageProcessor
Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
setPixels(int, FloatProcessor) ShortProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object) ByteProcessor
setPixels(Object) ColorProcessor
setPixels(Object) FloatProcessor
setPixels(Object) ImageProcessor
Sets a new pixel array for the image.
setPixels(Object) ShortProcessor
setPixels(Object, int) PlotVirtualStack
setPixels(Object, int) ImageStack
Assigns a pixel array to the specified slice,
were 1<=n<=nslices.
setPixels(Object, int) VirtualStack
Assigns a pixel array to the specified slice,
were 1<=n<=nslices.
setPlot(Plot) PlotCanvas
Tells the PlotCanvas which plot to use for zooming etc.
setPlot(Plot) PlotWindow
Sets the Plot object shown in this PlotWindow.
setPlotMaker(PlotMaker) Plot
setPlotObjectStyles(int, String) Plot
Set the style of the i-th PlotObject (curve, label, ...) in the sequence
they are plotted (i.e., foreground last), from a String with comma delimiters:
Main Color, Secondary Color (or "none"), Line Width [, Symbol shape for XY_DATA] [,hidden]
setPointType(int) PointRoi
Sets the point type (0=hybrid, 1=crosshair, 2=dot, 3=circle).
setPolygon(int[], int[], int) PolygonFiller
Specifies the polygon to be filled.
setPosition(int) Roi
Sets the stack position (image number) of this ROI.
setPosition(int) ImagePlus
Set the current hyperstack position based on the stack index 'n' (one-based).
setPosition(int, int, int) Roi
Sets the hyperstack position of this ROI.
setPosition(int, int, int) StackWindow
setPosition(int, int, int) ImagePlus
Sets the current hyperstack position and updates the display,
where 'channel', 'slice' and 'frame' are one-based indexes.
setPosition(ImagePlus) Roi
Sets the position of this ROI based on the stack position of the specified image.
setPositionWithoutUpdate(int, int, int) ImagePlus
Sets the current hyperstack position without updating the display,
where 'channel', 'slice' and 'frame' are one-based indexes.
setPrecision(int) ResultsTable
Sets the decimal places (digits to the right of decimal point)
that are used when this table is displayed.
setPrecision(int) Analyzer
Sets the number of digits displayed to the right of decimal point.
setPreviousMinMax() Plot
reverts plot range to previous values and updates the image
setProcessor(ImageProcessor) ImageRoi
setProcessor(ImageProcessor) ImagePlus
Replaces the ImageProcessor with the one specified and updates the
display.
setProcessor(ImageProcessor, int) ImageStack
Assigns the pixel array of an ImageProcessor to the
specified slice, were 1<=n<=nslices.
setProcessor(String, ImageProcessor) ImagePlus
Replaces the ImageProcessor with the one specified and updates the display.
setProcessStack(boolean) ContrastEnhancer
setProgressBar(ProgressBar) ImageProcessor
Assigns a progress bar to this processor.
setProperties(String) Roi
setProperty(String, Object) IJ
Adds a key-value pair to IJ.properties.
setProperty(String, Object) ImagePlus
Adds a key-value pair to this image's properties.
setProperty(String, String) Roi
setPrototypeOverlay(Overlay) Roi
setQuality(int) JpegWriter
Deprecated.
setRandomSeed(double) ImageProcessor
setRandomSeed(int) Minimizer
Set a seed to initialize the random number generator, which is used for initialization
of the simplex.
setRawThreshold(ImagePlus, double, double, String) IJ
This is a version of setThreshold() that always uses raw (uncalibrated) values
in the range 0-255 for 8-bit images and 0-65535 for 16-bit images.
setRedirectImage(ImagePlus) Analyzer
Set the "Redirect To" image.
setRestarts(int) CurveFitter
Set maximum number of simplex restarts to do.
setResultsTable(ResultsTable) Analyzer
setResultsTable(ResultsTable) ParticleAnalyzer
Sets the ResultsTable to be used by the next
ParticleAnalyzer instance.
setResultsTable(ResultsTable) TextPanel
Sets the ResultsTable associated with this TextPanel.
setRGB(byte[], byte[], byte[]) ColorProcessor
Sets the current pixels from 3 byte arrays (reg, green, blue).
setRGBWeights(double[]) ColorProcessor
This is a thread-safe (non-static) version of setWeightingFactors().
setRGBWeights(double, double, double) ColorProcessor
This is a thread-safe (non-static) version of setWeightingFactors().
setRoi(int, int, int, int) ImagePlus
Creates a rectangular selection.
setRoi(int, int, int, int) 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) ImagePlus
Assigns the specified ROI to this image and displays it.
setRoi(Roi) ImageProcessor
Defines a non-rectangular region of interest that will consist of a
rectangular ROI and a mask.
setRoi(Roi, boolean) ImagePlus
Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.
setRoi(Roi, int) RoiManager
Replaces the ROI at the specified index.
setRoi(Polygon) ImageProcessor
Defines a polygonal region of interest that will consist of a
rectangular ROI and a mask.
setRoi(Rectangle) ImagePlus
Creates a rectangular selection.
setRoi(Rectangle) ImageStack
setRoi(Rectangle) ImageProcessor
Defines a rectangular region of interest and sets the mask
to null if this ROI is not the same size as the previous one.
setRoiManager(RoiManager) ParticleAnalyzer
Sets the RoiManager to be used by the next ParticleAnalyzer
instance.
setRotationCenter(double, double) Roi
setRoundRectArcSize(int) Roi
Obsolete; replaced by setCornerDiameter().
setRoundRectArcSize(int) Toolbar
Sets the rounded rectangle corner diameter (pixels).
setScale(float) Plot
Sets the scale.
setScaleToFit(boolean) ImageCanvas
setSelectedIndexes(int[]) RoiManager
Selects multiple ROIs, where 'indexes' is an array of integers, each
greater than or equal to 0 and less than the value returned by getCount().
setSelection(int, int) TextPanel
Creates a selection and insures that it is visible.
setShowAllColor(Color) ImageCanvas
Obsolete
setShowAllList(Overlay) ImageCanvas
setShowAllROIs(boolean) ImageCanvas
Obsolete
setShowConflictMessage(boolean) FileOpener
setShowCursorStatus(boolean) ImageCanvas
Called by IJ.showStatus() to prevent status bar text from
being overwritten until the cursor moves at least 12 pixels.
setShowLabels(boolean) PointRoi
setShowProgress(boolean) FHT
Enables/disables display of the progress bar during transforms.
setSigned16BitCalibration() Calibration
Sets up a calibration function that subtracts 32,768 from pixel values.
setSilentMode(boolean) Opener
The "Opening: path" status message is not displayed in silent mode.
setSize(int) PointRoi
Sets the point size, where 'size' is 0-4.
setSize(int) ArrayUtil
setSize(int, int) ImageCanvas
setSize(int, int) Plot
Sets the canvas size in (unscaled) pixels and sets the scale to 1.0.
setSlice(int) IJ
Switches to the specified stack slice, where 1<='slice'<=stack-size.
setSlice(int) ImagePlus
Displays the specified stack image, where 1<=n<=stackSize.
setSliceLabel(String, int) ImageStack
Sets the label of the specified slice, were 1<=n<=nslices.
setSliceLabel(String, int) VirtualStack
Does nothing.
setSliceNumber(int) ImageProcessor
PlugInFilterRunner uses this method to set the slice number.
setSliceWithoutUpdate(int) ImagePlus
Displays the specified stack image (1<=n<=stackSize)
without updating the display.
setSliderHeight(int) ImageWindow
setSmartRecording(boolean) GenericDialog
Unchanged parameters are not recorder in 'smart recording' mode.
setSnapshotCopyMode(boolean) ImageProcessor
The getPixelsCopy() method returns a reference to the
snapshot buffer if it is not null and 'snapshotCopyMode' is true.
setSnapshotPixels(Object) ByteProcessor
setSnapshotPixels(Object) ColorProcessor
setSnapshotPixels(Object) FloatProcessor
setSnapshotPixels(Object) ImageProcessor
Sets a new pixel array for the snapshot (undo) buffer.
setSnapshotPixels(Object) ShortProcessor
setSourceRect(Rectangle) ImageCanvas
Sets the region of the image (in pixels) to be displayed.
setSourceRect(Rectangle) PlotCanvas
Scrolling a PlotCanvas is updating the plot, not viewing part of the plot, unless the plot is frozen
setStack(ImageStack) ImagePlus
Replaces the image with the specified stack and updates the display.
setStack(ImageStack, int, int, int) ImagePlus
setStack(String, ImageStack) ImagePlus
Replaces the image with the specified stack and updates
the display.
setStart(int, int) WandToolOptions
setStartSlice(int) ZProjector
setStatusAndEsc(String, boolean) CurveFitter
Create output on the number of iterations in the ImageJ Status line, e.g.
setStatusAndEsc(String, boolean) Minimizer
Create output on the number of iterations in the ImageJ Status line, e.g.
