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

A

ABF - Class in org.javaabf
A class that provides a means of transparently accessing .abf files in ABF2.0, pClamp 9, and ABF1.8 file formats.
ABF(String) - Constructor for class org.javaabf.ABF
Associates this ABF class with the .abf file passed as argument.
ABF(File) - Constructor for class org.javaabf.ABF
Associates this ABF class with the .abf file passed as argument.
ABF(File, boolean) - Constructor for class org.javaabf.ABF
 
ABF18_parser - Class in org.javaabf
 
ABF18_parser(String, boolean) - Constructor for class org.javaabf.ABF18_parser
 
ABF2_parser - Class in org.javaabf
 
ABF2_parser(String, boolean) - Constructor for class org.javaabf.ABF2_parser
 
ABF_ADCInfo - Class in org.javaabf
 
ABF_ADCInfo() - Constructor for class org.javaabf.ABF_ADCInfo
 
ABF_FileInfo - Class in org.javaabf
 
ABF_FileInfo() - Constructor for class org.javaabf.ABF_FileInfo
 
ABF_parser - Interface in org.javaabf
A generic .abf file parser interface.
ABF_parserFactory - Class in org.javaabf
Provides a means of transparently determining the appropriate .abf file parser corresponding to a given version of .abf file.
ABF_parserFactory() - Constructor for class org.javaabf.ABF_parserFactory
 
ABF_ProtocolInfo - Class in org.javaabf
 
ABF_ProtocolInfo() - Constructor for class org.javaabf.ABF_ProtocolInfo
 
ABF_Section - Class in org.javaabf
 
ABF_Section() - Constructor for class org.javaabf.ABF_Section
 
ABF_utils - Class in org.javaabf
 
ABF_utils() - Constructor for class org.javaabf.ABF_utils
 
ABFpClamp9_parser - Class in org.javaabf
 
ABFpClamp9_parser(String, boolean) - Constructor for class org.javaabf.ABFpClamp9_parser
 
ABFWaveProxy - Class in ij.wave
A bridge between the ABF classes and the PhysImage Wave class, so that we can dynamically pull data from the .abf file while abiding by the Wave interface.
ABFWaveProxy(ABF, int) - Constructor for class ij.wave.ABFWaveProxy
 
ABFWaveProxy(ABF, int, double, double) - Constructor for class ij.wave.ABFWaveProxy
 
ABGR - Static variable in class ij.io.FileInfo
32-bit interleaved ABGR.
abort() - Static method in class ij.Macro
Aborts the currently running macro or any plugin using IJ.run().
abort() - Static method in class ij.macro.Interpreter
Aborts currently running macro.
abort(Interpreter) - Static method in class ij.macro.Interpreter
Absolete, replaced by abortMacro().
abort() - Method in class ij.measure.Minimizer
Aborts minimization.
ABORTED - Static variable in class ij.measure.Minimizer
Status returned: aborted by call to abort method.
abortExecution() - Method in class ij.plugin.frame.Jython_Console
 
abortMacro() - Method in class ij.macro.Interpreter
Aborts this macro.
abortPaste() - Method in class ij.gui.Roi
 
ABOUT_MENU - Static variable in class ij.Menus
 
AboutBox - Class in ij.plugin
This plugin implements the Help/About ImageJ command by opening the about.jpg in ij.jar, scaling it 400% and adding some text.
AboutBox() - Constructor for class ij.plugin.AboutBox
 
ABS - Static variable in interface ij.macro.MacroConstants
 
abs() - Method in class ij.process.FloatProcessor
 
abs() - Method in class ij.process.ImageProcessor
If this is a 32-bit or signed 16-bit image, performs an absolute value transform, otherwise does nothing.
abs() - Method in class ij.process.ShortProcessor
 
abs() - Method in class ij.wave.Wave
 
AbstractABF_parser - Class in org.javaabf
A generic .abf file parser implementation that is extended for specific .abf versions.
AbstractABF_parser() - Constructor for class org.javaabf.AbstractABF_parser
 
accept(File, String) - Method in class ij.plugin.Compiler
 
accumulateImages(Vector, String) - Static method in class ij.wave.CTA_Utils
 
ACOS - Static variable in interface ij.macro.MacroConstants
 
actionPerformed(ActionEvent) - Method in class ij.gui.GenericDialog
 
actionPerformed(ActionEvent) - Method in class ij.gui.HistogramWindow
 
actionPerformed(ActionEvent) - Method in class ij.gui.HTMLDialog
 
actionPerformed(ActionEvent) - Method in class ij.gui.MessageDialog
 
actionPerformed(ActionEvent) - Method in class ij.gui.NonBlockingGenericDialog
 
actionPerformed(ActionEvent) - Method in class ij.gui.PlotWindow
 
actionPerformed(ActionEvent) - Method in class ij.gui.SaveChangesDialog
 
actionPerformed(ActionEvent) - Method in class ij.gui.StackWindow
 
actionPerformed(ActionEvent) - Method in class ij.gui.Toolbar
 
actionPerformed(ActionEvent) - Method in class ij.gui.WaitForUserDialog
 
actionPerformed(ActionEvent) - Method in class ij.gui.YesNoCancelDialog
 
actionPerformed(ActionEvent) - Method in class ij.ImageJ
Handle menu events.
actionPerformed(ActionEvent) - Method in class ij.macro.FunctionFinder
 
actionPerformed(ActionEvent) - Method in class ij.plugin.BatchConverter
 
actionPerformed(ActionEvent) - Method in class ij.plugin.BatchProcesser
 
actionPerformed(ActionEvent) - Method in class ij.plugin.CommandFinder
 
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Calibrator
 
actionPerformed(ActionEvent) - Method in class ij.plugin.filter.Convolver
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Channels
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ColorThresholder
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ContrastAdjuster
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Editor
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Fitter
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Jython_Console
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.LayoutPanel
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.PlugInFrame
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.Recorder
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.RoiManager
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.SyncWindows
Implementation of ActionListener interface.
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
 
actionPerformed(ActionEvent) - Method in class ij.plugin.frame.WaveManager
 
actionPerformed(ActionEvent) - Method in class ij.plugin.LUT_Editor
 
actionPerformed(ActionEvent) - Method in class ij.plugin.MacroInstaller
 
actionPerformed(ActionEvent) - Method in class ij.plugin.Orthogonal_Views
 
actionPerformed(ActionEvent) - Method in class ij.plugin.Reorder_Components
 
actionPerformed(ActionEvent) - Method in class ij.text.TextPanel
 
actionPerformed(ActionEvent) - Method in class ij.text.TextWindow
 
ADCNAMELEN - Static variable in interface org.javaabf.ABF_parser
 
ADCUNITLEN - Static variable in interface org.javaabf.ABF_parser
 
add(Component) - Method in class ij.gui.GenericDialog
 
add(Component) - Method in class ij.gui.ImageWindow
 
add(Roi) - Method in class ij.gui.Overlay
Adds an Roi to this Overlay.
add(ImageProcessor, double) - Method in class ij.plugin.filter.SaltAndPepper
 
add(ImagePlus, Roi, int) - Method in class ij.plugin.frame.RoiManager
Adds the specified ROI to the list.
add(Wave) - Static method in class ij.plugin.frame.WaveManager
 
add(Wave, int) - Method in class ij.plugin.frame.WaveManager
Adds the specified Wave to the list.
ADD - Static variable in interface ij.process.Blitter
dst=dst+src
add(int) - Method in class ij.process.FloatProcessor
 
add(double) - Method in class ij.process.FloatProcessor
 
add(int) - Method in class ij.process.ImageProcessor
Adds 'value' to each pixel in the image or ROI.
add(double) - Method in class ij.process.ImageProcessor
Adds 'value' to each pixel in the image or ROI.
add(int) - Method in class ij.process.ShortProcessor
 
add(double) - Method in class ij.process.ShortProcessor
 
add(double) - Method in class ij.wave.Wave
Adds each element within this Wave by the value passed as argument and fires a waveChanged event.
add(Comment) - Method in class org.javaabf.Comments
 
ADD_TO_MANAGER - Static variable in class ij.plugin.filter.ParticleAnalyzer
Add particles to ROI Manager.
ADD_TO_OVERLAY - Static variable in interface ij.measure.Measurements
 
addAdjustmentListener(AdjustmentListener) - Method in class ij.gui.ScrollbarWithLabel
 
addAnnotation(XYAnnotation) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds any kinds of XYAnnotation to the chart
addAnnotations(XYAnnotation[]) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds any kinds of XYAnnotations to the chart
addAnnotationsFrom(ChartFramePlugIn) - Method in class ij.plugin.frame.ChartFramePlugIn
Add XYAnnotations from another chart to the current chart.
addArrayName(String) - Method in class com.jmatio.io.MatFileFilter
Add array name to the filter.
addBatchModeImage(ImagePlus) - Static method in class ij.macro.Interpreter
 
addBurst(Burst) - Method in class ij.wave.Bursts
 
addChar(char) - Method in class ij.gui.TextRoi
This method is used by the text tool to add typed characters to displayed text selections.
addCheckbox(String, boolean) - Method in class ij.gui.GenericDialog
Adds a checkbox.
addCheckboxGroup(int, int, String[], boolean[]) - Method in class ij.gui.GenericDialog
Adds a group of checkboxs using a grid layout.
addCheckboxGroup(int, int, String[], boolean[], String[]) - Method in class ij.gui.GenericDialog
Adds a group of checkboxs using a grid layout.
addChoice(String, String[], String) - Method in class ij.gui.GenericDialog
Adds a popup menu.
addClusterAverageWave(String, ArrayList, Color, ChartFramePlugIn) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
addColumns() - Method in class ij.measure.ResultsTable
Obsolete; the addValue() method automatically adds columns as needed.
addCommandListener(CommandListener) - Static method in class ij.Executer
Adds the specified command listener.
addComment(Comment) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds a single Comment to the chart.
addComments(Comments) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds the Comments to the chart.
addComponent(String, int, int) - Method in class ij.plugin.frame.Layout
 
addComponent(ImagePlus) - Method in class ij.plugin.frame.Layout
 
addComponent(PlugInFrame, int, int) - Method in class ij.plugin.frame.Layout
 
addComponent(ChartFramePlugIn) - Method in class ij.plugin.frame.Layout
 
addComponent(LayoutComponent) - Method in class ij.plugin.frame.Layout
 
addComponent() - Method in class ij.plugin.frame.LayoutPanel
 
addComponent(String, int, int) - Method in class ij.plugin.frame.LayoutPanel
 
addComponent(ImagePlus) - Method in class ij.plugin.frame.LayoutPanel
 
addComponent(ChartFramePlugIn) - Method in class ij.plugin.frame.LayoutPanel
 
addComponent(ClusterFramePlugIn) - Method in class ij.plugin.frame.LayoutPanel
 
addComponent(LayoutComponent) - Method in class ij.plugin.frame.LayoutPanel
 
addDialogListener(DialogListener) - Method in class ij.gui.GenericDialog
Add an Object implementing the DialogListener interface.
addElement(Roi) - Method in class ij.gui.Overlay
Adds an Roi to this Overlay.
addElement(double) - Method in class ij.wave.DynamicSeries
 
addElement(double) - Method in class ij.wave.Wave
Appends a value to the end of this array and fires a waveChanged event.
addElement(double, boolean) - Method in class ij.wave.Wave
Appends a value to this array with the option of firing a waveChanged event.
addEpoch(Epoch) - Method in class ij.plugin.frame.table.EpochTableModel
 
addEpochPopupMenu() - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
addErrorBars(float[]) - Method in class ij.gui.Plot
Adds error bars to the plot.
addErrorBars(double[]) - Method in class ij.gui.Plot
Adds error bars to the plot.
addErrorBars(String, float[]) - Method in class ij.gui.Plot
This is a version of addErrorBars that works with JavaScript.
addErrorBars(float[]) - Method in class ij.gui.PlotWindow
Adds error bars to the plot.
addEventListener(IJEventListener) - Static method in class ij.IJ
 
addHelp(String) - Method in class ij.gui.GenericDialog
Adds a "Help" button that opens the specified URL in the default browser.
addImageListener(ImageListener) - Static method in class ij.ImagePlus
 
addKeyListener(KeyListener) - Method in class ij.gui.ScrollbarWithLabel
 
addKeyListener(KeyListener) - Method in class ij.text.TextPanel
Unused keyPressed and keyTyped events will be passed to 'listener'.
addLabel(double, double, String) - Method in class ij.gui.Plot
Draws text at the specified location, where (0,0) is the upper left corner of the the plot frame and (1,1) is the lower right corner.
addLabel(double, double, String) - Method in class ij.gui.PlotWindow
Draws a label.
addLabel(String) - Method in class ij.measure.ResultsTable
Adds a label to the beginning of the current row.
addLabel(String, String) - Method in class ij.measure.ResultsTable
Adds a label to the beginning of the current row.
addLayoutComponent(String, Component) - Method in class ij.gui.ImageLayout
Not used by this class.
addMacroTool(String, MacroInstaller, int) - Method in class ij.gui.Toolbar
Used by the MacroInstaller class to install a set of macro tools.
addMacroTool(String, MacroInstaller) - Method in class ij.gui.Toolbar
Used by the MacroInstaller class to add a macro tool to the toolbar.
addMarker(WaveMarker) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds a single WaveMarker to the chart.
addMarkers(ArrayList) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds each of the WaveMarkers in the list to the current chart.
addMaskFromRois(ImagePlus, Color, Roi[]) - Static method in class ij.plugin.frame.RoiManager
 
addMaskFromWaves(ImagePlus, Color, Waves) - Static method in class ij.plugin.frame.RoiManager
 
addMessage(String) - Method in class ij.gui.GenericDialog
Adds a message consisting of one or more lines of text.
addMessage(String, Font) - Method in class ij.gui.GenericDialog
Adds a message consisting of one or more lines of text, which will be displayed using the specified font.
addMessage(String, Font, Color) - Method in class ij.gui.GenericDialog
Adds a message consisting of one or more lines of text, which will be displayed using the specified font and color.
addMouseListener(MouseListener) - Method in class ij.text.TextPanel
 
addNotesPopupMenu() - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
addNotify() - Method in class ij.gui.MultiLineLabel
 
addNumericField(String, double, int) - Method in class ij.gui.GenericDialog
Adds a numeric field.
addNumericField(String, double, int, int, String) - Method in class ij.gui.GenericDialog
Adds a numeric field.
addOffset() - Method in class ij.gui.PolygonRoi
 
addOpenBaseDirScriptsSubMenu(Menu, ImageJ) - Method in class ij.Menus
 
addOpenProcessingDirScriptsSubMenu(Menu, ImageJ) - Method in class ij.Menus
 
addOpenRecentItem(String) - Static method in class ij.Menus
Adds a file path to the beginning of the File/Open Recent submenu.
addPanel(Panel) - Method in class ij.gui.GenericDialog
Adds a Panel to the dialog.
addPanel(Panel, int, Insets) - Method in class ij.gui.GenericDialog
Adds a Panel to the dialog with custom contraint and insets.
addPlugInTool(PlugInTool) - Static method in class ij.gui.Toolbar
Adds a plugin tool to the first available toolbar slot, or to the last slot if the toolbar is full.
addPoint(double, double) - Method in class ij.gui.PointRoi
Returns a copy of this PointRoi with a point at (x,y) added.
addPoint(int, int) - Method in class ij.gui.PointRoi
 
addPoint(float, float) - Method in class ij.process.FloatPolygon
 
addPoint(double, double) - Method in class ij.process.FloatPolygon
 
addPoints(float[], float[], int) - Method in class ij.gui.Plot
Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(double[], double[], int) - Method in class ij.gui.Plot
Adds a set of points to the plot using double arrays.
addPoints(String, float[], float[], int) - Method in class ij.gui.Plot
This a version of addPoints that works with JavaScript.
addPoints(ArrayList, ArrayList, int) - Method in class ij.gui.Plot
Adds a set of points to the plot using double ArrayLists.
addPoints(double[], double[], double[], int) - Method in class ij.gui.Plot
Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(ArrayList, ArrayList, ArrayList, int) - Method in class ij.gui.Plot
Adds a set of points to the plot using double ArrayLists.
addPoints(float[], float[], int) - Method in class ij.gui.PlotWindow
Adds a set of points to the plot or adds a curve if shape is set to LINE.
addPoints(double[], double[], int) - Method in class ij.gui.PlotWindow
Adds a set of points to the plot using double arrays.
addPopupMenu() - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
addPopupMenu() - Method in class ij.plugin.frame.LayoutPanel
 
addPreviewCheckbox(PlugInFilterRunner) - Method in class ij.gui.GenericDialog
Adds a checkbox labelled "Preview" for "automatic" preview.
addPreviewCheckbox(PlugInFilterRunner, String) - Method in class ij.gui.GenericDialog
Add the preview checkbox with user-defined label; for details see the addPreviewCheckbox method with standard "Preview" label.
addRadioButtonGroup(String, String[], int, int, String) - Method in class ij.gui.GenericDialog
Adds a radio button group.
addResults() - Method in class ij.measure.ResultsTable
Adds the last row in this table to the Results window without updating it.
addRoi(Roi) - Method in class ij.plugin.frame.RoiManager
Adds the specified ROI.
addSlice(String, Object) - Method in class ij.ImageStack
Adds an image in the form of a pixel array to the end of the stack.
addSlice(ImageProcessor) - Method in class ij.ImageStack
Adds the image in 'ip' to the end of the stack.
addSlice(String, ImageProcessor) - Method in class ij.ImageStack
Adds the image in 'ip' to the end of the stack, setting the string 'sliceLabel' as the slice metadata.
addSlice(String, ImageProcessor, int) - Method in class ij.ImageStack
Adds the image in 'ip' to the stack following slice 'n'.
addSlice(String) - Method in class ij.VirtualStack
Adds an image to the end of the stack.
addSlice(String, Object) - Method in class ij.VirtualStack
Does nothing.
addSlice(String, ImageProcessor) - Method in class ij.VirtualStack
Does nothing..
addSlice(String, ImageProcessor, int) - Method in class ij.VirtualStack
Does noting.
addSlider(String, double, double, double) - Method in class ij.gui.GenericDialog
Adds a slider (scroll bar) to the dialog box.
addStringField(String, String) - Method in class ij.gui.GenericDialog
Adds an 8 column text field.
addStringField(String, String, int) - Method in class ij.gui.GenericDialog
Adds a text field.
addText(String, int, int) - Method in class ij.plugin.frame.Layout
 
addText(String, Color, int, int) - Method in class ij.plugin.frame.Layout
 
addText(String, Color, Font, int, int) - Method in class ij.plugin.frame.Layout
 
addText() - Method in class ij.plugin.frame.LayoutPanel
 
addText(String, Color, int, int) - Method in class ij.plugin.frame.LayoutPanel
 
addText(String, Color, Font, int, int) - Method in class ij.plugin.frame.LayoutPanel
 
addText(String, Color, Font) - Method in class ij.plugin.frame.LayoutPanel
 
addTextAreas(String, String, int, int) - Method in class ij.gui.GenericDialog
Adds one or two (side by side) text areas.
addToManager - Variable in class ij.plugin.filter.ParticleAnalyzer
 
addTool(String) - Method in class ij.gui.Toolbar
Adds a tool to the toolbar.
addUnsignedShortSlice(String, Object) - Method in class ij.ImageStack
Deprecated. Short images are always unsigned.
addValue(int, double) - Method in class ij.measure.ResultsTable
Adds a value to the end of the given column.
addValue(String, double) - Method in class ij.measure.ResultsTable
Adds a value to the end of the given column.
addValue(String, String) - Method in class ij.measure.ResultsTable
Adds a string value to the end of the given column.
addWave(String) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds a Wave from the WaveManager to the Chart by name.
addWave(Wave) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds a Wave to the chart.
addWave(Wave, Color) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds a Wave with the given Color to the chart.
addWave(Wave) - Method in class ij.plugin.frame.WaveManager
Adds the specified Wave.
addWave(ABF, Epoch, String, int) - Method in class ij.plugin.frame.WaveManager
 
addWave(Wave, boolean) - Method in class ij.plugin.frame.WaveManager
 
addWave(Wave) - Method in class ij.wave.Wave
Adds the contents of the Wave passed as argument, to this Wave instance index-by-index.
addWave(Wave) - Method in class ij.wave.Waves
Adds the Wave to the end of the collection.
addWaves(Waves) - Method in class ij.plugin.frame.ChartFramePlugIn
Adds all the Waves to the current chart.
addWaves(WaveXYZDataset, Waves, Color) - Method in class ij.plugin.frame.ChartFramePlugIn
 
addWaves(WaveXYZDataset, Waves, double, double, Color) - Method in class ij.plugin.frame.ChartFramePlugIn
 
addWaves(Waves, Color) - Method in class ij.plugin.frame.ChartFramePlugIn
 
addWaves(Waves, double, double, Color) - Method in class ij.plugin.frame.ChartFramePlugIn
 
addWaves(Waves) - Method in class ij.plugin.frame.WaveManager
 
addWaves(Epoch, String) - Method in class ij.plugin.frame.WaveManager
 
addWaves(Epoch) - Method in class ij.plugin.frame.WaveManager
 
addWaves(String, ABF, Epoch) - Method in class ij.plugin.frame.WaveManager
 
addWaves(Waves) - Method in class ij.wave.Waves
Adds each Wave from the Waves to the current collection in the order they appear in the argument's collection.
addWaveSeries(Wave, Wave) - Method in class ij.wave.WaveXYDataset
 
addWaveSeries(Wave) - Method in class ij.wave.WaveXYDataset
 
addWaveSeries(Wave, Wave) - Method in class ij.wave.WaveXYZDataset
 
addWaveSeries(Wave) - Method in class ij.wave.WaveXYZDataset
 
addWindow(Window) - Static method in class ij.WindowManager
Adds the specified window to the Window menu.
addWindow(Frame) - Static method in class ij.WindowManager
Adds the specified Frame to the Window menu.
addXYZPlot(Waves) - Method in class ij.plugin.frame.ChartFramePlugIn
 
addXYZPlot(Waves, Color) - Static method in class ij.util.PlotterUtils
 
addY(int, double) - Method in class ij.wave.DynamicXYDataset
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.ColorChooser
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.GenericDialog
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.ScrollbarWithLabel
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.gui.StackWindow
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ColorThresholder
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ContrastAdjuster
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.plugin.Orthogonal_Views
 
adjustmentValueChanged(AdjustmentEvent) - Method in class ij.text.TextPanel
 
ALL_KEYS - Static variable in class ij.IJ
 
allocate() - Method in class com.jmatio.types.MLNumericArray
 
allocate() - Method in class com.jmatio.types.MLSparse
 
allPoints() - Static method in class ij.gui.Wand
 
altKeyDown() - Static method in class ij.IJ
Returns true if the alt key is down.
alwaysOnTop - Static variable in class ij.Prefs
 
analyze(ImagePlus) - Method in class ij.plugin.filter.LineGraphAnalyzer
Uses ImageJ's particle analyzer to extract a set of coordinate pairs from a digitized line graph.
analyze(ImagePlus) - Method in class ij.plugin.filter.ParticleAnalyzer
Performs particle analysis on the specified image.
analyze(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
Performs particle analysis on the specified ImagePlus and ImageProcessor.
analyze(ImagePlus, ImageProcessor, Vector) - Method in class ij.plugin.filter.ParticleAnalyzer
Performs particle analysis on the specified ImagePlus and ImageProcessor.
Analyzer - Class in ij.plugin.filter
This plugin implements ImageJ's Analyze/Measure and Analyze/Set Measurements commands.
Analyzer() - Constructor for class ij.plugin.filter.Analyzer
 
Analyzer(ImagePlus) - Constructor for class ij.plugin.filter.Analyzer
Constructs a new Analyzer using the specified ImagePlus object and the current measurement options and default results table.
Analyzer(ImagePlus, int, ResultsTable) - Constructor for class ij.plugin.filter.Analyzer
Construct a new Analyzer using an ImagePlus object and private measurement options and results table.
analyzer - Variable in class ij.plugin.filter.ParticleAnalyzer
 
and(ShapeRoi) - Method in class ij.gui.ShapeRoi
Unary intersection operator.
AND - Static variable in interface ij.process.Blitter
dst=dst AND src
and(int) - Method in class ij.process.FloatProcessor
 
and(int) - Method in class ij.process.ImageProcessor
Binary AND of each pixel in the image or ROI with 'value'.
and(int) - Method in class ij.process.ShortProcessor
 
ANGLE - Static variable in class ij.gui.Roi
 
ANGLE - Static variable in class ij.gui.Toolbar
 
ANGLE - Static variable in class ij.measure.ResultsTable
 
angle - Variable in class ij.process.EllipseFitter
Angle in degrees
angle - Variable in class ij.process.ImageStatistics
Angle in degrees of fitted ellipse
angstromSymbol - Static variable in class ij.IJ
 
Animator - Class in ij.plugin
This plugin animates stacks.
Animator() - Constructor for class ij.plugin.Animator
 
antialiasedText - Static variable in class ij.Prefs
No longer used
antialiasedText - Variable in class ij.process.ImageProcessor
 
antialiasedTools - Static variable in class ij.Prefs
Draw tool icons using antialiasing.
antiAliasPlots - Static variable in class ij.util.PlotterUtils
 
AppearanceOptions - Class in ij.plugin
This plugin implements the Edit/Options/Appearance command.
AppearanceOptions() - Constructor for class ij.plugin.AppearanceOptions
 
append(String, String) - Static method in class ij.IJ
Appends a string to the end of a file.
append(String) - Method in class ij.plugin.frame.Editor
 
append(String) - Method in class ij.text.TextPanel
Adds one or more lines to the end of this TextPanel.
append(ArrayList) - Method in class ij.text.TextPanel
Adds strings contained in an ArrayList to the end of this TextPanel.
append(String) - Method in class ij.text.TextWindow
Adds one or lines of text to the window.
append(Wave) - Method in class ij.wave.Wave
Appends the contents of the Wave passed as argument to the end of this Wave instance.
appendLine(String) - Method in class ij.text.TextPanel
Adds a single line to the end of this TextPanel.
appendSelectedWaves() - Method in class ij.plugin.frame.WaveManager
 
appendWithoutUpdate(String) - Method in class ij.text.TextPanel
Adds a single line to the end of this TextPanel without updating the display.
applyLut() - Method in class ij.process.ByteProcessor
 
applyMacro(ImageProcessor, String, boolean) - Static method in class ij.plugin.filter.ImageMath
 
applyMacro(String) - Method in class ij.process.ImageProcessor
Uses the Process/Math/Macro command to apply macro code to this image.
applyTable(int[]) - Method in class ij.process.ByteProcessor
 
applyTable(int[]) - Method in class ij.process.ColorProcessor
 
applyTable(int[], int) - Method in class ij.process.ColorProcessor
 
applyTable(int[]) - Method in class ij.process.FloatProcessor
 
applyTable(int[]) - Method in class ij.process.ImageProcessor
Transforms the image or ROI using a lookup table.
applyTable(int[]) - Method in class ij.process.ShortProcessor
Transforms the pixel data using a 65536 entry lookup table.
applyTable(int[]) - Method in class ij.process.StackProcessor
 
applyWindowFunction() - Method in class ij.wave.Wave
 
AREA - Static variable in interface ij.measure.Measurements
 
AREA - Static variable in class ij.measure.ResultsTable
 
area - Variable in class ij.process.ImageStatistics
 
AREA_FRACTION - Static variable in interface ij.measure.Measurements
 
AREA_FRACTION - Static variable in class ij.measure.ResultsTable
 
areaFraction - Variable in class ij.process.ImageStatistics
 
areEpisodic() - Method in class ij.wave.Waves
Returns true if ALL the Waves in this instance are EpisodicWaves
ARG_ARRAY - Static variable in interface ij.macro.MacroExtension
 
ARG_NUMBER - Static variable in interface ij.macro.MacroExtension
 
ARG_OPTIONAL - Static variable in interface ij.macro.MacroExtension
 
ARG_OUTPUT - Static variable in interface ij.macro.MacroExtension
 
ARG_STRING - Static variable in interface ij.macro.MacroExtension
 
ARGB - Static variable in class ij.io.FileInfo
32-bit interleaved ARGB.
argTypes - Variable in class ij.macro.ExtensionDescriptor
 
ARRAY - Static variable in interface ij.macro.MacroConstants
 
ARRAY_FUNC - Static variable in interface ij.macro.MacroConstants
 
ARRAY_FUNCTION - Static variable in interface ij.macro.MacroConstants
 
arrayFunctionIDs - Static variable in interface ij.macro.MacroConstants
 
arrayFunctions - Static variable in interface ij.macro.MacroConstants
 
ArrayUtil - Class in ij.util
 
ArrayUtil(int) - Constructor for class ij.util.ArrayUtil
constructeur
ArrayUtil(float[]) - Constructor for class ij.util.ArrayUtil
constructeur
Arrow - Class in ij.gui
This is an Roi subclass for creating and displaying arrows.
Arrow(double, double, double, double) - Constructor for class ij.gui.Arrow
 
Arrow(int, int, ImagePlus) - Constructor for class ij.gui.Arrow
 
ARROW - Static variable in class ij.io.RoiDecoder
 
ARROW_HEAD_SIZE - Static variable in class ij.io.RoiDecoder
 
ARROW_STYLE - Static variable in class ij.io.RoiDecoder
 
ArrowTool - Class in ij.plugin.tool
 
ArrowTool() - Constructor for class ij.plugin.tool.ArrowTool
 
ARTEST - Static variable in class ij.io.TiffDecoder
 
ASCENDING - Static variable in class ij.wave.Burst
 
ASIN - Static variable in interface ij.macro.MacroConstants
 
asp_bk - Variable in class ij.gui.Roi
 
aspect - Variable in class ij.gui.Roi
 
ASPECT_RATIO - Static variable in class ij.measure.ResultsTable
 
ATAN - Static variable in interface ij.macro.MacroConstants
 
ATAN2 - Static variable in interface ij.macro.MacroConstants
 
attributes - Variable in class com.jmatio.types.MLArray
 
AUTO_UPDATE - Static variable in interface ij.macro.MacroConstants
 
autoClose - Static variable in class ij.gui.PlotWindow
Automatically close window after saving values.
autoContrast - Static variable in class ij.Prefs
Adjust contrast when scrolling stacks (or hold shift key down)
autonameSelectedROIs(String) - Method in class ij.plugin.frame.RoiManager
 
autonameSelectedROIs() - Method in class ij.plugin.frame.RoiManager
 
autonameSelectedWaves(String) - Method in class ij.plugin.frame.WaveManager
 
autonameSelectedWaves() - Method in class ij.plugin.frame.WaveManager
 
autoOutline(int, int, double, double, int) - Method in class ij.gui.Wand
Traces an object defined by lower and upper threshold values.
autoOutline(int, int, double, double) - Method in class ij.gui.Wand
Traces an object defined by lower and upper threshold values or an interior hole; whatever is found first ('legacy mode').
autoOutline(int, int, int, int) - Method in class ij.gui.Wand
This is a variation of legacy autoOutline that uses int threshold arguments.
autoOutline(int, int) - Method in class ij.gui.Wand
Traces the boundary of an area of uniform color, where 'startX' and 'startY' are somewhere inside the area.
autoOutline(int, int, double, int) - Method in class ij.gui.Wand
Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel at the starting location.
autoThreshold() - Method in class ij.process.ColorProcessor
 
autoThreshold() - Method in class ij.process.FloatProcessor
Not implemented.
autoThreshold() - Method in class ij.process.ImageProcessor
Converts the image to binary using an automatically determined threshold.
AutoThresholder - Class in ij.process
Autothresholding methods from the Auto_Threshold plugin (http://pacific.mpi-cbg.de/wiki/index.php/Auto_Threshold) by G.Landini at bham dot ac dot uk.
AutoThresholder() - Constructor for class ij.process.AutoThresholder
 
AutoThresholder.Method - Enum in ij.process
 
AVAILABLE_BYTE1 - Static variable in class ij.io.RoiDecoder
 
AVERAGE - Static variable in class ij.plugin.Binner
 
AVERAGE - Static variable in interface ij.process.Blitter
dst=(dst+src)/2
averageCycleWindows(Vector) - Static method in class ij.wave.CTA_Utils
 
averageSelectedWaves() - Method in class ij.plugin.frame.WaveManager
 
averageWaves() - Method in class ij.wave.Waves
Returns a Wave named 'WaveAvg' by averaging each of the Waves at each sampling point.
averageWindow(double[], int, int) - Method in class ij.wave.Wave
 
