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 _

S

s2ints(String) - Method in class ij.plugin.ControlPanel
Breaks the specified string into an array of ints.
s2ints(String) - Method in class ij.plugin.filter.FractalBoxCounter
Breaks the specified string into an array of ints.
S_END - Static variable in class ij.plugin.frame.jedit.tokenmarker.PerlTokenMarker
 
S_ONE - Static variable in class ij.plugin.frame.jedit.tokenmarker.PerlTokenMarker
 
S_TWO - Static variable in class ij.plugin.frame.jedit.tokenmarker.PerlTokenMarker
 
SaltAndPepper - Class in ij.plugin.filter
Implements ImageJ's Process/Noise/Salt and Pepper command.
SaltAndPepper() - Constructor for class ij.plugin.filter.SaltAndPepper
 
SAMPLE_FORMAT - Static variable in class ij.io.TiffDecoder
 
sampleModel - Variable in class ij.process.ImageProcessor
 
SAMPLES_PER_PIXEL - Static variable in class ij.io.TiffDecoder
 
samplesPerPixel - Variable in class ij.io.FileInfo
 
SansSerif12 - Static variable in class ij.ImageJ
SansSerif, 12-point, plain font.
SAT - Static variable in class com.bric.swing.ColorPicker
Used to indicate when we're in "saturation mode".
SAT - Static variable in class ij2x.plugin.frame.JColorPicker
Used to indicate when we're in "saturation mode".
save - Variable in class ij.gui.HistogramWindow
 
save(String) - Static method in class ij.IJ
Saves the current image, lookup table, selection or text window to the specified file path.
save(ImagePlus, String) - Static method in class ij.IJ
Saves the specified image, lookup table or selection to the specified file path.
save() - Method in class ij.io.FileSaver
Resaves the image.
SAVE - Static variable in interface ij.macro.MacroConstants
 
save(ImagePlus, String, int) - Static method in class ij.plugin.JpegWriter
Thread-safe method.
save(String) - Method in class ij.plugin.MeasurementsWriter
 
save(PrintWriter) - Method in class ij.text.TextPanel
Writes all the text in this TextPanel to a file.
SAVE_AS - Static variable in interface ij.macro.MacroConstants
 
SAVE_AS_MENU - Static variable in class ij.Menus
 
SAVE_SETTINGS - Static variable in interface ij.macro.MacroConstants
 
saveAction - Static variable in class ij.plugin.frame.Editor
 
saveAction - Static variable in class ij2x.plugin.frame.Editor
 
saveAction - Static variable in class ij2x.plugin.frame.MonoEditor
 
saveAs(String, String) - Static method in class ij.IJ
 
saveAs(ImagePlus, String, String) - Static method in class ij.IJ
 
saveAs(String) - Static method in class ij.Macro
 
saveAs(String) - Method in class ij.measure.ResultsTable
Saves this ResultsTable as a tab or comma delimited text file.
saveAs(String) - Method in class ij.text.TextPanel
Saves all the text in this TextPanel to a file.
saveAsAction - Static variable in class ij.plugin.frame.Editor
 
saveAsAction - Static variable in class ij2x.plugin.frame.Editor
 
saveAsAction - Static variable in class ij2x.plugin.frame.MonoEditor
 
saveAsBmp() - Method in class ij.io.FileSaver
Save the image in BMP format using a save file dialog.
saveAsBmp(String) - Method in class ij.io.FileSaver
Save the image in BMP format using the specified path.
saveAsByteArray(Roi) - Static method in class ij.io.RoiEncoder
Saves the specified ROI as a byte array.
saveAsFits() - Method in class ij.io.FileSaver
Save the image in FITS format using a save file dialog.
saveAsFits(String) - Method in class ij.io.FileSaver
Save the image in FITS format using the specified path.
saveAsGif() - Method in class ij.io.FileSaver
Save the image in GIF format using a save file dialog.
saveAsGif(String) - Method in class ij.io.FileSaver
Save the image in Gif format using the specified path.
saveAsJava(File, ImagePlus) - Method in class ij2x.plugin.Lut2Java
 
saveAsJava(PrintWriter, ImagePlus) - Method in class ij2x.plugin.Lut2Java
 
saveAsJavaButton - Variable in class ij2x.plugin.LutPanel
 
saveAsJpeg() - Method in class ij.io.FileSaver
Save the image in JPEG format using a save file dialog.
saveAsJpeg(String) - Method in class ij.io.FileSaver
Save the image in JPEG format using the specified path.
saveAsLut() - Method in class ij.io.FileSaver
Save the current LUT using a save file dialog.
saveAsLut(String) - Method in class ij.io.FileSaver
Save the current LUT using the specified path.
saveAsPgm() - Method in class ij.io.FileSaver
Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using a save file dialog.
saveAsPgm(String) - Method in class ij.io.FileSaver
Saves grayscale images in PGM (portable graymap) format and RGB images in PPM (portable pixmap) format, using the specified path.
saveAsPng() - Method in class ij.io.FileSaver
Save the image in PNG format using a save file dialog.
saveAsPng(String) - Method in class ij.io.FileSaver
Save the image in PNG format using the specified path.
saveAsRaw() - Method in class ij.io.FileSaver
Save the image or stack as raw data using a save file dialog.
saveAsRaw(String) - Method in class ij.io.FileSaver
Save the image as raw data using the specified path.
saveAsRawStack(String) - Method in class ij.io.FileSaver
Save the stack as raw data using the specified path.
saveAsText() - Method in class ij.io.FileSaver
Save the image as tab-delimited text using a save file dialog.
saveAsText(String) - Method in class ij.io.FileSaver
Save the image as tab-delimited text using the specified path.
saveAsTiff() - Method in class ij.io.FileSaver
Save the image or stack in TIFF format using a save file dialog.
saveAsTiff(String) - Method in class ij.io.FileSaver
Save the image in TIFF format using the specified path.
saveAsTiffStack(String) - Method in class ij.io.FileSaver
Save the stack as a multi-image TIFF using the specified path.
saveAsZip() - Method in class ij.io.FileSaver
Uses a save file dialog to save the image or stack as a TIFF in a ZIP archive.
saveAsZip(String) - Method in class ij.io.FileSaver
Save the image or stack in TIFF/ZIP format using the specified path.
saveBackup(File, int, String, String, String) - Static method in class ij.plugin.frame.jedit.MiscUtilities
Saves a backup (optionally numbered) of a file.
saveBackup(File, int, String, String, String, int) - Static method in class ij.plugin.frame.jedit.MiscUtilities
Saves a backup (optionally numbered) of a file.
saveBitmap(String, Image, int, int) - Method in class ij.plugin.BMP_Writer
 
saveChanges(int) - Method in class ij.VirtualStack
Currently not implemented
SaveChangesDialog - Class in ij.gui
A modal dialog box with a one line message and "Don't Save", "Cancel" and "Save" buttons.
SaveChangesDialog(JFrame, String) - Constructor for class ij.gui.SaveChangesDialog
 
saveChangesDialog() - Method in class ij.plugin.frame.Editor
 
saveCommand() - Static method in class ij.plugin.frame.Recorder
Writes the current command and options to the Recorder window.
SaveDialog - Class in ij.io
This class displays a dialog window from which the user can save a file.
SaveDialog(String, String, String) - Constructor for class ij.io.SaveDialog
Displays a file save dialog with 'title' as the title, 'defaultName' as the initial file name, and 'extension' (e.g. ".tif") as the default extension.
SaveDialog(String, String, String, String) - Constructor for class ij.io.SaveDialog
Displays a file save dialog, using the specified default directory and file name and extension.
saveGlobals(Program) - Method in class ij.macro.Interpreter
Saves global variables.
saveImageDescription(byte[], FileInfo) - Method in class ij.io.TiffDecoder
Save the image description in the specified FileInfo.
saveLocation(String, Point) - Static method in class ij.Prefs
Saves the Point loc in the preferences file as a string using the keyword key.
saveMetadata(String, String) - Method in class ij.io.TiffDecoder
 
savePreferences(Properties) - Static method in class ij.gui.NewImage
Called when ImageJ quits.
savePreferences(Properties) - Static method in class ij.gui.PlotWindow
Called once when ImageJ quits.
savePreferences(Properties) - Method in class ij.ImageJ
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.io.ImportDialog
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.Menus
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.Analyzer
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.filter.ParticleAnalyzer
Called once when ImageJ quits.
savePreferences(Properties) - Static method in class ij.plugin.frame.Editor
Called once when ImageJ quits.
savePreferences() - Static method in class ij.Prefs
Saves user preferences in the IJ_Prefs.txt properties file.
savePrefs(Properties, String) - Static method in class ij.Prefs
 
savePressed() - Method in class ij.gui.SaveChangesDialog
Returns true if the user dismissed dialog by pressing "Save".
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.Analyzer
Saves the measurements specified in the "Set Measurements" dialog, or by calling setMeasurements(), in the default results table.
saveResults(ImageStatistics, Roi) - Method in class ij.plugin.filter.ParticleAnalyzer
Saves statistics for one particle in a results table.
saveRoi() - Method in class ij.ImagePlus
 
saveRoi(ImagePlus) - Method in class ij.plugin.filter.RoiWriter
 
savesettingsAction - Static variable in class ij.plugin.frame.Editor
 
savesettingsAction - Static variable in class ij2x.plugin.frame.Editor
 
savesettingsAction - Static variable in class ij2x.plugin.frame.MonoEditor
 
saveString(String, String) - Static method in class ij.IJ
Saves a string as a file.
saveXValues - Static variable in class ij.gui.PlotWindow
Save x-values only.
saveXYCoordinates(ImagePlus) - Method in class ij.plugin.filter.XYWriter
 
scale(double, double) - Method in class ij.process.ByteProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ColorProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.FloatProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.ImageProcessor
Scales the image by the specified factors.
scale(double, double) - Method in class ij.process.ShortProcessor
Scales the image or selection using the specified scale factors.
scale(double, double) - Method in class ij.process.StackProcessor
 
scale(double, double, double) - Method in class ij.process.StackProcessor
 
SCALE_T - Static variable in class ij.plugin.Resizer
 
ScaleAll - Class in ij2x.plugin
This plugin implements the Image/Scale command.
ScaleAll() - Constructor for class ij2x.plugin.ScaleAll
 
ScaleBar - Class in ij.plugin
This plugin implements the Analyze/Tools/Draw Scale Bar command.
ScaleBar() - Constructor for class ij.plugin.ScaleBar
 
scaleButton - Variable in class ij2x.plugin.TransformPanel
 
scaled() - Method in class ij.measure.Calibration
Returns true if this image is spatially calibrated.
ScaleDialog - Class in ij.plugin.filter
Implements the Analyze/Set Scale command.
ScaleDialog() - Constructor for class ij.plugin.filter.ScaleDialog
 
scalefactor - Variable in class ij.plugin.filter.Printer
 
Scaler - Class in ij.plugin
This plugin implements the Image/Scale command.
Scaler() - Constructor for class ij.plugin.Scaler
 
SCIENTIFIC_NOTATION - Static variable in interface ij.measure.Measurements
 
SCREEN_HEIGHT - Static variable in interface ij.macro.MacroConstants
 
SCREEN_WIDTH - Static variable in interface ij.macro.MacroConstants
 
ScreenGrabber - Class in ij.plugin
This plugin implements the Image/Flatten, Plugins/Utilities/Capture Screen and Plugins/Utilities/Capture Image commands.
ScreenGrabber() - Constructor for class ij.plugin.ScreenGrabber
 
screenX(int) - Method in class ij.gui.ImageCanvas
Converts an offscreen x-coordinate to a screen x-coordinate.
screenX(int) - Method in class ij.gui.Roi
 
screenXD(double) - Method in class ij.gui.ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenXD(double) - Method in class ij.gui.Roi
 
screenY(int) - Method in class ij.gui.ImageCanvas
Converts an offscreen y-coordinate to a screen y-coordinate.
screenY(int) - Method in class ij.gui.Roi
 
screenYD(double) - Method in class ij.gui.ImageCanvas
Converts a floating-point offscreen x-coordinate to a screen x-coordinate.
screenYD(double) - Method in class ij.gui.Roi
 
SCRIPT - Static variable in class ij.plugin.frame.jedit.tokenmarker.PHPTokenMarker
 
scriptMode() - Static method in class ij.plugin.frame.Recorder
 
scroll(int, int) - Method in class ij.gui.ImageCanvas
 
scrollBarsInitialized - Variable in class ij.plugin.frame.jedit.JEditTextArea
 
ScrollbarWithLabel - Class in ij.gui
This class, based on Joachim Walter's Image5D package, adds "c", "z" labels and play-pause icons (T) to the stack and hyperstacks dimension sliders.
ScrollbarWithLabel() - Constructor for class ij.gui.ScrollbarWithLabel
 
ScrollbarWithLabel(StackWindow, int, int, int, int, char) - Constructor for class ij.gui.ScrollbarWithLabel
 
scrollTo(int, int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Ensures that the specified line and offset is visible by scrolling the text area if necessary.
scrollToCaret() - Method in class ij.plugin.frame.jedit.JEditTextArea
Ensures that the caret is visible by scrolling the text area if necessary.
scrollToTop() - Method in class ij.text.TextPanel
 