setStopSlice(int) ZProjector
setStroke(BasicStroke) Roi
Sets the Stroke used to draw this ROI.
setStrokeColor(Color) Overlay
Sets the stroke color of all the ROIs in this overlay.
setStrokeColor(Color) Roi
Sets the color used by this ROI to draw its outline.
setStrokeWidth(double) Roi
This is a version of setStrokeWidth() that accepts a double argument.
setStrokeWidth(float) Line
setStrokeWidth(float) Roi
Sets the width of the line used to draw this ROI.
setStyle(int) Arrow
setStyle(String) Arrow
setSystemLookAndFeel() Java2
Sets the Swing look and feel to the system look and feel (Windows only).
setT(int) ImagePlus
Sets the hyperstack frame position (one based).
setT(ImageWindow, int) SyncWindows
setTempCurrentImage(ImagePlus) WindowManager
Makes the specified image temporarily the active
image for this thread.
setTempCurrentImage(Thread, ImagePlus) WindowManager
Sets a temporary image for the specified thread.
setText(String) MultiLineLabel
setTextPanel(TextPanel) IJ
TextWindow calls this method with a null argument when the "Results" window is closed.
setThreads(int) Prefs
Sets the number of threads (1-32) used by PlugInFilters to process stacks.
setThreshold(double, double) IJ
Sets the lower and upper threshold levels and displays the image
using red to highlight thresholded pixels.
setThreshold(double, double, int) ByteProcessor
setThreshold(double, double, int) FloatProcessor
setThreshold(double, double, int) ImageProcessor
Sets the lower and upper threshold levels.
setThreshold(double, double, int) ShortProcessor
setThreshold(double, double, String) IJ
Sets the lower and upper threshold levels and displays the image using
the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
setThreshold(ImagePlus, double, double) IJ
Sets the lower and upper threshold levels of the specified image.
setThreshold(ImagePlus, double, double, String) IJ
Sets the lower and upper threshold levels of the specified image and updates the display using
the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
setTickLength(int) Plot
Sets the length of the major tick in pixels.
setTimeUnit(String) Calibration
Sets the time unit (e.g.
setTitle(String) ImagePlus
Sets the image name.
setTitle(String) TextPanel
setTool(int) Toolbar
setTool(int) IJ
Switches to the specified tool, where id = Toolbar.RECTANGLE (0),
Toolbar.OVAL (1), etc.
setTool(String) Toolbar
setTool(String) IJ
Switches to the specified tool, where 'name' is "rect", "elliptical",
"brush", etc.
setTransparentColor(Color) Blitter
Sets the transparent color used in the COPY_TRANSPARENT
mode (default is Color.white).
setTransparentColor(Color) ByteBlitter
setTransparentColor(Color) ColorBlitter
setTransparentColor(Color) FloatBlitter
setTransparentColor(Color) ShortBlitter
setTransparentIndex(int) Prefs
Sets the transparent index (0-255), or set to -1 to disable transparency.
setType(int) ImagePlus
setUnderColor(int, int, int) ImageProcessor
Set the lower Over/Under thresholding color.
setUnit(String) Calibration
Sets the default length unit (e.g.
setUnitIncrement(int) ScrollbarWithLabel
setUnsavedMeasurements(boolean) Analyzer
setup() GenericDialog
setup() HistogramWindow
setup(int, ImagePlus) Undo
setup(String, ImagePlus) Analyzer
setup(String, ImagePlus) AVI_Writer
setup(String, ImagePlus) BackgroundSubtracter
setup(String, ImagePlus) Benchmark
setup(String, ImagePlus) Binary
setup(String, ImagePlus) Calibrator
setup(String, ImagePlus) Convolver
setup(String, ImagePlus) Duplicater
Deprecated.
setup(String, ImagePlus) EDM
Prepare for processing; also called at the very end with argument 'final'
to show any newly created output image.
setup(String, ImagePlus) FFTCustomFilter
setup(String, ImagePlus) FFTFilter
setup(String, ImagePlus) Filler
setup(String, ImagePlus) Filters
setup(String, ImagePlus) FractalBoxCounter
setup(String, ImagePlus) GaussianBlur
Method to return types supported
setup(String, ImagePlus) ImageMath
setup(String, ImagePlus) ImageProperties
setup(String, ImagePlus) Info
Deprecated.
setup(String, ImagePlus) LineGraphAnalyzer
setup(String, ImagePlus) LutApplier
setup(String, ImagePlus) LutViewer
setup(String, ImagePlus) MaximumFinder
Method to return types supported
setup(String, ImagePlus) ParticleAnalyzer
setup(String, ImagePlus) PlugInFilter
This method is called once when the filter is loaded.
setup(String, ImagePlus) Printer
setup(String, ImagePlus) RankFilters
Setup of the PlugInFilter.
setup(String, ImagePlus) RGBStackSplitter
setup(String, ImagePlus) RoiWriter
setup(String, ImagePlus) Rotator
setup(String, ImagePlus) SaltAndPepper
setup(String, ImagePlus) ScaleDialog
setup(String, ImagePlus) Shadows
setup(String, ImagePlus) StackLabeler
setup(String, ImagePlus) ThresholdToSelection
setup(String, ImagePlus) Transformer
setup(String, ImagePlus) Translator
setup(String, ImagePlus) UnsharpMask
Method to return types supported
setup(String, ImagePlus) Writer
Deprecated.
setup(String, ImagePlus) XYWriter
SETUP_UNDO MacroConstants
setupDialog(ImagePlus, int) IJ
Displays a "Process all images?" dialog.
setupScroll(int, int) ImageCanvas
setupScroll(int, int) PlotCanvas
overrides ImageCanvas.setupScroll; if plot is not frozen, scrolling modifies the plot data range
setUseBicubic(boolean) ImageProcessor
setUseStackHistogram(boolean) ContrastEnhancer
setValue(double) ByteProcessor
Sets the default fill/draw value, where 0<=value<=255.
setValue(double) ColorProcessor
Sets the default fill/draw value, where value is interpreted as an RGB int.
setValue(double) FloatProcessor
Sets the default fill/draw value.
setValue(double) ImageProcessor
Sets the default fill/draw value.
setValue(double) ShortProcessor
Sets the default fill/draw value, where 0<=value<=65535).
setValue(int) ScrollbarWithLabel
setValue(int, int, double) ResultsTable
Sets the value of the given column and row, where
where 0<=column<=(lastRow+1 and 0<=row<=size().
setValue(int, int, String) ResultsTable
Sets the string value of the given column and row, where
where 0<=column<=(lastRow+1 and 0<=row<=size().
setValue(String, int, double) ResultsTable
Sets the value of the given column and row, where
where 0<=row<size().
setValue(String, int, String) ResultsTable
Sets the string value of the given column and row, where
where 0<=row<size().
setValueUnit(String) Calibration
Sets the value unit.
setVariable(String, double) Interpreter
setVariable(String, String) Interpreter
setVirtual(boolean) AVI_Reader
Open as virtual stack?
setVisibleAmount(int) ScrollbarWithLabel
setVoxel(int, int, int, double) ImageStack
setVoxels(int, int, int, int, int, int, float[]) ImageStack
Experimental
setVoxels(int, int, int, int, int, int, float[], int) ImageStack
Experimental
setWeightingFactors(double, double, double) ColorProcessor
Sets the weighting factors used by getPixelValue(), getHistogram()
and convertToByte() to do color conversions.
setWidth(int) Line
setWildcardChars(char, char) WildcardMatch
Sets new characters to be used as wildcard characters, overriding the
the default of '?' for any single character match and '*' for any
amount of characters, including 0 characters.
setWindow(ImageWindow) ImagePlus
This method should only be called from an ImageWindow.
setWindow(Frame) WindowManager
The specified frame becomes the front window, the one returnd by getFrontWindow().
setWindow(Window) WindowManager
The specified Window becomes the front window.
setXLabelFont(Font) Plot
Sets the xLabelFont; must not be mull.
setXMinorTicks(boolean) Plot
Sets whether to show minor ticks on the x axis (if linear).
setXTicks(boolean) Plot
Sets whether to show major ticks at the x axis.
setXUnit(String) Calibration
Sets the X length unit.
setXYLabels(String, String) Plot
Sets the labels of the x and y axes.
setYLabelFont(Font) Plot
Sets the yLabelFont; must not be null.
setYMinorTicks(boolean) Plot
Sets whether to show minor ticks on the y axis (if linear).
setYTicks(boolean) Plot
Sets whether to show major ticks at the y axis.
setYUnit(String) Calibration
Sets the Y length unit.
setZ(int) ImagePlus
Sets the hyperstack slice position (one based).
setZ(ImageWindow, int) SyncWindows
setZeroTransparent(boolean) ImageRoi
setZUnit(String) Calibration
Sets the Z length unit.
Shadows ij.plugin.filter
Implements the commands in the Process/Shadows submenu.
Shadows() Shadows
Shanbhag AutoThresholder.Method
SHAPE_DESCRIPTORS Measurements
SHAPE_ROI_SIZE RoiDecoder
ShapeRoi ij.gui
A subclass of ij.gui.Roi (2D Regions Of Interest) implemented in terms of java.awt.Shape.