AVG_METHOD - Static variable in class ij.plugin.ZProjector
 
AVI - Static variable in class ij.io.Opener
 
AVI_Reader - Class in ij.plugin
ImageJ Plugin for reading an AVI file into an image stack (one slice per video frame) Restrictions and Notes: - Only few formats supported: - uncompressed 8 bit with palette (=LUT) - uncompressed 8 & 16 bit grayscale - uncompressed 24 & 32 bit RGB (alpha channel ignored) - uncompressed 32 bit AYUV (alpha channel ignored) - various YUV 4:2:2 and 4:2:0 compressed formats (i.e., formats with full luminance resolution, but reduced chroma resolution - png or jpeg-encoded individual frames.
AVI_Reader() - Constructor for class ij.plugin.AVI_Reader
 
AVI_Writer - Class in ij.plugin.filter
This plugin implements the File/Save As/AVI command.
AVI_Writer() - Constructor for class ij.plugin.filter.AVI_Writer
 
avoidResliceInterpolation - Static variable in class ij.Prefs
Avoid interpolation when re-slicing
axisChanged(AxisChangeEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
axisChanged(AxisChangeEvent) - Method in class ij.wave.DynamicXYDataset
 
axisChanged(AxisChangeEvent) - Method in class ij.wave.WaveXYDataset
 
axisChanged(AxisChangeEvent) - Method in class ij.wave.WaveXYZDataset
 

B

BACKGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
 
backgroundColor - Static variable in class ij.ImageJ
 
backgrounds - Static variable in class ij.plugin.Thresholder
 
BackgroundSubtracter - Class in ij.plugin.filter
Implements ImageJ's Subtract Background command.
BackgroundSubtracter() - Constructor for class ij.plugin.filter.BackgroundSubtracter
 
BAR - Static variable in class ij.gui.Arrow
 
BARE_OUTLINES - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
BARG - Static variable in class ij.io.FileInfo
32-bit interleaved BARG (MCID).
baseCM - Variable in class ij.process.ImageProcessor
 
BaseDirScriptsOpener - Class in ij
Opens, in a separate thread, files selected from the File/Open BaseDir Scripts submenu.
BatchConverter - Class in ij.plugin
This plugin implements the File/Batch/Convert command, which converts the images in a folder to a specified format.
BatchConverter() - Constructor for class ij.plugin.BatchConverter
 
BatchMeasure - Class in ij.plugin
This plugin implements the File/Batch/Measure command, which measures all the images in a user-specified folder.
BatchMeasure() - Constructor for class ij.plugin.BatchMeasure
 
batchMode - Static variable in class ij.macro.Interpreter
 
BatchProcesser - Class in ij.plugin
This plugin implements the File/Batch/Macro and File/Batch/Virtual Stack commands.
BatchProcesser() - Constructor for class ij.plugin.BatchProcesser
 
BCOLOR - Static variable in class ij.Prefs
 
beep() - Static method in class ij.IJ
Emits an audio beep.
BEEP - Static variable in interface ij.macro.MacroConstants
 
Benchmark - Class in ij.plugin.filter
Implements the Plugins/Utilities/Run Benchmark command.
Benchmark() - Constructor for class ij.plugin.filter.Benchmark
 
BGR - Static variable in class ij.io.FileInfo
24-bit interleaved BGR.
BICUBIC - Static variable in class ij.process.ImageProcessor
Interpolation methods
BILINEAR - Static variable in class ij.process.ImageProcessor
Interpolation methods
bin(int) - Method in class ij.process.ImageProcessor
Returns a copy of this image that has been reduced in size using binning.
Binary - Class in ij.plugin.filter
Implements the Erode, Dilate, Open, Close, Outline, Skeletonize and Fill Holes commands in the Process/Binary submenu.
Binary() - Constructor for class ij.plugin.filter.Binary
 
BinaryProcessor - Class in ij.process
This class processes binary images.
BinaryProcessor(ByteProcessor) - Constructor for class ij.process.BinaryProcessor
Creates a BinaryProcessor from a ByteProcessor.
Binner - Class in ij.plugin
This plugin implements the Image/Transform/Bin command.
Binner() - Constructor for class ij.plugin.Binner
 
binSize - Variable in class ij.process.ImageStatistics
 
BIT_DEPTH - Static variable in interface ij.macro.MacroConstants
 
BitBuffer - Class in ij.io
A class for reading arbitrary numbers of bits from a byte array.
BitBuffer(byte[]) - Constructor for class ij.io.BitBuffer
 
BITMAP - Static variable in class ij.io.FileInfo
1-bit black and white.
BITS_PER_SAMPLE - Static variable in class ij.io.TiffDecoder
 
BLACK - Static variable in class ij.process.ImageProcessor
Value of pixels included in masks.
BLACK_AND_WHITE_LUT - Static variable in class ij.process.ImageProcessor
 
blackBackground - Static variable in class ij.Prefs
Backgound is black in binary images
blackCanvas - Static variable in class ij.Prefs
Use black image border.
Blitter - Interface in ij.process
ImageJ bit blitting classes must implement this interface.
blue - Variable in class ij.plugin.filter.RGBStackSplitter
 
blues - Variable in class ij.io.FileInfo
 
blur(ImageProcessor, double) - Method in class ij.plugin.filter.GaussianBlur
Deprecated. 
blur1Direction(FloatProcessor, double, double, boolean, int) - Method in class ij.plugin.filter.GaussianBlur
Blur an image in one direction (x or y) by a Gaussian.
BLUR_MORE - Static variable in class ij.process.ImageProcessor
 
blurFloat(FloatProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur
Gaussian Filtering of a FloatProcessor.
blurGaussian(ImageProcessor, double, double, double) - Method in class ij.plugin.filter.GaussianBlur
Gaussian Filtering of an ImageProcessor.
blurGaussian(double) - Method in class ij.process.ImageProcessor
Blurs the image by convolving with a Gaussian function.
bLUT1 - Variable in class ij.process.ImageProcessor
 
bLUT2 - Variable in class ij.process.ImageProcessor
 
BMP - Static variable in class ij.io.FileInfo
 
BMP - Static variable in class ij.io.Opener
 
BMP_Reader - Class in ij.plugin
This plugin reads BMP files.
BMP_Reader() - Constructor for class ij.plugin.BMP_Reader
 
BMP_Writer - Class in ij.plugin
Implements the File/Save As/BMP command.
BMP_Writer() - Constructor for class ij.plugin.BMP_Writer
 
boldFont - Variable in class ij.process.ImageProcessor
 
BOTTOM - Static variable in class ij.io.RoiDecoder
 
BOTTOM_MARGIN - Static variable in class ij.gui.Plot
the margin width below the plot frame
boundingRect(int, int, int, int) - Method in class ij.plugin.frame.SyncWindows
Compute bounding rectangle given current and old cursor locations.
BOX - Static variable in class ij.gui.Plot
Display points using an box-shaped mark.
BOX - Static variable in class ij.gui.PlotWindow
Display points using an box-shaped mark.
BREAK - Static variable in interface ij.macro.MacroConstants
 
BrowserLauncher - Class in ij.plugin
This plugin implements the File/Import/URL command and the commands in the Help menu that open web pages.
BrowserLauncher() - Constructor for class ij.plugin.BrowserLauncher
 
BRUSH_ROI - Static variable in class ij.gui.Toolbar
 
BrushTool - Class in ij.plugin.tool
 
BrushTool() - Constructor for class ij.plugin.tool.BrushTool
 
bSyncAll - Variable in class ij.plugin.frame.SyncWindows
Buttons for user control.
BufferedRandomAccessFile - Class in org.jah
 
BufferedRandomAccessFile(String, String) - Constructor for class org.jah.BufferedRandomAccessFile
 
BufferedRandomAccessFile(File, String) - Constructor for class org.jah.BufferedRandomAccessFile
 
BUILD - Static variable in class ij.ImageJ
 
buildControlDialog(int, int) - Method in class ij.plugin.ZProjector
Builds dialog to query users for projection parameters.
buildControlPanel() - Method in class ij.plugin.frame.SyncWindows
Builds panel containing control buttons.
buildWindowList() - Method in class ij.plugin.frame.SyncWindows
Builds list of open ImageWindows
buldFromBytes(byte[]) - Method in interface com.jmatio.types.ByteStorageSupport
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLDouble
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLInt16
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLInt32
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLInt64
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLInt8
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLSingle
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLSparse
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLUInt64
 
buldFromBytes(byte[]) - Method in class com.jmatio.types.MLUInt8
 
bUnsyncAll - Variable in class ij.plugin.frame.SyncWindows
Buttons for user control.
Burst - Class in ij.wave
Represents the waveform (burst envelope) of a given burst cycle in the context of a larger Wave.
Burst() - Constructor for class ij.wave.Burst
 
Burst(double, Wave) - Constructor for class ij.wave.Burst
 
Burst(double, double) - Constructor for class ij.wave.Burst
 
Burst(double, double, double) - Constructor for class ij.wave.Burst
 
BURST - Static variable in class ij.wave.WaveMarker
 
BURST_TYPE - Static variable in class ij.wave.Wave
 
Burst_Utils - Class in ij.wave
 
Burst_Utils() - Constructor for class ij.wave.Burst_Utils
 
Bursts - Class in ij.wave
A collection of Burst instances that can be easily used to calculate broader statistics or generate graphical markers of bursts.
Bursts() - Constructor for class ij.wave.Bursts
 
button - Variable in class ij.gui.MessageDialog
 
button - Variable in class ij.gui.WaitForUserDialog
 
BYTE - Static variable in class ij.plugin.filter.EDM
Output type: new 8-bit image
BYTE_OVERWRITE - Static variable in class ij.plugin.filter.EDM
Output type: overwrite current 8-bit image
ByteBlitter - Class in ij.process
This class does bit blitting of byte images.
ByteBlitter(ByteProcessor) - Constructor for class ij.process.ByteBlitter
Constructs a ByteBlitter from a ByteProcessor.
ByteProcessor - Class in ij.process
This is an 8-bit image and methods that operate on that image.
ByteProcessor(Image) - Constructor for class ij.process.ByteProcessor
Creates a ByteProcessor from an AWT Image.
ByteProcessor(int, int) - Constructor for class ij.process.ByteProcessor
Creates a blank ByteProcessor of the specified dimensions.
ByteProcessor(int, int, byte[]) - Constructor for class ij.process.ByteProcessor
Creates a ByteProcessor from a byte array.
ByteProcessor(int, int, byte[], ColorModel) - Constructor for class ij.process.ByteProcessor
Creates a ByteProcessor from a pixel array and IndexColorModel.
ByteProcessor(BufferedImage) - Constructor for class ij.process.ByteProcessor
Creates a ByteProcessor from a TYPE_BYTE_GRAY BufferedImage.
ByteProcessor(ImageProcessor, boolean) - Constructor for class ij.process.ByteProcessor
Creates a ByteProcessor from an ImageProcessor. 16-bit and 32-bit pixel data are scaled from min-max to 0-255 if 'scale' is true.
ByteStatistics - Class in ij.process
8-bit image statistics, including histogram.
ByteStatistics(ImageProcessor) - Constructor for class ij.process.ByteStatistics
Construct an ImageStatistics object from a ByteProcessor using the standard measurement options (area, mean, mode, min and max) and no calibration.
ByteStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ByteStatistics
Constructs a ByteStatistics object from a ByteProcessor using the specified measurement and calibration.
ByteStorageSupport<T extends java.lang.Number> - Interface in com.jmatio.types
 

C

c2hex(Color) - Static method in class ij.util.Tools
Converts a Color to an 7 byte hex string starting with '#'.
C_POSITION - Static variable in class ij.io.RoiDecoder
 
CACHE_BYTE_SIZE - Static variable in interface org.javaabf.ABF_parser
 
cachedMask - Variable in class ij.gui.Roi
 
cal - Variable in class ij.gui.HistogramWindow
 
cal - Variable in class ij.process.ImageStatistics
 
calculate(String, ImagePlus, ImagePlus) - Method in class ij.plugin.ImageCalculator
Deprecated. replaced by run(String,ImagePlus,ImagePlus)
calculateDistance(int, int, int, int) - Method in class ij.gui.Plot
 
CALCULATOR - Static variable in interface ij.macro.MacroConstants
 
CALIBRATE - Static variable in interface ij.macro.MacroConstants
 
calibrate(ImagePlus) - Method in class ij.plugin.filter.Calibrator
Calibrate an image with the function type defined previously.
calibrated() - Method in class ij.measure.Calibration
Returns true if this image is density calibrated.
Calibration - Class in ij.measure
Calibration objects contain an image's spatial and density calibration data.
Calibration(ImagePlus) - Constructor for class ij.measure.Calibration
Constructs a new Calibration object using the default values.
Calibration() - Constructor for class ij.measure.Calibration
Constructs a new Calibration object using the default values.
CalibrationBar - Class in ij.plugin
This plugin implements the Analyze/Tools/Calibration Bar command.
CalibrationBar() - Constructor for class ij.plugin.CalibrationBar
 
calibrationFunction - Variable in class ij.io.FileInfo
 
Calibrator - Class in ij.plugin.filter
Implements the Analyze/Calibrate command.
Calibrator() - Constructor for class ij.plugin.filter.Calibrator
 
CALL - Static variable in interface ij.macro.MacroConstants
 
CANCELED - Static variable in class ij.IJ
 
cancelPressed() - Method in class ij.gui.SaveChangesDialog
Returns true if the user dismissed dialog by pressing "Cancel".
cancelPressed() - Method in class ij.gui.YesNoCancelDialog
Returns true if the user dismissed dialog by pressing "Cancel".
canEnlarge(int, int) - Method in class ij.gui.ImageCanvas
 
canInitializeLJ() - Method in interface org.jah.Labjack
 
canInitializeLJ() - Method in class org.jah.Labjack32bit
 
canInitializeLJ() - Method in class org.jah.SimpleLabjackControl
 
CanvasResizer - Class in ij.plugin
This plugin implements the Image/Adjust/Canvas Size command.
CanvasResizer() - Constructor for class ij.plugin.CanvasResizer
 
captureImage() - Method in class ij.plugin.ScreenGrabber
Captures the active image window and returns it as an ImagePlus.
captureScreen() - Method in class ij.plugin.ScreenGrabber
Captures the entire screen and returns it as an ImagePlus.
cChannel - Variable in class ij.plugin.frame.SyncWindows
Checkboxes for user control.
cCoords - Variable in class ij.plugin.frame.SyncWindows
Checkboxes for user control.
cCursor - Variable in class ij.plugin.frame.SyncWindows
Checkboxes for user control.
ccWindow - Variable in class ij.wave.ClusterHints
 
cells() - Method in class com.jmatio.types.MLCell
 
center(Window) - Static method in class ij.gui.GUI
Positions the specified window in the center of the screen.
CENTER - Static variable in class ij.gui.Plot
Text justification.
center - Variable in class ij.gui.Roi
 
CENTER - Static variable in class ij.gui.TextRoi
 
center(String, int) - Static method in class org.javaabf.ABF_utils
 
center(String, int, String) - Static method in class org.javaabf.ABF_utils
 
CENTER_JUSTIFY - Static variable in class ij.process.ImageProcessor
Center justify text.
CENTER_OF_MASS - Static variable in interface ij.measure.Measurements
 
centerAboutZero() - Method in class ij.wave.Wave
Centers the amplitudes of this Wave about zero and fires a waveChanged event.
centerBottom(Window) - Static method in class ij.gui.GUI
Positions the specified window in the center-bottom of the screen.
centerDialog(boolean) - Method in class ij.gui.GenericDialog
Display dialog centered on the primary screen?
centerNextImage() - Static method in class ij.gui.ImageWindow
Causes the next image to be opened to be centered on the screen and displayed without informational text above the image.
centralFiniteDifference(double[], int) - Static method in class ij.wave.WaveUtils
 
centralFiniteDifference(Wave, int) - Static method in class ij.wave.WaveUtils
 
CENTROID - Static variable in interface ij.measure.Measurements
 
cFrame - Variable in class ij.plugin.frame.SyncWindows
Checkboxes for user control.
CHANGE_VALUES - Static variable in interface ij.macro.MacroConstants
 
changeComment(int) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
changeComment(int, String) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
changeComment(int, String) - Method in class org.javaabf.Comments
 
changeFont(Font) - Method in class ij.gui.Plot
Obsolete; replaced by setFont().
changeFont(Font) - Method in class ij.gui.PlotWindow
Changes the font.
changes - Variable in class ij.ImagePlus
True if any changes have been made to this image.
CHANNEL - Static variable in class ij.measure.ResultsTable
 
channelLuts - Variable in class ij.io.FileInfo
 
Channels - Class in ij.plugin.frame
Displays the ImageJ Channels window.
Channels() - Constructor for class ij.plugin.frame.Channels
 
ChannelSplitter - Class in ij.plugin
This plugin implements the Image/Color/Split Channels command.
ChannelSplitter() - Constructor for class ij.plugin.ChannelSplitter
 
CHAPMAN - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
CHAR - Static variable in interface org.javaabf.ABF_parser
 
CHAR_CODE_AT - Static variable in interface ij.macro.MacroConstants
 
CHART - Static variable in class ij.io.Opener
 
CHART - Static variable in class ij.plugin.frame.Layout
 
CHART_TYPE - Static variable in class ij.WindowManager
 
ChartFramePlugIn - Class in ij.plugin.frame
This class provides JFreeChart library plotting functionality as an ImageJ/PhysImage plugin.
ChartFramePlugIn(String, JFreeChart) - Constructor for class ij.plugin.frame.ChartFramePlugIn
 
chartMouseClicked(ChartMouseEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
chartMouseMoved(ChartMouseEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
chartTitle - Static variable in class ij.util.PlotterUtils
 
ChartWriter - Class in ij.plugin
This plugin implements the File/Save As/Chart command.
ChartWriter() - Constructor for class ij.plugin.ChartWriter
 
CHECK_AVAILABLE_MEMORY - Static variable in class ij.gui.NewImage
 
checkArguments(Object[]) - Method in class ij.macro.ExtensionDescriptor
 
checkbox - Variable in class ij.gui.GenericDialog
 
checkForDuplicateName - Static variable in class ij.WindowManager
 
choice - Variable in class ij.gui.GenericDialog
 
CIRCLE - Static variable in class ij.gui.Plot
Display points using a circle 5 pixels in diameter.
CIRCLE - Static variable in class ij.gui.PlotWindow
Display points using a circle 5 pixels in diameter.
CIRCULARITY - Static variable in interface ij.measure.Measurements
 
CIRCULARITY - Static variable in class ij.measure.ResultsTable
 
ClassChecker - Class in ij.plugin
Checks for duplicate class and JAR files in the plugins folders and deletes older duplicates.
ClassChecker() - Constructor for class ij.plugin.ClassChecker
 
clear() - Method in class ij.gui.Overlay
Removes all the Rois in this Overlay.
clear(ImageProcessor) - Method in class ij.gui.TextRoi
 
clear(ImageProcessor) - Method in class ij.plugin.filter.Filler
 
clear() - Method in class ij.plugin.frame.RoiManager
 
clear() - Method in class ij.plugin.frame.WaveManager
 
clear() - Method in class ij.text.TextPanel
Deletes all the lines.
clear() - Method in class ij.wave.Wave
Removes all elements from this Wave.
CLEAR_WORKSHEET - Static variable in class ij.plugin.filter.ParticleAnalyzer
Clear ImageJ console before starting.
clearCache() - Method in class org.jah.ElectrophysManager
 
clearEpochs() - Method in class ij.plugin.frame.table.EpochTableModel
 
clearOutside(ImageProcessor) - Method in class ij.plugin.filter.Filler
Deprecated. replaced by ImageProcessor.fillOutside(Roi)
clearSelection() - Method in class ij.text.TextPanel
Deletes the selected lines.
clipboard - Variable in class ij.gui.Roi
 
Clipboard - Class in ij.plugin
Copies and pastes images to the clipboard.
Clipboard() - Constructor for class ij.plugin.Clipboard
 
clipHeight - Variable in class ij.gui.Roi
 
clipRectMargin() - Method in class ij.gui.Arrow
 
clipRectMargin() - Method in class ij.gui.Line
 
clipRectMargin() - Method in class ij.gui.PolygonRoi
 
clipRectMargin() - Method in class ij.gui.Roi
 
clipWidth - Variable in class ij.gui.Roi
 
clipX - Variable in class ij.gui.Roi
 
clipXMax - Variable in class ij.process.ImageProcessor
 
clipXMin - Variable in class ij.process.ImageProcessor
 
clipY - Variable in class ij.gui.Roi
 
clipYMax - Variable in class ij.process.ImageProcessor
 
clipYMin - Variable in class ij.process.ImageProcessor
 
clone() - Method in class ij.gui.ImageRoi
 
clone() - Method in class ij.gui.LayoutComponent
 
clone() - Method in class ij.gui.PolygonRoi
Returns a copy of this PolygonRoi.
clone() - Method in class ij.gui.Roi
Returns a copy of this roi.
clone() - Method in class ij.gui.ShapeRoi
Returns a deep copy of this.
clone() - Method in class ij.gui.TextRoi
Returns a copy of this TextRoi.
clone() - Method in class ij.ImagePlus
Returns a shallow copy of this ImagePlus.
clone() - Method in class ij.io.FileInfo
 
clone() - Method in class ij.measure.Calibration
 
clone() - Method in class ij.measure.ResultsTable
Duplicates this ResultsTable.
clone() - Method in class ij.plugin.frame.ChartFramePlugIn
 
clone() - Method in class ij.process.ImageProcessor
Returns a shallow copy of this ImageProcessor, where this image and the copy share pixel data.
clone() - Method in class ij.process.LUT
 
clone() - Method in class ij.wave.ABFWaveProxy
 
clone() - Method in class ij.wave.Wave
 
clone() - Method in class ij.wave.WaveProxy
Returns a clone of this proxy and corresponding source.
clone() - Method in class ij.wave.Waves
Returns a deep-copy of this Waves' instance.
cloneMetadata(Wave) - Method in class ij.wave.CrosscorrelationWave
 
cloneMetadata(Wave) - Method in class ij.wave.Wave
 
close() - Method in class com.jmatio.io.MatFileIncrementalWriter
 
close() - Method in class ij.gui.ImageWindow
Removes this window from the window list and disposes of it.
close(boolean) - Method in class ij.gui.ImageWindow
Removes this window from the window list and disposes of it.
close() - Method in class ij.gui.StackWindow
 
close() - Method in class ij.gui.WaitForUserDialog
 
close() - Static method in class ij.IJ
 
close(String) - Static method in class ij.IJ
 
close(String, boolean) - Static method in class ij.IJ
 
close() - Method in class ij.ImagePlus
 
close(boolean) - Method in class ij.ImagePlus
Closes this image and sets the ImageProcessor to null.
close() - Method in class ij.io.ConsoleInputStream
 
close() - Method in class ij.io.ConsoleOutputStream
 
close() - Method in class ij.io.LogStream
 
close() - Method in class ij.io.RandomAccessStream
 
close() - Method in class ij.macro.FunctionFinder
 
CLOSE - Static variable in interface ij.macro.MacroConstants
 
CLOSE - Static variable in class ij.plugin.filter.RankFilters
 
close() - Method in class ij.plugin.frame.Channels
 
close() - Method in class ij.plugin.frame.ChartFramePlugIn
Closes this window.
close() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
close() - Method in class ij.plugin.frame.ColorThresholder
 
close() - Method in class ij.plugin.frame.ContrastAdjuster
Overrides close() in PlugInDialog.
close() - Method in class ij.plugin.frame.Editor
Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.Fonts
 
close() - Method in class ij.plugin.frame.LineWidthAdjuster
Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.PasteController
 
close() - Method in class ij.plugin.frame.PlugInDialog
Closes this window.
close() - Method in class ij.plugin.frame.PlugInFrame
Closes this window.
close() - Method in class ij.plugin.frame.Recorder
 
close() - Method in class ij.plugin.frame.RoiManager
Overrides PlugInFrame.close().
close() - Method in class ij.plugin.frame.SyncWindows
 
close() - Method in class ij.plugin.frame.ThresholdAdjuster
Overrides close() in PlugInFrame.
close() - Method in class ij.plugin.frame.WaveManager
Overrides PlugInFrame.close().
close() - Method in class ij.text.TextWindow
 
close(boolean) - Method in class ij.text.TextWindow
Closes this TextWindow.
closeAllWindows() - Static method in class ij.IJ
 
closeAllWindows() - Static method in class ij.WindowManager
Closes all windows.
closed - Variable in class ij.gui.ImageWindow
 
CLOSED - Static variable in class ij.ImagePlus
 
CLUSTER_TYPE - Static variable in class ij.WindowManager
 
ClusterFramePlugIn - Class in ij.plugin.frame
This class provides the JTreeView library plotting functionality as an ImageJ/PhysImage plugin.
ClusterFramePlugIn(String) - Constructor for class ij.plugin.frame.ClusterFramePlugIn
 
ClusterHints - Class in ij.wave
 
ClusterHints() - Constructor for class ij.wave.ClusterHints
 
ClusterHints(boolean) - Constructor for class ij.wave.ClusterHints
 
clusteringMethods - Static variable in class ij.wave.ClusterUtils
 
ClusterUtils - Class in ij.wave
A number of utility functions for working with the open source Cluster program and manipulating the inputs/outputs.
ClusterUtils() - Constructor for class ij.wave.ClusterUtils
 
cm - Variable in class ij.process.ImageProcessor
 
cm2 - Variable in class ij.process.ImageProcessor
 
CMYK - Static variable in class ij.io.FileInfo
32-bit interleaved CMYK.
coefficients - Variable in class ij.io.FileInfo
 
COLOR - Static variable in class ij.CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
color - Variable in class ij.gui.LineLayoutComponent
 
COLOR - Static variable in class ij.IJ
Image display modes
COLOR8 - Static variable in class ij.io.FileInfo
8-bit unsigned integer with color lookup table.
COLOR_256 - Static variable in class ij.ImagePlus
8-bit indexed color
COLOR_MAP - Static variable in class ij.io.TiffDecoder
 
COLOR_PICKER_CLOSED - Static variable in interface ij.IJEventListener
 
COLOR_RGB - Static variable in class ij.ImagePlus
32-bit RGB color
ColorBlitter - Class in ij.process
This class does bit blitting of RGB images.
ColorBlitter(ColorProcessor) - Constructor for class ij.process.ColorBlitter
Constructs a ColorBlitter from a ColorProcessor.
ColorChooser - Class in ij.gui
Displays a dialog that allows the user to select a color using three sliders.
ColorChooser(String, Color, boolean) - Constructor for class ij.gui.ColorChooser
Constructs a ColorChooser using the specified title and initial color.
ColorChooser(String, Color, boolean, Frame) - Constructor for class ij.gui.ColorChooser
 
ColorPicker - Class in ij.plugin
Implements the Image/Color/Color Picker command.
ColorPicker() - Constructor for class ij.plugin.ColorPicker
 
ColorProcessor - Class in ij.process
This is an 32-bit RGB image and methods that operate on that image..
ColorProcessor(Image) - Constructor for class ij.process.ColorProcessor
Creates a ColorProcessor from an AWT Image or BufferedImage.
ColorProcessor(int, int) - Constructor for class ij.process.ColorProcessor
Creates a blank ColorProcessor of the specified dimensions.
ColorProcessor(int, int, int[]) - Constructor for class ij.process.ColorProcessor
Creates a ColorProcessor from a pixel array.
Colors - Class in ij.plugin
This plugin implements most of the Edit/Options/Colors command.
Colors() - Constructor for class ij.plugin.Colors
 
colors - Static variable in class ij.plugin.Colors
 
colors - Static variable in class ij.util.PlotterUtils
 
ColorStatistics - Class in ij.process
RGB image statistics, including histogram.
ColorStatistics(ImageProcessor) - Constructor for class ij.process.ColorStatistics
Construct an ImageStatistics object from a ColorProcessor using the standard measurement options (area, mean, mode, min and max).
ColorStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.ColorStatistics
Constructs a ColorStatistics object from a ColorProcessor using the specified measurement options.
ColorThresholder - Class in ij.plugin.frame
Selects pixels according to hsb or rgb components.
ColorThresholder() - Constructor for class ij.plugin.frame.ColorThresholder
 
colorToString(Color) - Static method in class ij.plugin.Colors
Converts a Color into a string ("red", "green", #aa55ff, etc.).
colorToString2(Color) - Static method in class ij.plugin.Colors
Converts a Color into a string ("Red", "Green", #aa55ff, etc.).
COLUMN_IN_USE - Static variable in class ij.measure.ResultsTable
 
COLUMN_NOT_FOUND - Static variable in class ij.measure.ResultsTable
 
columnExists(int) - Method in class ij.measure.ResultsTable
Returns true if the specified column exists and is not empty.
com.jmatio.common - package com.jmatio.common
 
com.jmatio.io - package com.jmatio.io
 
com.jmatio.types - package com.jmatio.types
 
combineHorizontally(ImageStack, ImageStack) - Method in class ij.plugin.StackCombiner
 
combineVertically(ImageStack, ImageStack) - Method in class ij.plugin.StackCombiner
 
COMMAND_IN_USE - Static variable in class ij.Menus
 
COMMAND_NOT_FOUND - Static variable in class ij.Menus
 
commandExecuting(String) - Method in interface ij.CommandListener
 
commandExecuting(String) - Method in class ij.plugin.frame.Jython_Console
 
commandExecuting(String) - Method in class ij.plugin.Orthogonal_Views
 
CommandFinder - Class in ij.plugin
 
CommandFinder() - Constructor for class ij.plugin.CommandFinder
 
commandInUse(String) - Static method in class ij.Menus
 
CommandListener - Interface in ij
Plugins that implement this interface are notified when ImageJ is about to run a menu command.
CommandLister - Class in ij.plugin
Lists ImageJ commands or keyboard shortcuts in a text window.
CommandLister() - Constructor for class ij.plugin.CommandLister
 
commandPrefix - Static variable in class ij.plugin.MacroInstaller
 
Commands - Class in ij.plugin
Runs miscellaneous File and Window menu commands.
Commands() - Constructor for class ij.plugin.Commands
 
Comment - Class in org.javaabf
A class that represents a comment in an electrophysiological file (particularly of one of the .abf types).
Comment(Object, Object) - Constructor for class org.javaabf.Comment
 
COMMENT_PATTERN - Static variable in class org.javaabf.Epoch
 
comments - Variable in class ij.wave.Wave
 
Comments - Class in org.javaabf
A class that tracks a collection of electrophysiological comments.
Comments() - Constructor for class org.javaabf.Comments
 
commentsList - Variable in class org.javaabf.Comments
 
compareTo(Object) - Method in class ij.wave.WaveMarker
 
compareTo(Object) - Method in class org.javaabf.Comment
 
compareTo(Object) - Method in class org.javaabf.Tag
 
Compiler - Class in ij.plugin
Compiles and runs plugins using the javac compiler.
Compiler() - Constructor for class ij.plugin.Compiler
 
componentHidden(ComponentEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
componentMoved(ComponentEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
componentResized(ComponentEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
componentShown(ComponentEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
COMPOSITE - Static variable in class ij.CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
COMPOSITE - Static variable in class ij.gui.Roi
 
COMPOSITE - Static variable in class ij.IJ
Image display modes
CompositeConverter - Class in ij.plugin
This plugin implements the Image/Color/Make Composite command.
CompositeConverter() - Constructor for class ij.plugin.CompositeConverter
 
CompositeImage - Class in ij
 
CompositeImage(ImagePlus) - Constructor for class ij.CompositeImage
 
CompositeImage(ImagePlus, int) - Constructor for class ij.CompositeImage
 
compositeImage - Variable in class ij.ImagePlus
 
COMPOUND_FILTER - Static variable in class ij.Undo
 
COMPOUND_FILTER_DONE - Static variable in class ij.Undo
 
compression - Variable in class ij.io.FileInfo
 
COMPRESSION - Static variable in class ij.io.TiffDecoder
 
COMPRESSION_NONE - Static variable in class ij.io.FileInfo
 
COMPRESSION_UNKNOWN - Static variable in class ij.io.FileInfo
 
concatenate(ImagePlus, ImagePlus, boolean) - Method in class ij.plugin.Concatenator
 
concatenate(ImagePlus[], boolean) - Method in class ij.plugin.Concatenator
 
concatenateHyperstacks(ImagePlus[], String, boolean) - Method in class ij.plugin.Concatenator
 