SD_METHOD - Static variable in class ij.plugin.ZProjector
 
seek(long) - Method in class ij.io.RandomAccessStream
 
seek(int) - Method in class ij.io.RandomAccessStream
 
SEGMENTED - Static variable in class ij.plugin.filter.MaximumFinder
Output type watershed-segmented image
SELECT - Static variable in interface ij.macro.MacroConstants
 
select(int, int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Selects from the start offset to the end offset.
select(int) - Method in class ij.plugin.frame.RoiManager
Assigns the ROI at the specified index to the current image.
select(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager
Assigns the ROI at the specified index to 'imp'.
select(int, boolean, boolean) - Method in class ij.plugin.frame.RoiManager
 
select(int) - Method in class ij.plugin.frame.RoiManager0
Assigns the ROI at the specified index to the current image.
select(ImagePlus, int) - Method in class ij.plugin.frame.RoiManager0
Assigns the ROI at the specified index to 'imp'.
select(int, boolean, boolean) - Method in class ij.plugin.frame.RoiManager0
 
SELECT_ALL - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_DOC_END - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_DOC_HOME - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_END - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_HOME - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_IMAGE - Static variable in interface ij.macro.MacroConstants
 
SELECT_NEXT_CHAR - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_NEXT_LINE - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_NEXT_PAGE - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_NEXT_WORD - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_PREV_CHAR - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_PREV_LINE - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_PREV_PAGE - Static variable in class ij.plugin.frame.jedit.InputHandler
 
SELECT_PREV_WORD - Static variable in class ij.plugin.frame.jedit.InputHandler
 
selectAll() - Method in class ij.plugin.frame.jedit.JEditTextArea
Selects all text in the document.
selectAll() - Method in class ij.text.TextPanel
Selects all the lines in this TextPanel.
selectAllAction - Static variable in class ij.plugin.frame.Editor
 
selectButton - Variable in class ij2x.plugin.ControlBarPanel
 
selectButton - Variable in class ij2x.plugin.TransformPanel
 
SELECTED_COLOR_PROPERTY - Static variable in class com.bric.swing.ColorPicker
PropertyChangeEvents will be triggered for this property when the selected color changes.
SELECTED_COLOR_PROPERTY - Static variable in class ij2x.plugin.frame.JColorPicker
PropertyChangeEvents will be triggered for this property when the selected color changes.
Selection - Class in ij.plugin
This plugin implements the commands in the Edit/Section submenu.
Selection() - Constructor for class ij.plugin.Selection
 
SELECTION_CONTAINS - Static variable in interface ij.macro.MacroConstants
 
SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
 
SELECTION_TYPE - Static variable in interface ij.macro.MacroConstants
 
selectionColor - Variable in class ij.plugin.frame.jedit.LNTextAreaDefaults
 
selectionColor - Variable in class ij.plugin.frame.jedit.LNTextAreaPainter
 
selectionColor - Variable in class ij.plugin.frame.jedit.TextAreaDefaults
 
selectionColor - Variable in class ij.plugin.frame.jedit.TextAreaPainter
 
selectionEnd - Variable in class ij.plugin.frame.jedit.JEditTextArea
 
selectionEndLine - Variable in class ij.plugin.frame.jedit.JEditTextArea
 
selectionStart - Variable in class ij.plugin.frame.jedit.JEditTextArea
 
selectionStartLine - Variable in class ij.plugin.frame.jedit.JEditTextArea
 
selectNone() - Method in class ij.plugin.frame.jedit.JEditTextArea
Moves the mark to the caret position.
selectWindow(int) - Static method in class ij.IJ
For IDs less than zero, activates the image with the specified ID.
selectWindow(String) - Static method in class ij.IJ
Activates the window with the specified title.
send(EBMessage) - Static method in class ij.plugin.frame.jedit.EditBus
Sends a message to all components on the bus in turn.
separator - Static variable in class ij.Prefs
file.separator system property
SEQ - Static variable in class ij.plugin.frame.jedit.syntax.ParserRule
 
set(int) - Method in class gnu.regexp.RESyntax
Set a given bit in this syntax.
set(String, String) - Static method in class ij.Prefs
Saves the value of the string text in the preferences file using the keyword key.
set(String, int) - Static method in class ij.Prefs
Saves value in the preferences file using the keyword key.
set(String, double) - Static method in class ij.Prefs
Saves value in the preferences file using the keyword key.
set(String, boolean) - Static method in class ij.Prefs
Saves the boolean variable value in the preferences file using the keyword key.
set(int, int, int) - Method in class ij.process.ByteProcessor
 
set(int, int) - Method in class ij.process.ByteProcessor
 
set(int, int, int) - Method in class ij.process.ColorProcessor
 
set(int, int) - Method in class ij.process.ColorProcessor
 
set(int, int, int) - Method in class ij.process.FloatProcessor
 
set(int, int) - Method in class ij.process.FloatProcessor
 
set(int, int, int) - Method in class ij.process.ImageProcessor
This is a faster version of putPixel() that does not clip out of range values and does not do bounds checking.
set(int, int) - Method in class ij.process.ImageProcessor
 
set(int, int, int) - Method in class ij.process.ShortProcessor
 
set(int, int) - Method in class ij.process.ShortProcessor
 
SET_AUTO_THRESHOLD - Static variable in interface ij.macro.MacroConstants
 
SET_BACKGROUND - Static variable in interface ij.macro.MacroConstants
 
SET_BATCH_MODE - Static variable in interface ij.macro.MacroConstants
 
SET_COLOR - Static variable in interface ij.macro.MacroConstants
 
SET_FONT - Static variable in interface ij.macro.MacroConstants
 
SET_FOREGROUND - Static variable in interface ij.macro.MacroConstants
 
SET_JUSTIFICATION - Static variable in interface ij.macro.MacroConstants
 
SET_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
 
SET_LINE_WIDTH - Static variable in interface ij.macro.MacroConstants
 
SET_LOCATION - Static variable in interface ij.macro.MacroConstants
 
SET_LUT - Static variable in interface ij.macro.MacroConstants
 
SET_METADATA - Static variable in interface ij.macro.MacroConstants
 
SET_MIN_MAX - Static variable in interface ij.macro.MacroConstants
 
SET_OPTION - Static variable in interface ij.macro.MacroConstants
 
SET_PASTE_MODE - Static variable in interface ij.macro.MacroConstants
 
SET_PIXEL - Static variable in interface ij.macro.MacroConstants
 
SET_RESULT - Static variable in interface ij.macro.MacroConstants
 
SET_RGB_WEIGHTS - Static variable in interface ij.macro.MacroConstants
 
SET_SELECTION_LOC - Static variable in interface ij.macro.MacroConstants
 
SET_SELECTION_NAME - Static variable in interface ij.macro.MacroConstants
 
SET_SLICE - Static variable in interface ij.macro.MacroConstants
 
SET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
 
SET_TOOL - Static variable in interface ij.macro.MacroConstants
 
SET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
 
SET_Z_COORDINATE - Static variable in interface ij.macro.MacroConstants
 
setAbortable(boolean) - Method in class ij.util.WorkRequest
Sets if the request can be aborted.
setAbortable(boolean) - Method in class ij.util.WorkThread
Sets if the current request can be aborted.
setActivated() - Method in class ij.ImagePlus
Called by ImageWindow.windowActivated().
setAdditionalFunctions(String) - Static method in class ij.macro.Interpreter
The specified string, if not null, is added to strings passed to the run() method.
setAllPoints(boolean) - Static method in class ij.gui.Wand
 
setAnimate(boolean) - Method in class ij.gui.StackWindow
 
setAntialiased(Graphics, boolean) - Static method in class com.bric.swing.util.Java2
 
setAntialiased(boolean) - Method in class ij.gui.TextRoi
Sets the 'antialiased' instance variable.
setAntialiased(Graphics, boolean) - Static method in class ij.util.Java2
 
setAntialiasedText(Graphics, boolean) - Static method in class com.bric.swing.util.Java2
 
setAntialiasedText(boolean) - Method in class ij.process.ImageProcessor
Specifies whether or not text is drawn using antialiasing.
setAntialiasedText(Graphics, boolean) - Static method in class ij.util.Java2
 
setAutoThreshold(ImagePlus, String) - Static method in class ij.IJ
 
setAutoThreshold(String) - Method in class ij.process.ImageProcessor
 
setAutoThreshold(String, boolean, int) - Method in class ij.process.ImageProcessor
 
setAutoThreshold(AutoThresholder.Method, boolean) - Method in class ij.process.ImageProcessor
 
setAutoThreshold(AutoThresholder.Method, boolean, int) - Method in class ij.process.ImageProcessor
 
setAutoThreshold(int, int) - Method in class ij.process.ImageProcessor
Automatically sets the lower and upper threshold levels, where 'method' must be ISODATA or ISODATA2 and 'lutUpdate' must be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
setBackgroundColor(Color) - Static method in class ij.gui.Toolbar
 
setBackgroundColor(int, int, int) - Static method in class ij.IJ
Sets the background color.
setBackgroundValue(double) - Method in class ij.process.ByteProcessor
Sets the background fill value, where 0<=value<=255.
setBackgroundValue(double) - Method in class ij.process.ColorProcessor
Sets the background fill value, where value is interpreted as an RGB int.
setBackgroundValue(double) - Method in class ij.process.FloatProcessor
Does nothing.
setBackgroundValue(double) - Method in class ij.process.ImageProcessor
Sets the background fill value used by the rotate() and scale() methods.
setBackgroundValue(double) - Method in class ij.process.ShortProcessor
Does nothing.
setBatchMode(boolean) - Method in class ij.gui.ProgressBar
 
setBilinearInterpolation(Graphics, boolean) - Static method in class com.bric.swing.util.Java2
 
setBilinearInterpolation(Graphics, boolean) - Static method in class ij.util.Java2
 
setBinaryThreshold() - Method in class ij.process.ImageProcessor
 
setBitDepth(int) - Method in class ij.VirtualStack
Sets the bit depth (8, 16, 24 or 32).
setBlockCaretEnabled(boolean) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets if the caret should be drawn as a block, false otherwise.
setBlockCaretEnabled(boolean) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets if the caret should be drawn as a block, false otherwise.
setBlockIncrement(int) - Method in class ij.gui.ScrollbarWithLabel
 
setBracketHighlightColor(Color) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets the bracket highlight color.
setBracketHighlightColor(Color) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets the bracket highlight color.
setBracketHighlightEnabled(boolean) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Enables or disables bracket highlighting.
setBracketHighlightEnabled(boolean) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Enables or disables bracket highlighting.
setBrightness(FloatProcessor) - Method in class ij.process.ColorProcessor
Updates the brightness using the pixels in the specified FloatProcessor).
setBrushSize(int) - Static method in class ij.gui.Toolbar
Set the size of the brush tool, which must be greater than 4.
setButtonPanel(boolean) - Method in class ij2x.plugin.AdjustPanel
 
setButtonPanel(boolean) - Method in class ij2x.plugin.ImageTypePanel
 
setButtonPanel(boolean) - Method in class ij2x.plugin.LutPanel
 
setButtonPanel(boolean) - Method in class ij2x.plugin.MathPanel
 
setButtonPanel(boolean) - Method in class ij2x.plugin.ToolbarBoxControl
 
setCalibration(Calibration) - Method in class ij.ImagePlus
Sets this image's calibration.
setCalibrationTable(float[]) - Method in class ij.process.ImageProcessor
Set a lookup table used by getPixelValue(), getLine() and convertToFloat() to calibrate pixel values.
setCaretBlinkEnabled(boolean) - Method in class ij.plugin.frame.jedit.JEditTextArea
Toggles caret blinking.
setCaretColor(Color) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets the caret color.
setCaretColor(Color) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets the caret color.
setCaretPosition(int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the caret position.
setCaretVisible(boolean) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets if the caret should be visible.
setChannelColorModel(IndexColorModel) - Method in class ij.CompositeImage
 
setChannelLut(LUT) - Method in class ij.CompositeImage
 
setChannelLut(LUT, int) - Method in class ij.CompositeImage
 
setChannelsUpdated() - Method in class ij.CompositeImage
 
setCharWidth(int) - Method in class ij.plugin.frame.jedit.syntax.SyntaxStyle
Sets the character width of the monospaced font.
setClipRect(Rectangle) - Method in class ij.process.ImageProcessor
Updates the clipping rectangle used by lineTo(), drawLine(), drawDot() and drawPixel().
setColor(Color) - Method in class com.bric.swing.ColorPicker
Sets the current color of this ColorPicker.
setColor(Color) - Method in class ij.gui.Plot
Changes the drawing color.
setColor(Color) - Method in class ij.gui.PlotWindow
Changes the drawing color.
setColor(Color) - Static method in class ij.gui.Roi
Sets the default (global) color used for ROI outlines.
setColor(Color) - Method in class ij.gui.Toolbar
Deprecated. replaced by setForegroundColor()
setColor(Color) - Method in class ij.ImagePlus
Sets current foreground color.
setColor(Color) - Method in class ij.process.ByteProcessor
Sets the foreground drawing color.
setColor(Color) - Method in class ij.process.ColorProcessor
Sets the foreground color.
setColor(int) - Method in class ij.process.ColorProcessor
Sets the fill/draw color, where color is an RGB int.
setColor(Color) - Method in class ij.process.FloatProcessor
Sets the foreground fill/draw color.
setColor(Color) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value to the pixel value closest to the specified color.
setColor(int) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value.
setColor(Color) - Method in class ij.process.ShortProcessor
Sets the foreground fill/draw color.
setColor(Color) - Method in class ij2x.plugin.ColorIcon
 
setColorModel(ColorModel) - Method in class ij.ImageStack
Assigns a new color model to this stack.
setColorModel(ColorModel) - Method in class ij.process.ImageProcessor
Sets the color model.
setColumnHeadings(String) - Static method in class ij.IJ
Clears the "Results" window and sets the column headings to those in the tab-delimited 'headings' String.
setColumnHeadings(String) - Method in class ij.text.TextPanel
Clears this TextPanel and sets the column headings to those in the tab-delimited 'headings' String.
setCommand(String) - Static method in class ij.plugin.frame.Recorder
Starts recording a command.
setCommand(int) - Method in class ij2x.plugin.event.ShapesEvent
 