ShapeRoi(float[]) ShapeRoi
Constructs a ShapeRoi from an array of variable length path segments.
ShapeRoi(int, int, Shape) ShapeRoi
Constructs a ShapeRoi from a Shape.
ShapeRoi(Roi) ShapeRoi
Constructs a ShapeRoi from an Roi.
ShapeRoi(Shape) ShapeRoi
Constructs a ShapeRoi from a Shape.
shapeToRoi() ShapeRoi
Attempts to convert this ShapeRoi into a non-composite Roi.
sharpen() ImageProcessor
Sharpens the image or ROI using a 3x3 convolution kernel.
sharpenFloat(FloatProcessor, double, float) UnsharpMask
Unsharp Mask filtering of a float image.
SHIFT_LEFT MacroConstants
SHIFT_RIGHT MacroConstants
shiftKeyDown() IJ
Returns true if the shift key is down.
SHORT EDM
Output type: new 16-bit image
ShortBlitter ij.process
This class does bit blitting of 16-bit images.
ShortBlitter(ShortProcessor) ShortBlitter
Constructs a ShortBlitter from a ShortProcessor.
SHORTCUT_IN_USE Menus
shortcutInUse(String) Menus
Returns 'true' if this keyboard shortcut is in use.
SHORTCUTS_MENU Menus
ShortProcessor ij.process
ShortProcessors contain a 16-bit unsigned image
and methods that operate on that image.
ShortProcessor(int, int) ShortProcessor
Creates a blank ShortProcessor using the default grayscale LUT that
displays zero as black.
ShortProcessor(int, int, boolean) ShortProcessor
Obsolete.
ShortProcessor(int, int, short[], ColorModel) ShortProcessor
Creates a new ShortProcessor using the specified pixel array and ColorModel.
ShortProcessor(int, int, short[], ColorModel, boolean) ShortProcessor
Deprecated.
ShortProcessor(BufferedImage) ShortProcessor
Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage.
ShortStatistics ij.process
16-bit image statistics, including histogram.
ShortStatistics(ImageProcessor) ShortStatistics
Construct an ImageStatistics object from a ShortProcessor
using the standard measurement options (area, mean,
mode, min and max).
ShortStatistics(ImageProcessor, int, Calibration) ShortStatistics
Constructs a ShortStatistics object from a ShortProcessor using
the specified measurement options.
show() Plot
Displays the plot in a PlotWindow and returns a reference to the PlotWindow.
show() WaitForUserDialog
show() ImagePlus
Opens a window to display this image and clears the status bar.
show(double) ProgressBar
Updates the progress bar, where abs(progress) should run from 0 to 1.
show(double, boolean) ProgressBar
Updates the progress bar, where abs(progress) should run from 0 to 1.
show(int, int) ProgressBar
Updates the progress bar, where the length of the bar is set to
((abs(currentIndex)+1)/abs(finalIndex) of the maximum bar
length.
show(String) ImagePlus
Opens a window to display this image and displays
'statusMessage' in the status bar.
show(String) ResultsTable
Displays the contents of this ResultsTable in a window with
the specified title, or updates an existing results window.
SHOW_ALL_COLOR Prefs
SHOW_MASKS ParticleAnalyzer
Display image containing binary masks of measured particles.
SHOW_MESSAGE MacroConstants
SHOW_MESSAGE_WITH_CANCEL MacroConstants
SHOW_NONE ParticleAnalyzer
Do not display particle outline image.
SHOW_OUTLINES ParticleAnalyzer
Display image containing outlines of measured particles.
SHOW_OVERLAY_MASKS ParticleAnalyzer
Display filled particle as an overlay.
SHOW_OVERLAY_OUTLINES ParticleAnalyzer
Display particle outlines as an overlay.
SHOW_PROGRESS MacroConstants
SHOW_PROGRESS ParticleAnalyzer
Display a progress bar.
SHOW_RESULTS ParticleAnalyzer
Display results in the ImageJ console.
SHOW_ROI_MASKS ParticleAnalyzer
Display image containing grayscales masks that identify measured particles.
SHOW_STATUS MacroConstants
SHOW_SUMMARY ParticleAnalyzer
Obsolete, replaced by DISPLAY_SUMMARY
SHOW_TEXT MacroConstants
showAllPoints Prefs
Ignore stack positions when displaying points.
showAllSliceOnly Prefs
Only show ROIs associated with current slice in Roi Manager "Show All" mode.
showArrayInspector(int) Interpreter
Shows array elements after clicking an array variable in Debug
window
N.
showCompositeAdvisory(ImagePlus, String) GUI
showDialog() GenericDialog
Displays this dialog box.
showDialog() NonBlockingGenericDialog
showDialog() RoiProperties
Displays the dialog box and returns 'false' if the user cancels it.
showDialog() Compiler
showDialog() FFTMath
showDialog() ParticleAnalyzer
Displays a modal options dialog.
showDialog() NewPlugin
showDialog() OverlayLabels
showDialog() RoiScaler
showDialog(double) RoiRotator
showDialog(ImagePlus) Calibrator
showDialog(ImagePlus, double) RoiEnlarger
showDialog(ImagePlus, String, PlugInFilterRunner) BackgroundSubtracter
showDialog(ImagePlus, String, PlugInFilterRunner) Binary
showDialog(ImagePlus, String, PlugInFilterRunner) Convolver
showDialog(ImagePlus, String, PlugInFilterRunner) EDM
Called by the PlugInFilterRunner after setup.
showDialog(ImagePlus, String, PlugInFilterRunner) ExtendedPlugInFilter
This method is called after setup(arg, imp) unless the
DONE flag has been set.
showDialog(ImagePlus, String, PlugInFilterRunner) GaussianBlur
Ask the user for the parameters
showDialog(ImagePlus, String, PlugInFilterRunner) ImageMath
showDialog(ImagePlus, String, PlugInFilterRunner) MaximumFinder
showDialog(ImagePlus, String, PlugInFilterRunner) RankFilters
showDialog(ImagePlus, String, PlugInFilterRunner) Rotator
showDialog(ImagePlus, String, PlugInFilterRunner) StackLabeler
showDialog(ImagePlus, String, PlugInFilterRunner) Translator
showDialog(ImagePlus, String, PlugInFilterRunner) UnsharpMask
Ask the user for the parameters
showDialog(ImageStack) StackReducer
showDialog(Frame) PlotContentsStyleDialog
Shows the dialog, with a given parent Frame
showDialog(Frame) PlotDialog
Asks the user for axis scaling; then replot with new scale on the same ImageProcessor.
showHistogram(ImagePlus, int) HistogramWindow
Draws the histogram using the specified title and number of bins.
showHistogram(ImagePlus, int, double, double) HistogramWindow
Draws the histogram using the specified title, number of bins and histogram range.
showHistogram(ImagePlus, ImageStatistics) HistogramWindow
Draws the histogram using the specified title and ImageStatistics.
showImageDialog(String) RoiProperties
showList() HistogramWindow
showList() WindowManager
showLogWindow() Editor
showMacroFunctions() Editor
showMessage(String) IJ
Displays a message in a dialog box titled "Message".
showMessage(String, String) IJ
Displays a message in a dialog box with the specified title.
showMessageWithCancel(String, String) IJ
Displays a message in a dialog box with the specified title.
showOptionsDialog() ArrowTool
showOptionsDialog() BrushTool
showOptionsDialog() OverlayBrushTool
showOptionsDialog() PixelInspectionTool
showOptionsDialog() PlugInTool
showOptionsDialog() RoiRotationTool
showPopupMenu(MouseEvent, Toolbar) PlugInTool
showProgress ParticleAnalyzer
showProgress(boolean) GaussianBlur
showProgress(double) IJ
Updates the progress bar, where 0<=progress<=1.0.
showProgress(double) ImageProcessor
showProgress(int, int) IJ
Updates the progress bar, where the length of the bar is set to
(currentValue+1)/finalValue of the maximum bar length.
showResults ParticleAnalyzer
showRowNumbers(boolean) ResultsTable
showSizeDistribution ParticleAnalyzer
showSlice(int) StackWindow
Displays the specified slice and updates the stack scrollbar.
showStatus() Roi
showStatus(boolean) ThresholdToSelection
Determines whether to show status messages and a progress bar
showStatus(String) IJ
Displays a message in the ImageJ status bar.
showTime(ImagePlus, long, String) IJ
showTime(ImagePlus, long, String, int) IJ
shrink(ImagePlus, int, int, int, int) Binner
shrink(ImageProcessor, int, int, int) Binner
shrinkHyperstackZ(ImagePlus, int) Binner
shuffle(ImagePlus, int) 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 ij.plugin
This plugin implements the Plugins/Utilities/Unlock, Image/Rename
and Plugins/Utilities/Search commands.