Concatenator - Class in ij.plugin
This plugin, which concatenates two or more images or stacks, implements the Image/Stacks/Tools/Concatenate command.
Concatenator() - Constructor for class ij.plugin.Concatenator
 
Configuration_ - Class in org.jah
 
Configuration_() - Constructor for class org.jah.Configuration_
 
conjugateMultiply(FHT) - Method in class ij.process.FHT
Returns the image resulting from the point by point Hartley conjugate multiplication of this image and the specified image.
connect() - Static method in class org.jah.PhysImageServerProxy
 
console - Variable in class ij.plugin.frame.Jython_Console
 
ConsoleInputStream - Class in ij.io
Data written to this will be displayed into the console
ConsoleInputStream(Jython_Console) - Constructor for class ij.io.ConsoleInputStream
 
ConsoleOutputStream - Class in ij.io
Data written to this will be displayed into the console
ConsoleOutputStream(Jython_Console) - Constructor for class ij.io.ConsoleOutputStream
 
consolePush(String) - Method in class ij.plugin.frame.Jython_Console
Executes and DOES copy to the GUI the command passed as argument.
consolePush(String, boolean, boolean) - Method in class ij.plugin.frame.Jython_Console
The function that passes the command to be executed.
constrain - Variable in class ij.gui.Roi
 
CONSTRUCTING - Static variable in class ij.gui.Roi
 
contains(int, int) - Method in class ij.gui.Arrow
 
contains(int, int) - Method in class ij.gui.LayoutComponent
 
contains(int, int) - Method in class ij.gui.Line
 
contains(int, int) - Method in class ij.gui.OvalRoi
Tests if the specified point is inside the boundary of this OvalRoi.
contains(Roi) - Method in class ij.gui.Overlay
Returns 'true' if this Overlay contains the specified Roi.
contains(int, int) - Method in class ij.gui.PointRoi
Returns true if (x,y) is one of the points in this collection.
contains(int, int) - Method in class ij.gui.PolygonRoi
 
contains(int, int) - Method in class ij.gui.Roi
 
contains(int, int) - Method in class ij.gui.ShapeRoi
Checks whether the specified coordinates are inside a on this ROI's shape boundaries.
contains(float, float) - Method in class ij.process.FloatPolygon
Returns 'true' if the point (x,y) is inside this polygon.
contains(int, int) - Method in class ij.wave.WaveMarker
 
contents - Variable in class ij.wave.Wave
 
contentToString() - Method in class com.jmatio.types.MLArray
 
contentToString() - Method in class com.jmatio.types.MLCell
 
contentToString() - Method in class com.jmatio.types.MLChar
 
contentToString() - Method in class com.jmatio.types.MLNumericArray
 
contentToString() - Method in class com.jmatio.types.MLSparse
 
contentToString() - Method in class com.jmatio.types.MLStructure
 
CONTINUE - Static variable in interface ij.macro.MacroConstants
 
Continuous_Gaussian_Pulse_Runner - Class in org.jah
 
Continuous_Gaussian_Pulse_Runner() - Constructor for class org.jah.Continuous_Gaussian_Pulse_Runner
 
Continuous_Uniform_Pulse_Runner - Class in org.jah
 
Continuous_Uniform_Pulse_Runner() - Constructor for class org.jah.Continuous_Uniform_Pulse_Runner
 
ContrastAdjuster - Class in ij.plugin.frame
This plugin implements the Brightness/Contrast, Window/level and Color Balance commands, all in the Image/Adjust sub-menu.
ContrastAdjuster() - Constructor for class ij.plugin.frame.ContrastAdjuster
 
ContrastEnhancer - Class in ij.plugin
Implements ImageJ's Process/Enhance Contrast command.
ContrastEnhancer() - Constructor for class ij.plugin.ContrastEnhancer
 
controlKeyDown() - Static method in class ij.IJ
Returns true if the control key is down.
ControlPanel - Class in ij.plugin
ControlPanel.
ControlPanel() - Constructor for class ij.plugin.ControlPanel
 
controlPanel() - Method in class ij.plugin.frame.SyncWindows
Build window list display and button controls.
convert(String) - Method in class ij.plugin.Converter
Converts the ImagePlus to the specified image type.
convert(ImageProcessor) - Method in class ij.plugin.filter.ThresholdToSelection
 
convert(int) - Method in class ij.process.MedianCut
Uses Heckbert's median-cut algorithm to divide the color space defined by "hist" into "maxcubes" cubes.
CONVERT_TO_FLOAT - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag to have the ImageProcessor that is passed to the run() method converted to a FloatProcessor.
convertAvailableComponentsToChoices(Vector) - Method in class ij.plugin.frame.LayoutPanel
 
Converter - Class in ij.plugin
Implements the conversion commands in the Image/Type submenu.
Converter() - Constructor for class ij.plugin.Converter
 
convertGrayJpegTo8Bits(ImagePlus) - Static method in class ij.io.Opener
If the specified image is grayscale, convert it to 8-bits.
convertHSBToRGB() - Method in class ij.process.ImageConverter
Converts a 3-slice (hue, saturation, brightness) 8-bit stack to RGB.
convertHyperstack(ImagePlus, ImagePlus) - Method in class ij.plugin.RGBStackConverter
 
convertImagesToStack() - Method in class ij.plugin.ImagesToStack
 
convertImagesToStack() - Method in class ij.plugin.StackEditor
 
convertIndexToPosition(int) - Method in class ij.ImagePlus
Converts the stack index 'n' (one-based) into a hyperstack position (channel, slice, frame).
convertOutputType(Variable, Object) - Static method in class ij.macro.ExtensionDescriptor
 
convertRGBStackToRGB() - Method in class ij.process.ImageConverter
Converts a 2 or 3 slice 8-bit stack to RGB.
convertRGBtoIndexedColor(int) - Method in class ij.process.ImageConverter
Converts an RGB image to 8-bits indexed color.
convertShortcutToCode(String) - Static method in class ij.Menus
 
convertStackToImages(ImagePlus) - Method in class ij.plugin.StackEditor
 
convertToByte(boolean) - Method in class ij.process.ImageProcessor
Returns an 8-bit version of this image as a ByteProcessor.
convertToByte(int) - Method in class ij.process.MedianCut
This is a version of convert that returns a ByteProcessor.
convertToByte() - Method in class ij.process.TypeConverter
Converts processor to a ByteProcessor.
convertToByteProcessor() - Method in class ij.process.ImageProcessor
Returns an 8-bit version of this image as a ByteProcessor. 16-bit and 32-bit pixel data are scaled from min-max to 0-255.
convertToByteProcessor(boolean) - Method in class ij.process.ImageProcessor
Returns an 8-bit version of this image as a ByteProcessor. 16-bit and 32-bit pixel data are scaled from min-max to 0-255 if 'scale' is true.
convertToColorProcessor() - Method in class ij.process.ImageProcessor
Returns an RGB version of this image as a ColorProcessor.
convertToFloat() - Method in class ij.ImageStack
Creates a float version of this stack.
convertToFloat() - Method in class ij.process.ImageProcessor
Returns a 32-bit float version of this image as a FloatProcessor.
convertToFloat(float[]) - Method in class ij.process.TypeConverter
Converts processor to a FloatProcessor.
convertToFloatProcessor() - Method in class ij.process.ImageProcessor
Returns a 32-bit float version of this image as a FloatProcessor.
convertToGray16() - Method in class ij.process.ImageConverter
Converts this ImagePlus to 16-bit grayscale.
convertToGray16() - Method in class ij.process.StackConverter
Converts this Stack to 16-bit grayscale.
convertToGray32() - Method in class ij.process.ImageConverter
Converts this ImagePlus to 32-bit grayscale.
convertToGray32() - Method in class ij.process.StackConverter
Converts this Stack to 32-bit (float) grayscale.
convertToGray32(ImagePlus) - Static method in class org.jah.JAH_Utils
A utility function for converting an ImagePlus image or stack of images to 32-bit.
convertToGray8() - Method in class ij.process.ImageConverter
Converts this ImagePlus to 8-bit grayscale.
convertToGray8() - Method in class ij.process.StackConverter
Converts this Stack to 8-bit grayscale.
convertToHSB() - Method in class ij.process.ImageConverter
Converts an RGB image to a HSB (hue, saturation and brightness) stack.
convertToHSBHyperstack() - Method in class ij.process.StackConverter
Converts the stack (which must be RGB) to a 3 channel (hue, saturation and brightness) hyperstack.
convertToIndexedColor(int) - Method in class ij.process.StackConverter
Converts the stack to 8-bits indexed color.
convertToRGB(ImagePlus) - Static method in class ij.plugin.RGBStackConverter
Converts the specified multi-channel (composite) image to RGB.
convertToRGB() - Method in class ij.process.ImageConverter
Converts this ImagePlus to RGB.
convertToRGB() - Method in class ij.process.ImageProcessor
Returns an RGB version of this image as a ColorProcessor.
convertToRGB() - Method in class ij.process.StackConverter
Converts the Stack to RGB.
convertToRGB() - Method in class ij.process.TypeConverter
Converts processor to a ColorProcessor.
convertToRGBHyperstack() - Method in class ij.process.StackConverter
Converts the stack (which must be RGB) to a 3 channel (red, green and blue) hyperstack.
convertToRGBStack() - Method in class ij.process.ImageConverter
Converts an RGB image to an RGB (red, green and blue) stack.
convertToShort(boolean) - Method in class ij.process.ImageProcessor
Returns a 16-bit version of this image as a ShortProcessor.
convertToShort() - Method in class ij.process.TypeConverter
Converts processor to a ShortProcessor.
convertToShortProcessor() - Method in class ij.process.ImageProcessor
Returns a 16-bit version of this image as a ShortProcessor. 32-bit pixel data are scaled from min-max to 0-255.
convertToShortProcessor(boolean) - Method in class ij.process.ImageProcessor
Returns a 16-bit version of this image as a ShortProcessor. 32-bit pixel data are scaled from min-max to 0-255 if 'scale' is true.
convertVariable(Interpreter, int, Variable) - Static method in class ij.macro.ExtensionDescriptor
 
convertVectorToDoubleArray(Vector) - Method in class org.javaabf.ABF18_parser
 
convertVectorToDoubleArray(Vector) - Method in class org.javaabf.ABF2_parser
 
convertVectorToDoubleArray(Vector) - Static method in class org.javaabf.ABF_utils
 
convertVectorToIntArray(Vector) - Method in class org.javaabf.ABF18_parser
 
convertVectorToIntArray(Vector) - Method in class org.javaabf.ABF2_parser
 
convertVectorToIntArray(Vector) - Static method in class org.javaabf.ABF_utils
 
convertVectorToStringArray(Vector) - Method in class org.javaabf.ABF18_parser
 
convertVectorToStringArray(Vector) - Method in class org.javaabf.ABF2_parser
 
convertVectorToStringArray(Vector) - Static method in class org.javaabf.ABF_utils
 
convolve(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
Convolves ip with a kernel of width kw and height kh.
convolve(float[], int, int) - Method in class ij.process.ByteProcessor
Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ColorProcessor
Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.FloatProcessor
Performs a convolution operation using the specified kernel.
CONVOLVE - Static variable in class ij.process.ImageProcessor
 
convolve(float[], int, int) - Method in class ij.process.ImageProcessor
Performs a convolution operation using the specified kernel.
convolve(float[], int, int) - Method in class ij.process.ShortProcessor
Performs a convolution operation using the specified kernel.
convolve(Wave) - Method in class ij.wave.Wave
 
convolve(double[]) - Method in class ij.wave.Wave
 
convolve(Wave) - Method in class ij.wave.Waves
Convolves each Wave in this instance with the Wave passed as argument.
convolve3x3(int[]) - Method in class ij.process.ByteProcessor
 
convolve3x3(int[]) - Method in class ij.process.ColorProcessor
3x3 convolution contributed by Glynne Casteel.
convolve3x3(int[]) - Method in class ij.process.FloatProcessor
Does 3x3 convolution.
convolve3x3(int[]) - Method in class ij.process.ImageProcessor
Convolves the image or ROI with the specified 3x3 integer convolution kernel.
convolve3x3(int[]) - Method in class ij.process.ShortProcessor
Does 3x3 convolution.
convolveFloat(ImageProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
Convolves the float image ip with a kernel of width kw and height kh.
convolveFloat1D(FloatProcessor, float[], int, int) - Method in class ij.plugin.filter.Convolver
Convolves the image ip with a kernel of width kw and height kh.
convolveFloat1D(FloatProcessor, float[], int, int, double) - Method in class ij.plugin.filter.Convolver
Convolves the image ip with a kernel of width kw and height kh.
Convolver - Class in ij.plugin.filter
This plugin convolves images using user user defined kernels.
Convolver() - Constructor for class ij.plugin.filter.Convolver
 
COORDINATES - Static variable in class ij.io.RoiDecoder
 
copy - Variable in class ij.gui.HistogramWindow
 
copy(boolean) - Method in class ij.gui.ImageWindow
Copies the current ROI to the clipboard.
copy() - Method in class ij.ImagePlus
Copies the contents of the current selection, or the entire image if there is no selection, to the internal clipboard.
copy(boolean) - Method in class ij.ImagePlus
Copies the contents of the current selection to the internal clipboard.
copy() - Method in class ij.measure.Calibration
Returns a clone of this object.
COPY - Static variable in interface ij.process.Blitter
dst=src
COPY_INVERTED - Static variable in interface ij.process.Blitter
dst=255-src (8-bits and RGB)
COPY_TRANSPARENT - Static variable in interface ij.process.Blitter
Copies with white pixels transparent.
COPY_ZERO_TRANSPARENT - Static variable in interface ij.process.Blitter
Copies with zero pixels transparent.
copyAttributes(Roi) - Method in class ij.gui.Roi
Copy the attributes (outline color, fill color, outline width) of 'roi2' to the this selection.
copyAttributes(ImagePlus) - Method in class ij.ImagePlus
Copies attributes (name, ID, calibration, path) of the specified image to this image.
copyBits(ImageProcessor, int, int, int) - Method in interface ij.process.Blitter
Copies the image in 'src' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteBlitter
Copies the byte image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ByteProcessor
Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorBlitter
Copies the RGB image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ColorProcessor
Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatBlitter
Copies the float image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.FloatProcessor
Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ImageProcessor
Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortBlitter
Copies the 16-bit image in 'ip' to (x,y) using the specified mode.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.ShortProcessor
Copies the image contained in 'ip' to (xloc, yloc) using one of the transfer modes defined in the Blitter interface.
copyBits(ImageProcessor, int, int, int) - Method in class ij.process.StackProcessor
 
copyBits(ImageStack, int, int, int) - Method in class ij.process.StackProcessor
 
copyColumnHeaders - Static variable in class ij.Prefs
Include column headers when copying tables to clipboard.
copyFile(File, File) - Static method in class ij.macro.Functions
 
copyLuts(ImagePlus) - Method in class ij.CompositeImage
Copies the LUTs and display mode of 'imp' to this image.
copyScale(ImagePlus) - Method in class ij.ImagePlus
Copies the calibration of the specified image to this image.
copySelectedAsText() - Method in class ij.plugin.frame.WaveManager
 
copySelectedAsText(String, int) - Method in class ij.plugin.frame.WaveManager
 
copySelection() - Method in class ij.text.TextPanel
Copies the current selection to the system clipboard.
copyToClipboard() - Method in class ij.gui.HistogramWindow
 
CORNER_DIAMETER - Static variable in class ij.gui.Toolbar
 
correlationThreshold - Variable in class ij.wave.ClusterHints
 
COS - Static variable in interface ij.macro.MacroConstants
 
count - Variable in class ij.gui.HistogramWindow
 
COUNT - Static variable in class ij.plugin.filter.MaximumFinder
Do not create an image, just count maxima and add count to Results table
create(int, int, int, int) - Static method in class ij.ImageStack
Creates a new ImageStack.
create(String, String) - Method in class ij.plugin.frame.Editor
 
create8BitImage() - Method in class ij.process.FloatProcessor
 
createArray(int, int) - Method in interface com.jmatio.types.GenericArrayCreator
 
createArray(int, int) - Method in class com.jmatio.types.MLChar
 
createArray(int, int) - Method in class com.jmatio.types.MLDouble
 
createArray(int, int) - Method in class com.jmatio.types.MLInt16
 
createArray(int, int) - Method in class com.jmatio.types.MLInt32
 
createArray(int, int) - Method in class com.jmatio.types.MLInt64
 
createArray(int, int) - Method in class com.jmatio.types.MLInt8
 
createArray(int, int) - Method in class com.jmatio.types.MLSingle
 
createArray(int, int) - Method in class com.jmatio.types.MLSparse
 
createArray(int, int) - Method in class com.jmatio.types.MLUInt64
 
createArray(int, int) - Method in class com.jmatio.types.MLUInt8
 
createBlankImage(int, int) - Static method in class ij.gui.GUI
Creates a white AWT Image image of the specified size.
createByteImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
 
createColorModel(FileInfo) - Method in class ij.io.FileOpener
Returns an IndexColorModel for the image specified by this FileInfo.
createComment(String) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
createComposite(int, int, int, ImageStack[], boolean) - Method in class ij.plugin.RGBStackMerge
Deprecated; replaced by mergeChannels().
createContentsBufferIfNecessary() - Method in class ij.wave.Wave
 
createDoubleBuffer() - Method in class ij.plugin.frame.LayoutPanel
 
createEmptyStack() - Method in class ij.ImagePlus
Returns an empty image stack that has the same width, height and color table as this image.
createFloatImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
 
createGrayscaleColorModel(boolean) - Static method in class ij.LookUpTable
 
createHeader() - Static method in class com.jmatio.io.MatFileHeader
A factory.
createHyperStack(String, int, int, int, int, int, int) - Static method in class ij.IJ
Creates a new hyperstack.
createHyperStack(String, int, int, int, int) - Method in class ij.ImagePlus
This method has been replaced by IJ.createHyperStack().
createImage(String, int, int, int, int, int) - Static method in class ij.gui.NewImage
 
createImage(String, int, int, int, int) - Static method in class ij.IJ
Creates a new image.
createImage(String, String, int, int, int) - Static method in class ij.IJ
Creates a new imagePlus.
createImage(String, String, int, int, int, int, int) - Static method in class ij.IJ
Creates a new hyperstack.
createImage(IndexColorModel) - Static method in class ij.plugin.LutLoader
Creates a 256x32 image from an IndexColorModel.
createImage() - Method in class ij.process.ByteProcessor
 
createImage() - Method in class ij.process.ColorProcessor
 
createImage() - Method in class ij.process.FloatProcessor
Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImage() - Method in class ij.process.ImageProcessor
Returns a copy of this image is the form of an AWT Image.
createImage() - Method in class ij.process.ShortProcessor
Create an 8-bit AWT image by scaling pixels in the range min-max to 0-255.
createImagePlus() - Method in class ij.ImagePlus
Returns a new ImagePlus with this image's attributes (e.g. spatial scale), but no image.
createInputStream(FileInfo) - Method in class ij.io.FileOpener
Returns an InputStream for the image described by this FileInfo.
createInvertedLut() - Method in class ij.process.LUT
 
createLut() - Method in class ij.ImagePlus
Creates a LookUpTable object that corresponds to this image.
createLutFromColor(Color) - Method in class ij.CompositeImage
 
createLutFromColor(Color) - Static method in class ij.process.LUT
Creates a color LUT from a Color.
createMacro(String, String) - Method in class ij.plugin.frame.Editor
 
createMacro(String) - Method in class ij.plugin.NewPlugin
 
createNewRoi(int, int) - Method in class ij.ImagePlus
Starts the process of creating a new selection, where sx and sy are the starting screen coordinates.
createOverlay() - Static method in class ij.plugin.OverlayLabels
Creates an empty Overlay that has the current label settings.
createPlugin(String, int, String) - Method in class ij.plugin.NewPlugin
 
createProcessor(int, int) - Method in class ij.process.ByteProcessor
Returns a new, blank ByteProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ColorProcessor
Returns a new, blank ColorProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.FloatProcessor
Returns a new, blank FloatProcessor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ImageProcessor
Returns a new, blank processor with the specified width and height.
createProcessor(int, int) - Method in class ij.process.ShortProcessor
Returns a new, blank ShortProcessor with the specified width and height.
createRGBImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
 
createShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
Creates an unsigned short image.
createSubtitle() - Method in class ij.gui.ImageWindow
Creates the subtitle.
createSubtitle() - Method in class ij.gui.StackWindow
 
createTableFromImage(ImageProcessor) - Static method in class ij.measure.ResultsTable
Creates a ResultsTable from an image or image selection.
createTableModel(String) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
createThreadArray(int) - Static method in class ij.util.ThreadUtil
 
createThreadArray() - Static method in class ij.util.ThreadUtil
 
createUnsignedShortImage(String, int, int, int, int) - Static method in class ij.gui.NewImage
Deprecated. Short images are always unsigned.
createWindow() - Method in class ij.gui.ProfilePlot
Displays this profile plot in a window.
crop(Rectangle) - Method in class ij.gui.Overlay
 
crop(int, int) - Method in class ij.gui.Overlay
Removes ROIs having positions outside of the interval defined by firstSlice and lastSlice.
crop(int, int, int, int, int, int) - Method in class ij.gui.Overlay
Removes ROIs having a C, Z or T coordinate outside the volume defined by firstC, lastC, firstZ, lastZ, firstT and lastT.
crop(int, int, int, int, int, int) - Method in class ij.ImageStack
Creates a new stack by cropping this one.
crop() - Method in class ij.process.ByteProcessor
 
crop() - Method in class ij.process.ColorProcessor
 
crop() - Method in class ij.process.FloatProcessor
 
crop() - Method in class ij.process.ImageProcessor
Creates a new processor containing an image that corresponds to the current ROI.
crop() - Method in class ij.process.ShortProcessor
 
crop(int, int, int, int) - Method in class ij.process.StackProcessor
Crops the stack to the specified rectangle.
cropOverlay(Overlay, Rectangle) - Static method in class ij.plugin.Duplicator
 
CROSS - Static variable in class ij.gui.Plot
Display points using an cross-shaped mark.
CROSS - Static variable in class ij.gui.PlotWindow
Display points using an cross-shaped mark.
crosscorrelate(Wave, Wave, double) - Static method in class ij.wave.ClusterUtils
 
crosscorrelate(double[], double[], int) - Static method in class ij.wave.ClusterUtils
 
crosscorrelate(Wave[], boolean, double) - Static method in class ij.wave.ClusterUtils
 
crosscorrelate(double[], double[], int) - Static method in class ij.wave.CrosscorrelationWave
 
crosscorrelate(Wave, Wave, double) - Static method in class ij.wave.CrosscorrelationWave
 
CROSSCORRELATION_TYPE - Static variable in class ij.wave.Wave
 
CrosscorrelationWave - Class in ij.wave
 
CrosscorrelationWave(double[]) - Constructor for class ij.wave.CrosscorrelationWave
 
CrosscorrelationWave(Wave) - Constructor for class ij.wave.CrosscorrelationWave
 
CrosscorrelationWave(Wave, Wave, double) - Constructor for class ij.wave.CrosscorrelationWave
 
CrosscorrelationWave(Wave, Wave, double, Roi, Roi) - Constructor for class ij.wave.CrosscorrelationWave
 
CROSSHAIR - Static variable in class ij.gui.Toolbar
 
crosshairCursor - Static variable in class ij.gui.ImageCanvas
 
cScaling - Variable in class ij.plugin.frame.SyncWindows
Checkboxes for user control.
cSelector - Variable in class ij.gui.StackWindow
 
cSlice - Variable in class ij.plugin.frame.SyncWindows
Checkboxes for user control.
CTA_Utils - Class in ij.wave
 
CTA_Utils() - Constructor for class ij.wave.CTA_Utils
 
cTable - Variable in class ij.process.ImageProcessor
 
CTZ - Static variable in class ij.plugin.HyperStackConverter
 
cubic(double) - Static method in class ij.process.ImageProcessor
 
currentMemory() - Static method in class ij.IJ
Returns the amount of memory currently being used by ImageJ.
currentSlice - Variable in class ij.ImagePlus
 
cursorOverImage() - Method in class ij.gui.ImageCanvas
Returns 'true' if the cursor is over this image.
CurveFitter - Class in ij.measure
Curve fitting class based on the Simplex method in the Minimizer class Notes on fitting polynomial functions: (i) The range of x values should not be too far from 0, especially for higher-order polynomials.
CurveFitter(double[], double[]) - Constructor for class ij.measure.CurveFitter
Construct a new CurveFitter.
CUSTOM - Static variable in class ij.io.Opener
 
CUSTOM - Static variable in class ij.measure.Calibration
 
CUSTOM1 - Static variable in class ij.gui.Toolbar
 
CUSTOM2 - Static variable in class ij.gui.Toolbar
 
CUSTOM3 - Static variable in class ij.gui.Toolbar
 
CUSTOM4 - Static variable in class ij.gui.Toolbar
 
CUSTOM5 - Static variable in class ij.gui.Toolbar
 
CUSTOM6 - Static variable in class ij.gui.Toolbar
 
CUSTOM7 - Static variable in class ij.gui.Toolbar
 
CustomWave - Class in ij.wave
 
CustomWave() - Constructor for class ij.wave.CustomWave
 
cx - Variable in class ij.process.ImageProcessor
 
cy - Variable in class ij.process.ImageProcessor
 
CZT - Static variable in class ij.plugin.HyperStackConverter
 

D

d2s(double) - Static method in class ij.IJ
Converts a number to a formatted string using 2 digits to the right of the decimal point.
d2s(double, int) - Static method in class ij.IJ
Converts a number to a rounded formatted string.
d2s(double, int, int) - Static method in class ij.IJ
Converts a number to a rounded formatted string.
D2S - Static variable in interface ij.macro.MacroConstants
 
d2s(double, int) - Static method in class ij.measure.ResultsTable
This is a version of IJ.d2s() that uses scientific notation for small numbes that would otherwise display as zero.
DARK_BACKGROUND - Static variable in class ij.plugin.frame.ThresholdAdjuster
 
darkBlue - Static variable in class ij.plugin.filter.Analyzer
 
DATE_TIME - Static variable in class ij.io.TiffDecoder
 
DEBUG - Static variable in class ij.ImageJ
Run ImageJ in debug mode.
DEBUG - Static variable in interface ij.macro.MacroConstants
 
debug(Interpreter, int) - Method in class ij.plugin.frame.Editor
 
debug(String) - Method in class ij.plugin.frame.LayoutPanel
 
debug - Variable in class org.javaabf.ABF
 
DEBUG_LOC_KEY - Static variable in class ij.text.TextWindow
 
debugInfo - Variable in class ij.io.FileInfo
 
debugMode - Static variable in class ij.IJ
Use setDebugMode(boolean) to enable/disable debug mode.
debugMode - Variable in class ij.io.TiffDecoder
 
decimalPlaces - Variable in class ij.gui.HistogramWindow
 
decimate(int) - Method in class ij.wave.Wave
 
decimateSelectedWaves() - Method in class ij.plugin.frame.WaveManager
 
decimateSelectedWaves(int) - Method in class ij.plugin.frame.WaveManager
 
decode(String, Color) - Static method in class ij.plugin.Colors
 
decodeDescriptionString(FileInfo) - Method in class ij.io.FileOpener
 
decodeToken(int) - Method in class ij.macro.Program
 
DEFAULT_FLAGS - Static variable in class ij.gui.Plot
the default flags
DEFAULT_JPEG_QUALITY - Static variable in class ij.io.FileSaver
 
DEFAULT_PORT - Static variable in class ij.ImageJ
Address of socket where Image accepts commands
DEFAULT_QUALITY - Static variable in class ij.plugin.JpegWriter
 
DEFAULT_VALUE_UNIT - Static variable in class ij.measure.Calibration
 
defaultColorModel - Static variable in class ij.process.ImageProcessor
 
defaultCursor - Static variable in class ij.gui.ImageCanvas
 
defaultDirectory - Static variable in class ij.gui.HistogramWindow
 
defaultFillColor - Static variable in class ij.gui.Roi
 
defaultText - Variable in class ij.gui.GenericDialog
 
defaultValues - Variable in class ij.gui.GenericDialog
 
degreeSymbol - Static variable in class ij.IJ
 
delete(int) - Method in class ij.plugin.frame.RoiManager
 
delete(boolean) - Method in class ij.plugin.frame.RoiManager
 
delete(int) - Method in class ij.plugin.frame.WaveManager
 
deleteAll() - Method in class ij.plugin.frame.RoiManager
 
deleteAll() - Method in class ij.plugin.frame.WaveManager
 
deleteHandle(double, double) - Method in class ij.gui.PolygonRoi
 
deleteLastSlice() - Method in class ij.ImageStack
Deletes the last slice in the stack.
deleteLastSlice() - Method in class ij.VirtualStack
Deletes the last slice in the stack.
deleteRoi() - Method in class ij.ImagePlus
Deletes the current region of interest.
deleteRow(int) - Method in class ij.measure.ResultsTable
Deletes the specified row.
deleteRows(int, int) - Static method in class ij.IJ
Deletes 'row1' through 'row2' of the "Results" window.
deleteSelected() - Method in class ij.plugin.frame.RoiManager
 
deleteSelected() - Method in class ij.plugin.frame.WaveManager
 
deleteSlice(int) - Method in class ij.ImageStack
Deletes the specified slice, were 1<=n<=nslices.
deleteSlice(int) - Method in class ij.plugin.AVI_Reader
Deletes the specified image from this virtual stack (if it is one), where 1<=n<=nslices.
deleteSlice(int) - Method in class ij.plugin.FileInfoVirtualStack
Deletes the specified image, were 1<=n<=nImages.
deleteSlice(int) - Method in class ij.plugin.ListVirtualStack
Deletes the specified image, were 1<=n<=nslices.
deleteSlice(int) - Method in class ij.VirtualStack
Deletes the specified slice, were 1<=n<=nslices.
DESCENDING - Static variable in class ij.wave.Burst
 
description - Variable in class ij.io.FileInfo
 
deselect(int) - Method in class ij.plugin.frame.RoiManager
 
deselect(String) - Method in class ij.plugin.frame.WaveManager
 
deselect(int) - Method in class ij.plugin.frame.WaveManager
 
deselectAll() - Method in class ij.plugin.frame.Layout
 
deselectAll() - Method in class ij.plugin.frame.LayoutPanel
 
deselectAll() - Method in class ij.plugin.frame.RoiManager
 
deselectAll() - Method in class ij.plugin.frame.WaveManager
 
deselectLayoutComponent(LayoutComponent) - Method in class ij.plugin.frame.Layout
 
deselectLayoutComponent(LayoutComponent) - Method in class ij.plugin.frame.LayoutPanel
 
deserialize(byte[]) - Method in class ij.io.Opener
Deserialize a byte array that was serialized using the FileSaver.serialize().
DESPECKLE - Static variable in class ij.plugin.filter.RankFilters
 
destroy() - Method in class ij.ImageJApplet
 
dfht3(float[], int, boolean, int) - Method in class ij.process.FHT
Performs an optimized 1D FHT.
DIALOG - Static variable in interface ij.macro.MacroConstants
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in interface ij.gui.DialogListener
This method is invoked by a Generic Dialog if any of the inputs have changed (CANCEL does not trigger it; OK and running the dialog from a macro only trigger the first DialogListener added to a GenericDialog).
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.AppearanceOptions
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.BackgroundSubtracter
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Binary
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Convolver
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.GaussianBlur
Listener to modifications of the input fields of the dialog
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.ImageMath
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.MaximumFinder
Read the parameters (during preview or after showing the dialog)
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.PlugInFilterRunner
The listener to any change in the dialog.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.RankFilters
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Rotator
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.StackLabeler
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.Translator
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.filter.UnsharpMask
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.HyperStackReducer
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.OverlayLabels
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RectToolOptions
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.RGBStackConverter
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class ij.plugin.SpecifyROI
 
DialogListener - Interface in ij.gui
PlugIns or PlugInFilters that want to listen to changes in a GenericDialog without adding listeners for each dialog field should implementthis method.
DICOM - Static variable in class ij.io.FileInfo
 
DICOM - Static variable in class ij.io.Opener
 
DICOM - Class in ij.plugin
This plugin decodes DICOM files.
DICOM() - Constructor for class ij.plugin.DICOM
Default constructor.
DICOM(InputStream) - Constructor for class ij.plugin.DICOM
Constructs a DICOM reader that using an InputStream.
DICOM(BufferedInputStream) - Constructor for class ij.plugin.DICOM
Constructs a DICOM reader that using an BufferredInputStream.
DICOM_Sorter - Class in ij.plugin
 