setComposite(Composite) - Method in class ij.gui.ImageRoi
Sets the composite mode.
setCornerDiameter(int) - Method in class ij.gui.Roi
Sets the rounded rectangle corner diameter (pixels).
setCrossLoc(int, int, int) - Method in class ij.plugin.Orthogonal_Views
 
setCTable(float[], String) - Method in class ij.measure.Calibration
Sets the calibration table.
setCurrentFont(Font) - Method in class ij.gui.TextRoi
Set the current (instance) font.
setCurrentWindow(ImageWindow) - Static method in class ij.WindowManager
Makes the image contained in the specified window the active image.
setCursor(int, int, int, int) - Method in class ij.gui.ImageCanvas
Sets the cursor based on the current tool and cursor location.
setCustomRoi(boolean) - Method in class ij.gui.ImageCanvas
Allows plugins (e.g., Orthogonal_Views) to create a custom ROI using a display list.
setDate(Date) - Method in class ij2x.plugin.ControlBarPanel
 
setDebugMode(int) - Method in class ij.macro.Interpreter
 
setDefault(byte) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setDefault16bitRange(int) - Static method in class ij.ImagePlus
Set the default 16-bit display range, where 'bitDepth' must be 0 (auto-scaling), 8 (0-255), 10 (0-1023), 12 (0-4095, 15 (0-32767) or 16 (0-65535).
setDefaultDirectory(String) - Static method in class ij.io.DirectoryChooser
Sets the default directory presented in the dialog.
setDefaultDirectory(String) - Static method in class ij.io.OpenDialog
Sets the current working directory.
setDefaultDirectory(String) - Static method in class ij.plugin.frame.Editor
 
setDefaultDirectory(String) - Static method in class ij2x.plugin.frame.Editor
 
setDefaultDirectory(String) - Static method in class ij2x.plugin.frame.MonoEditor
 
setDefaultDoubleHeaded(boolean) - Static method in class ij.gui.Arrow
 
setDefaultFillColor(Color) - Static method in class ij.gui.Roi
 
setDefaultHeadings() - Method in class ij.measure.ResultsTable
Sets the headings used by the Measure command ("Area", "Mean", etc.).
setDefaultHeadings() - Static method in class ij.plugin.filter.Analyzer
Sets the default headings ("Area", "Mean", etc.).
setDefaultHeadSize(double) - Static method in class ij.gui.Arrow
 
setDefaultOutline(boolean) - Static method in class ij.gui.Arrow
 
setDefaultStyle(int) - Static method in class ij.gui.Arrow
 
setDefaultWidth(double) - Static method in class ij.gui.Arrow
 
setDialog(GenericDialog) - Method in class ij.plugin.filter.PlugInFilterRunner
 
setDigitRegexp(RE) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setDimensions(int, int, int) - Method in class ij.ImagePlus
Sets the 3rd, 4th and 5th dimensions, where nChannels*nSlices*nFrames must be equal to the stack size.
setDisplayList(Vector) - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.setOverlay(ij.gui.Overlay)
setDisplayList(Shape, Color, BasicStroke) - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.setOverlay(Shape, Color, BasicStroke)
setDisplayList(Roi, Color) - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.setOverlay(Roi, Color, int, Color)
setDisplayRange(double, double) - Method in class ij.CompositeImage
 
setDisplayRange(double, double) - Method in class ij.ImagePlus
Sets the display range of the current channel.
setDisplayRange(double, double, int) - Method in class ij.ImagePlus
Sets the display range of specified channels in an RGB image, where 4=red, 2=green, 1=blue, 6=red+green, etc.
setDocument(SyntaxDocument) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the document this text area is editing.
setDoScaling(boolean) - Static method in class ij.process.ImageConverter
Set true to scale to 0-255 when converting short to byte or float to byte and to 0-65535 when converting float to short.
setDoubleHeaded(boolean) - Method in class ij.gui.Arrow
 
setDrawingColor(int, int, boolean) - Method in class ij.gui.ImageCanvas
 
setDrawingSize(int, int) - Method in class ij.gui.ImageCanvas
 
setEchoChar(char) - Method in class ij.gui.GenericDialog
Sets the echo character for the next string field.
setEditable(boolean) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets if this component is editable.
setEditMode(ImagePlus, boolean) - Method in class ij.plugin.frame.RoiManager
 
setEditMode(ImagePlus, boolean) - Method in class ij.plugin.frame.RoiManager0
 
setEditor(Editor) - Method in class ij.macro.Interpreter
 
setElectricScroll(int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the number of lines from the top and bottom of the text area that are always visible
setEOLMarkerColor(Color) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets the EOL marker color.
setEOLMarkerColor(Color) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets the EOL marker color.
setEOLMarkersPainted(boolean) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets if EOL markers are to be drawn.
setEOLMarkersPainted(boolean) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets if EOL markers are to be drawn.
setEscapeRule(ParserRule) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setExceptionHandler(IJ.ExceptionHandler) - Static method in class ij.IJ
Installs a custom exception handler that overrides the handleException() method.
setExpertControlsVisible(boolean) - Method in class com.bric.swing.ColorPicker
The labels/spinners/buttons on the right side of a ColorPicker are optional.
setExtension(String, String) - Static method in class ij.io.SaveDialog
 
setf(int, int, float) - Method in class ij.process.ByteProcessor
 
setf(int, float) - Method in class ij.process.ByteProcessor
 
setf(int, int, float) - Method in class ij.process.ColorProcessor
 
setf(int, float) - Method in class ij.process.ColorProcessor
 
setf(int, int, float) - Method in class ij.process.FloatProcessor
 
setf(int, float) - Method in class ij.process.FloatProcessor
 
setf(int, int, float) - Method in class ij.process.ImageProcessor
 
setf(int, float) - Method in class ij.process.ImageProcessor
 
setf(int, int, float) - Method in class ij.process.ShortProcessor
 
setf(int, float) - Method in class ij.process.ShortProcessor
 
setFileInfo(FileInfo) - Method in class ij.ImagePlus
Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo().
setFileName(String) - Method in class ij.plugin.MacroInstaller
 
setFillColor(Color) - Method in class ij.gui.Overlay
Sets the fill color of all the Rois in this overlay.
setFillColor(Color) - Method in class ij.gui.Roi
Sets the color used to fill ROIs when they are in an overlay.
setFirstLine(int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the line displayed at the text area's origin without updating the scroll bars.
setFloatArray(float[][]) - Method in class ij.process.ImageProcessor
Replaces the pixel data with contents of the specified 2D float array.
setFocusable(boolean) - Method in class ij.gui.ScrollbarWithLabel
 
setFont(Font) - Method in class ij.gui.MultiLineLabel
 
setFont(String, int, int) - Static method in class ij.gui.TextRoi
Sets the global font face, size and style that will be used by TextROIs interactively created using the text tool.
setFont(String, int, int, boolean) - Static method in class ij.gui.TextRoi
Sets the font face, size, style and antialiasing mode that will be used by TextROIs interactively created using the text tool.
setFont(Font) - Method in class ij.plugin.frame.Editor
 
setFont(Font) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets the font for this component.
setFont(Font) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets the font for this component.
setFont(Font) - Method in class ij.process.ImageProcessor
Sets the font used by drawString().
setFont(Font, boolean) - Method in class ij.text.TextPanel
 
setFont(Font) - Method in class ij2x.plugin.frame.Editor
 
setFont(Font) - Method in class ij2x.plugin.frame.MonoEditor
 
setFontSize(int) - Static method in class ij.Menus
Set the size (in points) used for the fonts in ImageJ menus.
setForegroundColor(Color) - Static method in class ij.gui.Toolbar
 
setForegroundColor(int, int, int) - Static method in class ij.IJ
Sets the foreground color.
setFromFloatArrays(float[][]) - Method in class ij.process.ByteProcessor
 
setFromFloatProcessors(FloatProcessor[]) - Method in class ij.process.ByteProcessor
 
setFunction(int, double[], String) - Method in class ij.measure.Calibration
Sets the calibration function, coefficient table and unit (e.g.
setFunction(int, double[], String, boolean) - Method in class ij.measure.Calibration
 
setGlobalCalibration(Calibration) - Method in class ij.ImagePlus
Sets the system-wide calibration.
setGlobalJustification(int) - Static method in class ij.gui.TextRoi
Sets the 'justification' instance variable (must be LEFT, CENTER or RIGHT)
setGraphicsFlags(Graphics, Font) - Method in class ij.plugin.frame.jedit.SyntaxStyle
Sets the foreground color and font of the specified graphics context to that specified in this style.
setGrayPaletteColor(int, int, boolean) - Method in class ij2x.plugin.HorizontalGradient.ColorIconArea
 
setGrayPaletteColor(int, int, boolean) - Method in class ij2x.plugin.ThreeColor.ColorIconArea
 
setHandler(XmlHandler) - Method in class com.microstar.xml.XmlParser
Set the handler that will receive parsing events.
setHeading(int, String) - Method in class ij.measure.ResultsTable
Deprecated. replaced by addValue(String,double) and setValue(String,int,double)
setHeadSize(double) - Method in class ij.gui.Arrow
 
setHelpLabel(String) - Method in class ij.gui.GenericDialog
Sets a replacement label for the "Help" button.
setHexColor(String) - Method in class ij2x.plugin.HorizontalGradient
 
setHexColor(String) - Method in class ij2x.plugin.ThreeColor
 
setHexControlsVisible(boolean) - Method in class com.bric.swing.ColorPicker
This controls whether the hex field (and label) are visible or not.
setHideLabels(boolean) - Method in class ij.gui.PointRoi
 
setHideOutputImage(boolean) - Method in class ij.plugin.filter.ParticleAnalyzer
Set 'hideOutputImage' true to not display the "Show:" image.
setHideOverlay(boolean) - Method in class ij.ImagePlus
 
setHighlightDigits(boolean) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setHistogramRange(double, double) - Method in class ij.process.ImageProcessor
Set the range used for histograms of float images.
setHistogramSize(int) - Method in class ij.process.ImageProcessor
Set the number of bins to be used for histograms of float images.
setHorizontalOffset(int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the horizontal offset of drawn lines.
setHSB(float, float, float) - Method in class com.bric.swing.ColorPicker
Sets the current color of this ColorPicker
setHSB(float, float, float) - Method in class com.bric.swing.ColorPickerPanel
Sets the selected color of this panel.
setHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Sets the current pixels from 3 byte arrays (hue, saturation and brightness).
setHSBControlsVisible(boolean) - Method in class com.bric.swing.ColorPicker
This shows or hides the HSB spinner controls.
setIcon(JFrame) - Static method in class ij.util.Tools
 
setIgnoreCase(boolean) - Method in class ij.plugin.frame.jedit.KeywordMap
Sets if the keyword map should be case insensitive.
setIgnoreCase(boolean) - Method in class ij.plugin.frame.jedit.syntax.KeywordMap
Sets if the keyword map should be case insensitive.
setIgnoreCase(boolean) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setIgnoreFlush(boolean) - Method in class ij.ImagePlus
 
setImage(ImagePlus) - Method in class ij.gui.ImageWindow
 
setImage(ImagePlus) - Method in class ij.gui.Roi
 
setImage(Image) - Method in class ij.ImagePlus
Replaces the image, if any, with the one specified.
setImage(ImagePlus) - Method in class ij.ImagePlus
Replaces this image with the specified ImagePlus.
setImage(ImagePlus) - Method in class ij.measure.Calibration
Disables the density calibation if the specified image has a differenent bit depth.
setImage(ImagePlus) - Method in class ij.plugin.ZProjector
Explicitly set image to be projected.
setImagesURL(String) - Static method in class ij.Prefs
Sets the URL of the directory that contains the ImageJ sample images.
setImageUpdated() - Method in class ij.gui.ImageCanvas
ImagePlus.updateAndDraw calls this method to force the paint() method to update the image from the ImageProcessor.
setInitialParameters(double[]) - Method in class ij.measure.CurveFitter
Sets the initial parameters, which override the default initial parameters.
setInputEvent(InputEvent) - Static method in class ij.IJ
 
setInputHandler(InputHandler) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the input handler.
setInsets(int, int, int) - Method in class ij.gui.GenericDialog
Set the insets (margins), in pixels, that will be used for the next component added to the dialog.
setInsets(Insets) - Method in class ij2x.plugin.imageborder.ImageBorder
 
setInstanceColor(Color) - Method in class ij.gui.Roi
Deprecated. replaced by setStrokeColor()
setIntArray(int[][]) - Method in class ij.process.ImageProcessor
Replaces the pixel data with contents of the specified 2D int array.
setInterpolate(boolean) - Method in class ij.process.ImageProcessor
This method has been replaced by setInterpolationMethod().
setInterpolationMethod(int) - Method in class ij.process.ImageProcessor
Use this method to set the interpolation method (NONE, BILINEAR or BICUBIC) used by scale(), resize() and rotate().
setInvalidLinesPainted(boolean) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets if invalid lines are to be painted as red tildes.
setInvalidLinesPainted(boolean) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets if invalid lines are to be painted as red tildes.
setInvertY(boolean) - Method in class ij.measure.Calibration
Sets the 'invertY' flag.
setIsMacroWindow(boolean) - Method in class ij.plugin.frame.Editor
 