SimpleCommands() SimpleCommands
SIN MacroConstants
SINGLE_POINTS MaximumFinder
Output type single points
sixteenBitRanges ContrastAdjuster
size() Line
Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() OvalRoi
Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() Overlay
Returns the number of ROIs in this Overlay.
size() PolygonRoi
Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() Roi
Returns the number of points in this selection; equivalent to getPolygon().npoints.
size() ShapeRoi
If this ROI consists of a single polygon, retuns the number of vertices, otherwise returns 4.
size() ImageStack
Returns the number of slices in this stack.
size() ResultsTable
Returns the size of this ResultsTable.
SIZE_KEY Arrow
sizes PointRoi
skeletonize() 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() ByteProcessor
skewness ImageStatistics
SKEWNESS Measurements
SKEWNESS ResultsTable
skipRawDialog Prefs
Do not display dialog when opening .raw files
slice StackWindow
slice ParticleAnalyzer
SLICE Measurements
SLICE ResultsTable
sliceLabels FileInfo
Slicer ij.plugin
Implements the Image/Stacks/Reslice command.
Slicer() Slicer
sliceSelector StackWindow
slider GenericDialog
smooth() ImageProcessor
Replaces each pixel with the 3x3 neighborhood mean.
smoothWand Prefs
Wand tool "Smooth if thresholded" option
snapshot() ByteProcessor
Make a snapshot of the current image.
snapshot() ColorProcessor
snapshot() FloatProcessor
snapshot() ImageProcessor
Makes a copy of this image's pixel data that can be
later restored using reset() or reset(mask).
snapshot() ShortProcessor
SNAPSHOT MacroConstants
SNAPSHOT PlugInFilter
Set this flag if the filter requires a snapshot (copy of the pixels array).
snapshotHeight ImageProcessor
snapshotPixels ByteProcessor
snapshotPixels ColorProcessor
snapshotWidth ImageProcessor
SOFTWARE TiffDecoder
SOLIDITY ResultsTable
sort() ArrayUtil
sort(ImageStack) DicomTools
Sorts a DICOM stack by image number.
sort(String[]) StringSorter
Sorts the array.
sortByMetaData(boolean) FolderOpener
sortDicom(String[], String[], int) VirtualStack
sortedTypes CurveFitter
Nicer sequence of the built-in function types
sortFileList(String[]) FolderOpener
Sorts file names containing numerical components.
sortFileNames(boolean) FolderOpener
sortNumerically(String[]) StringSorter
Sorts file names containing numerical components.
source ImageProcessor
south(ImageProcessor) Shadows
southeast(ImageProcessor) Shadows
southwest(ImageProcessor) Shadows
spaceBarDown() IJ
Returns true if the space bar is down.
SPARE1 Toolbar
Obsolete public constants
SPARE2 Toolbar
Obsolete public constants
SPARE3 Toolbar
Obsolete public constants
SPARE4 Toolbar
Obsolete public constants
SPARE5 Toolbar
Obsolete public constants
SPARE6 Toolbar
Obsolete public constants
SPARE7 Toolbar
Obsolete public constants
SPARE8 Toolbar
Obsolete public constants
SPARE9 Toolbar
Obsolete public constants
SpecifyROI ij.plugin
This plugin implements the Edit/Selection/Specify command.
SpecifyROI() SpecifyROI
SPLINE_FIT RoiDecoder
splineFitLines Prefs
Automatically spline fit line selections
SplineFitter ij.measure
This class fits a spline function to a set of points.
SplineFitter(float[], float[], int) SplineFitter
SplineFitter(float[], float[], int, boolean) SplineFitter
For closed curves: the first and last y value should be identical;
internally, a periodic continuation with a few will be used at both
ends
SplineFitter(int[], int[], int) SplineFitter
splinePoints PolygonRoi
split(ImagePlus) ChannelSplitter
Splits the specified image into separate channels.
split(ImagePlus) RGBStackSplitter
Deprecated; replaced by ij.plugin.ChannelSplitter.
split(ImageStack, boolean) RGBStackSplitter
Deprecated; replaced by ChannelSplitter.splitRGB().
split(String) 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) Tools
Splits a string into substring using the characters
contained in the second argument as the delimiter set.
SPLIT MacroConstants
splitRGB(ImageStack, boolean) ChannelSplitter
Splits the specified RGB stack into three 8-bit grayscale stacks.
sqr() FloatProcessor
sqr() ImageProcessor
Performs a square transform on the image or ROI.
sqr() ShortProcessor
sqrt() FloatProcessor
sqrt() ImageProcessor
Performs a square root transform on the image or ROI.
sqrt() ShortProcessor
SQRT MacroConstants
SQRT2 EDM
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(2)
SQRT5 EDM
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(5)
srcEnd DownsizeTable
index of the last point of the source data that should be accessed
srcRect ImageCanvas
srcStart DownsizeTable
index of the first point of the source data that should be accessed
STACK MacroConstants
STACK_POSITION Measurements
STACK_REQUIRED PlugInFilter
Set this flag if the filter requires a stack.
Stack_Statistics ij.plugin
This plugin implements the Image/Stacks/Statistics command.
Stack_Statistics() Stack_Statistics
StackCombiner ij.plugin
This plugin implements the Image/Stacks/Combine command.
StackCombiner() StackCombiner
StackConverter ij.process
This class does stack type conversions.
StackConverter(ImagePlus) StackConverter
StackEditor ij.plugin
Implements the AddSlice, DeleteSlice and "Stack to Images" commands.
StackEditor() StackEditor
StackInserter ij.plugin
This plugin, which implements the Image/Stacks/Tools/Insert
command, inserts an image or stack into another image or stack.
StackInserter() StackInserter
StackLabeler ij.plugin.filter
This plugin implements the Image/Stacks/Label command.
StackLabeler() StackLabeler
StackMaker ij.plugin
The plugin implements the Image/Stacks/Tools/Montage to Stack command.
StackMaker() StackMaker
StackPlotter ij.plugin
StackPlotter() StackPlotter
StackProcessor ij.process
This class processes stacks.
StackProcessor(ImageStack) StackProcessor
Constructs a StackProcessor from a stack.
StackProcessor(ImageStack, ImageProcessor) StackProcessor
Constructs a StackProcessor from a stack.
StackReducer ij.plugin
This plugin implements the Image/Stacks/Tools/Reduce command.
StackReducer() StackReducer
StackReverser ij.plugin
This plugin implements the Image/Transform/Flip Z and
Image/Stacks/Tools/Reverse commands.
StackReverser() StackReverser
stackStatistics ImageStatistics
Used by HistogramWindow
StackStatistics ij.process
Statistics, including the histogram, of a stack.
StackStatistics(ImagePlus) StackStatistics
Creates a StackStatistics object from a stack, using 256
histogram bins and the entire stack pixel value range.
StackStatistics(ImagePlus, int, double, double) StackStatistics
Creates a StackStatistics object from a stack, using the specified
histogram bin count and x-axis range (pixel value tange).
StackWindow ij.gui
This class is an extended ImageWindow that displays stacks and hyperstacks.
StackWindow(ImagePlus) StackWindow
StackWindow(ImagePlus, ImageCanvas) StackWindow
StackWriter ij.plugin
This plugin, which saves the images in a stack as separate files,
implements the File/Save As/Image Sequence command.
StackWriter() StackWriter
STANDALONE ImageJ
Run as normal application.
startAndJoin(Thread[]) ThreadUtil
Start all given threads and wait on each of them until all are done.
startPaste(ImagePlus) Roi
STARTS_WITH MacroConstants
startServer() OtherInstance
startTiming() ImagePlus
Calls System.currentTimeMillis() to save the current
time so it can be retrieved later using getStartTime()
to calculate the elapsed time of an operation.
Startup ij.plugin
This plugin implements the Edit/Options/Startup command.
Startup() Startup
StartupRunner ij.macro
Runs the RunAtStartup (created by Edit/Options/Startup) and AutoRun (in StartupMacros) macros.
StartupRunner() StartupRunner
startxd Line
startyd Line
staticShowChoice ParticleAnalyzer
stats HistogramWindow
STATUS_STRING Minimizer
Strings describing the status codes
STD_DEV Measurements
STD_DEV ResultsTable
stdDev ImageStatistics
STEP Debugger
stop() Orthogonal_Views
str Symbol
STRAIGHT_LINE Calibration
STRAIGHT_LINE CurveFitter
Constants for the built-in fit functions
straighten(ImagePlus, Roi, int) Straightener
Straightener ij.plugin
This plugin implements the Edit/Selection/Straighten command.
Straightener() Straightener
straightenLine(ImagePlus, int) Straightener
straightenStack(ImagePlus, Roi, int) Straightener
stretchHistogram(ImagePlus, double) ContrastEnhancer
stretchHistogram(ImageProcessor, double) ContrastEnhancer
stretchHistogram(ImageProcessor, double, ImageStatistics) ContrastEnhancer
STRING MacroConstants
STRING_CONSTANT MacroConstants
STRING_FUNCTION MacroConstants
stringField GenericDialog
stringFunctionIDs MacroConstants
stringFunctions MacroConstants
StringSorter ij.util
A simple QuickSort for String arrays.