DICOM_Sorter() - Constructor for class ij.plugin.DICOM_Sorter
 
DicomTools - Class in ij.util
DICOM utilities
DicomTools() - Constructor for class ij.util.DicomTools
 
DIFFERENCE - Static variable in interface ij.process.Blitter
dst=abs(dst-src)
differentiate() - Method in class ij.wave.Wave
 
differentiate() - Method in class ij.wave.Waves
Differentiates each Wave in this instance.
digits - Variable in class ij.gui.HistogramWindow
 
dilate() - Method in class ij.process.ByteProcessor
 
dilate(int, int) - Method in class ij.process.ByteProcessor
 
dilate() - Method in class ij.process.ColorProcessor
 
dilate() - Method in class ij.process.FloatProcessor
Not implemented.
dilate() - Method in class ij.process.ImageProcessor
Dilates the image or ROI using a 3x3 minimum filter.
dilate() - Method in class ij.process.ShortProcessor
Not implemented.
dimensionsSet - Variable in class ij.ImagePlus
 
dims - Variable in class com.jmatio.types.MLArray
 
DIR_IMAGE - Static variable in class ij.Prefs
 
DIRECT_BYTE_BUFFER - Static variable in class com.jmatio.io.MatFileReader
 
directory - Variable in class ij.io.FileInfo
 
DirectoryChooser - Class in ij.io
This class displays a dialog box that allows the user can select a directory.
DirectoryChooser(String) - Constructor for class ij.io.DirectoryChooser
Display a dialog using the specified title.
disableDensityCalibration() - Method in class ij.measure.Calibration
 
disablePathRecording() - Static method in class ij.plugin.frame.Recorder
Temporarily disables path recording.
disablePopupMenu(boolean) - Method in class ij.gui.ImageCanvas
Disable/enable popup menu.
disableRowLabels() - Method in class ij.measure.ResultsTable
Set the row label column to null if the column label is "Label".
disableUndo - Static variable in class ij.Prefs
Disable Edit/Undo command.
disconnect() - Static method in class org.jah.PhysImageServerProxy
 
dispatch(Functions) - Method in class ij.macro.ExtensionDescriptor
 
display(String, String) - Method in class ij.plugin.frame.Editor
 
DISPLAY_SUMMARY - Static variable in class ij.plugin.filter.ParticleAnalyzer
Display a summary.
displayChanged(DisplayChangeEvent) - Method in class ij.plugin.frame.SyncWindows
Method to pass on changes of the z-slice of a stack.
displayComplex - Static variable in class ij.plugin.FFT
 
displayFHT - Static variable in class ij.plugin.FFT
 
displayRanges - Variable in class ij.io.FileInfo
 
displayRawPS - Static variable in class ij.plugin.FFT
 
displayResults() - Method in class ij.plugin.filter.Analyzer
Writes the last row in the system results table to the Results window.
displaySummary - Variable in class ij.plugin.filter.ParticleAnalyzer
 
dispose() - Method in class com.jmatio.types.MLArray
 
dispose() - Method in class com.jmatio.types.MLNumericArray
 
distanceMeasures - Static variable in class ij.wave.ClusterUtils
 
Distribution - Class in ij.plugin
This plugin implements the Analyze/Distribution command.
Distribution() - Constructor for class ij.plugin.Distribution
 
DIV_BY_ZERO_VALUE - Static variable in class ij.Prefs
 
DIV_EQUAL - Static variable in interface ij.macro.MacroConstants
 
DIVIDE - Static variable in interface ij.process.Blitter
dst=dst/src
divide(FHT) - Method in class ij.process.FHT
Returns the image resulting from the point by point Hartley division of this image by the specified image.
divide(double) - Method in class ij.wave.Wave
Divides each element within this Wave by the value passed as argument and fires a waveChanged event.
divideByZeroValue - Static variable in class ij.process.FloatBlitter
 
dmode - Variable in class ij.process.ImageStatistics
 
DO - Static variable in interface ij.macro.MacroConstants
 
DO_COMMAND - Static variable in interface ij.macro.MacroConstants
 
DO_WAND - Static variable in interface ij.macro.MacroConstants
 
doCommand(String) - Static method in class ij.IJ
Starts executing a menu command in a separete thread and returns immediately.
doCustomFit(String, double[], boolean) - Method in class ij.measure.CurveFitter
Fit a function defined as a macro String like "y = a + b*x + c*x*x".
doCustomFit(UserFunction, int, String, double[], double[], boolean) - Method in class ij.measure.CurveFitter
Fit a function defined in a user plugin implementing the UserFunction interface Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
DOES_16 - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter handles 16-bit images.
DOES_32 - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter handles float images.
DOES_8C - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter handles 8-bit indexed color images.
DOES_8G - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter handles 8-bit grayscale images.
DOES_ALL - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter handles all types of images.
DOES_RGB - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter handles RGB images.
DOES_STACKS - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter wants its run() method to be called for all the slices in a stack.
doesNotHaveValueAbove(ImageProcessor, double) - Static method in class org.jah.JAH_Utils
 
doFit(int) - Method in class ij.measure.CurveFitter
Perform curve fitting with one of the built-in functions doFit(fitType) does the fit quietly Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doFit(int, boolean) - Method in class ij.measure.CurveFitter
Perform curve fitting with one of the built-in functions doFit(fitType, true) pops up a dialog allowing the user to set the initial fit parameters and various numbers controlling the Minimizer Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and getParams() to access the result.
doFit(int) - Method in class ij.plugin.frame.Fitter
Fit data in the textArea, show result in log and create plot.
doHyperStackProjection(boolean) - Method in class ij.plugin.ZProjector
 
domainAxis - Variable in class ij.plugin.frame.ChartFramePlugIn
 
doMath(ImagePlus, ImagePlus) - Method in class ij.plugin.FFTMath
 
done - Variable in class ij.gui.StackWindow
 
done() - Method in class ij.macro.Interpreter
 
DONE - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the filter does not want its run method called.
dontSaveHeaders - Static variable in class ij.Prefs
Don't save Results table column headers
dontSaveRowNumbers - Static variable in class ij.Prefs
Don't save Results table row numbers
doOptions() - Method in class ij.plugin.Profiler
 
doProjection() - Method in class ij.plugin.ZProjector
Performs actual projection using specified method.
doProjection(boolean) - Method in class ij.plugin.ZProjector
Performs actual projection using specified method.
doProjections(ImagePlus) - Method in class ij.plugin.filter.Projector
 
doRGBProjection() - Method in class ij.plugin.ZProjector
 
doRGBProjection(boolean) - Method in class ij.plugin.ZProjector
 
doRGBProjections(ImagePlus) - Method in class ij.plugin.filter.Projector
 
DOT - Static variable in class ij.gui.Plot
Display points using a single pixel.
DOUBLE_CLICK_THRESHOLD - Static variable in class ij.gui.Toolbar
 
DOUBLE_HEADED - Static variable in class ij.io.RoiDecoder
 
DOUBLE_HEADED_KEY - Static variable in class ij.gui.Arrow
 
doubleBuffer - Static variable in class ij.Prefs
Double buffer display of selections and overlays.
DoubleBufferedScrollPane - Class in ij.plugin.frame
 
DoubleBufferedScrollPane() - Constructor for class ij.plugin.frame.DoubleBufferedScrollPane
 
doWand(int, int) - Static method in class ij.IJ
Equivalent to clicking on the current image at (x,y) with the wand tool.
doWand(int, int, double, String) - Static method in class ij.IJ
Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel at the starting location.
doWand(ImagePlus, int, int, double, String) - Static method in class ij.IJ
This version of doWand adds an ImagePlus argument.
download(String, String) - Static method in class ij.plugin.PluginInstaller
 
downloadJar(String) - Static method in class ij.plugin.Macro_Runner
 
DownsizeTable - Class in ij.process
A table for easier downsizing by convolution with a kernel.
DragAndDrop - Class in ij.plugin
This class opens images, roi's, luts and text files dragged and dropped on the "ImageJ" window.
DragAndDrop() - Constructor for class ij.plugin.DragAndDrop
 
dragComponent(int, int) - Method in class ij.plugin.frame.LayoutPanel
 
dragEnter(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
 
dragExit(DropTargetEvent) - Method in class ij.plugin.DragAndDrop
 
dragOver(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
 
draw(Graphics) - Method in class ij.gui.Arrow
Draws this arrow on the image.
draw(Graphics) - Method in class ij.gui.EllipseRoi
 
draw(Graphics) - Method in class ij.gui.ImageRoi
 
draw(Graphics) - Method in class ij.gui.Line
Draws this line on the image.
draw(Graphics) - Method in class ij.gui.OvalRoi
 
draw() - Method in class ij.gui.Plot
Draws the plot specified in the constructor.
draw() - Method in class ij.gui.PlotWindow
Displays the plot.
draw(Graphics) - Method in class ij.gui.PointRoi
Draws the points on the image.
draw(Graphics) - Method in class ij.gui.PolygonRoi
 
draw(Graphics) - Method in class ij.gui.Roi
 
draw(Graphics) - Method in class ij.gui.ShapeRoi
Non-destructively draws the shape of this object on the associated ImagePlus.
draw(Graphics) - Method in class ij.gui.TextRoi
Draws the text on the screen, clipped to the ROI.
draw() - Method in class ij.ImagePlus
Draws the image.
draw(int, int, int, int) - Method in class ij.ImagePlus
Draws image and roi outline using a clip rect.
draw(ImageProcessor) - Method in class ij.plugin.filter.Filler
Deprecated. replaced by ImageProcessor.draw(Roi)
draw(Roi) - Method in class ij.process.ImageProcessor
Draws the specified ROI on this image using the line width and color defined by ip.setLineWidth() and ip.setColor().
draw(Graphics2D, XYPlot, Rectangle2D, ValueAxis, ValueAxis, int, PlotRenderingInfo) - Method in class ij.wave.WaveMarker
 
DRAW_LINE - Static variable in interface ij.macro.MacroConstants
 
DRAW_OFFSET - Static variable in class ij.io.RoiDecoder
 
DRAW_OVAL - Static variable in interface ij.macro.MacroConstants
 
DRAW_RECT - Static variable in interface ij.macro.MacroConstants
 
DRAW_STRING - Static variable in interface ij.macro.MacroConstants
 
drawArrow(int, int, int, int, double) - Method in class ij.gui.Plot
 
drawBackgrounds(boolean) - Method in class ij.gui.Overlay
 
drawColorBar(Graphics, int, int, int, int) - Method in class ij.LookUpTable
 
drawDot(int, int) - Method in class ij.process.ImageProcessor
Draws a dot using the current line width and fill/draw value.
drawDot2(int, int) - Method in class ij.process.ImageProcessor
Deprecated.  
drawDottedLine(double, double, double, double, int) - Method in class ij.gui.Plot
 
drawEllipse(ImageProcessor) - Method in class ij.process.EllipseFitter
Draws the ellipse on the specified image.
drawEllipse(ImageProcessor) - Method in class ij.process.ImageStatistics
 
drawHistogram(ImageProcessor, boolean) - Method in class ij.gui.HistogramWindow
 
drawInfo(Graphics) - Method in class ij.gui.ImageWindow
Draws the subtitle.
drawingColor - Variable in class ij.process.ImageProcessor
 
drawLabel(ImagePlus, ImageProcessor, int, Rectangle) - Method in class ij.plugin.filter.Filler
 
drawLabels(boolean) - Method in class ij.gui.Overlay
 
drawLine(int, int) - Method in class ij.gui.Line
 
drawLine(double, double, double, double) - Method in class ij.gui.Plot
 
drawLine(int, int, int, int, Color, int) - Method in class ij.plugin.frame.Layout
 
drawLine(int, int, int, int, Color, int) - Method in class ij.plugin.frame.LayoutPanel
 
drawLine(int, int, int, int) - Method in class ij.process.ImageProcessor
Draws a line from (x1,y1) to (x2,y2).
drawNames(boolean) - Method in class ij.gui.Overlay
 
drawNormalizedLine(double, double, double, double) - Method in class ij.gui.Plot
 
drawOval(int, int, int, int) - Method in class ij.process.ImageProcessor
Draws an elliptical shape.
drawOverlay(Graphics) - Method in class ij.gui.Roi
 
drawOverlay(Graphics) - Method in class ij.gui.TextRoi
 
drawOverlay(Overlay) - Method in class ij.process.ImageProcessor
Draws the specified Overlay on this image.
drawParticle(ImageProcessor, Roi, ImageStatistics, ImageProcessor) - Method in class ij.plugin.filter.ParticleAnalyzer
Draws a selected particle in a separate image.
drawPixel(int, int) - Method in class ij.process.ByteProcessor
Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ColorProcessor
Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.FloatProcessor
Draws a pixel in the current foreground color.
drawPixel(int, int) - Method in class ij.process.ImageProcessor
Sets the pixel at (x,y) to the current fill/draw value.
drawPixel(int, int) - Method in class ij.process.ShortProcessor
Draws a pixel in the current foreground color.
drawPixels(ImageProcessor) - Method in class ij.gui.Arrow
 
drawPixels(ImageProcessor) - Method in class ij.gui.Line
 
drawPixels(ImageProcessor) - Method in class ij.gui.OvalRoi
Draws an outline of this OvalRoi on the image.
drawPixels(ImageProcessor) - Method in class ij.gui.PointRoi
 
drawPixels(ImageProcessor) - Method in class ij.gui.PolygonRoi
 
drawPixels() - Method in class ij.gui.Roi
Deprecated. replaced by drawPixels(ImageProcessor)
drawPixels(ImageProcessor) - Method in class ij.gui.Roi
Draws the selection outline on the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.ShapeRoi
Draws the shape of this object onto the specified ImageProcessor.
drawPixels(ImageProcessor) - Method in class ij.gui.TextRoi
Renders the text on the image.
drawPlot(Plot) - Method in class ij.gui.PlotWindow
Draws a new plot in this window.
drawPolygon(Polygon) - Method in class ij.process.ImageProcessor
Draws a polygon.
drawRect(int, int, int, int) - Method in class ij.process.ImageProcessor
Draws a rectangle.
drawRoi(Roi) - Method in class ij.process.ImageProcessor
Draws the specified ROI on this image using the stroke width, stroke color and fill color defined by roi.setStrokeWidth, roi.setStrokeColor() and roi.setFillColor().
drawRoiBrush(Graphics) - Method in class ij.gui.ShapeRoi
 
drawSphere(double, int, int, int) - Method in class ij.ImageStack
Experimental
drawString(String) - Method in class ij.process.ImageProcessor
Draws a string at the current location using the current fill/draw value.
drawString(String, int, int) - Method in class ij.process.ImageProcessor
Draws a string at the specified location using the current fill/draw value.
drawString(String, int, int, Color) - Method in class ij.process.ImageProcessor
Draws a string at the specified location with a filled background.
drawUnscaledColorBar(ImageProcessor, int, int, int, int) - Method in class ij.LookUpTable
 
drawVectors(double[], double[], double[], double[]) - Method in class ij.gui.Plot
Adds a set of points that will be drawn as ARROWs.
drawVectors(ArrayList, ArrayList, ArrayList, ArrayList) - Method in class ij.gui.Plot
Adds a set of vectors to the plot using double ArrayLists.
drop(DropTargetDropEvent) - Method in class ij.plugin.DragAndDrop
 
dropActionChanged(DropTargetDragEvent) - Method in class ij.plugin.DragAndDrop
 
DROPPER - Static variable in class ij.gui.Toolbar
 
dstHeight - Variable in class ij.gui.ImageCanvas
 
dstWidth - Variable in class ij.gui.ImageCanvas
 
DUMP - Static variable in interface ij.macro.MacroConstants
 
dump(String, String, boolean) - Static method in class org.javaabf.ABF_utils
 
dumpProgram() - Method in class ij.macro.Program
 
dumpSymbolTable() - Method in class ij.macro.Program
 
duplicate() - Method in class ij.gui.Overlay
Returns a clone of this Overlay.
duplicate() - Method in class ij.ImagePlus
Returns a copy (clone) of this ImagePlus.
duplicate() - Method in class ij.ImageStack
Duplicates this stack.
duplicate() - Method in class ij.process.ByteProcessor
Returns a duplicate of this image.
duplicate() - Method in class ij.process.ColorProcessor
Returns a duplicate of this image.
duplicate() - Method in class ij.process.FloatPolygon
 
duplicate() - Method in class ij.process.FloatProcessor
Returns a duplicate of this image.
duplicate() - Method in class ij.process.ImageProcessor
Returns a duplicate of this image.
duplicate() - Method in class ij.process.ShortProcessor
Returns a duplicate of this image.
Duplicater - Class in ij.plugin.filter
Deprecated. replaced by Duplicator class
Duplicater() - Constructor for class ij.plugin.filter.Duplicater
Deprecated.  
duplicateStack(ImagePlus, String) - Method in class ij.plugin.filter.Duplicater
Deprecated.  
duplicateSubstack(ImagePlus, String, int, int) - Method in class ij.plugin.filter.Duplicater
Deprecated.  
Duplicator - Class in ij.plugin
This plugin implements the Image/Duplicate command.
Duplicator() - Constructor for class ij.plugin.Duplicator
 
DynamicSeries - Class in ij.wave
 
DynamicSeries(double) - Constructor for class ij.wave.DynamicSeries
 
DynamicXYDataset - Class in ij.wave
 
DynamicXYDataset(NumberAxis) - Constructor for class ij.wave.DynamicXYDataset
 

E

east(ImageProcessor) - Method in class ij.plugin.filter.Shadows
 
Editor - Class in ij.plugin.frame
This is a simple TextArea based editor for editing and compiling plugins.
Editor() - Constructor for class ij.plugin.frame.Editor
 
Editor(int, int, int, int) - Constructor for class ij.plugin.frame.Editor
 
EDM - Class in ij.plugin.filter
This plugin implements the Euclidean Distance Map (EDM), Watershed, Ultimate Eroded Points and Voronoi commands in the Process/Binary submenu
EDM() - Constructor for class ij.plugin.filter.EDM
 
edPaste(String) - Method in class ij.macro.FunctionFinder
 
EIGHT_CONNECTED - Static variable in class ij.gui.Wand
Wand operation type: trace outline of 8-connected pixels
ELECTROPHYS_TYPE - Static variable in class ij.wave.Wave
 
ElectrophysManager - Class in org.jah
 
ElectrophysManager() - Constructor for class org.jah.ElectrophysManager
 
ElectrophysManager_Frame - Class in ij.plugin.frame
A GUI front-end for interacting with the ElectrophysManager instance back-end.
ElectrophysManager_Frame() - Constructor for class ij.plugin.frame.ElectrophysManager_Frame
 
ELLIPSE - Static variable in class ij.io.RoiDecoder
 
ELLIPSE - Static variable in interface ij.measure.Measurements
 
ELLIPSE_ASPECT_RATIO - Static variable in class ij.io.RoiDecoder
 
ELLIPSE_ROI - Static variable in class ij.gui.Toolbar
 
EllipseFitter - Class in ij.process
This class fits an ellipse to an ROI.
EllipseFitter() - Constructor for class ij.process.EllipseFitter
 
EllipseRoi - Class in ij.gui
Elliptical region of interest.
EllipseRoi(double, double, double, double, double) - Constructor for class ij.gui.EllipseRoi
 
EllipseRoi(int, int, ImagePlus) - Constructor for class ij.gui.EllipseRoi
 
ELLIPSES - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
ELSE - Static variable in interface ij.macro.MacroConstants
 
EMBEDDED - Static variable in class ij.ImageJ
Run embedded in another application.
enableDebugging() - Method in class ij.io.TiffDecoder
 
enableSubPixelResolution() - Method in class ij.gui.PolygonRoi
 
enableSubPixelResolution() - Method in class ij.gui.Roi
 
enableYesNoCancel() - Method in class ij.gui.GenericDialog
Make this a "Yes No Cancel" dialog.
enableYesNoCancel(String, String) - Method in class ij.gui.GenericDialog
Make this a "Yes No Cancel" dialog with custom labels.
endPaste() - Method in class ij.gui.Roi
 
ENDS_WITH - Static variable in interface ij.macro.MacroConstants
 
enhancedLineTool - Static variable in class ij.Prefs
Allow lines to be created with one click at start and another at the end
enlarge(Roi, double) - Static method in class ij.plugin.RoiEnlarger
 
EOF - Static variable in interface ij.macro.MacroConstants
 
EPISODIC_TYPE - Static variable in class ij.wave.Wave
 
EpisodicWave - Class in ij.wave
 
EpisodicWave(double[]) - Constructor for class ij.wave.EpisodicWave
 
Epoch - Class in org.javaabf
 
Epoch(long, long) - Constructor for class org.javaabf.Epoch
 
Epoch(String, long, long) - Constructor for class org.javaabf.Epoch
 
EpochTableModel - Class in ij.plugin.frame.table
 
EpochTableModel() - Constructor for class ij.plugin.frame.table.EpochTableModel
 
EpochUtils - Class in org.javaabf
 
EpochUtils() - Constructor for class org.javaabf.EpochUtils
 
EQ - Static variable in interface ij.macro.MacroConstants
 
equalize(ImagePlus) - Method in class ij.plugin.ContrastEnhancer
 
equalize(ImageProcessor) - Method in class ij.plugin.ContrastEnhancer
Changes the tone curves of images.
equals(Object) - Method in class com.jmatio.types.MLChar
 
equals(Object) - Method in class com.jmatio.types.MLNumericArray
 
equals(Object) - Method in class ij.gui.Roi
Checks whether two rectangles are equal.
equals(Calibration) - Method in class ij.measure.Calibration
Compares two Calibration objects for equality.
equals(Object) - Method in class ij.wave.Burst
 
equals(Object) - Method in class ij.wave.WaveMarker
 
erode() - Method in class ij.process.ByteProcessor
 
erode(int, int) - Method in class ij.process.ByteProcessor
 
erode() - Method in class ij.process.ColorProcessor
 
erode() - Method in class ij.process.FloatProcessor
Not implemented.
erode() - Method in class ij.process.ImageProcessor
Erodes the image or ROI using a 3x3 maximum filter.
erode() - Method in class ij.process.ShortProcessor
Not implemented.
error(String) - Static method in class ij.IJ
Displays a message in a dialog box titled "ImageJ".
error(String, String) - Static method in class ij.IJ
Displays a message in a dialog box with the specified title.
ErrorHandler(int, int, Exception) - Static method in class org.jah.Labjack32bit
 
escapePressed() - Method in class ij.gui.HTMLDialog
 
escapePressed() - Method in class ij.gui.MessageDialog
 
escapePressed() - Static method in class ij.IJ
Returns true if the Esc key was pressed since the last ImageJ command started to execute or since resetEscape() was called.
escPressed() - Method in class ij.gui.WaitForUserDialog
 
EVAL - Static variable in interface ij.macro.MacroConstants
 
evalSpline(double) - Method in class ij.measure.SplineFitter
Evalutes spline function at given point
evalSpline(int[], int[], int, double) - Method in class ij.measure.SplineFitter
 
evalSpline(float[], float[], int, double) - Method in class ij.measure.SplineFitter
 
eventOccurred(int) - Method in interface ij.IJEventListener
 
EXCLUDE_EDGE_PARTICLES - Static variable in class ij.plugin.filter.ParticleAnalyzer
Do not measure particles touching edge of image.
excludedFileType(String) - Static method in class ij.plugin.FolderOpener
 
excludeEdgeParticles - Variable in class ij.plugin.filter.ParticleAnalyzer
 
EXEC - Static variable in interface ij.macro.MacroConstants
 
Executer - Class in ij
Runs ImageJ menu commands in a separate thread.
Executer(String) - Constructor for class ij.Executer
Create an Executer to run the specified menu command in this thread using the active image.
Executer(String, ImagePlus) - Constructor for class ij.Executer
Create an Executer that runs the specified menu command in a separate thread using the specified image, or using the active image if 'imp' is null.
exists(String) - Static method in class ij.IJ
 
EXIT - Static variable in interface ij.macro.MacroConstants
 
exitConstructingMode() - Method in class ij.gui.PolygonRoi
 
exitWhenQuitting(boolean) - Method in class ij.ImageJ
ImageJ calls System.exit() when qutting when 'exitWhenQuitting' is true.
EXP - Static variable in interface ij.macro.MacroConstants
 
exp() - Method in class ij.process.FloatProcessor
 
exp() - Method in class ij.process.ImageProcessor
Performs a exponential transform on the image or ROI.
exp() - Method in class ij.process.ShortProcessor
 
EXP_RECOVERY - Static variable in class ij.measure.Calibration
 
EXP_RECOVERY - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
EXP_RECOVERY_NOOFFSET - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
EXP_REGRESSION - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
EXP_WITH_OFFSET - Static variable in class ij.measure.Calibration
 
EXP_WITH_OFFSET - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
expandImage(ImageProcessor, int, int, int, int) - Method in class ij.plugin.CanvasResizer
 
expandStack(ImageStack, int, int, int, int) - Method in class ij.plugin.CanvasResizer
 
EXPONENTIAL - Static variable in class ij.measure.Calibration
 
EXPONENTIAL - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
exponentialFit() - Method in class ij.wave.Wave
Applies an exponential fit to the contents of this Wave and fires a waveChanged event.
exponentialFit() - Method in class ij.wave.Waves
Scales each Wave in this instance with respect to its own pattern by an exponential fit.
exportChar() - Method in class com.jmatio.types.MLChar
 
exportImaginary() - Method in class com.jmatio.types.MLSparse
Returns the imaginary part (PI) array.
exportReal() - Method in class com.jmatio.types.MLSparse
Returns the real part (PR) array.
exportToEps() - Method in class ij.plugin.frame.Layout
 
exportToEps(String) - Method in class ij.plugin.frame.Layout
 
exportToEps() - Method in class ij.plugin.frame.LayoutPanel
 
exportToEps(String) - Method in class ij.plugin.frame.LayoutPanel
 
exportToJpeg() - Method in class ij.plugin.frame.Layout
 
exportToJpeg(String) - Method in class ij.plugin.frame.Layout
 
exportToJpeg() - Method in class ij.plugin.frame.LayoutPanel
 
exportToJpeg(String) - Method in class ij.plugin.frame.LayoutPanel
 
exportToPDF() - Method in class ij.plugin.frame.Layout
 
exportToPDF(String) - Method in class ij.plugin.frame.Layout
 
exportToPDF() - Method in class ij.plugin.frame.LayoutPanel
 
exportToPDF(String) - Method in class ij.plugin.frame.LayoutPanel
 
exportToTiff() - Method in class ij.plugin.frame.Layout
 
exportToTiff(String) - Method in class ij.plugin.frame.Layout
 
exportToTiff() - Method in class ij.plugin.frame.LayoutPanel
 
exportToTiff(String) - Method in class ij.plugin.frame.LayoutPanel
 
EXT - Static variable in interface ij.macro.MacroConstants
 
ExtendedPlugInFilter - Interface in ij.plugin.filter
ImageJ plugins that process an image may implement this interface.
ExtensionDescriptor - Class in ij.macro
 
ExtensionDescriptor(String, int[], MacroExtension) - Constructor for class ij.macro.ExtensionDescriptor
 

F

f(double[], double) - Method in class ij.measure.CurveFitter
Returns the formula value for parameters 'p' at 'x'.
f(int, double[], double) - Static method in class ij.measure.CurveFitter
Returns value of built-in 'fitType' formula value for parameters "p" at "x"
f2hex(float) - Static method in class ij.util.Tools
Converts a float to an 9 byte hex string starting with '#'.
FALSE - Static variable in interface ij.macro.MacroConstants
 
FAST_TRACE - Static variable in class ij.macro.Interpreter
 
FCOLOR - Static variable in class ij.Prefs
 
FERET - Static variable in interface ij.measure.Measurements
 
FERET - Static variable in class ij.measure.ResultsTable
 
FERET_ANGLE - Static variable in class ij.measure.ResultsTable
 
FERET_X - Static variable in class ij.measure.ResultsTable
 
FERET_Y - Static variable in class ij.measure.ResultsTable
 
FFT - Class in ij.plugin
This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands in the Process/FFT submenu.
FFT() - Constructor for class ij.plugin.FFT
 
FFTCustomFilter - Class in ij.plugin.filter
This class implements the Process/FFT/Custom Filter command.
FFTCustomFilter() - Constructor for class ij.plugin.filter.FFTCustomFilter
 
FFTFilter - Class in ij.plugin.filter
This class implements the Process/FFT/Bandpass Filter command.
FFTFilter() - Constructor for class ij.plugin.filter.FFTFilter
 
FFTMath - Class in ij.plugin
The class implements the Process/FFT/Math command.
FFTMath() - Constructor for class ij.plugin.FFTMath
 
FHT - Class in ij.process
This class contains a Java implementation of the Fast Hartley Transform.
FHT(ImageProcessor) - Constructor for class ij.process.FHT
Constructs a FHT object from an ImageProcessor.
FHT(ImageProcessor, boolean) - Constructor for class ij.process.FHT
 
FHT() - Constructor for class ij.process.FHT
 
FILE - Static variable in interface ij.macro.MacroConstants
 
fileChanged() - Method in class ij.plugin.frame.Editor
 
fileFormat - Variable in class ij.io.FileInfo
 
FileInfo - Class in ij.io
This class consists of public fields that describe an image file.
FileInfo() - Constructor for class ij.io.FileInfo
Creates a FileInfo object with all of its fields set to their default value.
FileInfoVirtualStack - Class in ij.plugin
This plugin opens a multi-page TIFF file as a virtual stack.
FileInfoVirtualStack() - Constructor for class ij.plugin.FileInfoVirtualStack
 
FileInfoVirtualStack(FileInfo) - Constructor for class ij.plugin.FileInfoVirtualStack
 
FileInfoVirtualStack(FileInfo, boolean) - Constructor for class ij.plugin.FileInfoVirtualStack
 
fileName - Variable in class ij.io.FileInfo
 
fileName - Static variable in class ij.plugin.FFT
 
filename - Variable in class org.jah.Continuous_Gaussian_Pulse_Runner
 
filename - Variable in class org.jah.Continuous_Uniform_Pulse_Runner
 
FileOpener - Class in ij.io
Opens or reverts an image specified by a FileInfo object.
FileOpener(FileInfo) - Constructor for class ij.io.FileOpener
 
FileSaver - Class in ij.io
Saves images in tiff, gif, jpeg, raw, zip and text format.
FileSaver(ImagePlus) - Constructor for class ij.io.FileSaver
Constructs a FileSaver from an ImagePlus.
fileType - Variable in class ij.io.FileInfo
 
FILL - Static variable in interface ij.macro.MacroConstants
 
fill(ImageProcessor) - Method in class ij.plugin.filter.Filler
Deprecated. replaced by ImageProcessor.fill(Roi)
fill(ImageProcessor) - Method in class ij.process.ByteProcessor
Fills pixels that are within roi and part of the mask.
fill(ImageProcessor) - Method in class ij.process.ColorProcessor
Fills pixels that are within roi and part of the mask.
fill() - Method in class ij.process.ColorProcessor
Fills the current rectangular ROI.
fill() - Method in class ij.process.FloatProcessor
Fills the current rectangular ROI.
fill(ImageProcessor) - Method in class ij.process.FloatProcessor
Fills pixels that are within roi and part of the mask.
fill(int, int) - Method in class ij.process.FloodFiller
Does a 4-connected flood fill using the current fill/draw value, which is defined by ImageProcessor.setValue().
fill() - Method in class ij.process.ImageProcessor
Fills the image or ROI bounding rectangle with the current fill/draw value.
fill(ImageProcessor) - Method in class ij.process.ImageProcessor
Fills pixels that are within the ROI bounding rectangle and part of the mask (i.e. pixels that have a value=BLACK in the mask array).
fill(Roi) - Method in class ij.process.ImageProcessor
Fills the ROI with the current fill/draw value.
fill(ImageProcessor, Rectangle) - Method in class ij.process.PolygonFiller
Fills the polygon using the ImageProcessor's current drawing color.
fill() - Method in class ij.process.ShortProcessor
Fills the current rectangular ROI.
fill(ImageProcessor) - Method in class ij.process.ShortProcessor
Fills pixels that are within roi and part of the mask.
fill8(int, int) - Method in class ij.process.FloodFiller
Does a 8-connected flood fill using the current fill/draw value, which is defined by ImageProcessor.setValue().
FILL_BLACK - Static variable in class ij.gui.NewImage
 