setIsMacroWindow(boolean) - Method in class ij2x.plugin.frame.Editor
 
setIsMacroWindow(boolean) - Method in class ij2x.plugin.frame.MonoEditor
 
setJpegQuality(int) - Static method in class ij.io.FileSaver
Specifies the image quality (0-100). 0 is poorest image quality, highest compression, and 100 is best image quality, lowest compression.
setJustification(int) - Method in class ij.gui.Plot
Sets the justification used by addLabel(), where justification is ImageProcessor.LEFT, ImageProcessor.CENTER or ImageProcessor.RIGHT.
setJustification(int) - Method in class ij.gui.TextRoi
Sets the 'justification' instance variable (must be LEFT, CENTER or RIGHT)
setJustification(int) - Method in class ij.process.ImageProcessor
Sets the justification used by drawString(), where justification is CENTER_JUSTIFY, RIGHT_JUSTIFY or LEFT_JUSTIFY.
setKeyDown(int) - Static method in class ij.IJ
 
setKeyUp(int) - Static method in class ij.IJ
 
setKeywords(KeywordMap) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setLabel(String, int) - Method in class ij.measure.ResultsTable
Adds a label to the beginning of the specified row, or updates an existing lable, where 0<=rowsetLabelColor(Color) - Method in class ij.gui.Overlay
 
setLabelFont(Font) - Method in class ij.gui.Overlay
 
setLastDirectory(String) - Static method in class ij.io.OpenDialog
Sets the path to the directory containing the last file opened by the user.
setLastName(String) - Static method in class ij.io.OpenDialog
Sets the name of the last file opened by the user.
setLimits(double, double, double, double) - Method in class ij.gui.Plot
Sets the x-axis and y-axis range.
setLimits(double, double, double, double) - Method in class ij.gui.PlotWindow
Sets the x-axis and y-axis range.
setLine(int, String) - Method in class ij.text.TextPanel
Replaces the contents of the specified line, where 'index' must be greater than or equal to zero and less than the value returned by getLineCount().
setLineContext(TokenMarker.LineContext) - Method in class ij.plugin.frame.jedit.syntax.DefaultTokenHandler
The token handler can compare this object with the object previously given for this line to see if the token type at the end of the line has changed (meaning subsequent lines might need to be retokenized).
setLineContext(TokenMarker.LineContext) - Method in class ij.plugin.frame.jedit.syntax.DummyTokenHandler
The token handler can compare this object with the object previously given for this line to see if the token type at the end of the line has changed (meaning subsequent lines might need to be retokenized).
setLineContext(TokenMarker.LineContext) - Method in interface ij.plugin.frame.jedit.syntax.TokenHandler
The token handler can compare this object with the object previously given for this line to see if the token type at the end of the line has changed (meaning subsequent lines might need to be retokenized).
setLineHighlightColor(Color) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets the line highlight color.
setLineHighlightColor(Color) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets the line highlight color.
setLineHighlightEnabled(boolean) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Enables or disables current line highlighting.
setLineHighlightEnabled(boolean) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Enables or disables current line highlighting.
setLineSeparator(String) - Method in class gnu.regexp.RESyntax
Changes the line separator string for regular expressions created using this RESyntax.
setLineWidth(int) - Method in class ij.gui.Plot
Changes the line width.
setLineWidth(int) - Method in class ij.gui.PlotWindow
Changes the line width.
setLineWidth(int) - Method in class ij.gui.Roi
Deprecated. replaced by setStrokeWidth(int)
setLineWidth(int) - Method in class ij.process.ImageProcessor
Sets the line width used by lineTo() and drawDot().
setLocation(int, int) - Method in class ij.gui.Roi
Set the location of the ROI in image coordinates.
setLocationAndSize(int, int, int, int) - Method in class ij.gui.ImageWindow
Moves and resizes this window.
setLogWriter(Writer) - Static method in class ij.util.Log
Writes all currently logged messages to this stream if there was no stream set previously, and sets the stream to write future log messages to.
setLoopBackAndForth(boolean) - Static method in class ij.measure.Calibration
Set the default state of the animation "Loop back and forth" flag
setLUT(FileInfo) - Method in class ij2x.plugin.HorizontalGradient
 
setLutAnimation(boolean) - Method in class ij.process.ImageProcessor
For 16 and 32 bit processors, set 'lutAnimation' true to have createImage() use the cached 8-bit version of the image.
setLuts(LUT[]) - Method in class ij.CompositeImage
 
setMacroRecorder(InputHandler.MacroRecorder) - Method in class ij.plugin.frame.jedit.InputHandler
Sets the macro recorder.
setMagicCaretPosition(int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the `magic' caret position.
setMagnification(double) - Method in class ij.gui.ImageCanvas
 
setMask(ImageProcessor) - Method in class ij.process.ImageProcessor
Defines a byte mask that limits processing to an irregular ROI.
setMaximum(int) - Method in class ij.gui.ScrollbarWithLabel
 
setMaxIterations(int) - Method in class ij.measure.CurveFitter
Set maximum number of iterations allowed
setMeasurement(int, boolean) - Static method in class ij.plugin.filter.Analyzer
Sets the specified system-wide measurement option.
setMeasurements(int) - Static method in class ij.plugin.filter.Analyzer
Sets the system-wide measurement options.
setMethod(int) - Method in class ij.plugin.ZProjector
 
setMinAndMax(double, double) - Static method in class ij.gui.ProfilePlot
Sets the y-axis min and max.
setMinAndMax(double, double) - Static method in class ij.IJ
Sets the display range (minimum and maximum displayed pixel values) of the current image.
setMinAndMax(ImagePlus, double, double) - Static method in class ij.IJ
Sets the display range (minimum and maximum displayed pixel values) of the specified image.
setMinAndMax(double, double, int) - Static method in class ij.IJ
Sets the minimum and maximum displayed pixel values on the specified RGB channels, where 4=red, 2=green and 1=blue.
setMinAndMax(double, double) - Method in class ij.process.ByteProcessor
Maps the entries in this image's LUT from min-max to 0-255.
setMinAndMax(double, double) - Method in class ij.process.ColorProcessor
Uses a table look-up to map the pixels in this image from min-max to 0-255.
setMinAndMax(double, double, int) - Method in class ij.process.ColorProcessor
 
setMinAndMax(double, double) - Method in class ij.process.FloatProcessor
Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setMinAndMax(double, double) - Method in class ij.process.ImageProcessor
This image will be displayed by mapping pixel values in the range min-max to screen values in the range 0-255.
setMinAndMax(double, double) - Method in class ij.process.ShortProcessor
Sets the min and max variables that control how real pixel values are mapped to 0-255 screen values.
setMinimum(int) - Method in class ij.gui.ScrollbarWithLabel
 
setMode(int) - Method in class com.bric.swing.ColorPicker
Sets the mode of this ColorPicker.
setMode(int) - Method in class com.bric.swing.ColorPickerPanel
Set the mode of this panel.
setMode(int) - Method in class ij.CompositeImage
 
setModeControlsVisible(boolean) - Method in class com.bric.swing.ColorPicker
This controls whether the radio buttons that adjust the mode are visible.
setMoviePanel(boolean) - Method in class ij2x.plugin.AdjustPanel
 
setMoviePanel(boolean) - Method in class ij2x.plugin.ImageTypePanel
 
setMoviePanel(boolean) - Method in class ij2x.plugin.LutPanel
 
setMoviePanel(boolean) - Method in class ij2x.plugin.MathPanel
 
setMoviePanel(boolean) - Method in class ij2x.plugin.ToolbarBoxControl
 
setName(String) - Method in class ij.gui.Roi
Sets the name of this ROI.
setNextLocation(Point) - Static method in class ij.gui.ImageWindow
Causes the next image to be displayed at the specified location.
setNonScalable(boolean) - Method in class ij.gui.Roi
Set 'nonScalable' true to have TextRois in a display list drawn at a fixed location and size.
setNormalize(boolean) - Method in class ij.plugin.filter.Convolver
 
setNoWordSep(String) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setNPasses(int) - Method in class ij.plugin.filter.BackgroundSubtracter
 
setNPasses(int) - Method in class ij.plugin.filter.Binary
 
setNPasses(int) - Method in class ij.plugin.filter.Convolver
 
setNPasses(int) - Method in class ij.plugin.filter.EDM
Prepare the progress bar.
setNPasses(int) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
This method is called by ImageJ to inform the plugin-filter about the passes to its run method.
setNPasses(int) - Method in class ij.plugin.filter.GaussianBlur
Set the number of passes of the blur1Direction method.
setNPasses(int) - Method in class ij.plugin.filter.ImageMath
 
setNPasses(int) - Method in class ij.plugin.filter.MaximumFinder
Set his to the number of images to process (for the watershed progress bar only).
setNPasses(int) - Method in class ij.plugin.filter.RankFilters
This method is called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar
setNPasses(int) - Method in class ij.plugin.filter.Rotator
 
setNPasses(int) - Method in class ij.plugin.filter.StackLabeler
 
setNPasses(int) - Method in class ij.plugin.filter.Translator
 
setNPasses(int) - Method in class ij.plugin.filter.UnsharpMask
Since most computing time is spent in GaussianBlur, forward the information about the number of passes to Gaussian Blur.
setNPasses(int) - Method in class ij2x.plugin.filter.RotateAll
 
setNPasses(int) - Method in class ij2x.plugin.RotateAll
 
setOKLabel(String) - Method in class ij.gui.GenericDialog
Sets a replacement label for the "OK" button.
setOpacity(float) - Method in class com.bric.swing.ColorPicker
Sets the currently selected opacity.
setOpacity(double) - Method in class ij.gui.ImageRoi
Sets the composite mode using the specified opacity (alpha), in the range 0.0-1.0, where 0.0 is fully transparent and 1.0 is fully opaque.
setOpacityVisible(boolean) - Method in class com.bric.swing.ColorPicker
This shows or hides the alpha controls.
setOpenAsHyperStack(boolean) - Method in class ij.ImagePlus
 
setOpenUsingPlugins(boolean) - Static method in class ij.io.Opener
Open all images using HandleExtraFileTypes.
setOption(String, boolean) - Static method in class ij.plugin.filter.Analyzer
 
setOptions(String) - Static method in class ij.Macro
Define a set of Macro options for the current Thread.
setOptions(Thread, String) - Static method in class ij.Macro
Define a set of Macro options for a Thread.
setOrigin(int, int) - Method in class ij.plugin.frame.jedit.JEditTextArea
A fast way of changing both the first line and horizontal offset.
setOutline(boolean) - Method in class ij.gui.Arrow
 
setOutputType(int) - Static method in class ij.plugin.filter.EDM
Sets the output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
setOverColor(int, int, int) - Static method in class ij.process.ImageProcessor
Sets the upper Over/Under threshold color.
setOverlay(Overlay) - Method in class ij.gui.ImageCanvas
Use ImagePlus.setOverlay(ij.gui.Overlay).
setOverlay(Overlay) - Method in class ij.ImagePlus
Installs a list of ROIs that will be drawn on this image as a non-destructive overlay.
setOverlay(Shape, Color, BasicStroke) - Method in class ij.ImagePlus
Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image.
setOverlay(Roi, Color, int, Color) - Method in class ij.ImagePlus
Creates an Overlay from the specified ROI, and assigns it to this image.
setOverwriteEnabled(boolean) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets if overwrite mode should be enabled.
setPaletteColor(int, int, boolean) - Method in class ij2x.plugin.HorizontalGradient.ColorIconArea
 
setPaletteColor(int, int, boolean) - Method in class ij2x.plugin.ThreeColor.ColorIconArea
 
setPasteMode(int) - Static method in class ij.gui.Roi
Sets the Paste transfer mode.
setPasteMode(String) - Static method in class ij.IJ
Sets the transfer mode used by the Edit/Paste command, where mode is "Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide".
setPixels(Object, int) - Method in class ij.ImageStack
Assigns a pixel array to the specified slice, were 1<=n<=nslices.
setPixels(Object) - Method in class ij.process.ByteProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.ByteProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object) - Method in class ij.process.ColorProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.ColorProcessor
Sets the pixels of one color channel from a FloatProcessor.
setPixels(Object) - Method in class ij.process.FloatProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.FloatProcessor
Sets the pixels, and min&max values from a FloatProcessor.
setPixels(Object) - Method in class ij.process.ImageProcessor
Sets a new pixel array for the image.
setPixels(int, FloatProcessor) - Method in class ij.process.ImageProcessor
Sets the pixels (of one color channel for RGB images) from a FloatProcessor.
setPixels(Object) - Method in class ij.process.ShortProcessor
 
setPixels(int, FloatProcessor) - Method in class ij.process.ShortProcessor
Sets the pixels from a FloatProcessor, no scaling.
setPixels(Object, int) - Method in class ij.VirtualStack
Assigns a pixel array to the specified slice, were 1<=n<=nslices.
setPolygon(int[], int[], int) - Method in class ij.process.PolygonFiller
Specifies the polygon to be filled.
setPosition(int) - Method in class ij.gui.Roi
Sets the stack position (image number) of this ROI.
setPosition(int, int, int) - Method in class ij.gui.Roi
Sets the hyperstack position of this ROI.
setPosition(int, int, int) - Method in class ij.gui.StackWindow
 