StringSorter() StringSorter
STRIP_BYTE_COUNT TiffDecoder
STRIP_OFFSETS TiffDecoder
stripLengths FileInfo
stripOffsets FileInfo
stroke Roi
STROKE_COLOR RoiDecoder
STROKE_WIDTH RoiDecoder
strokeColor Roi
STYLE_KEY Arrow
styles Arrow
SUB_PIXEL_RESOLUTION RoiDecoder
SubHyperstackMaker ij.plugin
This plugin is used by the Image/Stacks/Tools/Make Substack
command to create substacks of hyperstacks.
SubHyperstackMaker() SubHyperstackMaker
subPixelResolution Prefs
Use sub-pixel resolution with line selections
subPixelResolution() EllipseRoi
Always returns true.
subPixelResolution() Line
Always returns true.
subPixelResolution() PointRoi
Always returns true.
subPixelResolution() PolygonRoi
subPixelResolution() Roi
Returns true if this is a slection that supports sub-pixel resolution.
subPixelResolution() RotatedRectRoi
Always returns true.
SubstackMaker ij.plugin
This plugin implements the Image/Stacks/Tools/Make Substack command.
SubstackMaker() SubstackMaker
SUBSTRING MacroConstants
subtract(double) ImageProcessor
Subtracts 'value' from each pixel in the image or ROI.
SUBTRACT Blitter
dst=dst-src
subtractBackround(ImageProcessor, int) BackgroundSubtracter
Depracated.
subtractPoints(Roi) PointRoi
Subtract the points that intersect the specified ROI and return
the result.
subtractRGBBackround(ColorProcessor, int) BackgroundSubtracter
Depracated.
SUBTYPE RoiDecoder
SUCCESS Minimizer
Status returned: successful completion
SUM Binner
SUM_METHOD ZProjector
summarize() Analyzer
SUPPORTS_MASKING 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() IJ
Temporarily suppress "plugin not found" errors.
SurfacePlotter ij.plugin
SurfacePlotter() SurfacePlotter
swapPixelArrays() ByteProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() ColorProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() FloatProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() ImageProcessor
Swaps the pixel and snapshot (undo) buffers.
swapPixelArrays() ShortProcessor
Swaps the pixel and snapshot (undo) arrays.
swapQuadrants() FHT
Swap quadrants 1 and 3 and 2 and 4 of the image
contained in this FHT.
swapQuadrants(ImageProcessor) FHT
Swap quadrants 1 and 3 and 2 and 4 of the specified ImageProcessor
so the power spectrum origin is at the center of the image.
Symbol ij.macro
Objects of this class are used as entries in the macro language symbol table.
SyncWindows ij.plugin.frame
This class "synchronizes" mouse input in multiple windows.
SyncWindows() SyncWindows
Create window sync frame.
SyncWindows(String) SyncWindows
T
T_POSITION RoiDecoder
TABLE Opener
TABLE MacroConstants
TABLE NewPlugin
TABLE_FULL ResultsTable
TAN MacroConstants
TCZ HyperStackConverter
TEMPLATE NewPlugin
temporarilyHide() Roi
Deprecated
Text ij.plugin
This plugin implements the Edit/Options/Fonts command and
the dialog displayed when you double click on the text tool.
Text() Text
TEXT Toolbar
TEXT Opener
TEXT RoiDecoder
TEXT_FILE NewPlugin
textArea1 GenericDialog
textArea2 GenericDialog
TextEncoder ij.io
Saves an image described by an ImageProcessor object as a tab-delimited text file.
TextEncoder(ImageProcessor, Calibration, int) TextEncoder
Constructs a TextEncoder from an ImageProcessor and optional Calibration.
TextFileReader ij.plugin
This plugin displays the contents of a text file in a window.
TextFileReader() TextFileReader
TextPanel ij.text
This is an unlimited size text panel with tab-delimited,
labeled and resizable columns.
TextPanel() TextPanel
Constructs a new TextPanel.
TextPanel(String) TextPanel
Constructs a new TextPanel.
TextReader ij.plugin
This plugin opens a tab or comma delimeted text file as an image.
TextReader() TextReader
TextRoi ij.gui
This class is a rectangular ROI containing text.
TextRoi(double, double, double, double, String, Font) TextRoi
Creates a TextRoi using the specified sub-pixel location, size and Font.
TextRoi(double, double, String) TextRoi
Creates a TextRoi using sub-pixel coordinates.
TextRoi(double, double, String, Font) TextRoi
Creates a TextRoi using the specified sub-pixel location and Font.
TextRoi(int, int, ImagePlus) TextRoi
TextRoi(int, int, String) TextRoi
Creates a TextRoi.
TextRoi(int, int, String, Font) TextRoi
Creates a TextRoi using the specified location and Font.
TextRoi(int, int, String, Font, Color) TextRoi
Deprecated.
TextRoi(String, double, double, Font) TextRoi
Use this constructor as a drop-in replacement for ImageProcessor.drawString().
textValueChanged(TextEvent) ColorChooser
textValueChanged(TextEvent) GenericDialog
textValueChanged(TextEvent) FunctionFinder
textValueChanged(TextEvent) ChannelArranger
textValueChanged(TextEvent) Distribution
textValueChanged(TextEvent) Duplicator
textValueChanged(TextEvent) ImageProperties
textValueChanged(TextEvent) Editor
textValueChanged(TextEvent) LineWidthAdjuster
textValueChanged(TextEvent) Histogram
textValueChanged(TextEvent) Resizer
textValueChanged(TextEvent) Scaler
textValueChanged(TextEvent) Slicer
TextWindow ij.text
Uses a TextPanel to displays text in a window.
TextWindow(String, int, int) TextWindow
Opens a new text window containing the contents of a text file.
TextWindow(String, String, int, int) TextWindow
Opens a new single-column text window.
TextWindow(String, String, String, int, int) TextWindow
Opens a new multi-column text window.
TextWindow(String, String, ArrayList, int, int) TextWindow
Opens a new multi-column text window.
TextWriter ij.plugin
This plugin implements the File/Save As/Text command, which saves the
contents of Editor windows and TextWindows (e.g., "Log" and "Results").
TextWriter() TextWriter
theLabel GenericDialog
theta EllipseFitter
Angle in radians
thread StackWindow
ThreadLister ij.plugin
Displays thread information in a text window.
ThreadLister() ThreadLister
THREADS Prefs
ThreadUtil ij.util
ThreadUtil() ThreadUtil
threshold(int) ByteProcessor
Sets pixels less than or equal to level to 0 and all other pixels to 255.
threshold(int) ColorProcessor
Not implemented.
threshold(int) FloatProcessor
Not implemented.
threshold(int) ImageProcessor
Sets pixels less than or equal to level to 0 and all other
pixels to 255.
threshold(int) ShortProcessor
ThresholdAdjuster ij.plugin.frame
Adjusts the lower and upper threshold levels of the active image.
ThresholdAdjuster() ThresholdAdjuster
Thresholder ij.plugin
This plugin implements the Process/Binary/Make Binary
and Convert to Mask commands.
Thresholder() Thresholder
ThresholdToSelection ij.plugin.filter
ThresholdToSelection() ThresholdToSelection
TIFF FileInfo
TIFF Opener
TIFF_AND_DICOM Opener
TiffDecoder ij.io
Decodes single and multi-image TIFF files.
TiffDecoder(InputStream, String) TiffDecoder
TiffDecoder(String, String) TiffDecoder
TiffEncoder ij.io
Saves an image described by a FileInfo object as an uncompressed, big-endian TIFF file.
TiffEncoder(FileInfo) TiffEncoder
TILE_WIDTH TiffDecoder
tileMirror(ImageProcessor, int, int, int, int) FFTFilter
Puts ImageProcessor (ROI) into a new ImageProcessor of size width x height y at position (x,y).
time(ImagePlus, long) IJ
Experimental
TO_BINARY MacroConstants
TO_HEX MacroConstants
TO_LOWER_CASE MacroConstants
TO_SCALED MacroConstants
TO_STRING MacroConstants
TO_UNSCALED MacroConstants
TO_UPPER_CASE MacroConstants
toArray() Overlay
Returns on array containing the ROIs in this Overlay.
toByteArray() Plot
Writes this plot into a byte array containing (1) the serialized PlotProperties and
(2) the serialized Vector of all 'added' PlotObjects.
toDouble(float[]) Tools
Converts the float array 'a' to a double array.
toEDM(ImageProcessor) EDM
Converts a binary image into a 8-bit grayscale Euclidean Distance Map
(EDM).
toFloat(double[]) Tools
Converts the double array 'a' to a float array.
toFloat(int[]) Roi
Converts an int array to a float array.
toFloat(int, FloatProcessor) ByteProcessor
Returns a FloatProcessor with the same image, no scaling or calibration
(pixel values 0 to 255).
toFloat(int, FloatProcessor) ColorProcessor
Returns a FloatProcessor with one color channel of the image.
toFloat(int, FloatProcessor) FloatProcessor
Returns this FloatProcessor.
toFloat(int, FloatProcessor) ImageProcessor
Returns a FloatProcessor with the image or one color channel thereof.
toFloat(int, FloatProcessor) ShortProcessor
Returns a FloatProcessor with the same image, no scaling or calibration
(pixel values 0 to 65535).
toFloatArrays() ByteProcessor
toFloatProcessors() ByteProcessor
toFront(Frame) WindowManager
toHyperStack(ImagePlus, int, int, int) HyperStackConverter
Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and
't' frames using the default ordering ("xyczt") and display mode ("Composite").
toHyperStack(ImagePlus, int, int, int, String) HyperStackConverter
Converts the specified stack into a hyperstack with 'c' channels, 'z' slices and
't' frames using the default ordering ("xyczt") and the specified display
mode ("composite", "color" or "grayscale").
toHyperStack(ImagePlus, int, int, int, String, String) HyperStackConverter
Converts the specified stack into a hyperstack with 'c' channels,
'z' slices and 't' frames.
toInt(float[]) Roi
Converts a float array to an int array using truncation.
toInt(float[], int[], int) Roi
toIntR(float[]) Roi
Converts a float array to an int array using rounding.