FILL_COLOR - Static variable in class ij.io.RoiDecoder
 
FILL_OVAL - Static variable in interface ij.macro.MacroConstants
 
FILL_RAMP - Static variable in class ij.gui.NewImage
 
FILL_RANDOM - Static variable in class ij.gui.NewImage
 
FILL_RECT - Static variable in interface ij.macro.MacroConstants
 
FILL_WHITE - Static variable in class ij.gui.NewImage
 
fillColor - Variable in class ij.gui.Roi
 
fillContents() - Method in class ij.wave.CustomWave
Accepts the length of the wave in seconds
fillContents() - Method in class ij.wave.SimulatedUniformPulseWave
 
FILLED - Static variable in class ij.gui.Arrow
 
Filler - Class in ij.plugin.filter
This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.
Filler() - Constructor for class ij.plugin.filter.Filler
 
fillOutside(Roi) - Method in class ij.process.ImageProcessor
Fills outside an Roi.
fillOval(int, int, int, int) - Method in class ij.process.ImageProcessor
Fills an elliptical shape.
fillPolygon(Polygon) - Method in class ij.process.ImageProcessor
Fills a polygon.
filter(ImageStack, int, float, float, float) - Static method in class ij.plugin.Filters3D
 
filter(int) - Method in class ij.process.ByteProcessor
Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ColorProcessor
3x3 unweighted smoothing.
filter(int) - Method in class ij.process.FloatProcessor
Filters using a 3x3 neighborhood.
filter(int) - Method in class ij.process.ImageProcessor
A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES, MEDIAN_FILTER, MIN or MAX) determines the filter type.
filter(int) - Method in class ij.process.ShortProcessor
Filters using a 3x3 neighborhood.
FILTER - Static variable in class ij.Undo
 
filter(Waves, Waves) - Static method in class ij.wave.WaveUtils
waves1 should be the list of candidates to eliminate if they appear in waves2.
filter(Wave[], double, double) - Static method in class org.jah.FrequencyFilter
 
filter3D(ImageStack, float, float, float, int, int, int) - Method in class ij.process.StackProcessor
3D filter using threads
FILTER_MAX - Static variable in class ij.process.StackProcessor
 
FILTER_MAXLOCAL - Static variable in class ij.process.StackProcessor
 
FILTER_MEAN - Static variable in class ij.process.StackProcessor
 
FILTER_MEDIAN - Static variable in class ij.process.StackProcessor
 
FILTER_MIN - Static variable in class ij.process.StackProcessor
 
FILTER_VAR - Static variable in class ij.process.StackProcessor
 
filterOut(Waves) - Method in class ij.wave.Waves
This instance of Waves should be the list of candidates to eliminate if they appear in waves2.
filterRGB(int, double) - Method in class ij.process.ColorProcessor
Performs the specified filter on the red, green and blue planes of this image.
Filters - Class in ij.plugin.filter
This plugin implements the Invert, Smooth, Sharpen, Find Edges, and Add Noise commands.
Filters() - Constructor for class ij.plugin.filter.Filters
 
Filters3D - Class in ij.plugin
 
Filters3D() - Constructor for class ij.plugin.Filters3D
 
FILTERS_MENU - Static variable in class ij.Menus
 
filterString(String) - Method in class ij.JAHMenuItem
 
filterVector(Vector, double, double) - Static method in class org.jah.FrequencyFilter
 
FINAL_PROCESSING - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag if the setup method of the filter should be called again after the calls to the run(ip) have finished.
FIND_EDGES - Static variable in class ij.process.ImageProcessor
 
findAllMenuItems() - Method in class ij.plugin.CommandFinder
 
findBurstEnvelope(Wave) - Method in class ij.wave.Burst
Extracts the waveform corresponding to this burst from the reference Wave passed as argument.
findEdges() - Method in class ij.process.ColorProcessor
 
findEdges() - Method in class ij.process.ImageProcessor
Finds edges in the image or ROI using a Sobel operator.
findMaxima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder
Calculates peak positions of 1D array N.Vischer, 13-sep-2013
findMaxima(ImageProcessor, double, double, int, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder
Here the processing is done: Find the maxima of an image (does not find minima).
findMinAndMax() - Method in class ij.process.FloatProcessor
Calculates the minimum and maximum pixel value for the entire image.
findMinAndMax() - Method in class ij.process.ShortProcessor
 
findMinima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder
Returns minimum positions of array xx, sorted with decreasing strength
findNextTimeAbove(double, double) - Method in class ij.wave.Wave
 
findNextTimeBelow(double, double) - Method in class ij.wave.Wave
 
findNextWave(ArrayList, ArrayList) - Method in class ij.wave.Waves
 
findNthLowestNumber(float[], int, int) - Static method in class ij.plugin.filter.RankFilters
Find the n-th lowest number in part of an array
findRoi(String) - Static method in class org.jah.JAH_Utils
 
findWave(String) - Static method in class org.jah.JAH_Utils
 
FIO4 - Static variable in interface org.jah.Labjack
 
FIT - Static variable in interface ij.macro.MacroConstants
 
fit(ImageProcessor, ImageStatistics) - Method in class ij.process.EllipseFitter
Fits an ellipse to the current ROI.
fitList - Static variable in class ij.measure.CurveFitter
Names of the built-in fit functions
FITS - Static variable in class ij.io.FileInfo
 
FITS - Static variable in class ij.io.Opener
 
FITS_Reader - Class in ij.plugin
Opens and displays FITS images.
FITS_Reader() - Constructor for class ij.plugin.FITS_Reader
 
FITS_Writer - Class in ij.plugin
This plugin saves a 16 or 32 bit image in FITS format.
FITS_Writer() - Constructor for class ij.plugin.FITS_Writer
 
fitSpline(int) - Method in class ij.gui.PolygonRoi
 
fitSpline() - Method in class ij.gui.PolygonRoi
 
fitSplineForStraightening() - Method in class ij.gui.PolygonRoi
 
Fitter - Class in ij.plugin.frame
ImageJ plugin that does curve fitting using the modified CurveFitter class.
Fitter() - Constructor for class ij.plugin.frame.Fitter
 
fitToWindow() - Method in class ij.gui.ImageCanvas
 
fix(Scrollbar) - Static method in class ij.gui.GUI
Lightens overly dark scrollbar background on Windows 8.
fixLineEndings() - Method in class ij.plugin.frame.Editor
Changes Mac OS 9 (CR) and Windows (CRLF) line separators to line feeds (LF).
fixNewLines(String) - Static method in class ij.util.Tools
Converts carriage returns to line feeds.
flags - Variable in class ij.gui.ImageCanvas
 
flatten() - Method in class ij.ImagePlus
Returns a "flattened" version of this image, in RGB format.
flatten() - Method in class ij.plugin.frame.RoiManager
 
flattenStack() - Method in class ij.ImagePlus
Flattens all slices of this stack or HyperStack.
flipHorizontal() - Method in class ij.process.ImageProcessor
Flips the image or ROI horizontally.
flipHorizontal() - Method in class ij.process.StackProcessor
 
flipStack(ImagePlus) - Method in class ij.plugin.StackReverser
 
flipVertical() - Method in class ij.process.ByteProcessor
 
flipVertical() - Method in class ij.process.ColorProcessor
 
flipVertical() - Method in class ij.process.FloatProcessor
 
flipVertical() - Method in class ij.process.ImageProcessor
Flips the image or ROI vertically.
flipVertical() - Method in class ij.process.ShortProcessor
 
flipVertical() - Method in class ij.process.StackProcessor
 
flipXZ - Static variable in class ij.Prefs
Rotate XZ orthogonal views 180 degrees
fList - Static variable in class ij.measure.CurveFitter
Equations of the built-in fit functions
FLOAT - Static variable in class ij.plugin.filter.EDM
Output type: new 32-bit image
FLOAT - Static variable in interface org.javaabf.ABF_parser
 
FLOAT_STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
 
FloatBlitter - Class in ij.process
This class does bit blitting of 32-bit floating-point images.
FloatBlitter(FloatProcessor) - Constructor for class ij.process.FloatBlitter
Constructs a FloatBlitter from a FloatProcessor.
FloatPolygon - Class in ij.process
Used by the Roi classes to return float coordinate arrays and to determine if a point is inside or outside of spline fitted selections.
FloatPolygon() - Constructor for class ij.process.FloatPolygon
Constructs an empty FloatPolygon.
FloatPolygon(float[], float[]) - Constructor for class ij.process.FloatPolygon
Constructs a FloatPolygon from x and y arrays.
FloatPolygon(float[], float[], int) - Constructor for class ij.process.FloatPolygon
Constructs a FloatPolygon from x and y arrays.
FloatProcessor - Class in ij.process
This is an 32-bit floating-point image and methods that operate on that image.
FloatProcessor(int, int, float[]) - Constructor for class ij.process.FloatProcessor
Creates a new FloatProcessor using the specified pixel array.
FloatProcessor(int, int, float[], ColorModel) - Constructor for class ij.process.FloatProcessor
Creates a new FloatProcessor using the specified pixel array and ColorModel.
FloatProcessor(int, int) - Constructor for class ij.process.FloatProcessor
Creates a blank FloatProcessor using the default grayscale LUT that displays zero as black.
FloatProcessor(int, int, int[]) - Constructor for class ij.process.FloatProcessor
Creates a FloatProcessor from an int array using the default grayscale LUT.
FloatProcessor(int, int, double[]) - Constructor for class ij.process.FloatProcessor
Creates a FloatProcessor from a double array using the default grayscale LUT.
FloatProcessor(float[][]) - Constructor for class ij.process.FloatProcessor
Creates a FloatProcessor from a 2D float array using the default LUT.
FloatProcessor(int[][]) - Constructor for class ij.process.FloatProcessor
Creates a FloatProcessor from a 2D int array.
FloatStatistics - Class in ij.process
32-bit (float) image statistics, including histogram.
FloatStatistics(ImageProcessor) - Constructor for class ij.process.FloatStatistics
Constructs an ImageStatistics object from a FloatProcessor using the standard measurement options (area, mean, mode, min and max).
FloatStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.FloatStatistics
Constructs a FloatStatistics object from a FloatProcessor using the specified measurement options.
FLOOD_FILL - Static variable in interface ij.macro.MacroConstants
 
floodFill - Variable in class ij.plugin.filter.ParticleAnalyzer
 
FloodFiller - Class in ij.process
This class, which does flood filling, is used by the floodFill() macro function and by the particle analyzer The Wikipedia at "http://en.wikipedia.org/wiki/Flood_fill" has a good description of the algorithm used here as well as examples in C and Java.
FloodFiller(ImageProcessor) - Constructor for class ij.process.FloodFiller
 
FLOOR - Static variable in interface ij.macro.MacroConstants
 
flush() - Method in class ij.ImagePlus
Sets the ImageProcessor, Roi, AWT Image and stack image arrays to null.
flush() - Method in class ij.io.ConsoleInputStream
 
flush() - Method in class ij.io.ConsoleOutputStream
 
flush() - Method in class ij.io.LogStream
 
flush() - Static method in class org.jah.Logger
 
fmImage - Variable in class ij.process.ImageProcessor
 
focusGained(FocusEvent) - Method in class ij.gui.GenericDialog
 
focusGained(FocusEvent) - Method in class ij.gui.ImageWindow
 
focusGained(FocusEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
focusGained(FocusEvent) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
focusGained(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
 
focusGained(FocusEvent) - Method in class ij.plugin.frame.Jython_Console
 
focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
 
focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
 
focusGained(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
 
focusGained(FocusEvent) - Method in class ij.plugin.Scaler
 
focusGained(FocusEvent) - Method in class ij.text.TextWindow
 
focusLost(FocusEvent) - Method in class ij.gui.GenericDialog
 
focusLost(FocusEvent) - Method in class ij.gui.ImageWindow
 
focusLost(FocusEvent) - Method in class ij.plugin.frame.ChartFramePlugIn
 
focusLost(FocusEvent) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
focusLost(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
 
focusLost(FocusEvent) - Method in class ij.plugin.frame.Jython_Console
 
focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
 
focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
 
focusLost(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
 
focusLost(FocusEvent) - Method in class ij.plugin.Scaler
 
focusLost(FocusEvent) - Method in class ij.text.TextWindow
 
FolderOpener - Class in ij.plugin
Implements the File/Import/Image Sequence command, which opens a folder of images as a stack.
FolderOpener() - Constructor for class ij.plugin.FolderOpener
 
font - Variable in class ij.process.ImageProcessor
 
fontMetrics - Variable in class ij.process.ImageProcessor
 
Fonts - Class in ij.plugin.frame
Displays a window that allows the user to set the font, size and style.
Fonts() - Constructor for class ij.plugin.frame.Fonts
 
FOR - Static variable in interface ij.macro.MacroConstants
 
FOREGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
 
format(double, int) - Static method in class org.jah.JAH_Utils
 
FOUR_CONNECTED - Static variable in class ij.gui.Wand
Wand operation type: trace outline of 4-connected pixels
FOUR_CONNECTED - Static variable in class ij.plugin.filter.ParticleAnalyzer
Use 4-connected particle tracing.
fps - Variable in class ij.measure.Calibration
Frame rate in frames per second
FPS - Static variable in class ij.Prefs
 
FractalBoxCounter - Class in ij.plugin.filter
Calculate the so-called "capacity" fractal dimension.
FractalBoxCounter() - Constructor for class ij.plugin.filter.FractalBoxCounter
 
frame - Variable in class ij.gui.HistogramWindow
 
FRAME - Static variable in class ij.measure.ResultsTable
 
frameInterval - Variable in class ij.io.FileInfo
 
frameInterval - Variable in class ij.measure.Calibration
Frame interval in 'timeUnit's
FreehandRoi - Class in ij.gui
Freehand region of interest or freehand line of interest
FreehandRoi(int, int, ImagePlus) - Constructor for class ij.gui.FreehandRoi
 
FREELINE - Static variable in class ij.gui.Roi
 
FREELINE - Static variable in class ij.gui.Toolbar
 
freeMemory() - Static method in class ij.IJ
Runs the garbage collector and returns a string something like "64K of 256MB (25%)" that shows how much of the available memory is in use.
FREEROI - Static variable in class ij.gui.Roi
 
FREEROI - Static variable in class ij.gui.Toolbar
 
FrequencyAnalyzer - Class in org.jah
 
FrequencyAnalyzer() - Constructor for class org.jah.FrequencyAnalyzer
 
FrequencyFilter - Class in org.jah
 
FrequencyFilter() - Constructor for class org.jah.FrequencyFilter
 
FROM_CHAR_CODE - Static variable in interface ij.macro.MacroConstants
 
FUNCTION - Static variable in interface ij.macro.MacroConstants
 
FunctionFinder - Class in ij.macro
This class implements the text editor's Macros/Find Functions command.
FunctionFinder(Editor) - Constructor for class ij.macro.FunctionFinder
 
FunctionFinder() - Constructor for class ij.macro.FunctionFinder
 
functionIDs - Static variable in interface ij.macro.MacroConstants
 
Functions - Class in ij.macro
This class implements the built-in macro functions.
functions - Static variable in interface ij.macro.MacroConstants
 

G

gamma(double) - Method in class ij.process.FloatProcessor
 
gamma(double) - Method in class ij.process.ImageProcessor
Performs gamma correction of the image or ROI.
gamma(double) - Method in class ij.process.ShortProcessor
 
GAMMA_VARIATE - Static variable in class ij.measure.Calibration
 
GAMMA_VARIATE - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
gapBetweenImages - Variable in class ij.io.FileInfo
 
GAUSSIAN - Static variable in class ij.measure.Calibration
 
GAUSSIAN - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
GAUSSIAN_NOOFFSET - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
GaussianBlur - Class in ij.plugin.filter
This plug-in filter uses convolution with a Gaussian function for smoothing.
GaussianBlur() - Constructor for class ij.plugin.filter.GaussianBlur
 
GaussianBlur3D - Class in ij.plugin
 
GaussianBlur3D() - Constructor for class ij.plugin.GaussianBlur3D
 
GelAnalyzer - Class in ij.plugin
This plugin generates gel profile plots that can be analyzed using the wand tool.
GelAnalyzer() - Constructor for class ij.plugin.GelAnalyzer
 
generateWindowImages(ImagePlus, double, int, double, double, String, boolean, boolean) - Static method in class ij.wave.CTA_Utils
 
GenericArrayCreator<T> - Interface in com.jmatio.types
 
GenericDialog - Class in ij.gui
This class is a customizable modal dialog box.
GenericDialog() - Constructor for class ij.gui.GenericDialog
 
GenericDialog(String) - Constructor for class ij.gui.GenericDialog
Creates a new GenericDialog with the specified title.
GenericDialog(String, Frame) - Constructor for class ij.gui.GenericDialog
Creates a new GenericDialog using the specified title and parent frame.
get(int, int) - Method in class com.jmatio.types.MLCell
 
get(int) - Method in class com.jmatio.types.MLCell
 
get(int, int) - Method in class com.jmatio.types.MLNumericArray
Does the same as getReal.
get(int) - Method in class com.jmatio.types.MLNumericArray
 
get(int) - Method in class ij.gui.Overlay
Returns the Roi with the specified index.
get(String, String) - Static method in class ij.Prefs
Uses the keyword key to retrieve a string from the preferences file.
get(String, double) - Static method in class ij.Prefs
Uses the keyword key to retrieve a number from the preferences file.
get(String, boolean) - Static method in class ij.Prefs
Uses the keyword key to retrieve a boolean from the preferences file.
get(int, int) - Method in class ij.process.ByteProcessor
 
get(int) - Method in class ij.process.ByteProcessor
 
get(int, int) - Method in class ij.process.ColorProcessor
 
get(int) - Method in class ij.process.ColorProcessor
 
get(int, int) - Method in class ij.process.FloatProcessor
 
get(int) - Method in class ij.process.FloatProcessor
 
get(int, int) - Method in class ij.process.ImageProcessor
This is a faster version of getPixel() that does not do bounds checking.
get(int) - Method in class ij.process.ImageProcessor
 
get(int, int) - Method in class ij.process.ShortProcessor
 
get(int) - Method in class ij.process.ShortProcessor
 
get(int) - Method in class ij.wave.ABFWaveProxy
 
get(int) - Method in class ij.wave.Wave
 
get(int) - Method in class ij.wave.WaveProxy
Gets a specific value of the source with given index.
get(int) - Method in class ij.wave.Waves
A convenience method for calling getWave.
get(int) - Method in class org.javaabf.Comments
 
get16BitBufferedImage() - Method in class ij.process.ShortProcessor
Returns a copy of this image as a TYPE_USHORT_GRAY BufferedImage.
get16bitRangeIndex() - Static method in class ij.plugin.frame.ContrastAdjuster
 
GET_ARGUMENT - Static variable in interface ij.macro.MacroConstants
 
GET_BOOLEAN - Static variable in interface ij.macro.MacroConstants
 
GET_BOUNDING_RECT - Static variable in interface ij.macro.MacroConstants
 
GET_BOUNDS - Static variable in interface ij.macro.MacroConstants
 
GET_COORDINATES - Static variable in interface ij.macro.MacroConstants
 
GET_COUNT - Static variable in interface ij.macro.MacroConstants
 
GET_CURSOR_LOC - Static variable in interface ij.macro.MacroConstants
 
GET_DATE_AND_TIME - Static variable in interface ij.macro.MacroConstants
 
GET_DIMENSIONS - Static variable in interface ij.macro.MacroConstants
 
GET_DIRECTORY - Static variable in interface ij.macro.MacroConstants
 
GET_DISPLAYED_AREA - Static variable in interface ij.macro.MacroConstants
 
GET_FILE_LIST - Static variable in interface ij.macro.MacroConstants
 
GET_FONT_LIST - Static variable in interface ij.macro.MacroConstants
 
GET_HEIGHT - Static variable in interface ij.macro.MacroConstants
 
GET_HISTOGRAM - Static variable in interface ij.macro.MacroConstants
 
GET_ID - Static variable in interface ij.macro.MacroConstants
 
GET_IMAGE_INFO - Static variable in interface ij.macro.MacroConstants
 
GET_INFO - Static variable in interface ij.macro.MacroConstants
 
GET_LINE - Static variable in interface ij.macro.MacroConstants
 
GET_LIST - Static variable in interface ij.macro.MacroConstants
 
GET_LOCATION_AND_SIZE - Static variable in interface ij.macro.MacroConstants
 
GET_LUT - Static variable in interface ij.macro.MacroConstants
 
GET_METADATA - Static variable in interface ij.macro.MacroConstants
 
GET_MIN_AND_MAX - Static variable in interface ij.macro.MacroConstants
 
GET_NUMBER - Static variable in interface ij.macro.MacroConstants
 
GET_PIXEL - Static variable in interface ij.macro.MacroConstants
 
GET_PIXEL_SIZE - Static variable in interface ij.macro.MacroConstants
 
GET_PROFILE - Static variable in interface ij.macro.MacroConstants
 
GET_RAW_STATISTICS - Static variable in interface ij.macro.MacroConstants
 
GET_RESULT - Static variable in interface ij.macro.MacroConstants
 
GET_RESULT_LABEL - Static variable in interface ij.macro.MacroConstants
 
GET_RESULT_STRING - Static variable in interface ij.macro.MacroConstants
 
GET_SLICE_NUMBER - Static variable in interface ij.macro.MacroConstants
 
GET_STATISTICS - Static variable in interface ij.macro.MacroConstants
 
GET_STRING - Static variable in interface ij.macro.MacroConstants
 
GET_STRING_WIDTH - Static variable in interface ij.macro.MacroConstants
 
GET_THRESHOLD - Static variable in interface ij.macro.MacroConstants
 
GET_TIME - Static variable in interface ij.macro.MacroConstants
 
GET_TITLE - Static variable in interface ij.macro.MacroConstants
 
GET_VALUE - Static variable in interface ij.macro.MacroConstants
 
GET_VERSION - Static variable in interface ij.macro.MacroConstants
 
GET_VOXEL_SIZE - Static variable in interface ij.macro.MacroConstants
 
GET_WIDTH - Static variable in interface ij.macro.MacroConstants
 
GET_ZOOM - Static variable in interface ij.macro.MacroConstants
 
getABF(String) - Method in class org.jah.ElectrophysManager
Returns the ABF instance associated with the 'filename' where the filename DOES NOT contain the path to the file.
getABF1ADCInfos() - Method in class org.javaabf.ABF18_parser
 
getABF1ADCInfos() - Method in class org.javaabf.ABFpClamp9_parser
 
getABF1FileInfo() - Method in class org.javaabf.ABF18_parser
 
getABF1FileInfo() - Method in class org.javaabf.ABFpClamp9_parser
 
getABF1ProtocolInfo() - Method in class org.javaabf.ABF18_parser
 
getABF1ProtocolInfo() - Method in class org.javaabf.ABFpClamp9_parser
 
getABF2ADCInfo(ABF_Section) - Method in class org.javaabf.ABF18_parser
 
getABF2ADCInfo(ABF_Section) - Method in class org.javaabf.ABF2_parser
 
getABF2FileInfo() - Method in class org.javaabf.ABF18_parser
 
getABF2FileInfo() - Method in class org.javaabf.ABF2_parser
 
getABF_parser(String, boolean) - Static method in class org.javaabf.ABF_parserFactory
Transparently returns the appropriate .abf file parser corresponding to a given version of .abf file.
getABFFilename() - Method in class org.javaabf.Epoch
 
getABFVersion() - Method in class org.javaabf.ABF
 
getABFVersion() - Method in class org.javaabf.ABF18_parser
 
getABFVersion() - Method in class org.javaabf.ABF2_parser
 
getABFVersion() - Method in interface org.javaabf.ABF_parser
 
getABFVersion() - Method in class org.javaabf.AbstractABF_parser
 
getAbsoluteTime(long) - Method in class org.javaabf.ABF
 
getAbsoluteTime(long) - Method in class org.javaabf.ABF18_parser
Returns the absolute time for the sample row in milliseconds"""
getAbsoluteTime(long) - Method in class org.javaabf.ABF2_parser
Returns the absolute time for the sample row in milliseconds"""
getAbsoluteTime(long) - Method in interface org.javaabf.ABF_parser
Returns the absolute time for the sample row in milliseconds"""
getAbsoluteTime(long) - Method in class org.javaabf.AbstractABF_parser
Returns the absolute time for the sample row in milliseconds"""
getActiveChannels() - Method in class ij.CompositeImage
 
getActiveWindow() - Static method in class ij.WindowManager
Returns the front most window or null.
getAdditionalFunctions() - Static method in class ij.macro.Interpreter
 
getAllFields() - Method in class com.jmatio.types.MLStructure
Gets all field from sruct array as flat list of fields.
getAngle() - Method in class ij.gui.PolygonRoi
Returns the angle in degrees between the first two segments of this polyline.
getAngle(int, int, int, int) - Method in class ij.gui.Roi
Returns the angle in degrees between the specified line and a horizontal line.
getAngle() - Method in class ij.gui.TextRoi
 
getAnimate() - Method in class ij.gui.StackWindow
 
getAnnotatedImage(int, int) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getAnnotations() - Method in class ij.plugin.frame.ChartFramePlugIn
Returns a list of XYAnnotations on the chart.
getAntialiased() - Method in class ij.gui.TextRoi
Returns the state of the 'antialiased' instance variable.
getApplet() - Static method in class ij.IJ
Returns the Applet that created this ImageJ or null if running as an application.
getArea() - Method in class ij.wave.Burst
Returns the area under the full burst.
getArgs() - Static method in class ij.ImageJ
Returns the command line arguments passed to ImageJ.
getArray() - Method in class com.jmatio.types.MLDouble
Gets two-dimensional real array.
getArray() - Method in class com.jmatio.types.MLInt16
Gets two-dimensional real array.
getArray() - Method in class com.jmatio.types.MLInt32
Gets two-dimensional real array.
getArray() - Method in class com.jmatio.types.MLInt64
Gets two-dimensional real array.
getArray() - Method in class com.jmatio.types.MLInt8
Gets two-dimensional real array.
getArray() - Method in class com.jmatio.types.MLUInt64
Gets two-dimensional real array.
getArray() - Method in class com.jmatio.types.MLUInt8
Gets two-dimensional real array.
getArray() - Method in class ij.wave.Waves
Returns this collection of Waves as an array.
getAutoPulseLaser() - Static method in class org.jah.Configuration_
 
getAutoThreshold() - Method in class ij.process.ImageProcessor
Returns a pixel value (threshold) that can be used to divide the image into objects and background.
getAutoThreshold(int[]) - Method in class ij.process.ImageProcessor
This is a version of getAutoThreshold() that uses a histogram passed as an argument.
getAvailableLayoutComponents() - Static method in class ij.WindowManager
 
getAvailableLayoutComponents(String) - Static method in class ij.WindowManager
 
getAvailableLayoutComponents(String, boolean) - Static method in class ij.WindowManager
 
getAvailableLayouts() - Static method in class ij.WindowManager
 
getAverageDistanceBetweenROIs(Roi[]) - Static method in class org.jah.JAH_Utils
Calculates the Euclidean distance between the centroids of two Rois passed as arguments (in pixel values).
getAvgZProjection(ImagePlus, ImagePlus) - Static method in class org.jah.JAH_Utils
 
getAxes() - Method in class ij.plugin.frame.ChartFramePlugIn
Returns a list with all the axes.
getAxis(String) - Method in class ij.plugin.frame.ChartFramePlugIn
Returns the Axis corresponding to the axis label.
getAxisExtents(String) - Method in class ij.plugin.frame.ChartFramePlugIn
Returns the drawable extents for the axis given by the name.
getAxisRange(String) - Method in class ij.plugin.frame.ChartFramePlugIn
Returns the axis range
getBackgroundColor() - Static method in class ij.gui.Toolbar
 
getBackgroundRes(int) - Static method in class org.jah.HologConfiguration_
 
getBackgroundValue() - Method in class ij.process.ByteProcessor
Returns the background fill value.
getBackgroundValue() - Method in class ij.process.ColorProcessor
Returns the background fill value.
getBackgroundValue() - Method in class ij.process.FloatProcessor
Always returns 0.
getBackgroundValue() - Method in class ij.process.ImageProcessor
Returns the background fill value.
getBackgroundValue() - Method in class ij.process.ShortProcessor
Always returns 0.
getBaseDirectory() - Static method in class org.jah.Configuration_
 
getBatchModeImage(int) - Static method in class ij.macro.Interpreter
 
getBatchModeImageCount() - Static method in class ij.macro.Interpreter
 
getBatchModeImageIDs() - Static method in class ij.macro.Interpreter
 
getBatchModeRoiManager() - Static method in class ij.macro.Interpreter
Returns the batch mode RoiManager instance.
getBeamRes(int) - Static method in class org.jah.HologConfiguration_
 
getBestIndex(Color) - Method in class ij.process.ColorProcessor
Always returns 0 since RGB images do not use LUTs.
getBestIndex(Color) - Method in class ij.process.ImageProcessor
Returns the LUT index that's the best match for this color.
getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.FloatProcessor
This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
getBicubicInterpolatedPixel(double, double, ImageProcessor) - Method in class ij.process.ImageProcessor
This method is from Chapter 16 of "Digital Image Processing: An Algorithmic Introduction Using Java" by Burger and Burge (http://www.imagingbook.com/).
getBin3ImageHeight() - Static method in class org.jah.Configuration_
 
getBin3ImageWidth() - Static method in class org.jah.Configuration_
 
getBitDepth() - Method in class ij.ImagePlus
Returns the bit depth, 8, 16, 24 (RGB) or 32.
getBitDepth() - Method in class ij.ImageStack
Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).
getBitDepth() - Method in class ij.process.ByteProcessor
 
getBitDepth() - Method in class ij.process.ColorProcessor
 
getBitDepth() - Method in class ij.process.FloatProcessor
 
getBitDepth() - Method in class ij.process.ImageProcessor
Returns the bit depth, 8, 16, 24 (RGB) or 32.
getBitDepth() - Method in class ij.process.ShortProcessor
 
getBitDepth() - Method in class ij.VirtualStack
Returns the bit depth (8, 16, 24 or 32), or 0 if the bit depth is not known.
getBits(int) - Method in class ij.io.BitBuffer
 
getBlankImage(double) - Method in class ij.gui.LayoutComponent
 
getBlockIncrement() - Method in class ij.gui.ScrollbarWithLabel
 
getBlue(String) - Static method in class ij.plugin.Colors
 
getBlues() - Method in class ij.LookUpTable
 
getBoolean(String, boolean) - Static method in class ij.Prefs
Finds a boolean in IJ_Props or IJ_Prefs.txt.
getBottomProgressBar() - Method in class ij.ImageJ
 
getBoundingRect() - Method in class ij.gui.Roi
Deprecated. replaced by getBounds()
getBounds() - Method in class ij.gui.Arrow
Return the bounding rectangle of this arrow.
getBounds() - Method in class ij.gui.Line
Return the bounding rectangle of this line.
getBounds() - Method in class ij.gui.Roi
Return this selection's bounding rectangle.
getBounds() - Method in class ij.process.FloatPolygon
 
getBrightness() - Method in class ij.process.ColorProcessor
Returns brightness as a FloatProcessor.
getBrushSize() - Static method in class ij.gui.Toolbar
Returns the size of the brush tool, or 0 if the brush tool is not enabled.
getBufferedImage() - Method in class ij.ImagePlus
Returns a copy of this image as an 8-bit or RGB BufferedImage.
getBufferedImage() - Method in class ij.process.ByteProcessor
Returns this image as a BufferedImage.
getBufferedImage() - Method in class ij.process.FloatProcessor
Returns this image as an 8-bit BufferedImage.
getBufferedImage() - Method in class ij.process.ImageProcessor
Returns this image as a BufferedImage.
getBufferedImage() - Method in class ij.process.ShortProcessor
Returns this image as an 8-bit BufferedImage .
getBurst(int) - Method in class ij.wave.Bursts
 
getBurstCycleIndices(Wave, double, double, double, double) - Static method in class ij.wave.CTA_Utils
 
getBurstCycleIndices(Wave, double, double, double, double, boolean, boolean) - Static method in class ij.wave.CTA_Utils
 
getBurstCycleIndicesBelowThreshold(Wave, double, double, double, double) - Static method in class ij.wave.CTA_Utils
 
getBurstCycleIndicesBelowThreshold(Wave, double, double, double, double, boolean, boolean) - Static method in class ij.wave.CTA_Utils
I need to check that the advance step is working correctly here (probably not)
getBurstCycleIndicesFromTriggerMarkers(ArrayList) - Static method in class ij.wave.CTA_Utils
 