setPosition(int, int, int) - Method in class ij.ImagePlus
Sets the current hyperstack position and updates the display, where 'channel', 'slice' and 'frame' are one-based indexes.
setPosition(int) - Method in class ij.ImagePlus
Set the current hyperstack position based on the stack index 'n' (one-based).
setPositionWithoutUpdate(int, int, int) - Method in class ij.ImagePlus
Sets the current hyperstack position without updating the display, where 'channel', 'slice' and 'frame' are one-based indexes.
setPrecision(int) - Method in class ij.measure.ResultsTable
Sets the number of digits to the right of decimal point.
setPrecision(int) - Static method in class ij.plugin.filter.Analyzer
Sets the number of digits displayed to the right of decimal point.
setPreviewSwatchVisible(boolean) - Method in class com.bric.swing.ColorPicker
This controls whether the preview swatch visible or not.
setProcessor(ImageProcessor) - Method in class ij.ImagePlus
Replaces the ImageProcessor with the one specified and updates the display.
setProcessor(String, ImageProcessor) - Method in class ij.ImagePlus
Replaces the ImageProcessor with the one specified and updates the display.
setProgressBar(ProgressBar) - Method in class ij.process.ImageProcessor
Assigns a progress bar to this processor.
setProgressMaximum(int) - Method in class ij.util.WorkRequest
Sets the maximum progress value.
setProgressMaximum(int) - Method in class ij.util.WorkThread
Sets the maximum progress value.
setProgressValue(int) - Method in class ij.util.WorkRequest
Sets the progress value.
setProgressValue(int) - Method in class ij.util.WorkThread
Sets the progress value.
setProperties(Hashtable) - Method in class ij.plugin.frame.jedit.Mode
Should only be called by XModeHandler.
setProperties(Hashtable) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setProperty(String, Object) - Method in class ij.ImagePlus
Adds a key-value pair to this image's properties.
setProperty(String, Object) - Method in class ij.plugin.frame.jedit.Mode
Sets a mode property.
setPrototypeOverlay(Overlay) - Method in class ij.gui.Roi
 
setQuality(int) - Static method in class ij.plugin.JpegWriter
Deprecated. replaced by FileSaver.setJpegQuality()
setRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer
Set the "Redirect To" image.
setRepeatCount(int) - Method in class ij.plugin.frame.jedit.InputHandler
Sets the number of times the next action will be repeated.
setRepeatEnabled(boolean) - Method in class ij.plugin.frame.jedit.InputHandler
Enables repeating.
setRestarts(int) - Method in class ij.measure.CurveFitter
Set number of simplex restarts to do
setResultsTable(ResultsTable) - Static method in class ij.plugin.filter.Analyzer
 
setResultsTable(ResultsTable) - Method in class ij.text.TextPanel
Sets the ResultsTable associated with this TextPanel.
setRGB(int, int, int) - Method in class com.bric.swing.ColorPicker
Sets the current color of this ColorPicker
setRGB(int, int, int) - Method in class com.bric.swing.ColorPickerPanel
Sets the selected color of this panel.
setRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Sets the current pixels from 3 byte arrays (reg, green, blue).
setRGB(int, Color, Color, Color) - Method in class ij2x.plugin.HorizontalGradient.ColorIconArea
 
setRGB(int, Color, Color, Color) - Method in class ij2x.plugin.ThreeColor.ColorIconArea
 
setRGBControlsVisible(boolean) - Method in class com.bric.swing.ColorPicker
This shows or hides the RGB spinner controls.
setRightClickPopup(JPopupMenu) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the right click popup menu.
setRoi(Roi) - Method in class ij.ImagePlus
Assigns the specified ROI to this image and displays it.
setRoi(Roi, boolean) - Method in class ij.ImagePlus
Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.
setRoi(int, int, int, int) - Method in class ij.ImagePlus
Creates a rectangular selection.
setRoi(Rectangle) - Method in class ij.ImagePlus
Creates a rectangular selection.
setRoi(Rectangle) - Method in class ij.ImageStack
 
setRoi(Rectangle) - Method in class ij.process.ImageProcessor
Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoi(int, int, int, int) - Method in class ij.process.ImageProcessor
Defines a rectangular region of interest and sets the mask to null if this ROI is not the same size as the previous one.
setRoi(Roi) - Method in class ij.process.ImageProcessor
Defines a non-rectangular region of interest that will consist of a rectangular ROI and a mask.
setRoi(Polygon) - Method in class ij.process.ImageProcessor
Defines a polygonal region of interest that will consist of a rectangular ROI and a mask.
setRoundRectArcSize(int) - Method in class ij.gui.Roi
Obsolete; replaced by setCornerDiameter().
setRoundRectArcSize(int) - Static method in class ij.gui.Toolbar
Sets the rounded rectangle corner diameter (pixels).
setSelectedColor(Color) - Method in class ij2x.plugin.frame.JColorPicker
 
setSelectedColor(Color) - Method in class ij2x.plugin.HorizontalGradient
 
setSelectedColor(JPanel, Color) - Method in class ij2x.plugin.HorizontalGradient
 
setSelectedColor(Color) - Method in class ij2x.plugin.ThreeColor
 
setSelectedColor(JPanel, Color) - Method in class ij2x.plugin.ThreeColor
 
setSelectedIndexes(int[]) - Method in class ij.plugin.frame.RoiManager
 
setSelectedIndexes(int[]) - Method in class ij.plugin.frame.RoiManager0
 
setSelectedLutColor(Color) - Method in class ij2x.plugin.HorizontalGradient
 
setSelectedText(String) - Method in class ij.plugin.frame.jedit.JEditTextArea
Replaces the selection with the specified text.
setSelection(int, int) - Method in class ij.text.TextPanel
Creates a selection and insures that it is visible.
setSelectionColor(Color) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets the selection color.
setSelectionColor(Color) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets the selection color.
setSelectionEnd(int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the selection end.
setSelectionRectangular(boolean) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets if the selection should be rectangular.
setSelectionStart(int) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the selection start.
setShowAllColor(Color) - Static method in class ij.gui.ImageCanvas
Sets the color used used for "Show All" mode.
setShowAllROIs(boolean) - Method in class ij.gui.ImageCanvas
Enables/disables the ROI Manager "Show All" mode.
setShowConflictMessage(boolean) - Static method in class ij.io.FileOpener
 
setShowCursorStatus(boolean) - Method in class ij.gui.ImageCanvas
Called by IJ.showStatus() to prevent status bar text from being overwritten until the cursor moves at least 12 pixels.
setShowProgress(boolean) - Method in class ij.process.FHT
Enables/disables display of the progress bar during transforms.
setSigned16BitCalibration() - Method in class ij.measure.Calibration
Sets up a calibration function that subtracts 32,768 from pixel values.
setSilentMode(boolean) - Method in class ij.io.Opener
The "Opening: path" status message is not displayed in silent mode.
setSize(int, int) - Method in class ij.gui.Plot
Sets the canvas size (i.e., size of the resulting ImageProcessor).
setSlice(int) - Static method in class ij.IJ
Switches to the specified stack slice, where 1<='slice'<=stack-size.
setSlice(int) - Method in class ij.ImagePlus
Displays the specified stack image, where 1<=n<=stackSize.
setSliceLabel(String, int) - Method in class ij.ImageStack
Sets the label of the specified slice, were 1<=n<=nslices.
setSliceLabel(String, int) - Method in class ij.VirtualStack
Does nothing.
setSliceNumber(int) - Method in class ij.process.ImageProcessor
PlugInFilterRunner uses this method to set the slice number.
setSliceWithoutUpdate(int) - Method in class ij.ImagePlus
Displays the specified stack image (1<=n<=stackSize) without updating the display.
setSnapshotCopyMode(boolean) - Method in class ij.process.ImageProcessor
The getPixelsCopy() method returns a reference to the snapshot buffer if it is not null and 'snapshotCopyMode' is true.
setSnapshotPixels(Object) - Method in class ij.process.ByteProcessor
 
setSnapshotPixels(Object) - Method in class ij.process.ColorProcessor
 
setSnapshotPixels(Object) - Method in class ij.process.FloatProcessor
 
setSnapshotPixels(Object) - Method in class ij.process.ImageProcessor
Sets a new pixel array for the snapshot (undo) buffer.
setSnapshotPixels(Object) - Method in class ij.process.ShortProcessor
 
setSourceRect(Rectangle) - Method in class ij.gui.ImageCanvas
 
setStack(ImageStack) - Method in class ij.ImagePlus
Replaces the image with the specified stack and updates the display.
setStack(String, ImageStack) - Method in class ij.ImagePlus
Replaces the image with the specified stack and updates the display.
setStack(ImageStack, int, int, int) - Method in class ij.ImagePlus
 
setStartSlice(int) - Method in class ij.plugin.ZProjector
 
setStatus(String) - Method in class ij.util.WorkRequest
Sets the status text.
setStatus(String) - Method in class ij.util.WorkThread
Sets the status text.
setStopSlice(int) - Method in class ij.plugin.ZProjector
 
setStroke(BasicStroke) - Method in class ij.gui.Roi
Sets the Stroke used to draw this ROI.
setStrokeColor(Color) - Method in class ij.gui.Overlay
Sets the stroke color of all the Rois in this overlay.
setStrokeColor(Color) - Method in class ij.gui.Roi
Sets the color used by this ROI to draw its outline.
setStrokeWidth(float) - Method in class ij.gui.Line
 
setStrokeWidth(float) - Method in class ij.gui.Roi
Sets the width of the line used to draw this ROI.
setStrokeWidth(double) - Method in class ij.gui.Roi
This is a version of setStrokeWidth() that accepts a double argument.
setStyle(int) - Method in class ij.gui.Arrow
 
setStyles(SyntaxStyle[]) - Method in class ij.plugin.frame.jedit.LNTextAreaPainter
Sets the syntax styles used to paint colorized text.
setStyles(SyntaxStyle[]) - Method in class ij.plugin.frame.jedit.TextAreaPainter
Sets the syntax styles used to paint colorized text.
setSubToolbar() - Method in class ij.ImageJ
Set Control bar
setSystemLF(boolean) - Static method in class ij2x.plugin.frame.InteractiveTestCase
PENDING: JW - this is about toggling the LF, does nothing to update the UI.
setSystemLF(boolean) - Static method in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
PENDING: JW - this is about toggling the LF, does nothing to update the UI.
setSystemLookAndFeel() - Static method in class com.bric.swing.util.Java2
Sets the Swing look and feel to the system look and feel.
setSystemLookAndFeel(int) - Static method in class com.bric.swing.util.Java2
Sets the Swing look and feel to the system look and feel.
setSystemLookAndFeel() - Static method in class ij.util.Java2
Sets the Swing look and feel to the system look and feel.
setSystemLookAndFeel(int) - Static method in class ij.util.Java2
Sets the Swing look and feel to the system look and feel.
setTempCurrentImage(ImagePlus) - Static method in class ij.WindowManager
Makes the specified image temporarily the active image for this thread.
setTempCurrentImage(Thread, ImagePlus) - Static method in class ij.WindowManager
Sets a temporary image for the specified thread.
setTemporaryProperty(String, String) - Method in class ij.plugin.frame.jedit.PropertyManager
 
setTerminateChar(int) - Method in class ij.plugin.frame.jedit.syntax.ParserRuleSet
 
setText(String) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the entire text of this text area.
setTextPanel(TextPanel) - Static method in class ij.IJ
TextWindow calls this method with a null argument when the "Results" window is closed.
setThreads(int) - Static method in class ij.Prefs
Sets the number of threads (1-32) used by PlugInFilters to process stacks.
setThreshold(double, double) - Static method in class ij.IJ
Sets the lower and upper threshold levels and displays the image using red to highlight thresholded pixels.
setThreshold(double, double, String) - Static method in class ij.IJ
Sets the lower and upper threshold levels and displays the image using the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
setThreshold(ImagePlus, double, double) - Static method in class ij.IJ
Sets the lower and upper threshold levels of the specified image.
setThreshold(ImagePlus, double, double, String) - Static method in class ij.IJ
Sets the lower and upper threshold levels of the specified image and updates the display using the specified displayMode ("Red", "Black & White", "Over/Under" or "No Update").
setThreshold(double, double, int) - Method in class ij.process.ByteProcessor
 
setThreshold(double, double, int) - Method in class ij.process.FloatProcessor
 
setThreshold(double, double, int) - Method in class ij.process.ImageProcessor
Sets the lower and upper threshold levels.
setThreshold(double, double, int) - Method in class ij.process.ShortProcessor
 
setTimeFormatToString(String) - Method in class ij2x.plugin.ControlBarPanel
 
setTimeUnit(String) - Method in class ij.measure.Calibration
Sets the time unit (e.g.
settingColor - Static variable in class ij2x.plugin.HorizontalGradient
 
settingColor - Static variable in class ij2x.plugin.ThreeColor
 
setTitle(String) - Method in class ij.ImagePlus
Sets the image name.
setTitle(String) - Method in class ij.text.TextPanel
 
setTokenMarker(TokenMarker) - Method in class ij.plugin.frame.jedit.JEditTextArea
Sets the document's token marker.
setTokenMarker(TokenMarker) - Method in class ij.plugin.frame.jedit.Mode
Sets the token marker for this mode.
setTokenMarker(TokenMarker) - Method in class ij.plugin.frame.jedit.SyntaxDocument
Sets the token marker that is to be used to split lines of this document up into tokens.
setTool(String) - Method in class ij.gui.Toolbar
 
setTool(int) - Method in class ij.gui.Toolbar
 
setTool(int) - Static method in class ij.IJ
Switches to the specified tool, where id = Toolbar.RECTANGLE (0), Toolbar.OVAL (1), etc.
setTool(String) - Static method in class ij.IJ
Switches to the specified tool, where 'name' is "rect", "elliptical", "brush", etc.
setToolbarDim(int) - Method in class ij.gui.Toolbar
 
setTransparentColor(Color) - Method in interface ij.process.Blitter
Sets the transparent color used in the COPY_TRANSPARENT mode (default is Color.white).
setTransparentColor(Color) - Method in class ij.process.ByteBlitter
 
setTransparentColor(Color) - Method in class ij.process.ColorBlitter
 
setTransparentColor(Color) - Method in class ij.process.FloatBlitter
 
setTransparentColor(Color) - Method in class ij.process.ShortBlitter
 
setTransparentIndex(int) - Static method in class ij.Prefs
Sets the transparent index (0-255), or set to -1 to disable transparency.
setType(int) - Method in class ij.ImagePlus
 