TOK_MASK MacroConstants
TOK_SHIFT MacroConstants
tokenize(String) Tokenizer
Uses a StreamTokenizer to convert an ImageJ macro file into a token stream.
Tokenizer ij.macro
This class converts an imageJ macro file file into a token stream.
Tokenizer() Tokenizer
TOOL_CHANGED IJEventListener
TOOL_ID MacroConstants
TOOL_KEY Toolbar
Toolbar ij.gui
The ImageJ toolbar.
Toolbar() Toolbar
Tools ij.util
This class contains static utility methods.
Tools() Tools
TOOLS_MENU Menus
TOP RoiDecoder
TOP_LEFT Plot
Legend positions
TOP_MARGIN Plot
Deprecated.
TOP_RIGHT Plot
Legend positions
toShape(String) Plot
Returns the number for a given plot symbol shape, -1 for xError and -2 for yError (all case-insensitive)
toString() ImageWindow
toString() Overlay
toString() PointRoi
toString() Roi
toString() ImagePlus
toString() ImageStack
toString() FileInfo
toString() Symbol
toString() Variable
toString() Calibration
toString() ResultsTable
toString() JavaScriptEvaluator
toString() FHT
Returns a string containing information about this FHT.
toString() FloatPolygon
toString() ImageProcessor
Returns a string containing information about this ImageProcessor.
toString() ImageStatistics
toString() LUT
toString() ArrayUtil
information to be displayed
toWatershed(ImageProcessor) EDM
Do watershed segmentation based on the EDM of the
foreground objects (nonzero pixels) in an 8-bit image.
TRACE Debugger
TRACED_ROI Roi
transform() FHT
Performs a forward transform, converting this image into the frequency domain.
TRANSFORM Undo
transform1D(float[]) FHT
Performs an optimized 1D Fast Hartley Transform (FHT) of an array.
Transformer ij.plugin.filter
Implements the Flip and Rotate commands in the Image/Transform submenu.
Transformer() Transformer
translate(double, double) Overlay
Moves all the ROIs in this overlay.
translate(double, double) RoiManager
Moves the selected ROIs or all the ROIs if none are selected.
translate(double, double) ImageProcessor
Moves the image or selection vertically or horizontally by a specified
number of pixels.
translate(int, int) Overlay
Moves all the ROIs in this overlay.
translate(int, int, boolean) ImageProcessor
Deprecated.
Translator ij.plugin.filter
This plugin implements the Image/Translate command.
Translator() Translator
TRANSPARENT CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
Triangle AutoThresholder.Method
TRIANGLE Plot
Display points using an tiangular mark.
TRIANGLE PlotWindow
Display points using an tiangular mark.
trim() ImageStack
Frees memory by deleting a few slices from the end of the stack.
trim() VirtualStack
Does nothing.
trimFileList(String[]) FolderOpener
Removes names that start with "." or end with ".db", ".txt", ".lut", "roi", ".pty", ".hdr", ".py", etc.
trimKey(String) Macro
TrimmedButton ij.gui
This is an extended Button class used to reduce the width of the HUGE buttons on Mac OS X.
TrimmedButton(String, int) TrimmedButton
trimProcessor() ImagePlus
Frees RAM by setting the snapshot (undo) buffer in
the current ImageProcessor to null.
TRUE MacroConstants
tSelector StackWindow
type Roi
type Symbol
TYPE RoiDecoder
TYPE_CONVERSION Undo
TypeConverter ij.process
This class converts an ImageProcessor to another data type.
TypeConverter(ImageProcessor, boolean) TypeConverter
types PointRoi
types Opener
TZC HyperStackConverter
U
umean ImageStatistics
Uncalibrated mean
UNCALIBRATED_OD Calibration
undo() Undo
Undo ij
This class consists of static methods and
fields that implement ImageJ's Undo command.
Undo() Undo
uninstallPlugin(String) Menus
Deletes a command installed by Plugins/Shortcuts/Add Shortcut.
unit FileInfo
units ProfilePlot
UNKNOWN FileInfo
UNKNOWN Opener
unlock() ImagePlus
Unlocks the image.
UnsharpMask ij.plugin.filter
This plugin-filter implements ImageJ's Unsharp Mask command.
UnsharpMask() UnsharpMask
UNUSED Toolbar
unzoom() ImageCanvas
Implements the Image/Zoom/Original Scale command.
unzoom() PlotCanvas
Implements the Image/Zoom/Original Scale command.
update() Channels
update() ContrastAdjuster
Updates the ContrastAdjuster.
update() LineWidthAdjuster
update() ThresholdAdjuster
Notifies the ThresholdAdjuster that the image has changed.
update() PointToolOptions
update(boolean, boolean) Roi
If 'add' is true, adds this selection to the previous one.
update(int, ImagePlus, Roi) ResultsTable
update(ImageProcessor) ImageStack
Updates this stack so its attributes, such as min, max,
calibration table and color model, are the same as 'ip'.
update(Graphics) ImageCanvas
update(Graphics) ProgressBar
UPDATE_DISPLAY MacroConstants
UPDATE_RESULTS MacroConstants
updateAllChannelsAndDraw() CompositeImage
updateAndDraw() CompositeImage
updateAndDraw() ImagePlus
Updates this image from the pixel data in its
associated ImageProcessor, then displays it.
updateAndDraw() ContrastAdjuster
Resets this ContrastAdjuster and brings it to the front.
updateAndRepaintWindow() ImagePlus
Calls updateAndDraw to update from the pixel data
and draw the image, and also repaints the image
window to force the information displayed above
the image (dimension, type, size) to be updated.
updateArrayInspector() Interpreter
Updates Array inspector if variable exists, otherwise closes
ArrayInspector
updateChannelAndDraw() CompositeImage
updateChannelAndDraw() ImagePlus
Updates this image from the pixel data in its
associated ImageProcessor, then displays it.
updateChannels() Channels
updateClassName(String, String) Editor
Changes a plugins class name to reflect a new file name.
updateClipRect() Roi
updateColumnHeadings(String) TextPanel
updateComposite(int[], int) ColorProcessor
updateComposite(int[], int) ImageProcessor
CompositeImage calls this method to generate an updated color image.
UPDATED ImagePlus
updateDebugWindow(String[], TextWindow) Interpreter
updateDisplay() TextPanel
updateFullWindow Roi
updateHeadings() Analyzer
Redisplays the results table.
updateImage() CompositeImage
updateImage() Plot
Draws the plot again, ignored if the plot has not been drawn before or the plot is frozen
If the ImagePlus exist, updates it and its calibration.
updateImage() ImagePlus
ImageCanvas.paint() calls this method when the
ImageProcessor has generated a new image.
updateImage(ImagePlus) ImageWindow
updateImageJMenus() Menus
updateImagePlus(String, int) FileSaver
updateMenus() Menus
Updates the Image/Type and Window menus.
updatePlayPauseIcon() ScrollbarWithLabel
updatePolygon() PolygonRoi
updatePosition(int, int, int) ImagePlus
updateResults() ResultsTable
Updates the Results window.
updateSliceSelector() StackWindow
Updates the stack scrollbar.
updateStatusbarValue() ImagePlus
Redisplays the (x,y) coordinates and pixel value (which may
have changed) in the status bar.
updateUrl(String) Opener
Can't open imagej.nih.gov URLs due to encryption so redirect to mirror.nih.net.
updateWideLine(float) Roi
updateWindowList() SyncWindows
updateWindowMenuItem(ImagePlus, String, String) Menus
Changes the name of an item in the Window menu.
updateWindowMenuItem(String, String) Menus
Changes the name of an item in the Window menu.
updateY(double, int) Analyzer
Returns an updated Y coordinate based on
the current "Invert Y Coordinates" flag.
updateY(int, int) Analyzer
Returns an updated Y coordinate based on
the current "Invert Y Coordinates" flag.
upperThreshold ImageStatistics
Maximum threshold when "Limit to threshold" enabled
url FileInfo
URL IJ
URLOpener ij.plugin
Opens TIFFs, ZIP compressed TIFFs, DICOMs, GIFs and JPEGs using a URL.