getBurstMarkers() - Method in class ij.wave.Bursts
Returns a list of WaveMarkers that can be added to the ChartFramePlugins.
getBurstMarkers(ArrayList) - Static method in class ij.wave.WaveUtils
Returns the WaveMarkers of type BURST in the list passed as argument.
getBurstPeriodAverage(ArrayList) - Static method in class ij.wave.WaveUtils
 
getBurstPeriodAverage(ArrayList, boolean) - Static method in class ij.wave.WaveUtils
 
getBurstPeriods(ArrayList) - Static method in class ij.wave.WaveUtils
 
getBurstPeriods(ArrayList, boolean) - Static method in class ij.wave.WaveUtils
 
getBurstPeriodStderr(ArrayList) - Static method in class ij.wave.WaveUtils
 
getBurstPeriodStdev(ArrayList) - Static method in class ij.wave.WaveUtils
 
getBurstPeriodStdev(ArrayList, boolean) - Static method in class ij.wave.WaveUtils
 
getBursts(Wave, String, Vector) - Static method in class ij.wave.Burst_Utils
Returns the bursts indicated by the indiceVectors (time values) from the Wave passed as argument.
getBursts(Wave[], String, Vector) - Static method in class ij.wave.Burst_Utils
Returns an array of bursts indicated by the indiceVectors from the array of Waves passed as argument.
getBursts(double) - Method in class ij.wave.Wave
Identifies bursts based on an absolute threshold crossing algorithm.
getBursts(double, boolean) - Method in class ij.wave.Wave
Identifies bursts based on an absolute threshold crossing algorithm.
getBursts(String, double, double, double, double, boolean) - Method in class ij.wave.Wave
Identifies bursts based on an absolute threshold crossing algorithm.
getBursts(String, Vector) - Method in class ij.wave.Wave
 
getBurstsFromLocalMaxima(double, double, Wave) - Method in class ij.wave.Wave
 
getBurstsFromPeakDetector(double, double, double) - Method in class ij.wave.Wave
 
getBurstStartIndex() - Method in class ij.wave.Burst
Returns the index that this burst's wave starts at relative to a longer wave period.
getBurstsWithinPeakAmplitudeRange(double, double) - Method in class ij.wave.Bursts
Returns the Bursts from this instance that have peaks within the range passed as arguments.
getBurstTimes() - Method in class ij.wave.Bursts
Returns the peak times for all of the bursts in this instance.
getButton() - Method in class ij.gui.WaitForUserDialog
Returns a reference to the 'OK' button
getButtons() - Method in class ij.gui.GenericDialog
Returns references to the "OK" ("Yes"), "Cancel", and if present, "No" buttons as an array.
getButtonSize() - Static method in class ij.gui.Toolbar
 
getByteArray(T) - Method in interface com.jmatio.types.ByteStorageSupport
 
getByteArray(Double) - Method in class com.jmatio.types.MLDouble
 
getByteArray(Short) - Method in class com.jmatio.types.MLInt16
 
getByteArray(Integer) - Method in class com.jmatio.types.MLInt32
 
getByteArray(Long) - Method in class com.jmatio.types.MLInt64
 
getByteArray(Byte) - Method in class com.jmatio.types.MLInt8
 
getByteArray(Float) - Method in class com.jmatio.types.MLSingle
 
getByteArray(Double) - Method in class com.jmatio.types.MLSparse
 
getByteArray(Long) - Method in class com.jmatio.types.MLUInt64
 
getByteArray(Byte) - Method in class com.jmatio.types.MLUInt8
 
getByteBuffer() - Method in class com.jmatio.io.HeapBufferDataOutputStream
 
getByteRow(ImageStack, int, int, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
 
getBytes() - Method in class ij.process.LUT
 
getBytesAllocated() - Method in interface com.jmatio.types.ByteStorageSupport
 
getBytesAllocated() - Method in class com.jmatio.types.MLDouble
 
getBytesAllocated() - Method in class com.jmatio.types.MLInt16
 
getBytesAllocated() - Method in class com.jmatio.types.MLInt32
 
getBytesAllocated() - Method in class com.jmatio.types.MLInt64
 
getBytesAllocated() - Method in class com.jmatio.types.MLInt8
 
getBytesAllocated() - Method in class com.jmatio.types.MLSingle
 
getBytesAllocated() - Method in class com.jmatio.types.MLSparse
 
getBytesAllocated() - Method in class com.jmatio.types.MLUInt64
 
getBytesAllocated() - Method in class com.jmatio.types.MLUInt8
 
getBytesPerPixel() - Method in class ij.ImagePlus
Returns the number of bytes per pixel.
getBytesPerPixel() - Method in class ij.io.FileInfo
Returns the number of bytes used per pixel.
getC() - Method in class ij.ImagePlus
Returns the current hyperstack channel position.
getCalibration() - Method in class ij.ImagePlus
Returns this image's calibration.
getCalibrationTable() - Method in class ij.process.ImageProcessor
Returns the calibration table or null.
getCanvas() - Method in class ij.gui.ImageWindow
 
getCanvas() - Method in class ij.ImagePlus
Returns the ImageCanvas being used to display this image, or null.
getCaseSensitive() - Method in class ij.util.WildcardMatch
Returns the current state of case sensitivity.
getChannel() - Method in class ij.ImagePlus
 
getChannel(ImagePlus, int) - Static method in class ij.plugin.ChannelSplitter
 
getChannel(int) - Method in class ij.process.ColorProcessor
Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a byte array.
getChannel(int, ByteProcessor) - Method in class ij.process.ColorProcessor
Returns the specified plane (1=red, 2=green, 3=blue, 4=alpha) as a ByteProcessor.
getChannelColor() - Method in class ij.CompositeImage
 
getChannelData(int) - Method in class org.javaabf.ABF
 
getChannelData(int, double, double, int) - Method in class org.javaabf.ABF
 
getChannelData(int, int) - Method in class org.javaabf.ABF
 
getChannelData(int) - Method in class org.javaabf.ABF18_parser
Returns a list of the whole channel"s data."""
getChannelData(int, int) - Method in class org.javaabf.ABF18_parser
 
getChannelData(int) - Method in interface org.javaabf.ABF_parser
Returns a list of the whole channel"s data."""
getChannelData(int, int) - Method in interface org.javaabf.ABF_parser
 
getChannelData(int, double, double, int) - Method in interface org.javaabf.ABF_parser
 
getChannelData(int) - Method in class org.javaabf.AbstractABF_parser
Returns a list of the whole channel"s data."""
getChannelData(int, double, double, int) - Method in class org.javaabf.AbstractABF_parser
 
getChannelData(int, int) - Method in class org.javaabf.AbstractABF_parser
 
getChannelDataByEpoch(Epoch, int, int) - Method in class org.javaabf.ABF
 
getChannelDataByEpoch(Epoch, int, int) - Method in interface org.javaabf.ABF_parser
 
getChannelDataByEpoch(Epoch, int, int) - Method in class org.javaabf.AbstractABF_parser
 
getChannelDataByName(String) - Method in class org.javaabf.ABF
 
getChannelIndexByName(String) - Method in class org.javaabf.ABF
 
getChannelIndices() - Method in class org.javaabf.ABF
 
getChannelIndices() - Method in class org.javaabf.ABF18_parser
Returns a list of the channel indices, which is simply the order in which the channels appear in the file."""
getChannelIndices() - Method in class org.javaabf.ABF2_parser
Returns a list of the channel indices, which is simply the order in which the channels appear in the file."""
getChannelIndices() - Method in interface org.javaabf.ABF_parser
Returns a list of the channel indices, which is simply the order in which the channels appear in the file."""
getChannelIndices() - Method in class org.javaabf.AbstractABF_parser
Returns a list of the channel indices, which is simply the order in which the channels appear in the file."""
getChannelLut(int) - Method in class ij.CompositeImage
 
getChannelLut() - Method in class ij.CompositeImage
 
getChannelNameByIndex(int) - Method in class org.javaabf.ABF
 
getChannelNames(String) - Method in class org.jah.ElectrophysManager
 
getChannelNames() - Method in class org.javaabf.ABF
 
getChannelNames() - Method in class org.javaabf.ABF18_parser
 
getChannelNames() - Method in class org.javaabf.ABF2_parser
 
getChannelNames() - Method in interface org.javaabf.ABF_parser
 
getChannelNames() - Method in class org.javaabf.ABFpClamp9_parser
 
getChannelNames() - Method in class org.javaabf.AbstractABF_parser
 
getChannelNumberByIndex(int) - Method in class org.javaabf.AbstractABF_parser
 
getChannelNumbers() - Method in class org.javaabf.ABF
 
getChannelNumbers() - Method in class org.javaabf.ABF18_parser
 
getChannelNumbers() - Method in class org.javaabf.ABF2_parser
 
getChannelNumbers() - Method in interface org.javaabf.ABF_parser
 
getChannelNumbers() - Method in class org.javaabf.ABFpClamp9_parser
 
getChannelNumbers(boolean) - Method in class org.javaabf.ABFpClamp9_parser
 
getChannelNumbers() - Method in class org.javaabf.AbstractABF_parser
 
getChannelProcessor() - Method in class ij.CompositeImage
 
getChannelProcessor() - Method in class ij.ImagePlus
Returns a reference to the current ImageProcessor.
getChannelUnits() - Method in class org.javaabf.ABF
 
getChannelUnits() - Method in class org.javaabf.ABF18_parser
 
getChannelUnits() - Method in class org.javaabf.ABF2_parser
 
getChannelUnits() - Method in interface org.javaabf.ABF_parser
 
getChannelUnits() - Method in class org.javaabf.ABFpClamp9_parser
 
getChannelUnits() - Method in class org.javaabf.AbstractABF_parser
 
getChar(int, int) - Method in class com.jmatio.types.MLChar
 
getChart() - Method in class ij.plugin.frame.ChartFramePlugIn
 
getCharts() - Static method in class ij.WindowManager
 
getCheckboxes() - Method in class ij.gui.GenericDialog
Returns the Vector containing the Checkboxes.
getChoices() - Method in class ij.gui.GenericDialog
Returns the Vector containing the Choices.
getChunk(long, long) - Method in class org.javaabf.ABF18_parser
 
getChunk(long, long) - Method in class org.javaabf.ABF2_parser
 
getChunk(long, long) - Method in class org.javaabf.AbstractABF_parser
 
getClassLoader() - Static method in class ij.IJ
Returns the class loader ImageJ uses to run plugins or the system class loader if Menus.getPlugInsPath() returns null.
getClassName() - Method in class com.jmatio.types.MLJavaObject
 
getClassName() - Method in class com.jmatio.types.MLObject
 
getCleanZscore() - Method in class ij.wave.Wave
 
getCleanZscore(double) - Method in class ij.wave.Wave
 
getClipboard() - Static method in class ij.ImagePlus
Returns the internal clipboard or null if the internal clipboard is empty.
getCluster1() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getCluster2() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getCluster3() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getCluster4() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getClusteredWaves(ViewFrame) - Method in class ij.wave.Waves
Returns the Waves associated with the front ClusterFramePlugIn's selected cluster.
getClusters() - Static method in class ij.WindowManager
 
getClustersLowerBound(Range, Range, Range, Range) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getClustersUpperBound(Range, Range, Range, Range) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getCode() - Method in class ij.macro.Program
 
getCoefficients() - Method in class ij.measure.Calibration
Returns the calibration function coefficients.
getColor() - Method in class ij.gui.ColorChooser
Displays a color selection dialog and returns the color selected by the user.
getColor() - Method in class ij.gui.LineLayoutComponent
 
getColor() - Static method in class ij.gui.Roi
Returns the default (global) color used for drawing ROI outlines.
getColor() - Method in class ij.gui.Toolbar
Deprecated. replaced by getForegroundColor()
getColor(String, Color) - Static method in class ij.plugin.Colors
 
getColor(String, Color) - Static method in class ij.Prefs
Finds a color in IJ_Props or IJ_Prefs.txt.
getColor(int, int) - Method in class ij.process.ColorProcessor
 
getColor() - Method in class ij.wave.WaveMarker
 
getColorModel() - Method in class ij.ImageStack
Returns this stack's color model.
getColorModel() - Method in class ij.LookUpTable
 
getColorModel() - Method in class ij.process.ImageProcessor
Returns this processor's color model.
getColorName(Color, String) - Static method in class ij.plugin.Colors
 
getColors(String...) - Static method in class ij.plugin.Colors
 
getColumn(int) - Method in class ij.measure.ResultsTable
Returns a copy of the given column as a float array, or null if the column is empty.
getColumn(int, int, int[], int) - Method in class ij.process.ImageProcessor
Returns the pixel values down the column starting at (x,y).
getColumnAsDoubles(int) - Method in class ij.measure.ResultsTable
Returns a copy of the given column as a double array, or null if the column is empty.
getColumnClass(int) - Method in class ij.plugin.frame.table.EpochTableModel
 
getColumnCount() - Method in class ij.plugin.frame.table.EpochTableModel
 
getColumnHeading(int) - Method in class ij.measure.ResultsTable
Returns the heading of the specified column or null if the column is empty.
getColumnHeadings() - Method in class ij.measure.ResultsTable
Returns a tab or comma delimited string containing the column headings.
getColumnHeadings() - Method in class ij.text.TextPanel
Returns the column headings as a tab-delimited string.
getColumnIndex(String) - Method in class ij.measure.ResultsTable
Returns the index of the first column with the given heading.
getColumnName(int) - Method in class ij.plugin.frame.table.EpochTableModel
 
getCombinedDomainXYPlot(Waves, boolean, int, double, double) - Static method in class ij.util.PlotterUtils
 
getCommand() - Static method in class ij.Executer
Returns the last command executed.
getCommand() - Static method in class ij.plugin.frame.Recorder
Returns the name of the command currently being recorded, or null.
getCommandName() - Static method in class ij.ImageJ
 
getCommandOptions() - Static method in class ij.plugin.frame.Recorder
Used by GenericDialog to determine if any options have been recorded.
getCommands() - Static method in class ij.Menus
Returns the hashtable that associates commands with plugins.
getComments() - Method in class ij.wave.Wave
 
getComments() - Method in class org.javaabf.ABF
 
getComments(Epoch) - Method in class org.javaabf.ABF
 
getComments(String) - Method in interface org.javaabf.ABF_parser
 
getComments(Epoch, String) - Method in interface org.javaabf.ABF_parser
 
getComments() - Method in class org.javaabf.AbstractABF_parser
 
getComments(String) - Method in class org.javaabf.AbstractABF_parser
 
getComments(Epoch, String) - Method in class org.javaabf.AbstractABF_parser
 
getComments() - Method in class org.javaabf.Comments
 
getCommentsByEpoch(double, double) - Method in class org.jah.ElectrophysManager
 
getCommentsByPattern(String) - Method in class org.javaabf.AbstractABF_parser
 
getCommentsInEpochRange(String, String) - Method in class org.jah.ElectrophysManager
 
getCommentsList() - Method in class org.javaabf.Comments
 
getCompletedMinimizations() - Method in class ij.measure.Minimizer
Get number of minimizations completed (i.e. not aborted or stopped because the number of minimization was exceeded).
getComplexTransform() - Method in class ij.process.FHT
Converts this FHT to a complex Fourier transform and returns it as a two slice stack.
getCompositeMode() - Method in class ij.ImagePlus
Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.
getContent() - Method in class com.jmatio.io.MatFileReader
Returns a map of MLArray objects that were inside MAT-file.
getContrast() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getControlPanelProperties() - Static method in class ij.Prefs
 
getConvexHull() - Method in class ij.gui.PolygonRoi
Uses the gift wrap algorithm to find the convex hull and returns it as a Polygon.
getConvexHull() - Method in class ij.gui.Roi
 
getConvexHull() - Method in class ij.gui.ShapeRoi
 
getCopy() - Method in class ij.process.FHT
Returns a clone of this FHT.
getCornerDiameter() - Method in class ij.gui.Roi
Returns the rounded rectangle corner diameter (pixels).
getCorrelationTime() - Method in class ij.wave.Wave
 
getCorrelationValue() - Method in class ij.wave.Wave
 
getCount() - Method in class ij.plugin.frame.RoiManager
Returns the ROI count.
getCount() - Method in class ij.plugin.frame.WaveManager
Returns the Wave count.
getCounter() - Method in class ij.measure.ResultsTable
Returns the current value of the measurement counter.
getCounter() - Static method in class ij.plugin.filter.Analyzer
Returns the current measurement count.
getCPosition() - Method in class ij.gui.Roi
Returns the channel position of this ROI, or zero if this ROI is not associated with a particular channel.
getCrossLoc() - Method in class ij.plugin.Orthogonal_Views
 
getCTable() - Method in class ij.measure.Calibration
Returns the calibration table.
getCurrentColorModel() - Method in class ij.process.ImageProcessor
Returns the current color model, which may have been modified by setMinAndMax() or setThreshold().
getCurrentErrStream() - Static method in class ij.io.LogStream
Returns the redirection stream for System.err if it exists.
getCurrentFont() - Method in class ij.gui.TextRoi
Returns the current (instance) font.
getCurrentImage() - Static method in class ij.WindowManager
Returns a reference to the active image or null if there isn't one.
getCurrentOutStream() - Static method in class ij.io.LogStream
Returns the redirection stream for System.out if it exists.
getCurrentPasteMode() - Static method in class ij.gui.Roi
Returns the current paste transfer mode.
getCurrentSlice() - Method in class ij.ImagePlus
Returns the current stack index (one-based) or 1 if this is a single image.
getCurrentWindow() - Static method in class ij.WindowManager
Returns the active ImageWindow.
getCursorLoc() - Method in class ij.gui.ImageCanvas
Returns the current cursor location in image coordinates.
getCustomRoi() - Method in class ij.gui.ImageCanvas
 
getCValue(int) - Method in class ij.measure.Calibration
Converts a raw pixel value to a density calibrated value.
getCValue(double) - Method in class ij.measure.Calibration
Converts a raw pixel value to a density calibrated value.
getData() - Method in class com.jmatio.io.MatFileReader
Deprecated. use getContent which returns a Map to provide easier access to MLArrays contained in MAT-file
getData(long, int) - Method in class org.javaabf.ABF
 
getData(long, int) - Method in class org.javaabf.ABF18_parser
"""Returns a specific data value at a time point in a specific channel."""
getData(long, int) - Method in interface org.javaabf.ABF_parser
"""Returns a specific data value at a time point in a specific channel."""
getData(long, int) - Method in class org.javaabf.AbstractABF_parser
"""Returns a specific data value at a time point in a specific channel."""
getDataByAbsoluteTime(long, int) - Method in class org.javaabf.ABF
 
getDataByRelativeTime(long, int) - Method in class org.javaabf.ABF
 
getDataFormat() - Method in class org.javaabf.ABF
 
getDataFormat() - Method in class org.javaabf.ABF18_parser
 
getDataFormat() - Method in class org.javaabf.ABF2_parser
 
getDataFormat() - Method in interface org.javaabf.ABF_parser
 
getDataFormat() - Method in class org.javaabf.AbstractABF_parser
 
getDatasets(ArrayList, XYPlot) - Method in class ij.plugin.frame.ChartFramePlugIn
 
getDatasets() - Method in class ij.plugin.frame.ChartFramePlugIn
 
getDebugInfo() - Method in class ij.gui.PolygonRoi
 
getDebugInfo() - Method in class ij.gui.Roi
 
getDecimalPlaces(double, double) - Static method in class ij.util.Tools
Returns the number of decimal places need to display two numbers.
getDefault16bitRange() - Static method in class ij.ImagePlus
Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 15 or 16.
getDefaultBackgroundRes(int) - Static method in class org.jah.HologConfiguration_
 
getDefaultBeamRes(int) - Static method in class org.jah.HologConfiguration_
 
getDefaultChartHeight() - Static method in class org.jah.Configuration_
 
getDefaultChartWidth() - Static method in class org.jah.Configuration_
 
getDefaultColorModel() - Method in class ij.process.ImageProcessor
Returns the default grayscale IndexColorModel.
getDefaultDirectory() - Static method in class ij.io.OpenDialog
Returns the current working directory, which may be null.
getDefaultDirectory() - Static method in class ij.Prefs
Returns the default directory, if any, or null.
getDefaultDoubleHeaded() - Static method in class ij.gui.Arrow
 
getDefaultFillColor() - Static method in class ij.gui.Roi
 
getDefaultHeading(int) - Static method in class ij.measure.ResultsTable
 
getDefaultHeadSize() - Static method in class ij.gui.Arrow
 
getDefaultLeanDisplay() - Static method in class org.jah.Configuration_
 
getDefaultOutline() - Static method in class ij.gui.Arrow
 
getDefaultSourceWidth(int) - Static method in class org.jah.HologConfiguration_
 
getDefaultStrokeColor() - Static method in class ij.plugin.RectToolOptions
 
getDefaultStrokeWidth() - Static method in class ij.plugin.RectToolOptions
 
getDefaultStyle() - Static method in class ij.gui.Arrow
 
getDefaultWidth() - Static method in class ij.gui.Arrow
 
getDefaultXOffset(int) - Static method in class org.jah.HologConfiguration_
 
getDefaultYOffset(int) - Static method in class org.jah.HologConfiguration_
 
getDendroView() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getDensity() - Method in class ij.wave.Burst
Returns the area divided by the duration of the full burst.
getDescription() - Method in class com.jmatio.io.MatFileHeader
Gets descriptive text
getDescriptionString() - Method in class ij.io.FileSaver
Returns a string containing information about the specified image.
getDimensions() - Method in class com.jmatio.types.MLArray
 
getDimensions() - Method in class ij.ImagePlus
Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.
getDimensions(boolean) - Method in class ij.ImagePlus
 
getDir(String) - Method in class ij.io.Opener
 
getDir(String) - Static method in class ij.Macro
 
getDirectory(String) - Static method in class ij.IJ
Returns the path to the home ("user.home"), startup, ImageJ, plugins, macros, luts, temp, current or image directory if title is "home", "startup", "imagej", "plugins", "macros", "luts", "temp", "current", "default", "image", otherwise, displays a dialog and returns the path to the directory selected by the user.
getDirectory() - Method in class ij.io.DirectoryChooser
Returns the directory selected by the user.
getDirectory() - Method in class ij.io.OpenDialog
Returns the selected directory.
getDirectory() - Method in class ij.io.SaveDialog
Returns the selected directory.
getDirectory() - Method in class ij.macro.Functions
 
getDirectory() - Method in class ij.VirtualStack
Returns the path to the directory containing the images.
getDirectoryURL(String) - Static method in class ij.IJ
 
getDisplayList() - Method in class ij.gui.ImageCanvas
Deprecated. replaced by ImagePlus.getOverlay()
getDisplayRangeMax() - Method in class ij.CompositeImage
 
getDisplayRangeMax() - Method in class ij.ImagePlus
 
getDisplayRangeMin() - Method in class ij.CompositeImage
 
getDisplayRangeMin() - Method in class ij.ImagePlus
 
getDistanceBetweenRois() - Method in class ij.wave.CrosscorrelationWave
 
getDomainAxes() - Method in class ij.plugin.frame.ChartFramePlugIn
Returns a list with all the domain axes.
getDoScaling() - Static method in class ij.process.ImageConverter
Returns true if scaling is enabled.
getDouble(String, double) - Static method in class ij.Prefs
Looks up a real number in IJ_Props or IJ_Prefs.txt.
getDoubleFromArrayList(ArrayList) - Method in class ij.gui.Plot
 
getDoubleHeaded() - Method in class ij.gui.Arrow
 
getDrawBackgrounds() - Method in class ij.gui.Overlay
 
getDrawLabels() - Method in class ij.gui.Overlay
 
getDrawLabels() - Method in class ij.plugin.frame.RoiManager
 
getDrawNames() - Method in class ij.gui.Overlay
 
getDrawOffset() - Method in class ij.gui.Line
 
getDrawOffset() - Method in class ij.gui.PolygonRoi
 
getDrawOffset() - Method in class ij.gui.Roi
Returns true if this is a PolygonRoi that supports sub-pixel resolution and polygons are drawn on zoomed images offset down and to the right by 0.5 pixels..
getDrawStringMode() - Method in class ij.gui.TextRoi
 
getDuration() - Method in class ij.wave.Burst
Returns the length of the full burst in seconds.
getEditor() - Method in class ij.macro.Interpreter
 
getEditor() - Method in class ij.plugin.NewPlugin
Returns the Editor the newly created macro or plugin was opened in.
getElectrophysComments() - Method in class org.jah.ElectrophysManager
 
getElectrophysFiles() - Method in class org.jah.ElectrophysManager
 
getElectrophysSamplingRateHz() - Static method in class org.jah.Configuration_
 
getEnd() - Method in class org.javaabf.Epoch
 
getEnd_s() - Method in class org.javaabf.Epoch
 
getEndianIndicator() - Method in class com.jmatio.io.MatFileHeader
Gets endian indicator.
getEndTime() - Method in class org.javaabf.ABF
 
getEndTime_s(String) - Method in class org.jah.ElectrophysManager
 
getEnsembleFiles() - Static method in class ij.wave.WaveUtils
 
getEnsembleFiles(String) - Static method in class ij.wave.WaveUtils
 
getEnsembles() - Static method in class ij.wave.WaveUtils
 
getEnsembles(File[]) - Static method in class ij.wave.WaveUtils
 
getEpisodes() - Method in class ij.wave.EpisodicWave
 
getEpoch(int) - Method in class ij.plugin.frame.table.EpochTableModel
 
getEpoch(String) - Method in class ij.plugin.frame.table.EpochTableModel
 
getEpoch(String) - Static method in class org.javaabf.EpochUtils
 
getEpochByName(String) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
getEpochChannelName() - Static method in class org.jah.Configuration_
 
getEpochCommentMaxLength() - Static method in class org.jah.Configuration_
 
getEpochCommentPattern() - Static method in class org.jah.Configuration_
 
getEpochFactor() - Static method in class org.jah.Configuration_
 
getEpochsByCommentPattern(String) - Method in class org.jah.ElectrophysManager
 
getEpochsByCommentPattern(String, String) - Method in class org.jah.ElectrophysManager
 
getEpochsByCommentPattern(String) - Method in class org.javaabf.ABF
 
getEpochsByCommentPattern(String) - Method in interface org.javaabf.ABF_parser
 
getEpochsByCommentPattern(String) - Method in class org.javaabf.AbstractABF_parser
 
getEpochThreshold() - Static method in class org.jah.Configuration_
 
getErrorMessage() - Method in class ij.gui.GenericDialog
Returns an error message if getNextNumber was unable to convert a string into a number, otherwise, returns null.
getErrorMessage() - Static method in class ij.IJ
Returns the last error message written by IJ.error() or null if there was no error since the last time this method was called.
getEscapeChar() - Method in class ij.util.WildcardMatch
Returns the character used to escape the wildcard functionality of a wildcard character.
getExperimentDuration() - Method in class org.javaabf.ABF
 
getExperimentDuration() - Method in class org.javaabf.ABF18_parser
Returns the duration of the experiment in milliseconds"""
getExperimentDuration() - Method in class org.javaabf.ABF2_parser
Returns the duration of the experiment in milliseconds"""
getExperimentDuration() - Method in interface org.javaabf.ABF_parser
Returns the duration of the experiment in milliseconds"""
getExperimentDuration() - Method in class org.javaabf.AbstractABF_parser
Returns the duration of the experiment in milliseconds"""
getExperiments() - Method in class org.jah.ElectrophysManager
 
getExtensionFunctions() - Method in interface ij.macro.MacroExtension
 
getf(int, int) - Method in class ij.process.ByteProcessor
 
getf(int) - Method in class ij.process.ByteProcessor
 
getf(int, int) - Method in class ij.process.ColorProcessor
 
getf(int) - Method in class ij.process.ColorProcessor
 
getf(int, int) - Method in class ij.process.FloatProcessor
 
getf(int) - Method in class ij.process.FloatProcessor
 
getf(int, int) - Method in class ij.process.ImageProcessor
Returns the value of the pixel at (x,y) as a float.
getf(int) - Method in class ij.process.ImageProcessor
 
getf(int, int) - Method in class ij.process.ShortProcessor
 
getf(int) - Method in class ij.process.ShortProcessor
 
getFallTime() - Method in class ij.wave.Burst
Returns the time of the maximum amplitude relative to the end of the burst (in seconds).
getFallTimeToFwhm() - Method in class ij.wave.Burst
Not implemented yet
getFeretsDiameter() - Method in class ij.gui.Roi
Returns Feret's diameter, the greatest distance between any two points along the ROI boundary.
getFeretValues() - Method in class ij.gui.EllipseRoi
 
getFeretValues() - Method in class ij.gui.Roi
Caculates "Feret" (maximum caliper width), "FeretAngle" and "MinFeret" (minimum caliper width), "FeretX" and "FeretY".
getFeretValues() - Method in class ij.gui.ShapeRoi
Caculates "Feret" (maximum caliper width) and "MinFeret" (minimum caliper width).
getField(String) - Method in class com.jmatio.types.MLStructure
Gets a value of the field described by name from current struct in struct array or null if the field doesn't exist.
getField(String, int, int) - Method in class com.jmatio.types.MLStructure
Gets a value of the field described by name from (m,n)'th struct in struct array or null if the field doesn't exist.
getField(String, int) - Method in class com.jmatio.types.MLStructure
Gets a value of the field described by name from index'th struct in struct array or null if the field doesn't exist.
getFieldNames() - Method in class com.jmatio.types.MLStructure
Returns the Collection of keys for this structure.
getFileFormat(String) - Static method in class ij.io.Opener
 
getFileInfo() - Method in class ij.ImagePlus
Returns a FileInfo object containing information, including the pixel array, needed to save this image.
getFileInfo() - Method in class ij.io.ImportDialog
Displays the dialog and returns a FileInfo object that can be used to open the image.
getFileName() - Method in class ij.io.OpenDialog
Returns the selected file name.
getFileName() - Method in class ij.io.SaveDialog
Returns the selected file name.
getFileName() - Static method in class ij.plugin.MacroInstaller
 
getFileName(int) - Method in class ij.VirtualStack
Returns the file name of the specified slice, were 1<=n<=nslices.
getFilename() - Method in class org.javaabf.ABF
Returns the .abf file associated with this ABF class.
getFilePath(String) - Static method in class ij.IJ
Displays an open file dialog and returns the path to the choosen file, or returns null if the dialog is canceled.
getFilePointer() - Method in class ij.io.RandomAccessStream
 
getFileSeparator() - Static method in class ij.Prefs
Returns the file.separator system property.
getFileType(String) - Method in class ij.io.Opener
Attempts to determine the image file type by looking for 'magic numbers' and the file name extension.
getFillColor() - Method in class ij.gui.Roi
Returns the fill color used to display this ROI, or null if it is displayed transparently.
getFit() - Method in class ij.measure.CurveFitter
returns the code of the fit type of the fit performed
getFitCode(String) - Static method in class ij.measure.CurveFitter
Returns the code for a fit with given name as defined in fitList, or -1 if not found
getFitGoodness() - Method in class ij.measure.CurveFitter
Get a measure of "goodness of fit" where 1.0 is best.
getFixedMax() - Static method in class ij.gui.ProfilePlot
Returns the profile plot y-axis max.
getFixedMin() - Static method in class ij.gui.ProfilePlot
Returns the profile plot y-axis min.
getFlags() - Method in class com.jmatio.types.MLArray
 
getFloatAngle(double, double, double, double) - Method in class ij.gui.Roi
Returns the angle in degrees between the specified line and a horizontal line.
getFloatArray() - Method in class ij.process.ImageProcessor
Returns a copy of the pixel data as a 2D float array with dimensions [x=0..width-1][y=0..height-1].
getFloatBounds() - Method in class ij.gui.Roi
Return this selection's bounding rectangle.
getFloatBounds() - Method in class ij.process.FloatPolygon
 
getFloatHeight() - Method in class ij.gui.Roi
 
getFloatPoints() - Method in class ij.gui.Line
Returns, as a FloatPolygon, the two points that define this line.
getFloatPolygon() - Method in class ij.gui.Line
If the width of this line is less than or equal to one, returns the starting and ending coordinates as a 2-point FloatPolygon, or, if the width is greater than one, returns an outline of the line as a 4-point FloatPolygon.
getFloatPolygon() - Method in class ij.gui.OvalRoi
Returns this OvalRoi as a FloatPolygon.
getFloatPolygon() - Method in class ij.gui.PolygonRoi
Returns this polygon or polyline as float arrays.
getFloatPolygon() - Method in class ij.gui.Roi
 