setUnderColor(int, int, int) - Static method in class ij.process.ImageProcessor
Set the lower Over/Under thresholding color.
setUnit(String) - Method in class ij.measure.Calibration
Sets the default length unit (e.g.
setUnitIncrement(int) - Method in class ij.gui.ScrollbarWithLabel
 
setUnsavedMeasurements(boolean) - Static method in class ij.plugin.filter.Analyzer
 
setup() - Method in class ij.gui.GenericDialog
 
setup() - Method in class ij.gui.HistogramWindow
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Analyzer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.AVI_Writer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.BackgroundSubtracter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Benchmark
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Binary
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.CalibrationBar
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Calibrator
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Convolver
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Duplicater
Deprecated.  
setup(String, ImagePlus) - Method in class ij.plugin.filter.EDM
Prepare for processing; also called at the very end with argument 'final' to show any newly created output image.
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTCustomFilter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.FFTFilter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filler
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Filters
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.FractalBoxCounter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.GaussianBlur
Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageMath
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ImageProperties
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Info
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutApplier
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.LutViewer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.MaximumFinder
Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
 
setup(String, ImagePlus) - Method in interface ij.plugin.filter.PlugInFilter
This method is called once when the filter is loaded.
setup(String, ImagePlus) - Method in class ij.plugin.filter.Printer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Profiler
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.RankFilters
Setup of the PlugInFilter.
setup(String, ImagePlus) - Method in class ij.plugin.filter.Resizer
Deprecated.  
setup(String, ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.RoiWriter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Rotator
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.SaltAndPepper
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ScaleDialog
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Shadows
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.StackLabeler
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ThresholdToSelection
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Transformer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.Translator
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.UnsharpMask
Method to return types supported
setup(String, ImagePlus) - Method in class ij.plugin.filter.Writer
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.XYWriter
 
setup(String, ImagePlus) - Method in class ij.plugin.filter.ZAxisProfiler
 
setup(int, ImagePlus) - Static method in class ij.Undo
 
setup(String, ImagePlus) - Method in class ij2x.plugin.filter.RotateAll
The AffineTransform class represents a 2D affine transform that performs a linear mapping from 2D coordinates to other 2D coordinates that preserves the "straightness" and "parallelness" of lines.
setup(String, ImagePlus) - Method in class ij2x.plugin.Lut2Java
 
setup(String, ImagePlus) - Method in class ij2x.plugin.RotateAll
The AffineTransform class represents a 2D affine transform that performs a linear mapping from 2D coordinates to other 2D coordinates that preserves the "straightness" and "parallelness" of lines.
SETUP_UNDO - Static variable in interface ij.macro.MacroConstants
 
setupDialog(ImagePlus, int) - Static method in class ij.IJ
Displays a "Process all images?"
setupScroll(int, int) - Method in class ij.gui.ImageCanvas
 
setUseBicubic(boolean) - Static method in class ij.process.ImageProcessor
 
setValue(int) - Method in class ij.gui.ScrollbarWithLabel
 
setValue(String, int, double) - Method in class ij.measure.ResultsTable
Sets the value of the given column and row, where where 0<=row<counter.
setValue(int, int, double) - Method in class ij.measure.ResultsTable
Sets the value of the given column and row, where where 0<=column<=(lastRow+1 and 0<=row<counter.
setValue(double) - Method in class ij.process.ByteProcessor
Sets the default fill/draw value, where 0<=value<=255.
setValue(double) - Method in class ij.process.ColorProcessor
Sets the default fill/draw value, where value is interpreted as an RGB int.
setValue(double) - Method in class ij.process.FloatProcessor
Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ImageProcessor
Sets the default fill/draw value.
setValue(double) - Method in class ij.process.ShortProcessor
Sets the default fill/draw value, where 0<=value<=65535).
setValueUnit(String) - Method in class ij.measure.Calibration
Sets the value unit.
setVariable(String, double) - Method in class ij.macro.Interpreter
 
setVisibleAmount(int) - Method in class ij.gui.ScrollbarWithLabel
 
setVoxel(int, int, int, double) - Method in class ij.ImageStack
Sets the value of the specified voxel (experimental).
setWeightingFactors(double, double, double) - Static method in class ij.process.ColorProcessor
Sets the weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
setWidth(int) - Static method in class ij.gui.Line
 
setWindow(ImageWindow) - Method in class ij.ImagePlus
This method should only be called from an ImageWindow.
setWindow(JFrame) - Static method in class ij.WindowManager
The specified frame becomes the front window, the one returnd by getFrontWindow().
setXUnit(String) - Method in class ij.measure.Calibration
Sets the X length unit.
setYUnit(String) - Method in class ij.measure.Calibration
Sets the Y length unit.
setZUnit(String) - Method in class ij.measure.Calibration
Sets the Z length unit.
Shadows - Class in ij.plugin.filter
Implements the commands in the Process/Shadows submenu.
Shadows() - Constructor for class ij.plugin.filter.Shadows
 
shape - Variable in class ij2x.plugin.event.ShapesEvent
 
SHAPE_DESCRIPTORS - Static variable in interface ij.measure.Measurements
 
SHAPE_ROI_SIZE - Static variable in class ij.io.RoiDecoder
 
shapeDrawn(ShapesEvent) - Method in interface ij2x.plugin.event.ShapesEventListener
 
shapeEventListeners - Variable in class ij2x.plugin.ColorIcon
 
ShapeRoi - Class in ij.gui
A subclass of ij.gui.Roi (2D Regions Of Interest) implemented in terms of java.awt.Shape.
ShapeRoi(Roi) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from an Roi.
ShapeRoi(Shape) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from a Shape.
ShapeRoi(int, int, Shape) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from a Shape.
ShapeRoi(float[]) - Constructor for class ij.gui.ShapeRoi
Constructs a ShapeRoi from an array of variable length path segments.
ShapesEvent - Class in ij2x.plugin.event
ShapesEvent Class.
ShapesEvent(Object, ShapeRoi) - Constructor for class ij2x.plugin.event.ShapesEvent
 
ShapesEventListener - Interface in ij2x.plugin.event
Title: Description: Copyright: Copyright (c) 2006 Company:
shapeToRoi() - Method in class ij.gui.ShapeRoi
Attempts to convert this ShapeRoi into a non-composite Roi.
sharpen() - Method in class ij.process.ImageProcessor
Sharpens the image or ROI using a 3x3 convolution kernel.
sharpenFloat(FloatProcessor, double, float) - Method in class ij.plugin.filter.UnsharpMask
Unsharp Mask filtering of a float image.
ShellScriptTokenMarker - Class in ij.plugin.frame.jedit.tokenmarker
Shell script token marker.
ShellScriptTokenMarker() - Constructor for class ij.plugin.frame.jedit.tokenmarker.ShellScriptTokenMarker
 
SHIFT_LEFT - Static variable in interface ij.macro.MacroConstants
 
SHIFT_RIGHT - Static variable in interface ij.macro.MacroConstants
 
shiftKeyDown() - Static method in class ij.IJ
Returns true if the shift key is down.
SHORT - Static variable in class ij.plugin.filter.EDM
Output type: new 16-bit image
ShortBlitter - Class in ij.process
This class does bit blitting of 16-bit images.
ShortBlitter(ShortProcessor) - Constructor for class ij.process.ShortBlitter
Constructs a ShortBlitter from a ShortProcessor.
SHORTCUT_IN_USE - Static variable in class ij.Menus
 
shortcutInUse(String) - Static method in class ij.Menus
 
shortcutKeyi - Static variable in interface ij.plugin.frame.KeyCode
 
shortcutKeys - Static variable in interface ij.plugin.frame.KeyCode
 
SHORTCUTS_MENU - Static variable in class ij.Menus
 
ShortProcessor - Class in ij.process
ShortProcessors contain a 16-bit unsigned image and methods that operate on that image.
ShortProcessor(int, int, short[], ColorModel) - Constructor for class ij.process.ShortProcessor
Creates a new ShortProcessor using the specified pixel array and ColorModel.
ShortProcessor(int, int) - Constructor for class ij.process.ShortProcessor
Creates a blank ShortProcessor using the default grayscale LUT that displays zero as black.
ShortProcessor(BufferedImage) - Constructor for class ij.process.ShortProcessor
Creates a ShortProcessor from a TYPE_USHORT_GRAY BufferedImage.
ShortProcessor(int, int, short[], ColorModel, boolean) - Constructor for class ij.process.ShortProcessor
Deprecated. 16 bit images are normally unsigned but signed images can be simulated by subtracting 32768 and using a calibration function to restore the original values.
ShortProcessor(int, int, boolean) - Constructor for class ij.process.ShortProcessor
Obsolete. 16 bit images are normally unsigned but signed images can be used by subtracting 32768 and using a calibration function to restore the original values.
ShortStatistics - Class in ij.process
16-bit image statistics, including histogram.
ShortStatistics(ImageProcessor) - Constructor for class ij.process.ShortStatistics
Construct an ImageStatistics object from a ShortProcessor using the standard measurement options (area, mean, mode, min and max).
ShortStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ShortStatistics
Constructs a ShortStatistics object from a ShortProcessor using the specified measurement options.
show() - Method in class ij.gui.Plot
Displays the plot in a PlotWindow and returns a reference to the PlotWindow.
show(double) - Method in class ij.gui.ProgressBar
Updates the progress bar, where percent should run from 0 to 1.
show(double, boolean) - Method in class ij.gui.ProgressBar
Updates the progress bar, where percent should run from 0 to 1.
show(int, int) - Method in class ij.gui.ProgressBar
Updates the progress bar, where the length of the bar is set to (currentValue+1)/finalValue of the maximum bar length.
show() - Method in class ij.gui.WaitForUserDialog
 
show() - Method in class ij.ImagePlus
Opens a window to display this image and clears the status bar.
show(String) - Method in class ij.ImagePlus
Opens a window to display this image and displays 'statusMessage' in the status bar.
show(String) - Method in class ij.measure.ResultsTable
Displays the contents of this ResultsTable in a window with the specified title.
show(JXFrame) - Method in class ij2x.plugin.frame.InteractiveTestCase
Packs and shows the frame.
show(JXFrame, int, int) - Method in class ij2x.plugin.frame.InteractiveTestCase
Packs, sizes and shows the frame.
show(JXFrame) - Method in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
Packs and shows the frame.
show(JXFrame, int, int) - Method in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
Packs, sizes and shows the frame.
SHOW_ALL_COLOR - Static variable in class ij.Prefs
 
SHOW_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display image containing binary masks of measured particles.
SHOW_MESSAGE - Static variable in interface ij.macro.MacroConstants
 
SHOW_MESSAGE_WITH_CANCEL - Static variable in interface ij.macro.MacroConstants
 
SHOW_NONE - Static variable in class ij.plugin.filter.ParticleAnalyzer
Do not display particle outline image.
SHOW_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display image containing outlines of measured particles.
SHOW_OVERLAY_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display filled particle as an overlay.
SHOW_OVERLAY_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display particle outlines as an overlay.
SHOW_PROGRESS - Static variable in interface ij.macro.MacroConstants
 
SHOW_PROGRESS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display a progress bar.
SHOW_RESULTS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display results in the ImageJ console.
SHOW_ROI_MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display image containing grayscales masks that identify measured particles.
SHOW_STATUS - Static variable in interface ij.macro.MacroConstants
 
SHOW_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer
Obsolete
SHOW_TEXT - Static variable in interface ij.macro.MacroConstants
 
showAllSliceOnly - Static variable in class ij.Prefs
Only show ROIs associated with current slice in Roi Manager "Show All" mode.
showDialog(Container, Color) - Static method in class com.bric.swing.ColorPicker
 
showDialog(Window, Color) - Static method in class com.bric.swing.ColorPicker
This creates a modal dialog prompting the user to select a color.
showDialog(Window, Color, boolean) - Static method in class com.bric.swing.ColorPicker
This creates a modal dialog prompting the user to select a color.
showDialog(Window, String, Color, boolean) - Static method in class com.bric.swing.ColorPicker
This creates a modal dialog prompting the user to select a color.
showDialog() - Method in class ij.gui.GenericDialog
Displays this dialog box.
showDialog() - Method in class ij.gui.NonBlockingGenericDialog
 
showDialog() - Method in class ij.gui.RoiProperties
Displays the dialog box and returns 'false' if the user cancels the dialog.
showDialog() - Method in class ij.plugin.Compiler
 
showDialog() - Method in class ij.plugin.FFTMath
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.BackgroundSubtracter
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Binary
 
showDialog(ImagePlus) - Method in class ij.plugin.filter.Calibrator
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Convolver
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.EDM
Called by the PlugInFilterRunner after setup.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in interface ij.plugin.filter.ExtendedPlugInFilter
This method is called after setup(arg, imp) unless the DONE flag has been set.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.GaussianBlur
Ask the user for the parameters
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.ImageMath
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.MaximumFinder
 
showDialog() - Method in class ij.plugin.filter.ParticleAnalyzer
Displays a modal options dialog.
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.RankFilters
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Rotator
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.StackLabeler
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.Translator
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij.plugin.filter.UnsharpMask
Ask the user for the parameters
showDialog() - Method in class ij.plugin.NewPlugin
 
showDialog(ImageStack) - Method in class ij.plugin.StackReducer
 
showDialog() - Method in class ij2x.plugin.Concatenator
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij2x.plugin.filter.RotateAll
 
showDialog(ImagePlus, String, PlugInFilterRunner) - Method in class ij2x.plugin.RotateAll
 