URLOpener() URLOpener
useFileChooser Prefs
Use the file chooser to import and export image sequences on Windows and Linux
useInvertingLut Prefs
Open 8-bit images with inverting LUT so 0 is white and 255 is black.
useJFileChooser Prefs
Use JFileChooser instead of FileDialog to open and save files.
useNamesAsLabels Prefs
Use ROI names as "show all" labels in the ROI Manager
usePointer ImageCanvas
usePointerCursor Prefs
Use pointer cursor instead of cross
USER_FUNCTION MacroConstants
userFunction(double[], double) CurveFitter
This function is called by the Minimizer and calculates the sum of squared
residuals for given parameters.
userFunction(double[], double) UserFunction
A user-supplied function
UserFunction ij.measure
A plugin should implement this interface for minimizing a single-valued function
or fitting a curve with a custom fit function.
useSystemProxies Prefs
Set the "java.net.useSystemProxies" property
useTemplate(Plot) Plot
Adjusts the format with another plot as a template, using the current
(usually default) flags of this plot.
useTemplate(Plot, int) Plot
Adjusts the format (style) with another plot as a template.
UTILITIES_MENU Menus
V
validDimensions() StackWindow
validExtensions PluginInstaller
value HistogramWindow
value Symbol
valueChanged(ListSelectionEvent) RoiManager
valueOf(String) AutoThresholder.Method
Returns the enum constant of this type with the specified name.
values() AutoThresholder.Method
Returns an array containing the constants of this enum type, in
the order they are declared.
valueUnit FileInfo
VAR MacroConstants
VAR Filters3D
Variable ij.macro
Variable() Variable
Variable(double) Variable
Variable(Variable[]) Variable
Variable(String) Variable
VARIABLE_FUNCTION MacroConstants
variableFunctionIDs MacroConstants
variableFunctions MacroConstants
VARIANCE RankFilters
VERSION ImageJ
Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string.
VERSION_OFFSET RoiDecoder
versionLessThan(String) IJ
Displays an error message and returns true if the
ImageJ version is less than the one specified.
verticalProfile Prefs
Plot rectangular selectons vertically
VGAP ImageWindow
virtualStack FileInfo
VirtualStack ij
This class represents an array of disk-resident images.
VirtualStack() VirtualStack
Default constructor.
VirtualStack(int, int) VirtualStack
VirtualStack(int, int, int) VirtualStack
Creates a virtual stack with no backing storage.
VirtualStack(int, int, ColorModel, String) VirtualStack
Creates an empty virtual stack.
vistaHint Prefs
vListMap SyncWindows
Hashtable to map list ids to image window ids.
vwins SyncWindows
Indices of synchronized image windows are maintained in this Vector.
W
wait(int) IJ
Delays 'msecs' milliseconds.
WAIT MacroConstants
WAIT_FOR_USER MacroConstants
WaitForUserDialog 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) WaitForUserDialog
WaitForUserDialog(String, String) WaitForUserDialog
Wand ij.gui
This class implements ImageJ's wand (tracing) tool.
Wand(ImageProcessor) Wand
Constructs a Wand object from an ImageProcessor.
WAND Toolbar
WandToolOptions ij.plugin
This plugin implements the Edit/Options/Wand Tool command.
WandToolOptions() WandToolOptions
wasCanceled() GenericDialog
Returns true if the user clicked on "Cancel".
wasError() Interpreter
wasOKed() GenericDialog
Returns true if the user has clicked on "OK" or a macro is running.
weightedColor Prefs
Color to grayscale conversion is weighted (0.299, 0.587, 0.114) if the variable is true.
weightedHistogram() ColorProcessor
weights DownsizeTable
For each source point, weights for adding it to the destination point
given in the corresponding element of 'indices'
west(ImageProcessor) Shadows
WHILE MacroConstants
whiteIsZero FileInfo
whitePoint ColorSpaceConverter
wideLine Roi
width ImagePlus
width FileInfo
width ImageProcessor
width ImageStatistics
WIDTH ProgressBar
WIDTH_KEY Arrow
WIDTH_KEY TextWindow
WIDTHD RoiDecoder
WildcardMatch ij.util
This class allows for simple wildcard pattern matching.
WildcardMatch() WildcardMatch
WildcardMatch(char, char) WildcardMatch
win ImagePlus
WINDOW_MENU_ITEMS Menus
windowActivated(WindowEvent) GenericDialog
windowActivated(WindowEvent) ImageWindow
windowActivated(WindowEvent) MessageDialog
windowActivated(WindowEvent) PlotWindow
Called when the window is activated (WindowListener)
Window layout is finished at latest a few millisec after windowActivated, then the
'wasActivated' boolean is set to tell the ImageCanvas that resize events should
lead to resizing the canvas (before, creating the layout can lead to resize events)
windowActivated(WindowEvent) YesNoCancelDialog
windowActivated(WindowEvent) ImageJ
windowActivated(WindowEvent) FunctionFinder
windowActivated(WindowEvent) CommandFinder
windowActivated(WindowEvent) ColorThresholder
windowActivated(WindowEvent) ContrastAdjuster
windowActivated(WindowEvent) Editor
Override windowActivated in PlugInFrame to
prevent Mac menu bar from being installed.
windowActivated(WindowEvent) LineWidthAdjuster
windowActivated(WindowEvent) PlugInDialog
windowActivated(WindowEvent) PlugInFrame
windowActivated(WindowEvent) Recorder
Override windowActivated in PlugInFrame.
windowActivated(WindowEvent) RoiManager
windowActivated(WindowEvent) ThresholdAdjuster
windowActivated(WindowEvent) Orthogonal_Views
windowClosed(WindowEvent) GenericDialog
windowClosed(WindowEvent) ImageWindow
windowClosed(WindowEvent) MessageDialog
windowClosed(WindowEvent) YesNoCancelDialog
windowClosed(WindowEvent) ImageJ
windowClosed(WindowEvent) FunctionFinder
windowClosed(WindowEvent) CommandFinder
windowClosed(WindowEvent) PlugInDialog
windowClosed(WindowEvent) PlugInFrame
windowClosed(WindowEvent) Orthogonal_Views
windowClosing(WindowEvent) GenericDialog
windowClosing(WindowEvent) ImageWindow
windowClosing(WindowEvent) MessageDialog
windowClosing(WindowEvent) NonBlockingGenericDialog
windowClosing(WindowEvent) YesNoCancelDialog
windowClosing(WindowEvent) ImageJ
windowClosing(WindowEvent) FunctionFinder
windowClosing(WindowEvent) CommandFinder
windowClosing(WindowEvent) PlugInDialog
windowClosing(WindowEvent) PlugInFrame
windowClosing(WindowEvent) SyncWindows
Override parent windowClosing method to clean up synchronized
resources on exit.
windowClosing(WindowEvent) Orthogonal_Views
windowDeactivated(WindowEvent) GenericDialog
windowDeactivated(WindowEvent) ImageWindow
windowDeactivated(WindowEvent) MessageDialog
windowDeactivated(WindowEvent) YesNoCancelDialog
windowDeactivated(WindowEvent) ImageJ
windowDeactivated(WindowEvent) FunctionFinder
windowDeactivated(WindowEvent) CommandFinder
windowDeactivated(WindowEvent) PlugInDialog
windowDeactivated(WindowEvent) PlugInFrame
windowDeactivated(WindowEvent) Orthogonal_Views
windowDeiconified(WindowEvent) GenericDialog
windowDeiconified(WindowEvent) ImageWindow
windowDeiconified(WindowEvent) MessageDialog
windowDeiconified(WindowEvent) YesNoCancelDialog
windowDeiconified(WindowEvent) ImageJ
windowDeiconified(WindowEvent) FunctionFinder
windowDeiconified(WindowEvent) CommandFinder
windowDeiconified(WindowEvent) PlugInDialog
windowDeiconified(WindowEvent) PlugInFrame
windowDeiconified(WindowEvent) Orthogonal_Views
windowIconified(WindowEvent) GenericDialog
windowIconified(WindowEvent) ImageWindow
windowIconified(WindowEvent) MessageDialog
windowIconified(WindowEvent) YesNoCancelDialog
windowIconified(WindowEvent) ImageJ
windowIconified(WindowEvent) FunctionFinder
windowIconified(WindowEvent) CommandFinder
windowIconified(WindowEvent) PlugInDialog
windowIconified(WindowEvent) PlugInFrame
windowIconified(WindowEvent) Orthogonal_Views
WindowManager ij
This class consists of static methods used to manage ImageJ's windows.
windowOpened(WindowEvent) GenericDialog
windowOpened(WindowEvent) ImageWindow
windowOpened(WindowEvent) MessageDialog
windowOpened(WindowEvent) YesNoCancelDialog
windowOpened(WindowEvent) ImageJ
windowOpened(WindowEvent) FunctionFinder
windowOpened(WindowEvent) CommandFinder
windowOpened(WindowEvent) PlugInDialog
windowOpened(WindowEvent) PlugInFrame
windowOpened(WindowEvent) Orthogonal_Views
WindowOrganizer ij.plugin
This class implements the Window menu's "Show All", "Main Window", "Cascade" and "Tile" commands.