getFloatPolygon() - Method in class ij.gui.ShapeRoi
 
getFloatWidth() - Method in class ij.gui.Roi
 
getFont() - Static method in class ij.gui.TextRoi
Returns the name of the global (default) font.
getFont() - Static method in class ij.Menus
 
getFont() - Method in class ij.process.ImageProcessor
Returns the current font.
getFontMetrics() - Method in class ij.process.ImageProcessor
Returns the current FontMetrics.
getFontSize() - Static method in class ij.Menus
Returns the size (in points) used for the fonts in ImageJ menus.
getForegroundColor() - Static method in class ij.gui.Toolbar
 
getFormula() - Method in class ij.measure.CurveFitter
returns a String with the formula of the fit function used
getFrame() - Method in class ij.ImagePlus
 
getFrame(String) - Static method in class ij.WindowManager
Obsolete; replaced by getWindow().
getFrameRate() - Static method in class ij.plugin.Animator
Returns the current animation speed in frames per second.
getFreeColumn(String) - Method in class ij.measure.ResultsTable
Sets the heading of the the first available column and returns that column's index.
getFrontChart() - Static method in class ij.WindowManager
 
getFrontCluster() - Static method in class ij.WindowManager
 
getFrontImage() - Static method in class ij.WindowManager
 
getFrontLayout() - Static method in class ij.WindowManager
 
getFrontWindow() - Static method in class ij.WindowManager
Obsolete; replaced by getActiveWindow.
getFullVersion() - Static method in class ij.IJ
Returns the ImageJ version and build number as a String, for example "1.46n05", or 1.46n99 if there is no build number.
getFunction() - Method in class ij.measure.Calibration
Returns the calibration function ID.
getFunctionValue() - Method in class ij.measure.Minimizer
Get the value of the minimum, i.e. the value associated with the resulting parameters as obtained by getParams().
getFwhmDensity() - Method in class ij.wave.Burst
Returns the area divided by the FWHM duration.
getFwhmDuration() - Method in class ij.wave.Burst
Gets the full-width at half maximum (FWHM) in seconds.
getGlobalCalibration() - Method in class ij.ImagePlus
Returns the system-wide calibration, or null.
getGlobalJustification() - Static method in class ij.gui.TextRoi
Returns the global (default) justification (LEFT, CENTER or RIGHT).
getGlobals() - Method in class ij.macro.Program
 
getGreen(String) - Static method in class ij.plugin.Colors
 
getGreens() - Method in class ij.LookUpTable
 
getHashCode() - Method in class ij.gui.Roi
Returns a hashcode for this Roi that typically changes if it is moved, even though it is still the same object.
getHeader(ImagePlus) - Static method in class ij.plugin.FITS_Writer
Extracts the original FITS header from the Properties object of the ImagePlus image (or from the current slice label in the case of an ImageStack) and returns it as an array of String objects representing each card.
getHeadings() - Method in class ij.measure.ResultsTable
Returns the column headings as an array of Strings.
getHeadSize() - Method in class ij.gui.Arrow
 
getHeight() - Method in class ij.gui.LayoutComponent
 
getHeight() - Method in class ij.ImagePlus
 
getHeight() - Method in class ij.ImageStack
 
getHeight() - Method in class ij.plugin.AVI_Reader
Returns the image height of the virtual stack
getHeight() - Method in class ij.plugin.FileInfoVirtualStack
 
getHeight() - Method in class ij.plugin.ListVirtualStack
 
getHeight() - Method in class ij.process.ImageProcessor
Returns the height of this image in pixels.
getHideOverlay() - Method in class ij.ImagePlus
 
getHigherZoomLevel(double) - Static method in class ij.gui.ImageCanvas
 
getHistogram() - Method in class ij.gui.HistogramWindow
 
getHistogram() - Method in class ij.process.ByteProcessor
 
getHistogram(ImageProcessor) - Method in class ij.process.ByteProcessor
 
getHistogram() - Method in class ij.process.ColorProcessor
 
getHistogram(ImageProcessor) - Method in class ij.process.ColorProcessor
 
getHistogram() - Method in class ij.process.FloatProcessor
Not implemented.
getHistogram() - Method in class ij.process.ImageProcessor
Returns the histogram of the image or ROI.
getHistogram() - Method in class ij.process.ImageStatistics
Returns the histogram as an array of longs.
getHistogram() - Method in class ij.process.ShortProcessor
Returns 65536 bin histogram of the current ROI, which can be non-rectangular.
getHistogramDataset(double[], int) - Static method in class ij.wave.WaveUtils
 
getHistogramDataset(double[], int, double, double) - Static method in class ij.wave.WaveUtils
 
getHistogramMax() - Method in class ij.process.ImageProcessor
Returns the maximum histogram value used for histograms of float images.
getHistogramMin() - Method in class ij.process.ImageProcessor
Returns the minimum histogram value used for histograms of float images.
getHistogramSize() - Method in class ij.process.ImageProcessor
Returns the number of float image histogram bins.
getHomeDir() - Static method in class ij.Prefs
Obsolete, replaced by getImageJDir(), which, unlike this method, returns a path that ends with File.separator.
getHSB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Returns hue, saturation and brightness in 3 byte arrays.
getHSBStack() - Method in class ij.process.ColorProcessor
Returns an ImageStack with three 8-bit slices, representing hue, saturation and brightness
getID() - Method in class ij.ImagePlus
Returns this image's unique numeric ID.
getID() - Method in class org.javaabf.Epoch
 
getIDList() - Static method in class ij.WindowManager
Returns a list of the IDs of open images.
getImage() - Method in class ij.CompositeImage
 
getImage() - Method in class ij.gui.ImageCanvas
Returns the ImagePlus object that is associated with this ImageCanvas.
getImage(double) - Method in class ij.gui.LayoutComponent
 
getImage() - Method in class ij.gui.Roi
Returns the ImagePlus associated with this ROI, or null.
getImage() - Static method in class ij.IJ
Returns a reference to the active image, or displays an error message and aborts the plugin or macro if no images are open.
getImage() - Method in class ij.ImagePlus
Returns this image as a AWT image.
getImage() - Static method in class ij.plugin.Orthogonal_Views
 
getImage(int) - Static method in class ij.WindowManager
For IDs less than zero, returns the ImagePlus with the specified ID.
getImage(String) - Static method in class ij.WindowManager
Returns the first image that has the specified title or null if it is not found.
getImageArray() - Method in class ij.ImageStack
Returns the stack as an array of 1D pixel arrays.
getImageArray() - Method in class ij.VirtualStack
Returns null.
getImageCount() - Static method in class ij.WindowManager
Returns the number of open images.
getImageFromVector(int) - Method in class ij.plugin.frame.SyncWindows
Get ImagePlus from Windows-Vector vwins.
getImageID() - Method in class ij.gui.Roi
Returns the ID of the image associated with this ROI.
getImageInfo(ImagePlus, ImageProcessor) - Method in class ij.plugin.filter.Info
 
getImageJDir() - Static method in class ij.Prefs
Returns the path, ending in File.separator, to the ImageJ directory.
getImageJMenu(String) - Static method in class ij.Menus
Returns the specified ImageJ menu (e.g., "File>New") or null if it is not found.
getImagePlus() - Method in class ij.gui.ImageWindow
 
getImagePlus() - Method in class ij.gui.Plot
Returns the plot as an ImagePlus.
getImagePlus() - Method in class ij.plugin.AVI_Reader
Returns the ImagePlus opened by run().
getImages() - Static method in class ij.WindowManager
 
getImageStack() - Method in class ij.ImagePlus
Returns the base image stack.
getImageStackSize() - Method in class ij.ImagePlus
If this is a stack, returns the actual number of images in the stack, else returns 1.
getImagesURL() - Static method in class ij.Prefs
Returns the URL of the directory that contains the ImageJ sample images.
getImageTitleFromVector(int) - Method in class ij.plugin.frame.SyncWindows
Get the title of image n from Windows-Vector vwins.
getImageTitles() - Static method in class ij.WindowManager
 
getImageWindowsVector() - Static method in class ij.WindowManager
 
getImaginary(int, int) - Method in class com.jmatio.types.MLNumericArray
Gets single imaginary array element of A(m,n).
getImaginary(int) - Method in class com.jmatio.types.MLNumericArray
 
getImaginary(int, int) - Method in class com.jmatio.types.MLSparse
 
getImaginary(int) - Method in class com.jmatio.types.MLSparse
 
getImaginaryByteBuffer() - Method in class com.jmatio.types.MLNumericArray
 
getImagingSamplingRateHz() - Static method in class org.jah.Configuration_
 
getImports() - Method in class ij.plugin.PlugInInterpreter
Returns the import statements that are added to the script.
getIndex(int, int) - Method in class com.jmatio.types.MLArray
 
getIndex(int, int) - Method in class com.jmatio.types.MLCell
 
getIndex(String) - Method in class ij.gui.Overlay
Returns the index of the Roi with the specified name, or -1 if not found.
getIndexOfImage(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
Get index of "image" in vector of synchronized windows, if image is in vector.
getIndexSampleModel() - Method in class ij.process.ImageProcessor
 
getInfo() - Method in class ij.ImageJ
 
getInfo(String) - Method in class ij.plugin.DICOM
Returns the DICOM tags of the specified file as a string.
getInfo(StringBuffer, String, XYPlot) - Method in class ij.plugin.frame.ChartFramePlugIn
 
getInfo() - Method in class ij.plugin.frame.ChartFramePlugIn
 
getInfo() - Method in class ij.wave.Burst
Returns general burst statistics as a String.
getInfo() - Method in class ij.wave.CrosscorrelationWave
 
getInfo() - Method in class ij.wave.EpisodicWave
 
getInfo() - Method in class ij.wave.Wave
 
getInfo(String) - Method in class org.jah.ElectrophysManager
 
getInfo(String, boolean) - Method in class org.jah.ElectrophysManager
 
getInfo() - Static method in class org.jah.HologConfiguration_
 
getInfo() - Method in class org.javaabf.ABF
 
getInfoProperty() - Method in class ij.ImagePlus
Returns the "Info" property string, or null if it is not found.
getInitialMagnification() - Method in class ij.gui.ImageWindow
 
getInsets() - Method in class ij.gui.GenericDialog
 
getInsets() - Method in class ij.gui.ImageWindow
Override Container getInsets() to make room for some text above the image.
getInsets() - Method in class ij.plugin.frame.SyncWindows
 
getInstance() - Static method in class ij.gui.Toolbar
Returns a reference to the ImageJ toolbar.
getInstance() - Static method in class ij.IJ
Returns a reference to the "ImageJ" frame.
getInstance() - Static method in class ij.macro.Interpreter
 
getInstance() - Static method in class ij.plugin.frame.Channels
Obsolete; always returns null.
getInstance() - Static method in class ij.plugin.frame.Editor
 
getInstance() - Static method in class ij.plugin.frame.Jython_Console
 
getInstance() - Static method in class ij.plugin.frame.Recorder
 
getInstance() - Static method in class ij.plugin.frame.RoiManager
Returns a reference to the ROI Manager or null if it is not open.
getInstance() - Static method in class ij.plugin.frame.SyncWindows
 
getInstance() - Static method in class ij.plugin.frame.WaveManager
Returns a reference to the Wave Manager or null if it is not open.
getInstance() - Static method in class ij.plugin.Orthogonal_Views
 
getInstance() - Static method in class org.jah.ElectrophysManager
 
getInstance2() - Static method in class ij.plugin.frame.RoiManager
Returns a reference to the ROI Manager window or to the macro batch mode RoiManager, or null if neither exists.
getInt(Properties, String) - Static method in class ij.OtherInstance
 
getInt(String, int) - Static method in class ij.Prefs
Finds an int in IJ_Props or IJ_Prefs.txt.
getIntArray() - Method in class ij.process.ImageProcessor
Returns a copy of the pixel data as a 2D int array with dimensions [x=0..width-1][y=0..height-1].
getInterpolate() - Method in class ij.process.ImageProcessor
Returns the value of the interpolate field.
getInterpolatedPixel(double, double) - Method in class ij.process.ByteProcessor
Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ColorProcessor
Calls getPixelValue(x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.FloatProcessor
Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ImageProcessor
Uses the current interpolation method (bilinear or bicubic) to find the pixel value at real coordinates (x,y).
getInterpolatedPixel(double, double) - Method in class ij.process.ShortProcessor
Uses the current interpolation method (BILINEAR or BICUBIC) to calculate the pixel value at real coordinates (x,y).
getInterpolatedPolygon(double, boolean) - Method in class ij.gui.PolygonRoi
 
getInterpolatedPolygon() - Method in class ij.gui.Roi
Returns, as a FloatPolygon, an interpolated version of this selection that has points spaced 1.0 pixel apart.
getInterpolatedPolygon(double, boolean) - Method in class ij.gui.Roi
Returns, as a FloatPolygon, an interpolated version of this selection with points spaced 'interval' pixels apart.
getInterpolatedPolygon(FloatPolygon, double, boolean) - Method in class ij.gui.Roi
 
getInterpolatedRGBPixel(double, double) - Method in class ij.process.ColorProcessor
Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolatedValue(double, double) - Method in class ij.process.ImageProcessor
Uses bilinear interpolation to find the pixel value at real coordinates (x,y).
getInterpolationMethod() - Method in class ij.process.ImageProcessor
Returns the current interpolation method (NONE, BILINEAR or BICUBIC).
getInterpolationMethods() - Static method in class ij.process.ImageProcessor
 
getIntStrings(File) - Static method in class org.jah.JAH_Utils
 
getIR() - Method in class com.jmatio.types.MLSparse
Gets row indices ir points to an integer array of length nzmax containing the row indices of the corresponding elements in pr and pi.
getItemCount(int) - Method in class ij.wave.DynamicXYDataset
 
getItemCount(int) - Method in class ij.wave.WaveXYDataset
 
getItemCount(int) - Method in class ij.wave.WaveXYZDataset
 
getItemIndex(String) - Method in class ij.plugin.frame.RoiManager
 
getItemIndex(String) - Method in class ij.plugin.frame.WaveManager
 
getIterations() - Method in class ij.measure.CurveFitter
Get number of iterations performed.
getIterations() - Method in class ij.measure.Minimizer
Get number of iterations performed (includes all restarts).
getJarFileForMenuEntry(String) - Static method in class ij.Menus
 
getJavaABFVersion() - Static method in class org.javaabf.ABF_utils
 
getJC() - Method in class com.jmatio.types.MLSparse
Gets column indices.
getJpegQuality() - Static method in class ij.io.FileSaver
Returns the current JPEG quality setting (0-100).
getJSPrefix(String) - Static method in class ij.plugin.frame.Editor
 
getJustification() - Method in class ij.gui.TextRoi
Returns the value of the 'justification' instance variable (LEFT, CENTER or RIGHT).
getKeySetToByteArray() - Method in class com.jmatio.types.MLStructure
Dumps field names to byte array.
getLab(ImageProcessor, byte[], byte[], byte[]) - Method in class ij.plugin.frame.ColorThresholder
 
getLabel(int) - Method in class ij.measure.ResultsTable
Returns the label of the specified row.
getLabelColor() - Method in class ij.gui.Overlay
 
getLabelFont() - Method in class ij.gui.Overlay
 
getLabjack() - Static method in class org.jah.LabjackFactory
 
getLastBatchModeImage() - Static method in class ij.macro.Interpreter
 
getLastColumn() - Method in class ij.measure.ResultsTable
Returns the index of the last used column, or -1 if no columns are used.
getLastDirectory() - Static method in class ij.io.OpenDialog
Returns the path to the last directory opened by the user using a file open or file save dialog, or using drag and drop.
getLastFileIndexBefore(String) - Method in class org.javaabf.Comments
 
getLastFileInfo() - Static method in class ij.io.ImportDialog
Returns the FileInfo object used to import the last raw image, or null if a raw image has not been imported.
getLastName() - Static method in class ij.io.OpenDialog
Returns the name of the last file opened by the user using a file open or file save dialog, or using drag and drop.
getLastPromptIndex() - Method in class ij.plugin.frame.Jython_Console
 
getLastStreamLength() - Static method in class org.jah.Configuration_
 
getLastToken(String) - Static method in class org.jah.HologConfiguration_
 
getLayoutComponent(String) - Method in class ij.plugin.frame.Layout
 
getLayoutComponent(int, int) - Method in class ij.plugin.frame.Layout
 
getLayoutComponent(String) - Method in class ij.plugin.frame.LayoutPanel
 
getLayoutComponent(int, int) - Method in class ij.plugin.frame.LayoutPanel
 
getLayoutComponents() - Method in class ij.plugin.frame.Layout
 
getLayoutComponents(String) - Method in class ij.plugin.frame.Layout
 
getLayoutComponents() - Method in class ij.plugin.frame.LayoutPanel
 
getLayoutComponents(String) - Method in class ij.plugin.frame.LayoutPanel
 
getLayoutExportDPI() - Static method in class org.jah.Configuration_
 
getLayoutMode() - Method in class ij.plugin.frame.Layout
 
getLayoutPanel() - Method in class ij.plugin.frame.Layout
 
getLayoutSize() - Method in class ij.plugin.frame.Layout
 
getLeftHorizontalProportions() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getLeftVerticalProportions() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getLength() - Method in class ij.gui.EllipseRoi
Returns the perimeter of this ellipse.
getLength() - Method in class ij.gui.Line
Returns the length of this line.
getLength() - Method in class ij.gui.OvalRoi
Returns the perimeter length.
getLength() - Method in class ij.gui.PolygonRoi
Returns the perimeter (for ROIs) or length (for lines).
getLength() - Method in class ij.gui.Roi
Returns the perimeter length.
getLength() - Method in class ij.gui.ShapeRoi
Returns the perimeter if this ShapeRoi can be decomposed into simple ROIs, otherwise returns zero.
getLength(boolean) - Method in class ij.process.FloatPolygon
 
getLength() - Method in class ij.wave.ABFWaveProxy
 
getLength() - Method in class ij.wave.Wave
Returns the number of elements in this Wave.
getLength() - Method in class ij.wave.WaveProxy
Gets the length of the full source.
getLength() - Method in class org.javaabf.Epoch
 
getLength_s() - Method in class ij.wave.Wave
Returns the length of this Wave in seconds.
getLine(double, double, double, double) - Method in class ij.process.ImageProcessor
Returns an array containing the pixel values along the line starting at (x1,y1) and ending at (x2,y2).
getLine(int) - Method in class ij.text.TextPanel
Returns the specified line as a string.
getLineCount() - Method in class ij.text.TextPanel
Returns the number of lines of text in this TextPanel.
getLineNumber() - Method in class ij.macro.Interpreter
 
getLineWidth() - Method in class ij.process.ImageProcessor
Returns the current line width.
getList() - Method in class ij.plugin.frame.RoiManager
Returns the selection list.
getList() - Method in class ij.plugin.frame.WaveManager
Returns the selection list.
getListenerCount() - Static method in class ij.Executer
 
getLJDAC0ScalingFactor() - Static method in class org.jah.Configuration_
 
getLJDAC0YOffset() - Static method in class org.jah.Configuration_
 
getLoadRate(double, ImagePlus) - Static method in class ij.io.Opener
 
getLocalCalibration() - Method in class ij.ImagePlus
Returns this image's local calibration, ignoring the "Global" calibration flag.
getLocation(String) - Static method in class ij.Prefs
Uses the keyword key to retrieve a location from the preferences file.
getLocationAsString(int, int) - Method in class ij.ImagePlus
Converts the current cursor location to a string.
getLog() - Static method in class ij.IJ
Returns the contents of the Log window or null if the Log window is not open.
getLongFilePointer() - Method in class ij.io.RandomAccessStream
 
getLowerZoomLevel(double) - Static method in class ij.gui.ImageCanvas
 
getLut() - Method in class ij.process.ImageProcessor
 
getLuts() - Method in class ij.CompositeImage
 
getLuts() - Static method in class ij.IJ
Returns, as an array of strings, a list of the LUTs in the Image/Lookup Tables menu.
getLuts() - Method in class ij.ImagePlus
 
getLutUpdateMode() - Method in class ij.process.ImageProcessor
Returns the LUT update mode, which can be RED_LUT, BLACK_AND_WHITE_LUT, OVER_UNDER_LUT or NO_LUT_UPDATE.
getM() - Method in class com.jmatio.types.MLArray
 
getMacroCode(String, ImagePlus) - Method in class ij.gui.TextRoi
Returns code needed by Recorder for recording the "Draw" and "Add Selection..." commands.
getMacroCount() - Method in class ij.Menus
 
getMacroCount() - Method in class ij.plugin.MacroInstaller
 
getMacroCount() - Method in class ij.plugin.tool.MacroToolRunner
 
getMacroProgram() - Method in class ij.plugin.tool.MacroToolRunner
 
getMacroProgram() - Method in class ij.plugin.tool.PlugInTool
 
getMacroShortcuts() - Static method in class ij.Menus
Returns the hashtable that associates keyboard shortcuts with macros.
getMacrosMenu() - Static method in class ij.Menus
 
getMacrosPath() - Static method in class ij.Menus
Returns the path to the macros directory or null if the macros directory was not found.
getMagnification() - Method in class ij.gui.ImageCanvas
 
getMagnification() - Method in class ij.gui.Roi
 
getMapSize() - Method in class ij.LookUpTable
 
getMarkers() - Method in class ij.plugin.frame.ChartFramePlugIn
Returns a reference to the list of WaveMarkers on the chart.
getMarkers(String) - Method in class ij.plugin.frame.ChartFramePlugIn
Returns the list of a type of markers, but should only be used for read-only.
getMarkersByType(ArrayList, String) - Static method in class ij.wave.WaveUtils
Filters the WaveMarkers in the argument by type.
getMarkerTypes() - Method in class ij.plugin.frame.ChartFramePlugIn
 
getMask() - Method in class ij.gui.Arrow
 
getMask() - Method in class ij.gui.OvalRoi
 
getMask() - Method in class ij.gui.PointRoi
 
getMask() - Method in class ij.gui.PolygonRoi
Override Roi.nudge() to support splines.
getMask() - Method in class ij.gui.Roi
Always returns null for rectangular Roi's
getMask() - Method in class ij.gui.ShapeRoi
Returns this ROI's mask pixels as a ByteProcessor with pixels "in" the mask set to white (255) and pixels "outside" the mask set to black (0).
getMask() - Method in class ij.ImagePlus
For images with irregular ROIs, returns a byte mask, otherwise, returns null.
getMask() - Method in class ij.process.ImageProcessor
For images with irregular ROIs, returns a mask, otherwise, returns null.
getMask(int, int) - Method in class ij.process.PolygonFiller
Returns a byte mask containing a filled version of the polygon.
getMaskArray() - Method in class ij.process.ImageProcessor
Returns a reference to the mask pixel array, or null if there is no mask.
getMatchingCoords(ImageCanvas, ImageCanvas, int, int) - Method in class ij.plugin.frame.SyncWindows
Get Screen Coordinates for ImageCanvas ic matching the OffScreen Coordinates of the current ImageCanvas.
getMatFileHeader() - Method in class com.jmatio.io.MatFileReader
Gets MAT-file header
getMax() - Method in class ij.gui.ProfilePlot
Returns the calculated maximum value.
getMax(double[]) - Static method in class ij.measure.CurveFitter
Gets index of highest value in an array.
getMax() - Method in class ij.process.ByteProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ColorProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.FloatProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ImageProcessor
Returns the largest displayed pixel value.
getMax() - Method in class ij.process.ShortProcessor
Returns the largest displayed pixel value.
getMaxFieldLenth() - Method in class com.jmatio.types.MLStructure
Gets the maximum length of field descriptor
getMaxima(ImageProcessor, double, boolean) - Method in class ij.plugin.filter.MaximumFinder
Finds the image maxima and returns them as a Polygon.
getMaximum() - Method in class ij.gui.ScrollbarWithLabel
 
getMaximum() - Method in class ij.util.ArrayUtil
The maximum value
getMaximumAmplitude() - Method in class ij.wave.Burst
Should be the same as getPeakAmplitude()
getMaximumAmplitudeIndex() - Method in class ij.wave.Burst
The index within the burst period that the maximum amplitude is at.
getMaximumBounds() - Method in class ij.gui.ImageWindow
 
getMaxIterations() - Method in class ij.measure.CurveFitter
Get maximum number of iterations allowed (sum of iteration count for all restarts)
getMaxIterations() - Method in class ij.measure.Minimizer
Get maximum number of iterations allowed.
getMaxNZ() - Method in class com.jmatio.types.MLSparse
Gets maximum number of non-zero values
getMaxRestarts() - Method in class ij.measure.Minimizer
Get maximum number of minimization restarts to do
getMaxThreshold() - Method in class ij.process.ImageProcessor
Returns the upper threshold level.
getMaxValue() - Method in class ij.wave.Wave
 
getMaxValue(double, double) - Method in class ij.wave.Wave
 
getMaxValue(int, int) - Method in class ij.wave.Wave
 
getMaxValue() - Method in class ij.wave.Waves
Gets the maximum value across all the Waves in this instance.
getMaxValue(ImageProcessor) - Static method in class org.jah.JAH_Utils
 
getMaxValueTime() - Method in class ij.wave.Wave
 
getMaxValueTime(double, double) - Method in class ij.wave.Wave
Returns the time that the max value of the Wave is achieved (in seconds).
getMaxValueTime(int, int) - Method in class ij.wave.Wave
 
getMaxVisiblePlotPoints() - Static method in class org.jah.Configuration_
 
getMean() - Method in class ij.util.ArrayUtil
Average value
getMeanValue(double, double) - Method in class ij.wave.Wave
 
getMeanValue() - Method in class ij.wave.Wave
 
getMeasurements() - Static method in class ij.plugin.filter.Analyzer
 
getMedianValue(double, double) - Method in class ij.wave.Wave
 
getMedianValue() - Method in class ij.wave.Wave
 
getMemorySetting() - Method in class ij.plugin.Memory
 
getMenuBar() - Static method in class ij.Menus
 
getMenus() - Method in class ij.macro.Program
 
getMessage() - Method in class ij.gui.GenericDialog
Returns a reference to the Label or MultiLineLabel created by the last addMessage() call, or null if addMessage() was not called.
getMethod() - Static method in class ij.plugin.frame.ThresholdAdjuster
Returns the current method ("Default", "Huang", etc).
getMethods() - Static method in class ij.process.AutoThresholder
 
getMiddleDividerLocation() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getMin() - Method in class ij.gui.ProfilePlot
Returns the calculated minimum value.
getMin() - Method in class ij.process.ByteProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ColorProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.FloatProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ImageProcessor
Returns the smallest displayed pixel value.
getMin() - Method in class ij.process.ShortProcessor
Returns the smallest displayed pixel value.
getMinimizer() - Method in class ij.measure.CurveFitter
Returns a reference to the Minimizer used, for accessing Minimizer methods directly.
getMinimum() - Method in class ij.gui.ScrollbarWithLabel
 
getMinimum() - Method in class ij.util.ArrayUtil
The minimum value
getMinimumAmplitude() - Method in class ij.wave.Burst
The minimum amplitude in the burst envelope.
getMinimumPulseStepValue() - Static method in class org.jah.Configuration_
 
getMinimumSize() - Method in class ij.gui.MultiLineLabel
 
getMinimumSize() - Method in class ij.gui.ScrollbarWithLabel
 
getMinimumSize() - Method in class ij.gui.Toolbar
 
getMinimumSize() - Method in class ij.gui.TrimmedButton
 
getMinMax(double[]) - Static method in class ij.util.Tools
 
getMinMax(float[]) - Static method in class ij.util.Tools
 
getMinThreshold() - Method in class ij.process.ImageProcessor
Returns the lower threshold level.
getMinValue() - Method in class ij.wave.Wave
 
getMinValue(double, double) - Method in class ij.wave.Wave
 
getMinValue(int, int) - Method in class ij.wave.Wave
 
getMinValue() - Method in class ij.wave.Waves
Gets the minimum value across all the Waves in this instance.
getMinValueTime() - Method in class ij.wave.Wave
 
getMinValueTime(double, double) - Method in class ij.wave.Wave
Returns the time that the min value of the Wave is achieved (in seconds).
getMinValueTime(int, int) - Method in class ij.wave.Wave
 
getMLArray(String) - Method in class com.jmatio.io.MatFileReader
Returns the value to which the red file maps the specified array name.
getMode() - Method in class ij.CompositeImage
 
getMode() - Static method in class ij.plugin.frame.ThresholdAdjuster
Returns the current mode ("Red","B&W" or"Over/Under").
getMode() - Static method in class ij.plugin.WandToolOptions
 
getModeAsString() - Method in class ij.CompositeImage
 
getModifiers() - Method in class ij.gui.ImageCanvas
Returns the mouse event modifiers.
getMultipleWildcardChar() - Method in class ij.util.WildcardMatch
Returns the character used to specify any amount of characters.
getMultiPointMode() - Static method in class ij.gui.Toolbar
Returns 'true' if the multi-point tool is enabled.
getN() - Method in class com.jmatio.types.MLArray
 
getName() - Method in class com.jmatio.types.MLArray
Gets array name
getName() - Method in class ij.gui.Roi
Returns the name of this ROI, or null.
getName(String) - Method in class ij.io.Opener
 
getName(String) - Static method in class ij.Macro
 
getName() - Method in class ij.measure.CurveFitter
returns the name of the fit function of the fit performed
getName(int) - Method in class ij.plugin.frame.RoiManager
Returns the name of the ROI with the specified index, or null if the index is out of range.
getName(String) - Static method in class ij.plugin.frame.RoiManager
Returns the name of the ROI with the specified index.
getName(String) - Static method in class ij.plugin.frame.WaveManager
Returns the name of the Wave with the specified index.
getName(int) - Static method in class ij.plugin.frame.WaveManager
 
getName() - Method in class ij.plugin.PlugInInterpreter
Returns the name of this PlugInInterpreter.
getName() - Method in class ij.plugin.TextReader
Returns the file name.
getName() - Method in class ij.wave.Bursts
 
getName() - Method in class ij.wave.Wave
Sets the name of this wave
getName() - Method in class org.javaabf.ABF
 
getName() - Method in class org.javaabf.Epoch
 
getNames() - Method in class ij.wave.Waves
 
getNamesByCluster(TreeDrawerNode) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getNamesByCluster(TreeDrawerNode, ArrayList) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getNameToByteArray() - Method in class com.jmatio.types.MLArray
 
getNbCpus() - Static method in class ij.util.ThreadUtil
 
getNChannels() - Method in class ij.ImagePlus
Returns the number of channels.
getNChannels() - Method in class ij.process.ColorProcessor
Returns the number of color channels of the image, i.e., 3.
getNChannels() - Method in class ij.process.ImageProcessor
Returns the number of color channels in the image.
getNCoordinates() - Method in class ij.gui.PolygonRoi
Returns the number of XY coordinates.
getNDimensions() - Method in class com.jmatio.types.MLArray
 
getNDimensions() - Method in class ij.ImagePlus
Returns the number of dimensions (2, 3, 4 or 5).
getNeighborhood(int, int, double[][]) - Method in class ij.process.ImageProcessor
Experimental
getNextABF_Section() - Method in class org.javaabf.ABF18_parser
 
getNextABF_Section() - Method in class org.javaabf.ABF2_parser
 
getNextABF_Section() - Method in class org.javaabf.AbstractABF_parser
 
getNextBool() - Method in class org.javaabf.AbstractABF_parser
 
getNextBoolean() - Method in class ij.gui.GenericDialog
Returns the state of the next checkbox.
getNextChar() - Method in class org.javaabf.ABF18_parser
 
getNextChar() - Method in class org.javaabf.ABF2_parser
 
getNextChar() - Method in class org.javaabf.AbstractABF_parser
 
getNextChoice() - Method in class ij.gui.GenericDialog
Returns the selected item in the next popup menu.
getNextChoiceIndex() - Method in class ij.gui.GenericDialog
Returns the index of the selected item in the next popup menu.
getNextEpoch(String) - Method in class org.jah.ElectrophysManager
 
getNextEpoch(int) - Method in class org.javaabf.ABF
 
getNextEpoch(int) - Method in interface org.javaabf.ABF_parser
 
getNextEpoch(int) - Method in class org.javaabf.AbstractABF_parser
 
getNextFloat() - Method in class org.javaabf.AbstractABF_parser
 
getNextLong() - Method in class org.javaabf.AbstractABF_parser
 
getNextLongLong() - Method in class org.javaabf.AbstractABF_parser
 
getNextMYGUID() - Method in class org.javaabf.ABF18_parser
 
getNextMYGUID() - Method in class org.javaabf.ABF2_parser
 
getNextMYGUID() - Method in class org.javaabf.AbstractABF_parser
 
getNextNumber() - Method in class ij.gui.GenericDialog
Returns the contents of the next numeric field, or NaN if the field does not contain a number.
getNextRadioButton() - Method in class ij.gui.GenericDialog
Returns the selected item in the next radio button group.
getNextShort() - Method in class org.javaabf.AbstractABF_parser
 