showHistogram(ImagePlus, int) - Method in class ij.gui.HistogramWindow
Draws the histogram using the specified title and number of bins.
showHistogram(ImagePlus, int, double, double) - Method in class ij.gui.HistogramWindow
Draws the histogram using the specified title, number of bins and histogram range.
showHistogram(ImagePlus, ImageStatistics) - Method in class ij.gui.HistogramWindow
Draws the histogram using the specified title and ImageStatistics.
showImageDialog(String) - Method in class ij.gui.RoiProperties
 
showInFrame(JComponent, String) - Method in class ij2x.plugin.frame.InteractiveTestCase
Creates, shows and returns a JXFrame with the specified title, containing the component.
showInFrame(JComponent, String, boolean) - Method in class ij2x.plugin.frame.InteractiveTestCase
Creates, shows and returns a JXFrame with the specified title, containing the component.
showInFrame(JComponent, String) - Method in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
Creates, shows and returns a JXFrame with the specified title, containing the component.
showInFrame(JComponent, String, boolean) - Method in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
Creates, shows and returns a JXFrame with the specified title, containing the component.
showList() - Method in class ij.gui.HistogramWindow
 
showlutButton - Variable in class ij2x.plugin.LutPanel
 
showLutSlideButton - Variable in class ij2x.plugin.LutPanel
 
showMessage(String) - Static method in class ij.IJ
Displays a message in a dialog box titled "Message".
showMessage(String, String) - Static method in class ij.IJ
Displays a message in a dialog box with the specified title.
showMessageWithCancel(String, String) - Static method in class ij.IJ
Displays a message in a dialog box with the specified title.
showProgress(double) - Static method in class ij.IJ
Updates the progress bar, where 0<=progress<=1.0.
showProgress(int, int) - Static method in class ij.IJ
Updates the progress bar, where the length of the bar is set to (currentValue+1)/finalValue of the maximum bar length.
showProgress - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showProgress(double) - Method in class ij.process.ImageProcessor
 
showResults - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showSizeDialog() - Method in class ij.plugin.NewPlugin
 
showSizeDistribution - Variable in class ij.plugin.filter.ParticleAnalyzer
 
showSlice(int) - Method in class ij.gui.StackWindow
Displays the specified slice and updates the stack scrollbar.
showStatus() - Method in class ij.gui.Roi
 
showStatus(String) - Static method in class ij.IJ
Displays a message in the ImageJ status bar.
showTime(ImagePlus, long, String) - Static method in class ij.IJ
 
showTime(ImagePlus, long, String, int) - Static method in class ij.IJ
 
showToolbar() - Method in class ij.ImageJ
Toolbar implamanation
showWithScrollingInFrame(JComponent, String) - Method in class ij2x.plugin.frame.InteractiveTestCase
Creates, shows and returns a JXFrame with the specified title, containing the component wrapped into a JScrollPane.
showWithScrollingInFrame(JComponent, JComponent, String) - Method in class ij2x.plugin.frame.InteractiveTestCase
Creates and returns a JXFrame with the specified title, containing two components individually wrapped into a JScrollPane.
showWithScrollingInFrame(JComponent, String) - Method in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
Creates, shows and returns a JXFrame with the specified title, containing the component wrapped into a JScrollPane.
showWithScrollingInFrame(JComponent, JComponent, String) - Method in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
Creates and returns a JXFrame with the specified title, containing two components individually wrapped into a JScrollPane.
shuffle(ImagePlus, int) - Method in class ij.plugin.HyperStackConverter
Changes the dimension order of a 4D or 5D stack from the specified order (CTZ, ZCT, ZTC, TCZ or TZC) to the XYCZT order used by ImageJ.
SimpleCommands - Class in ij.plugin
This plugin implements the Plugins/Utilities/Unlock, Image/Rename and Plugins/Utilities/Search commands.
SimpleCommands() - Constructor for class ij.plugin.SimpleCommands
 
SIN - Static variable in interface ij.macro.MacroConstants
 
SINGLE_POINTS - Static variable in class ij.plugin.filter.MaximumFinder
Output type single points
size() - Method in class ij.gui.Overlay
Returns the number of Rois in this Overlay.
SIZE_KEY - Static variable in class ij.gui.Arrow
 
skeletonize() - Method in class ij.process.BinaryProcessor
Uses a lookup table to repeatably removes pixels from the edges of objects in a binary image, reducing them to single pixel wide skeletons.
skeletonize() - Method in class ij.process.ByteProcessor
 
SKEWNESS - Static variable in interface ij.measure.Measurements
 
SKEWNESS - Static variable in class ij.measure.ResultsTable
 
skewness - Variable in class ij.process.ImageStatistics
 
sleepAmount - Variable in class ij.plugin.Memory_Monitor.Surface
 
slice - Variable in class ij.gui.StackWindow
 
SLICE - Static variable in interface ij.measure.Measurements
 
SLICE - Static variable in class ij.measure.ResultsTable
 
slice - Variable in class ij.plugin.filter.ParticleAnalyzer
 
sliceLabels - Variable in class ij.io.FileInfo
 
Slicer - Class in ij.plugin
Implements the Image/Stacks/Reslice command.
Slicer() - Constructor for class ij.plugin.Slicer
 
sliceSelector - Variable in class ij.gui.StackWindow
 
slider - Variable in class ij.gui.GenericDialog
 
smalerAction - Static variable in class ij.plugin.frame.Editor
 
smalerAction - Static variable in class ij2x.plugin.frame.Editor
 
smalerAction - Static variable in class ij2x.plugin.frame.MonoEditor
 
SMART_HOME_END_PROPERTY - Static variable in class ij.plugin.frame.jedit.InputHandler
If this client property is set to Boolean.TRUE on the text area, the home/end keys will support 'smart' BRIEF-like behaviour (one press = start/end of line, two presses = start/end of viewscreen, three presses = start/end of document).
smooth() - Method in class ij.process.ImageProcessor
Replaces each pixel with the 3x3 neighborhood mean.
SNAPSHOT - Static variable in interface ij.macro.MacroConstants
 
SNAPSHOT - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter requires a snapshot (copy of the pixels array).
snapshot() - Method in class ij.process.ByteProcessor
Make a snapshot of the current image.
snapshot() - Method in class ij.process.ColorProcessor
 
snapshot() - Method in class ij.process.FloatProcessor
 
snapshot() - Method in class ij.process.ImageProcessor
Makes a copy of this image's pixel data that can be later restored using reset() or reset(mask).
snapshot() - Method in class ij.process.ShortProcessor
 
snapshotHeight - Variable in class ij.process.ImageProcessor
 
snapshotPixels - Variable in class ij.process.ByteProcessor
 
snapshotPixels - Variable in class ij.process.ColorProcessor
 
snapshotWidth - Variable in class ij.process.ImageProcessor
 
SocketListener - Class in ij
Runs commands sent to the port returned by ImageJ.getPort().
SocketListener() - Constructor for class ij.SocketListener
 
SOFTWARE - Static variable in class ij.io.TiffDecoder
 
SOLIDITY - Static variable in class ij.measure.ResultsTable
 
sort(ImageStack) - Static method in class ij.util.DicomTools
Sorts a DICOM stack by image number.
sort(String[]) - Static method in class ij.util.StringSorter
Sorts the array.
sortDicom(String[], String[], int) - Method in class ij.VirtualStack
 
sortFileList(String[]) - Method in class ij.plugin.FolderOpener
Sorts the file names into numeric order.
sortFileNames(boolean) - Method in class ij.plugin.FolderOpener
 
source - Variable in class ij.process.ImageProcessor
 
south(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
southeast(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
southwest(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
spaceBarDown() - Static method in class ij.IJ
Returns true if the space bar is down.
spaceLabel - Variable in class ij2x.plugin.ControlBarPanel
 
SPAN - Static variable in class ij.plugin.frame.jedit.syntax.ParserRule
 
spanEndSubst - Variable in class ij.plugin.frame.jedit.syntax.TokenMarker.LineContext
 
SPARE1 - Static variable in class ij.gui.Toolbar
 
SPARE2 - Static variable in class ij.gui.Toolbar
 
SPARE3 - Static variable in class ij.gui.Toolbar
 
SPARE4 - Static variable in class ij.gui.Toolbar
 
SPARE5 - Static variable in class ij.gui.Toolbar
 
SPARE6 - Static variable in class ij.gui.Toolbar
 
SPARE7 - Static variable in class ij.gui.Toolbar
 
SPARE8 - Static variable in class ij.gui.Toolbar
 
SPARE9 - Static variable in class ij.gui.Toolbar
 
specifyButton - Variable in class ij2x.plugin.ControlBarPanel
 
SpecifyROI - Class in ij.plugin
This plugin implements the Edit/Selection/Specify command.
SpecifyROI() - Constructor for class ij.plugin.SpecifyROI
 
speedButton - Variable in class ij2x.plugin.MovieControllerPanel
 
spinner - Variable in class ij.gui.GenericDialog
 
spinnerField - Variable in class ij.gui.GenericDialog
 
SPLINE_FIT - Static variable in class ij.io.RoiDecoder
 
splineButton - Variable in class ij2x.plugin.ControlBarPanel
 
SplineFitter - Class in ij.measure
This class fits a spline function to a set of points.
SplineFitter(int[], int[], int) - Constructor for class ij.measure.SplineFitter
 
splinePoints - Variable in class ij.gui.PolygonRoi
 
SPLIT - Static variable in interface ij.macro.MacroConstants
 
split(ImagePlus) - Method in class ij.plugin.filter.RGBStackSplitter
Splits the specified RGB image or stack into three 8-bit grayscale images or stacks.
split(ImageStack, boolean) - Method in class ij.plugin.filter.RGBStackSplitter
Splits the specified RGB stack into three 8-bit grayscale stacks.
split(String) - Static method in class ij.util.Tools
Splits a string into substrings using the default delimiter set, which is " \t\n\r" (space, tab, newline and carriage-return).
split(String, String) - Static method in class ij.util.Tools
Splits a string into substring using the characters contained in the second argument as the delimiter set.
split(Image, int, boolean) - Static method in class ij2x.plugin.ControlBarPanel
Splits an image into count subimages.
splitAll(Image, int, int, boolean) - Static method in class ij2x.plugin.ControlBarPanel
Splits an image into count subimages.
spliterButton - Variable in class ij2x.plugin.StackControlPanel
 
splitStackButton - Variable in class ij2x.plugin.StackControlPanel
 
SQLTokenMarker - Class in ij.plugin.frame.jedit.tokenmarker
SQL token marker.
SQLTokenMarker(KeywordMap) - Constructor for class ij.plugin.frame.jedit.tokenmarker.SQLTokenMarker
 
SQLTokenMarker(KeywordMap, boolean) - Constructor for class ij.plugin.frame.jedit.tokenmarker.SQLTokenMarker
 
sqr() - Method in class ij.process.FloatProcessor
 
sqr() - Method in class ij.process.ImageProcessor
Performs a square transform on the image or ROI.
sqr() - Method in class ij.process.ShortProcessor
 
SQRT - Static variable in interface ij.macro.MacroConstants
 
sqrt() - Method in class ij.process.FloatProcessor
 
sqrt() - Method in class ij.process.ImageProcessor
Performs a square root transform on the image or ROI.
sqrt() - Method in class ij.process.ShortProcessor
 
SQRT2 - Static variable in class ij.plugin.filter.EDM
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(2)
SQRT5 - Static variable in class ij.plugin.filter.EDM
In old make16bitEDM this pixel value corresponds to a pixel distance of sqrt(5)
srcEnd - Variable in class ij.process.DownsizeTable
index of the last point of the source data that should be accessed
srcRect - Variable in class ij.gui.ImageCanvas
 
srcRect - Variable in class ij2x.plugin.filter.RotateAll
 
srcRect - Variable in class ij2x.plugin.RoiRotator
 
srcRect - Variable in class ij2x.plugin.RotateAll
 
srcStart - Variable in class ij.process.DownsizeTable
index of the first point of the source data that should be accessed
STACK - Static variable in interface ij.macro.MacroConstants
 
STACK_POSITION - Static variable in interface ij.measure.Measurements
 
STACK_REQUIRED - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter requires a stack.
stackAction - Static variable in class ij2x.plugin.CollapsiblePane
 
stackButton - Variable in class ij2x.plugin.StackControlPanel
 
StackCombiner - Class in ij.plugin
This plugin implements the Image/Stacks/Combine command.
StackCombiner() - Constructor for class ij.plugin.StackCombiner
 
StackControlPanel - Class in ij2x.plugin
Title: Description: Copyright: Copyright (c) 2006 Company:
StackControlPanel() - Constructor for class ij2x.plugin.StackControlPanel
 
StackConverter - Class in ij.process
This class does stack type conversions.
StackConverter(ImagePlus) - Constructor for class ij.process.StackConverter
 
StackEditor - Class in ij.plugin
Implements the AddSlice, DeleteSlice and "Stack to Images" commands.
StackEditor() - Constructor for class ij.plugin.StackEditor
 
StackInserter - Class in ij.plugin
This plugin, which implements the Image>Stacks>Insert command, inserts an image or stack into a stack.
StackInserter() - Constructor for class ij.plugin.StackInserter
 
StackInserter - Class in ij2x.plugin
Inserts an image or stack into a stack.
StackInserter() - Constructor for class ij2x.plugin.StackInserter
 
StackLabeler - Class in ij.plugin.filter
This plugin implements the Image/Stacks/Label command.
StackLabeler() - Constructor for class ij.plugin.filter.StackLabeler
 
StackMaker - Class in ij.plugin
The plugin implements the Image/Stacks/Tools/Montage to Stack command.
StackMaker() - Constructor for class ij.plugin.StackMaker
 
StackMaker - Class in ij2x.plugin
Creates a w*h slice stack from an wxh image montage.
StackMaker() - Constructor for class ij2x.plugin.StackMaker
 