WindowOrganizer() WindowOrganizer
windowStateChanged(WindowEvent) ImageWindow
wipeBack() PolygonRoi
wList SyncWindows
List of currently displayed windows retrieved from ImageJ
window manager.
WORD MacroConstants
write(byte[]) LogStream
write(byte[], int, int) LogStream
write(int) LogStream
write(Roi) RoiEncoder
Save the Roi to the file of stream.
write(DataOutputStream) TextEncoder
Saves the image as a tab-delimited text file.
write(DataOutputStream) TiffEncoder
write(OutputStream) ImageWriter
Writes the image to the specified OutputStream.
write(OutputStream) TiffEncoder
Saves the image as a TIFF file.
write(String) IJ
Deprecated.
WRITE MacroConstants
writeImage(ImagePlus, String, int) PNG_Writer
writeImage(ImagePlus, String, int, int) AVI_Writer
Writes an ImagePlus (stack) as AVI file.
Writer ij.plugin.filter
Deprecated.
Writer() Writer
Deprecated.
X
x SyncWindows
X Plot
Display points using an X-shaped mark.
X PlotWindow
Display points using an X-shaped mark.
X_CENTER_OF_MASS ResultsTable
X_CENTROID ResultsTable
X_FORCE2GRID Plot
flag for forcing frame to coincide with the grid/ticks in x direction (results in unused space)
X_GRID Plot
flag for drawing vertical grid lines for x axis
X_LOG_NUMBERS Plot
flag for logarithmic x-axis
X_LOG_TICKS Plot
flag for ticks (major and minor, if space) on logarithmic x axis
X_MINOR_TICKS Plot
flag for drawing minor ticks on linear (non-logarithmic) x axis
X_NUMBERS Plot
flag for numeric labels of x-axis ticks
X_RANGE Plot
Flag for addressing the x axis, for copying from a template: copy/write x axis range.
X_RESOLUTION TiffDecoder
X_TICKS Plot
flag for drawing major ticks on linear (non-logarithmic) x axis
x1 Line
X1 RoiDecoder
x1d Line
x1R Line
x2 Line
X2 RoiDecoder
x2d Line
x2R Line
xCenter EllipseFitter
X centroid
xCenterOfMass ImageStatistics
xCentroid ImageStatistics
xCoordinates EllipseFitter
Initialized by makeRoi()
XD RoiDecoder
xInc ProfilePlot
XINC Editor
XINC MacroInstaller
xloc WaitForUserDialog
xMax Roi
xMax ImageProcessor
xMin ImageProcessor
xMouse ImageCanvas
xMouseStart ImageCanvas
xor(int) FloatProcessor
xor(int) ImageProcessor
Binary exclusive OR of each pixel in the image or ROI with 'value'.
xor(int) ShortProcessor
xor(ShapeRoi) ShapeRoi
Unary exclusive or operator.
XOR Blitter
dst=dst XOR src
xOrigin Calibration
X origin in pixels.
xp PolygonRoi
xp2 PolygonRoi
xpf PolygonRoi
xpoints Wand
The x-coordinates of the points in the outline.
xpoints FloatPolygon
xSpline PolygonRoi
xSrcStart ImageCanvas
xstart ImageStatistics
Used internally by AnalyzeParticles
xValues ProfilePlot
XY_Reader ij.plugin
This plugin implements the File/Import/XY Coordinates command.
XY_Reader() XY_Reader
XYCoordinates ij.plugin
Writes the XY coordinates and pixel values of all non-background
pixels to a tab-delimited text file.
XYCoordinates() XYCoordinates
XYWriter ij.plugin.filter
Saves the XY coordinates of the current ROI boundary.
XYWriter() XYWriter
xyYtoXYZ(double[]) ColorSpaceConverter
xyYtoXYZ(double, double, double) ColorSpaceConverter
XYZtoLAB(double[]) ColorSpaceConverter
Convert XYZ to LAB.
XYZtoLAB(double, double, double) ColorSpaceConverter
Convert XYZ to LAB.
XYZtoRGB(double[]) ColorSpaceConverter
Convert XYZ to RGB
XYZtoRGB(double, double, double) ColorSpaceConverter
Convert XYZ to RGB.
XYZtoxyY(double[]) ColorSpaceConverter
XYZtoxyY(double, double, double) ColorSpaceConverter
Y
y SyncWindows
Y_CENTER_OF_MASS ResultsTable
Y_CENTROID ResultsTable
Y_FORCE2GRID Plot
flag for forcing frame to coincide with the grid/ticks in y direction (results in unused space)
Y_GRID Plot
flag for drawing horizontal grid lines for y axis
Y_LOG_NUMBERS Plot
flag for logarithmic y axis
Y_LOG_TICKS Plot
flag for ticks (major and minor, if space) on logarithmic y axis
Y_MINOR_TICKS Plot
flag for drawing minor ticks on linear (non-logarithmic) y axis
Y_NUMBERS Plot
flag for numeric labels of x-axis ticks
Y_RANGE Plot
Flag for addressing the y axis, for copying from a template: copy/write y axis range
Y_RESOLUTION TiffDecoder
Y_TICKS Plot
flag for drawing major ticks on linear (non-logarithmic) y axis
y1 Line
Y1 RoiDecoder
y1d Line
y1R Line
y2 Line
Y2 RoiDecoder
y2d Line
y2R Line
yCenter EllipseFitter
X centroid
yCenterOfMass ImageStatistics
yCentroid ImageStatistics
yCoordinates EllipseFitter
Initialized by makeRoi()
YD RoiDecoder
Yen AutoThresholder.Method
YesNoCancelDialog ij.gui
A modal dialog box with a one line message and
"Yes", "No" and "Cancel" buttons.
YesNoCancelDialog(Frame, String, String) YesNoCancelDialog
YesNoCancelDialog(Frame, String, String, String, String) YesNoCancelDialog
yesPressed() YesNoCancelDialog
Returns true if the user dismissed dialog by pressing "Yes".
YINC Editor
YINC MacroInstaller
yLabel ProfilePlot
yloc WaitForUserDialog
yMax HistogramWindow
yMax Roi
yMax ImageProcessor
yMin ImageProcessor
yMouse ImageCanvas
yMouseStart ImageCanvas
yOrigin Calibration
Y origin in pixels.
yp PolygonRoi
yp2 PolygonRoi
ypf PolygonRoi
ypoints Wand
The y-coordinates of the points in the outline.
ypoints FloatPolygon
ySpline PolygonRoi
ySrcStart ImageCanvas
ystart ImageStatistics
Used internally by AnalyzeParticles
Z
Z_POSITION RoiDecoder
ZAxisProfiler ij.plugin
Implements the Image/Stacks/Plot Z-axis Profile command,
which plots the selection mean gray value versus slice number.
ZAxisProfiler() ZAxisProfiler
ZCT HyperStackConverter
ZERO_TRANSPARENT RoiDecoder
zeroClip() Calibration
Returns true if zero clipping is enabled.
ZIP FileInfo
ZIP Opener
ZIP_ARCHIVE FileInfo
zipUncompress(byte[]) ImageReader
TIFF Adobe ZIP support contributed by Jason Newton.
zoom(String) PlotCanvas
Zoom operations that are handled by ij.plugin.Zoom
Zoom ij.plugin
This plugin implements the commands in the Image/Zoom submenu.
Zoom() Zoom
zoom100Percent() ImageCanvas
Implements the Image/Zoom/View 100% command.
zoom100Percent() PlotCanvas
Implements the Image/Zoom/View 100% command: Sets the original frame size as specified
in Edit/Options/Plots (unless the plot is frozen)
zoomIn(int, int) ImageCanvas
Zooms in by making the window bigger.
zoomIn(int, int) PlotCanvas
Zooms in by modifying the plot range; sx and sy are screen coordinates
zoomOut(int, int) ImageCanvas
Zooms out by making the source rectangle (srcRect)
larger and centering it on (x,y).
zoomOut(int, int) PlotCanvas
Zooms out by modifying the plot range; sx and sy are screen coordinates
zoomTargetOX ImageCanvas
Image (=offscreen) coordinates where the cursor was moved to for zooming
zoomTargetOY ImageCanvas
zOrigin Calibration
Z origin in pixels.
ZProjector ij.plugin
This plugin performs a z-projection of the input stack.
ZProjector() ZProjector
ZProjector(ImagePlus) ZProjector
Construction of ZProjector with image to be projected.
zScale(ImagePlus, int, int) Resizer
zSelector StackWindow
ZTC HyperStackConverter
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
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