StackProcessor - Class in ij.process
This class processes stacks.
StackProcessor(ImageStack, ImageProcessor) - Constructor for class ij.process.StackProcessor
Constructs a StackProcessor from a stack.
StackReducer - Class in ij.plugin
This plugin implements the Image/Stacks/Misc/Reduce command.
StackReducer() - Constructor for class ij.plugin.StackReducer
 
StackReverser - Class in ij.plugin
Implements the Image/Transform/Flip Z command.
StackReverser() - Constructor for class ij.plugin.StackReverser
 
StackReverser - Class in ij2x.plugin
This plugin reverses the order of the slices in a stack.
StackReverser() - Constructor for class ij2x.plugin.StackReverser
 
StackStatistics - Class in ij.process
Statistics, including the histogram, of a stack.
StackStatistics(ImagePlus) - Constructor for class ij.process.StackStatistics
 
StackStatistics(ImagePlus, int, double, double) - Constructor for class ij.process.StackStatistics
 
StackWindow - Class in ij.gui
This class is an extended ImageWindow used to display image stacks.
StackWindow(ImagePlus) - Constructor for class ij.gui.StackWindow
 
StackWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.StackWindow
 
StackWriter - Class in ij.plugin
This plugin, which saves the images in a stack as separate files, implements the File/Save As/Image Sequence command.
StackWriter() - Constructor for class ij.plugin.StackWriter
 
STANDALONE - Static variable in class ij.ImageJ
Run as normal application.
start() - Method in class ij.plugin.frame.ColorThresholder
 
start - Variable in class ij.plugin.frame.jedit.syntax.ParserRule
 
start() - Method in class ij.plugin.Memory_Monitor.Surface
 
start() - Method in class ij.util.WorkThreadPool
Starts all the threads in this thread pool.
start() - Method in class ij2x.plugin.CollapsiblePane
 
start() - Method in class ij2x.plugin.ControlBarPanel
 
start() - Method in interface ij2x.plugin.MovieController
 
start() - Method in class ij2x.plugin.MovieControllerPanel
 
startButton - Variable in class ij2x.plugin.MovieControllerPanel
 
startDocument() - Method in class com.microstar.xml.HandlerBase
Handle the start of the document.
startDocument() - Method in interface com.microstar.xml.XmlHandler
Start the document.
startDocument() - Method in class ij.plugin.frame.jedit.syntax.XModeHandler
 
startElement(String) - Method in class com.microstar.xml.HandlerBase
Handle the start of an element.
startElement(String) - Method in interface com.microstar.xml.XmlHandler
Start an element.
startElement(String) - Method in class ij.plugin.frame.jedit.syntax.XModeHandler
 
startExternalEntity(String) - Method in class com.microstar.xml.HandlerBase
Handle the start of an external entity.
startExternalEntity(String) - Method in interface com.microstar.xml.XmlHandler
Begin an external entity.
startPaste(ImagePlus) - Method in class ij.gui.Roi
 
startPosMatch - Variable in class ij.plugin.frame.jedit.syntax.ParserRule
 
startRegexp - Variable in class ij.plugin.frame.jedit.syntax.ParserRule
 
STARTS_WITH - Static variable in interface ij.macro.MacroConstants
 
startStop - Variable in class ij2x.plugin.MovieControllerPanel
 
startStop - Variable in class ij2x.plugin.StackControlPanel
 
startStop - Variable in class ij2x.plugin.TransformPanel
 
startTiming() - Method in class ij.ImagePlus
Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation.
startxd - Variable in class ij.gui.Line
 
startyd - Variable in class ij.gui.Line
 
stateChanged(ChangeEvent) - Method in class ij2x.gui.ColorChooser
 
stateChanged(ChangeEvent) - Method in class ij2x.gui.JColorChooser
 
stateChanged(ChangeEvent) - Method in class ij2x.plugin.AlignRGB
 
stateChanged(ChangeEvent) - Method in class ij2x.plugin.filter.RotateAll
 
stateChanged(ChangeEvent) - Method in class ij2x.plugin.ImageTypePanel
 
stateChanged(ChangeEvent) - Method in class ij2x.plugin.RoiRotator
 
stateChanged(ChangeEvent) - Method in class ij2x.plugin.RotateAll
 
staticShowChoice - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
stats - Variable in class ij.gui.HistogramWindow
 
statusUpdate(WorkThreadPool, int) - Method in interface ij.util.WorkThreadProgressListener
 
STD_DEV - Static variable in interface ij.measure.Measurements
 
STD_DEV - Static variable in class ij.measure.ResultsTable
 
stdDev - Variable in class ij.process.ImageStatistics
 
STEP - Static variable in class ij.macro.Interpreter
 
stop() - Method in class ij.plugin.frame.ColorThresholder
 
stop() - Method in class ij.plugin.Memory_Monitor.Surface
 
stop() - Method in class ij2x.plugin.CollapsiblePane
 
stop() - Method in class ij2x.plugin.ControlBarPanel
 
stop() - Method in interface ij2x.plugin.MovieController
 
stop() - Method in class ij2x.plugin.MovieControllerPanel
 
stopButton - Variable in class ij2x.plugin.MovieControllerPanel
 
stopButton - Variable in class ij2x.plugin.StackControlPanel
 
stopButton - Variable in class ij2x.plugin.TransformPanel
 
str - Variable in class ij.macro.Symbol
 
str - Variable in class ij.plugin.frame.jedit.syntax.Chunk
 
STRAIGHT_LINE - Static variable in class ij.measure.Calibration
 
STRAIGHT_LINE - Static variable in class ij.measure.CurveFitter
 
straighten(ImagePlus, Roi, int) - Method in class ij.plugin.Straightener
 
Straightener - Class in ij.plugin
This plugin implements the Edit/Selection/Straighten command.
Straightener() - Constructor for class ij.plugin.Straightener
 
straightenLine(ImagePlus, int) - Method in class ij.plugin.Straightener
 
straightenStack(ImagePlus, Roi, int) - Method in class ij.plugin.Straightener
 
stretchHistogram(ImagePlus, double) - Method in class ij.plugin.ContrastEnhancer
 
stretchHistogram(ImageProcessor, double) - Method in class ij.plugin.ContrastEnhancer
 
stretchHistogram(ImageProcessor, double, ImageStatistics) - Method in class ij.plugin.ContrastEnhancer
 
STRING - Static variable in interface ij.macro.MacroConstants
 
STRING_CONSTANT - Static variable in interface ij.macro.MacroConstants
 
STRING_FUNCTION - Static variable in interface ij.macro.MacroConstants
 
stringField - Variable in class ij.gui.GenericDialog
 
stringFunctionIDs - Static variable in interface ij.macro.MacroConstants
 
stringFunctions - Static variable in interface ij.macro.MacroConstants
 
stringRGB - Variable in class ij2x.plugin.HorizontalGradient
 
stringRGB - Variable in class ij2x.plugin.ThreeColor
 
strings - Static variable in class com.bric.swing.ColorPicker
The localized strings used in this (and related) panel(s).
stringsEqual(String, String) - Static method in class ij.plugin.frame.jedit.MiscUtilities
Deprecated. Call objectsEqual() instead.
StringSorter - Class in ij.util
A simple QuickSort for String arrays.
StringSorter() - Constructor for class ij.util.StringSorter
 
stringToToken(String) - Static method in class ij.plugin.frame.jedit.syntax.Token
Converts a token type string to a token type constant.
STRIP_BYTE_COUNT - Static variable in class ij.io.TiffDecoder
 
STRIP_OFFSETS - Static variable in class ij.io.TiffDecoder
 
stripLengths - Variable in class ij.io.FileInfo
 
stripOffsets - Variable in class ij.io.FileInfo
 
stroke - Variable in class ij.gui.Roi
 
STROKE_COLOR - Static variable in class ij.io.RoiDecoder
 
STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
 
strokeColor - Variable in class ij.gui.Roi
 
stx - Variable in class ij2x.plugin.AlignRGB
 
sty - Variable in class ij2x.plugin.AlignRGB
 
style - Variable in class ij.plugin.frame.jedit.syntax.Chunk
 
STYLE_KEY - Static variable in class ij.gui.Arrow
 
styles - Static variable in class ij.gui.Arrow
 
styles - Variable in class ij.plugin.frame.jedit.LNTextAreaDefaults
 
styles - Variable in class ij.plugin.frame.jedit.LNTextAreaPainter
 
styles - Variable in class ij.plugin.frame.jedit.TextAreaDefaults
 
styles - Variable in class ij.plugin.frame.jedit.TextAreaPainter
 
subButton - Variable in class ij2x.plugin.MathPanel
 
SubstackMaker - Class in ij.plugin
This plugin extracts selected images from a stack to make a new substack.
SubstackMaker() - Constructor for class ij.plugin.SubstackMaker
 
substitute(Object, String) - Method in class gnu.regexp.RE
Substitutes the replacement text for the first match found in the input.
substitute(Object, String, int) - Method in class gnu.regexp.RE
Substitutes the replacement text for the first match found in the input beginning at the specified index position.
substitute(Object, String, int, int) - Method in class gnu.regexp.RE
Substitutes the replacement text for the first match found in the input string, beginning at the specified index position and using the specified execution flags.
substituteAll(Object, String) - Method in class gnu.regexp.RE
Substitutes the replacement text for each non-overlapping match found in the input text.
substituteAll(Object, String, int) - Method in class gnu.regexp.RE
Substitutes the replacement text for each non-overlapping match found in the input text, starting at the specified index.
substituteAll(Object, String, int, int) - Method in class gnu.regexp.RE
Substitutes the replacement text for each non-overlapping match found in the input text, starting at the specified index and using the specified execution flags.
substituteInto(String) - Method in class gnu.regexp.REMatch
Substitute the results of this match to create a new string.
SUBSTRING - Static variable in interface ij.macro.MacroConstants
 
SUBTRACT - Static variable in interface ij.process.Blitter
dst=dst-src
subtract(double) - Method in class ij.process.ImageProcessor
Subtracts 'value' from each pixel in the image or ROI.
subtractBackround(ImageProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
Depracated.
subtractPoints(Roi) - Method in class ij.gui.PointRoi
Subtract the points that intersect the specified ROI and return the result.
subtractRGBBackround(ColorProcessor, int) - Method in class ij.plugin.filter.BackgroundSubtracter
Depracated.
SUBTYPE - Static variable in class ij.io.RoiDecoder
 
SUM_METHOD - Static variable in class ij.plugin.ZProjector
 
summarize() - Method in class ij.plugin.filter.Analyzer
 
SUPPORTS_MASKING - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter wants ImageJ, for non-rectangular ROIs, to restore that part of the image that's inside the bounding rectangle but outside of the ROI.
supportsMultilineTokens() - Method in class ij.plugin.frame.jedit.tokenmarker.BatchFileTokenMarker
 
supportsMultilineTokens() - Method in class ij.plugin.frame.jedit.tokenmarker.PatchTokenMarker
 
supportsMultilineTokens() - Method in class ij.plugin.frame.jedit.tokenmarker.PropsTokenMarker
 
supportsMultilineTokens() - Method in class ij.plugin.frame.jedit.tokenmarker.TokenMarker
Returns if the token marker supports tokens that span multiple lines.
suppressPluginNotFoundError() - Static method in class ij.IJ
Temporarily suppress "plugin not found" errors.
SurfacePlotter - Class in ij.plugin
 
SurfacePlotter() - Constructor for class ij.plugin.SurfacePlotter
 
swapPixelArrays() - Method in class ij.process.ByteProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.ColorProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.FloatProcessor
Swaps the pixel and snapshot (undo) arrays.
swapPixelArrays() - Method in class ij.process.ImageProcessor
Swaps the pixel and snapshot (undo) buffers.
swapPixelArrays() - Method in class ij.process.ShortProcessor
Swaps the pixel and snapshot (undo) arrays.
swapQuadrants(ImageProcessor) - Method in class ij.process.FHT
Swap quadrants 1 and 3 and 2 and 4 of the specified ImageProcessor so the power spectrum origin is at the center of the image.
swapQuadrants() - Method in class ij.process.FHT
Swap quadrants 1 and 3 and 2 and 4 of the image contained in this FHT.
Symbol - Class in ij.macro
Objects of this class are used as entries in the macro language symbol table.
SyntaxDocument - Class in ij.plugin.frame.jedit
A document implementation that can be tokenized by the syntax highlighting system.
SyntaxDocument() - Constructor for class ij.plugin.frame.jedit.SyntaxDocument
 
SyntaxStyle - Class in ij.plugin.frame.jedit.syntax
A simple text style class.
SyntaxStyle(Color, Color, Font) - Constructor for class ij.plugin.frame.jedit.syntax.SyntaxStyle
Creates a new SyntaxStyle.
SyntaxStyle - Class in ij.plugin.frame.jedit
A simple text style class.
SyntaxStyle(Color, boolean, boolean) - Constructor for class ij.plugin.frame.jedit.SyntaxStyle
Creates a new SyntaxStyle.
SyntaxUtilities - Class in ij.plugin.frame.jedit.syntax
Contains utility functions used by the syntax highlighting code.
SyntaxUtilities() - Constructor for class ij.plugin.frame.jedit.syntax.SyntaxUtilities
 
SyntaxUtilities - Class in ij.plugin.frame.jedit
Class with several utility functions used by jEdit's syntax colorizing subsystem.
systemLF - Variable in class ij2x.plugin.CollapsiblePane
 
systemLF - Variable in class ij2x.plugin.frame.InteractiveTestCase
 
systemLF - Variable in class ij2x.plugin.frame.JXCollapsiblePaneVisualCheck
 

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