getNextString() - Method in class ij.gui.GenericDialog
Returns the contents of the next text field.
getNextText() - Method in class ij.gui.GenericDialog
Returns the contents of the next textarea.
getNextUnsignedInt() - Method in class org.javaabf.AbstractABF_parser
Could be problematic
getNextUnsignedLong() - Method in class org.javaabf.AbstractABF_parser
 
getNextUnsignedShort() - Method in class org.javaabf.AbstractABF_parser
 
getNFrames() - Method in class ij.ImagePlus
Returns the number of frames (time-points).
getNonImageTitles() - Static method in class ij.WindowManager
Returns an array containing the titles of non-image Frames and Dialogs.
getNonImageWindows() - Static method in class ij.WindowManager
Returns an array containing a list of the non-image Frames.
getNonImageWindowsVector() - Static method in class ij.WindowManager
 
getNonSplineCoordinates() - Method in class ij.gui.PolygonRoi
 
getNonSplineFloatPolygon() - Method in class ij.gui.PolygonRoi
 
getNormalizedZAxisProfile(Analyzer, Calibration, ImageStack, Roi) - Static method in class org.jah.JAH_Utils
 
getNScrollbars() - Method in class ij.gui.StackWindow
 
getNSlices() - Method in class ij.ImagePlus
Returns the image depth (number of z-slices).
getNthImageID(int) - Static method in class ij.WindowManager
Returns the ID of the Nth open image.
getNumber(String, double) - Static method in class ij.IJ
Allows the user to enter a number in a dialog box.
getNumberOfActualEpisodes() - Method in class org.javaabf.ABF18_parser
 
getNumberOfActualEpisodes() - Method in class org.javaabf.ABF2_parser
 
getNumberOfActualEpisodes() - Method in interface org.javaabf.ABF_parser
 
getNumberOfActualEpisodes() - Method in class org.javaabf.ABFpClamp9_parser
 
getNumberOfActualEpisodes() - Method in class org.javaabf.AbstractABF_parser
 
getNumberOfADC() - Method in class org.javaabf.ABF
 
getNumberOfADC() - Method in class org.javaabf.ABF18_parser
 
getNumberOfADC() - Method in class org.javaabf.ABF2_parser
 
getNumberOfADC() - Method in interface org.javaabf.ABF_parser
 
getNumberOfADC() - Method in class org.javaabf.ABFpClamp9_parser
 
getNumberOfADC() - Method in class org.javaabf.AbstractABF_parser
 
getNumberOfEpisodes() - Method in class ij.wave.EpisodicWave
 
getNumberOfEpisodes() - Method in class org.javaabf.ABF
 
getNumberOfEpisodes() - Method in class org.javaabf.ABF18_parser
 
getNumberOfEpisodes() - Method in class org.javaabf.ABF2_parser
 
getNumberOfEpisodes() - Method in interface org.javaabf.ABF_parser
 
getNumberOfEpisodes() - Method in class org.javaabf.AbstractABF_parser
 
getNumberOfPulseAmplitudeSteps() - Static method in class org.jah.Configuration_
 
getNumberOfPulsesInTrain() - Static method in class org.jah.Configuration_
 
getNumberOfRows() - Method in class org.javaabf.ABF
 
getNumberOfRows() - Method in class org.javaabf.ABF18_parser
"""Returns the number of sample rows."""
getNumberOfRows() - Method in class org.javaabf.ABF2_parser
"""Returns the number of sample rows."""
getNumberOfRows() - Method in interface org.javaabf.ABF_parser
"""Returns the number of sample rows."""
getNumberOfRows() - Method in class org.javaabf.AbstractABF_parser
"""Returns the number of sample rows."""
getNumberOfSamplesPerChannel() - Method in class org.javaabf.ABF
 
getNumberOfSamplesPerEpisode() - Method in class org.javaabf.ABF
 
getNumberOfSamplesPerEpisode() - Method in class org.javaabf.ABF18_parser
 
getNumberOfSamplesPerEpisode() - Method in class org.javaabf.ABF2_parser
 
getNumberOfSamplesPerEpisode() - Method in interface org.javaabf.ABF_parser
 
getNumberOfSamplesPerEpisode() - Method in class org.javaabf.AbstractABF_parser
 
getNumberOfSamplesPerEpisodePerChannel() - Method in class ij.wave.EpisodicWave
 
getNumElements() - Method in class ij.wave.Bursts
The number of bursts in this instance.
getNumericFields() - Method in class ij.gui.GenericDialog
Returns the Vector containing the numeric TextFields.
getNumParams() - Method in class ij.measure.CurveFitter
Get number of parameters for current fit formula Do not use before 'doFit', because the fit function would be undefined.
getNumTools() - Method in class ij.gui.Toolbar
 
getObject() - Method in class com.jmatio.types.MLJavaObject
 
getObject() - Method in class com.jmatio.types.MLObject
 
getObjectiveChoices() - Static method in class org.jah.HologConfiguration_
 
getObjectives() - Static method in class org.jah.HologConfiguration_
 
getOffset() - Method in class ij.io.FileInfo
Returns the offset as a long.
getOpacity() - Method in class ij.gui.ImageRoi
Returns the current opacity.
getOpenAsHyperStack() - Method in class ij.ImagePlus
 
getOpenBaseDirScriptsMenu() - Static method in class ij.Menus
 
getOpenProcessingDirScriptsMenu() - Static method in class ij.Menus
 
getOpenRecentMenu() - Static method in class ij.Menus
 
getOpenUsingPlugins() - Static method in class ij.io.Opener
Returns the state of the openUsingPlugins flag.
getOperationMode() - Method in class org.javaabf.ABF
 
getOperationMode() - Method in class org.javaabf.ABF18_parser
 
getOperationMode() - Method in class org.javaabf.ABF2_parser
 
getOperationMode() - Method in interface org.javaabf.ABF_parser
 
getOperationMode() - Method in class org.javaabf.ABFpClamp9_parser
 
getOperationMode() - Method in class org.javaabf.AbstractABF_parser
 
getOptions() - Static method in class ij.Macro
If a command started using run(name, options) is running, and the current thread is the same thread, returns the options string, otherwise, returns null.
getOrientation() - Method in class ij.gui.ScrollbarWithLabel
 
getOriginalFileInfo() - Method in class ij.ImagePlus
Returns the FileInfo object that was used to open this image.
getOutline() - Method in class ij.gui.Arrow
 
getOutputImage() - Method in class ij.plugin.filter.ParticleAnalyzer
Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is selected in the "Show:" menu.
getOutputType() - Static method in class ij.plugin.filter.EDM
Returns the current output type (BYTE_OVERWRITE, BYTE, SHORT or FLOAT)
getOvalToolType() - Static method in class ij.gui.Toolbar
Returns the oval tool type (OVAL_ROI, ELLIPSE_ROI or BRUSH_ROI).
getOverlay() - Method in class ij.gui.ImageCanvas
Use ImagePlus.getOverlay().
getOverlay() - Method in class ij.ImagePlus
Returns the current overly, or null if this image does not have an overlay.
getOverlay(ImagePlus) - Static method in class ij.io.FileSaver
 
getOverlay() - Method in class ij.process.ImageProcessor
 
getPaintPending() - Method in class ij.gui.ImageCanvas
 
getPaintScale(String, int) - Method in class ij.plugin.frame.ChartFramePlugIn
Gets the PaintScale for a Wave rendered using the XYBlockRenderer (e.g., 3D plots)
getPaintScale(XYPlot, int) - Method in class ij.plugin.frame.ChartFramePlugIn
 
getParams() - Method in class ij.gui.EllipseRoi
Returns x1, y1, x2, y2 and aspectRatio as a 5 element array.
getParams() - Method in class ij.measure.CurveFitter
Get the result of fitting, i.e. the set of parameter values for the best fit.
getParams() - Method in class ij.measure.Minimizer
Get the result, i.e., the set of parameter values (i.e., variable values) from the best corner of the simplex.
getParent() - Method in class ij.gui.LayoutComponent
 
getPasteMode() - Method in class ij.gui.Roi
Returns the current paste transfer mode, or NOT_PASTING (-1) if no paste operation is in progress.
getPath() - Method in class ij.io.OpenDialog
Returns the selected file path or null if the dialog was canceled.
getPeakAmp() - Method in class ij.wave.Burst
Gets the maximum amplitude for this burst period.
getPeakDetectionHighThreshold() - Static method in class org.jah.Configuration_
 
getPeakDetectionLowThreshold() - Static method in class org.jah.Configuration_
 
getPeakFrames(String) - Static method in class ij.wave.CTA_Utils
 
getPeakTime() - Method in class ij.wave.Burst
Gets the peak time in seconds relative to the longer wave period.
getPeriodCV() - Method in class ij.wave.Bursts
The coefficient of variation of the periods in this instance
getPeriodMean() - Method in class ij.wave.Bursts
The mean of the periods in this instance
getPeriodNumber() - Method in class ij.wave.Bursts
The number of periods in this instance (should be n-1)
getPeriods() - Method in class ij.wave.Bursts
Returns an array of all the periods between bursts (in seconds)
getPeriodStderr() - Method in class ij.wave.Bursts
The standard error of the periods in this instance
getPeriodStdev() - Method in class ij.wave.Bursts
The standard deviation of the periods in this instance
getPeriodsTimes() - Method in class ij.wave.Bursts
Returns an array of all the times the periods between bursts was computed (in seconds)
getPixel(int, int) - Method in class ij.ImagePlus
Returns the pixel value at (x,y) as a 4 element array.
getPixel(int, int) - Method in class ij.process.ByteProcessor
 
getPixel(int, int) - Method in class ij.process.ColorProcessor
 
getPixel(int, int, int[]) - Method in class ij.process.ColorProcessor
Returns the 3 samples for the pixel at (x,y) in an array of int.
getPixel(int, int) - Method in class ij.process.FloatProcessor
Returns a pixel value that must be converted using Float.intBitsToFloat().
getPixel(int, int, int[]) - Method in class ij.process.FloatProcessor
Returns the value of the pixel at (x,y) in a one element int array. iArray is an optiona preallocated array.
getPixel(int, int) - Method in class ij.process.ImageProcessor
Returns the value of the pixel at (x,y).
getPixel(int, int, int[]) - Method in class ij.process.ImageProcessor
Returns the samples for the pixel at (x,y) in an int array.
getPixel(int, int) - Method in class ij.process.ShortProcessor
 
getPixelCount() - Method in class ij.process.ImageProcessor
 
getPixelInterpolated(double, double) - Method in class ij.process.ByteProcessor
 
getPixelInterpolated(double, double) - Method in class ij.process.ColorProcessor
 
getPixelInterpolated(double, double) - Method in class ij.process.FloatProcessor
 
getPixelInterpolated(double, double) - Method in class ij.process.ImageProcessor
Uses the current interpolation method to find the pixel value at real coordinates (x,y).
getPixelInterpolated(double, double) - Method in class ij.process.ShortProcessor
 
getPixels() - Method in class ij.gui.Line
Returns the pixel values along this line.
getPixels(int) - Method in class ij.ImageStack
Returns the pixel array for the specified slice, were 1<=n<=nslices.
getPixels() - Method in class ij.process.ByteProcessor
Returns a reference to the byte array containing this image's pixel data.
getPixels() - Method in class ij.process.ColorProcessor
Returns a reference to the int array containing this image's pixel data.
getPixels() - Method in class ij.process.FloatProcessor
Returns a reference to the float array containing this image's pixel data.
getPixels() - Method in class ij.process.ImageProcessor
Returns a reference to this image's pixel array.
getPixels() - Method in class ij.process.ShortProcessor
Returns a reference to the short array containing this image's pixel data.
getPixels(int) - Method in class ij.VirtualStack
Returns the pixel array for the specified slice, were 1<=n<=nslices.
getPixelsCopy() - Method in class ij.process.ByteProcessor
Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ColorProcessor
Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.FloatProcessor
Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ImageProcessor
Returns a copy of the pixel data.
getPixelsCopy() - Method in class ij.process.ShortProcessor
Returns a copy of the pixel data.
getPixelValue(int, int) - Method in class ij.process.ByteProcessor
 
getPixelValue(int, int) - Method in class ij.process.ColorProcessor
Converts the specified pixel to grayscale using the formula g=(r+g+b)/3 and returns it as a float.
getPixelValue(int, int) - Method in class ij.process.FloatProcessor
Returns the value of the pixel at (x,y) as a float.
getPixelValue(int, int) - Method in class ij.process.ImageProcessor
Returns the value of the pixel at (x,y).
getPixelValue(int, int) - Method in class ij.process.ShortProcessor
Returns the value of the pixel at (x,y) as a float.
getPlot() - Method in interface ij.gui.PlotMaker
Returns a profile plot.
getPlot() - Method in class ij.gui.ProfilePlot
 
getPlot() - Method in class ij.plugin.Profiler
 
getPlot() - Method in class ij.plugin.ZAxisProfiler
 
getPlotSize() - Method in class ij.gui.ProfilePlot
Returns the size of the plot that createWindow() creates.
getPluginCount() - Method in class ij.Menus
 
getPlugins() - Static method in class ij.Menus
Returns a list of the plugins in the plugins menu.
getPlugInsPath() - Static method in class ij.Menus
Returns the path to the user plugins directory or null if the plugins directory was not found.
getPlugInTool() - Static method in class ij.gui.Toolbar
 
getPoints() - Method in class ij.gui.Line
Returns, as a Polygon, the two points that define this line.
getPolygon() - Method in class ij.gui.Line
If the width of this line is less than or equal to one, returns the starting and ending coordinates as a 2-point Polygon, or, if the width is greater than one, returns an outline of the line as a 4-point Polygon.
getPolygon() - Method in class ij.gui.OvalRoi
Returns this OvalRoi as a Polygon.
getPolygon() - Method in class ij.gui.PolygonRoi
Returns this PolygonRoi as a Polygon.
getPolygon() - Method in class ij.gui.Roi
Returns the outline of this selection as a Polygon, or null if this is a straight line selection.
getPolygon() - Method in class ij.gui.ShapeRoi
 
getPopupMenu() - Static method in class ij.Menus
 
getPort() - Static method in class ij.ImageJ
Returns the port that ImageJ checks on startup to see if another instance is running.
getPosition() - Method in class ij.gui.Roi
Returns the stack position (image number) of this ROI, or zero if the ROI is not associated with a particular stack image.
getPostPulseDetectionDelay() - Static method in class org.jah.Configuration_
 
getPowerSpectrum() - Method in class ij.process.FHT
Returns an 8-bit power spectrum, log-scaled to 1-254.
getPrecision() - Static method in class ij.plugin.filter.Analyzer
Returns the number of digits displayed to the right of decimal point.
getPreferredLocation() - Method in class ij.ImageJ
 
getPreferredSize() - Method in class ij.gui.ImageCanvas
 
getPreferredSize() - Method in class ij.gui.MultiLineLabel
 
getPreferredSize() - Method in class ij.gui.ProgressBar
 
getPreferredSize() - Method in class ij.gui.ScrollbarWithLabel
 
getPreferredSize() - Method in class ij.gui.Toolbar
 
getPreferredSize() - Method in class ij.gui.TrimmedButton
 
getPrefsDir() - Static method in class ij.Prefs
Gets the path to the directory where the preferences file (IJPrefs.txt) is saved.
getPrefsDirectory() - Static method in class ij.OtherInstance
 
getPreviewCheckbox() - Method in class ij.gui.GenericDialog
Returns a reference to the Preview Checkbox.
getPreviousEpoch(String) - Method in class org.jah.ElectrophysManager
 
getPreviousEpoch(int) - Method in class org.javaabf.ABF
 
getPreviousEpoch(int) - Method in interface org.javaabf.ABF_parser
 
getPreviousEpoch(int) - Method in class org.javaabf.AbstractABF_parser
 
getProcessingDirectory() - Static method in class org.jah.Configuration_
 
getProcessor(int) - Method in class ij.CompositeImage
 
getProcessor() - Method in class ij.gui.Plot
Returns the plot as an ImageProcessor.
getProcessor() - Static method in class ij.IJ
Returns the active image or stack slice as an ImageProcessor, or displays an error message and aborts the plugin or macro if no images are open.
getProcessor() - Method in class ij.ImagePlus
Returns a reference to the current ImageProcessor.
getProcessor(int) - Method in class ij.ImageStack
Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
getProcessor(int) - Method in class ij.plugin.AVI_Reader
Returns an ImageProcessor for the specified slice of this virtual stack (if it is one) where 1<=n<=nslices.
getProcessor(int) - Method in class ij.plugin.FileInfoVirtualStack
Returns an ImageProcessor for the specified image, were 1<=n<=nImages.
getProcessor(int) - Method in class ij.plugin.ListVirtualStack
Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
getProcessor(int) - Method in class ij.VirtualStack
Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
getProfile() - Method in class ij.gui.ProfilePlot
Returns the profile plot data.
getProgram() - Method in class ij.plugin.MacroInstaller
 
getProgressBar() - Method in class ij.ImageJ
 
getProjection() - Method in class ij.plugin.ZProjector
Retrieve results of most recent projection operation.
getProp(String) - Method in class ij.ImagePlus
Returns the value from the "Info" property string associated with 'key', or null if the key is not found.
getProperties() - Method in class ij.gui.Roi
 
getProperties() - Method in class ij.ImagePlus
Returns this image's Properties.
getProperty(String) - Method in class ij.gui.Roi
 
getProperty(String) - Method in class ij.ImagePlus
Returns the property associated with 'key'.
getProperty(String, String) - Static method in class org.jah.Configuration_
 
getPropertyCount() - Method in class ij.gui.Roi
 
getPropertyDouble(String, String) - Static method in class org.jah.Configuration_
 
getPropertyFilenames() - Static method in class org.jah.PhysImage_Properties
Returns a list of files in the base directory that contain the 'prop' in their name as they are presumable property files.
getProtocolInfo(ABF_Section) - Method in class org.javaabf.ABF18_parser
 
getProtocolInfo(ABF_Section) - Method in class org.javaabf.ABF2_parser
 
getPrototypeOverlay() - Method in class ij.gui.Roi
 
getPSD(Wave) - Static method in class org.jah.FrequencyAnalyzer
 
getPulseAmplitude() - Static method in class org.jah.Configuration_
 
getPulseContinuousMax() - Static method in class org.jah.Configuration_
 
getPulseContinuousMin() - Static method in class org.jah.Configuration_
 
getPulseFrequency() - Static method in class org.jah.Configuration_
 
getPulseGaussianMean() - Static method in class org.jah.Configuration_
 
getPulseGaussianStdD() - Static method in class org.jah.Configuration_
 
getPulseLength() - Static method in class org.jah.Configuration_
 
getPulseStartDelay() - Static method in class org.jah.Configuration_
 
getPulseTrainStartDelay() - Static method in class org.jah.Configuration_
 
getQuality() - Static method in class ij.plugin.JpegWriter
Deprecated. replaced by FileSaver.getJpegQuality()
getRadioButtonGroups() - Method in class ij.gui.GenericDialog
Returns the Vector that contains the RadioButtonGroups.
getRangeAxes() - Method in class ij.plugin.frame.ChartFramePlugIn
Returns a list with all the range axes.
getRawLength() - Method in class ij.gui.Line
Returns the length of this line in pixels.
getRawType(int) - Static method in class ij.macro.ExtensionDescriptor
 
getRawValue(double) - Method in class ij.measure.Calibration
Converts a density calibrated value into a raw pixel value.
getRawX(double) - Method in class ij.measure.Calibration
Converts a x-coordinate in physical units to pixels.
getRawY(double) - Method in class ij.measure.Calibration
Converts a y-coodinate in physical units to pixels.
getRawY(double, int) - Method in class ij.measure.Calibration
Converts a y-coodinate in physical units to pixels, taking into account the 'invertY' flag.
getReal(int, int) - Method in class com.jmatio.types.MLNumericArray
Gets single real array element of A(m,n).
getReal(int) - Method in class com.jmatio.types.MLNumericArray
 
getReal(int, int) - Method in class com.jmatio.types.MLSparse
 
getReal(int) - Method in class com.jmatio.types.MLSparse
 
getRealByteBuffer() - Method in class com.jmatio.types.MLNumericArray
 
getRed(String) - Static method in class ij.plugin.Colors
 
getRedirectImage(ImagePlus) - Static method in class ij.plugin.filter.Analyzer
Returns the image selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog, or null if "None" is selected, the image was not found or the image is not the same size as currentImage.
getReds() - Method in class ij.LookUpTable
 
getRelativeEpochs(String, double) - Method in class org.javaabf.ABF
 
getRelativeEpochs(int, double) - Method in class org.javaabf.ABF
 
getRelativeTime(long) - Method in class org.javaabf.ABF
 
getRelativeTime(long) - Method in class org.javaabf.ABF18_parser
Returns the time relative to the start of the experiment in milliseconds"""
getRelativeTime(long) - Method in class org.javaabf.ABF2_parser
Returns the time relative to the start of the experiment in milliseconds"""
getRelativeTime(long) - Method in interface org.javaabf.ABF_parser
Returns the time relative to the start of the experiment in milliseconds"""
getRelativeTime(long) - Method in class org.javaabf.AbstractABF_parser
Returns the time relative to the start of the experiment in milliseconds"""
getResiduals() - Method in class ij.measure.CurveFitter
Returns residuals array, i.e., differences between data and curve.
getRestarts() - Method in class ij.measure.CurveFitter
Get maximum number of simplex restarts to do.
getResultsTable() - Method in class ij.gui.PlotWindow
Returns the X and Y plot values as a ResultsTable.
getResultsTable() - Static method in class ij.measure.ResultsTable
Returns the ResultsTable used by the Measure command.
getResultsTable() - Static method in class ij.plugin.filter.Analyzer
Returns the default results table.
getResultsTable() - Method in class ij.text.TextPanel
Returns the ResultsTable associated with this TextPanel, or null.
getResultString() - Method in class ij.measure.CurveFitter
Get a string with detailed description of the curve fitting results (several lines, including the fit parameters).
getResultsWindow() - Static method in class ij.measure.ResultsTable
Returns the "Results" TextWindow.
getReturnValue() - Method in class ij.plugin.PlugInInterpreter
Returns the value returned by the script, if any, or null.
getRGB(byte[], byte[], byte[]) - Method in class ij.process.ColorProcessor
Returns the red, green and blue planes as 3 byte arrays.
getRGBRow(ImageStack, int, int, int, int, int, int[]) - Method in class ij.plugin.filter.Projector
 
getRGBWeights() - Method in class ij.process.ColorProcessor
Returns the values set by setRGBWeights(), or null if setRGBWeights() has not been called.
getRight() - Method in class org.javaabf.Comment
 
getRiseTime() - Method in class ij.wave.Burst
Returns the time of the maximum amplitude relative to the start of the burst (in seconds).
getRiseTimeFromFwhm() - Method in class ij.wave.Burst
Not implemented yet
getRoi() - Method in class ij.ImagePlus
Returns the current selection, or null if there is no selection.
getRoi() - Method in class ij.ImageStack
 
getRoi() - Method in class ij.io.RoiDecoder
Returns the ROI.
getRoi(String) - Method in class ij.plugin.frame.RoiManager
 
getRoi() - Method in class ij.process.ImageProcessor
Returns a Rectangle that represents the current region of interest.
getRoi() - Method in class ij.wave.Wave
Returns an Roi associated with this Wave.
getRoi1() - Method in class ij.wave.CrosscorrelationWave
 
getRoi2() - Method in class ij.wave.CrosscorrelationWave
 
getRoiArea(Roi) - Static method in class org.jah.JAH_Utils
Calculates the area of the Roi passed as argument (in pixel values).
getRoiCentroid(Roi) - Static method in class org.jah.JAH_Utils
Calculates the centroid point of the Roi passed as argument (in pixel coordinates).
getRoiIndex(Roi) - Method in class ij.plugin.frame.RoiManager
 
getRois() - Method in class ij.gui.ShapeRoi
Converts a Shape into Roi object(s).
getROIs() - Method in class ij.plugin.frame.RoiManager
Returns the ROI Hashtable.
getRois() - Method in class ij.wave.Waves
Returns an array of Rois associated with each of the Waves in this instance.
getRoisAsArray() - Method in class ij.plugin.frame.RoiManager
Returns the ROIs as an array.
getRoisAsArray() - Static method in class org.jah.JAH_Utils
A utility function for returning all the Rois in the RoiManager.
getRoisByNames(ArrayList) - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getRoisForWaves(Waves) - Static method in class ij.plugin.frame.RoiManager
 
getRoiWave(ImagePlus, Roi) - Static method in class ij.wave.Wave
Creates a new Wave from Roi passed as argument the ImagePlus passed as argument.
getRoiWaves(ImagePlus) - Static method in class ij.wave.Wave
Creates a new set of Waves from the selected ROIs in the RoiManager and the ImagePlus passed as argument.
getRoiWaves(ImagePlus, Roi[]) - Static method in class ij.wave.Wave
 
getRoot() - Method in class ij.plugin.ControlPanel
 
getRoundRectArcSize() - Method in class ij.gui.Roi
Obsolete; replaced by getCornerDiameter().
getRoundRectArcSize() - Static method in class ij.gui.Toolbar
Returns the rounded rectangle arc size, or 0 if the rounded rectangle tool is not enabled.
getRow(int, int, int[], int) - Method in class ij.process.ImageProcessor
Returns the pixel values along the horizontal line starting at (x,y).
getRow(int, int, float[], int) - Method in class ij.process.ImageProcessor
Returns the pixel values along the horizontal line starting at (x,y).
getRow(long) - Method in class org.javaabf.ABF
 
getRow(long) - Method in class org.javaabf.ABF18_parser
 
getRow(long) - Method in interface org.javaabf.ABF_parser
 
getRow(long) - Method in class org.javaabf.AbstractABF_parser
 
getRowAsString(int) - Method in class ij.measure.ResultsTable
Returns a tab or comma delimited string representing the given row, where 0<=row<=counter-1.
getRowByAbsoluteTime(long) - Method in class org.javaabf.ABF
 
getRowByRelativeTime(long) - Method in class org.javaabf.ABF
 
getRowCount() - Method in class ij.plugin.frame.table.EpochTableModel
 
getRowNumberByAbsoluteTime(long) - Method in class org.javaabf.ABF
 
getRowNumberByAbsoluteTime(double) - Method in class org.javaabf.ABF18_parser
"""Returns the row number for the absolute time (assuming ms)."""
getRowNumberByAbsoluteTime(double) - Method in class org.javaabf.ABF2_parser
"""Returns the row number for the absolute time (assuming ms)."""
getRowNumberByAbsoluteTime(double) - Method in interface org.javaabf.ABF_parser
"""Returns the row number for the absolute time (assuming ms)."""
getRowNumberByAbsoluteTime(double) - Method in class org.javaabf.AbstractABF_parser
"""Returns the row number for the absolute time (assuming ms)."""
getRowNumberByRelativeTime(long) - Method in class org.javaabf.ABF
 
getRowNumberByRelativeTime(double) - Method in class org.javaabf.ABF18_parser
"""Returns the row number for the relative time (assuming ms)."""
getRowNumberByRelativeTime(double) - Method in class org.javaabf.ABF2_parser
"""Returns the row number for the relative time (assuming ms)."""
getRowNumberByRelativeTime(double) - Method in interface org.javaabf.ABF_parser
"""Returns the row number for the relative time (assuming ms)."""
getRowNumberByRelativeTime(double) - Method in class org.javaabf.AbstractABF_parser
"""Returns the row number for the relative time (assuming ms)."""
getRSquared() - Method in class ij.measure.CurveFitter
Returns R^2, where 1.0 is best.
getSampleImageNames() - Static method in class ij.plugin.URLOpener
 
getSamplingRate() - Method in class org.javaabf.ABF
 
getSamplingRate() - Method in class org.javaabf.ABF18_parser
 
getSamplingRate() - Method in class org.javaabf.ABF2_parser
 
getSamplingRate() - Method in interface org.javaabf.ABF_parser
 
getSamplingRate() - Method in class org.javaabf.AbstractABF_parser
 
getSamplingRateHz() - Method in class ij.wave.ABFWaveProxy
 
getSamplingRateHz() - Method in class ij.wave.Wave
Returns the sampling rate of this wave in Hz
getSamplingRateHz() - Method in class ij.wave.WaveProxy
Returns the sampling rate of the underlying source irrespective of its origin.
getSaveAsMenu() - Static method in class ij.Menus
 
getScale(float[]) - Static method in class ij.plugin.filter.Convolver
 
getScaledStroke() - Method in class ij.gui.Roi
 
getScaleFactor() - Method in class ij.gui.LayoutComponent
 
getScaleToFit() - Method in class ij.gui.ImageCanvas
 
getScrambledWave() - Method in class ij.wave.Wave
Returns the same Wave but with an new start location within the waveform depending on the value of a uniformly random number -- the new Wave wraps to maintain the same length as the original instance.
getScrambledWaves() - Method in class ij.wave.Waves
 
getScreenSize() - Static method in class ij.IJ
Returns the size, in pixels, of the primary display.
getSD() - Method in class ij.measure.CurveFitter
Returns the standard deviation of the residuals.
getSD() - Static method in class ij.plugin.filter.Filters
Returns the default standard deviation used by Process/Noise/Add Specified Noise.
getSelectedABF() - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
getSelectedEpoch() - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
getSelectedEpoch() - Method in class org.jah.ElectrophysManager
 
getSelectedEpochName() - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
getSelectedEpochName() - Method in class org.jah.ElectrophysManager
 
getSelectedIndex() - Method in class ij.plugin.frame.RoiManager
 
getSelectedIndexes() - Method in class ij.plugin.frame.RoiManager
 
getSelectedIndexes() - Method in class ij.plugin.frame.WaveManager
 
getSelectedRoi() - Method in class ij.plugin.frame.RoiManager
 
getSelectedRoisAsArray() - Method in class ij.plugin.frame.RoiManager
Returns the selected ROIs as an array, or all the ROIs if none are selected.
getSelectedRoisAsArray() - Static method in class org.jah.JAH_Utils
A utility function for returning the selected Rois in the RoiManager.
getSelectedRoisAsVector() - Static method in class org.jah.JAH_Utils
 
getSelectedWave() - Method in class ij.plugin.frame.WaveManager
 
getSelectedWaves() - Method in class ij.plugin.frame.WaveManager
 
getSelectedWavesAsArray() - Method in class ij.plugin.frame.WaveManager
Returns the selected Waves as an array, or all the Waves if none are selected.
getSelectedWavesAsArray() - Static method in class org.jah.JAH_Utils
A utility function for returning the selected Waves in the WaveManager.
getSelectedWavesAsVector() - Static method in class org.jah.JAH_Utils
 
getSelectionEnd() - Method in class ij.text.TextPanel
Returns the index of the last selected line, or -1 if there is no slection.
getSelectionStart() - Method in class ij.text.TextPanel
Returns the index of the first selected line, or -1 if there is no slection.
getSerializedImage() - Method in class ij.gui.ImageRoi
Returns a serialized version of the image.
getSeriesCount() - Method in class ij.wave.DynamicXYDataset
 
getSeriesCount() - Method in class ij.wave.WaveXYDataset
 
getSeriesCount() - Method in class ij.wave.WaveXYZDataset
 
getSeriesIndex(String) - Method in class ij.plugin.frame.ChartFramePlugIn
 
getSeriesKey(int) - Method in class ij.wave.DynamicXYDataset
 
getSeriesKey(int) - Method in class ij.wave.WaveXYDataset
 
getSeriesKey(int) - Method in class ij.wave.WaveXYZDataset
 
getServerAddress() - Static method in class org.jah.Configuration_
 
getShape() - Method in class ij.gui.ShapeRoi
Returns a reference to the Shape object encapsulated by this ShapeRoi.
getShapeAsArray() - Method in class ij.gui.ShapeRoi
Retrieves the end points and control points of the path as a float array.
getShapeRoi() - Method in class ij.io.RoiDecoder
 
getShortcuts() - Static method in class ij.Menus
Returns the hashtable that associates shortcuts with commands.
getShortSliceLabel(int) - Method in class ij.ImageStack
Returns a shortened version (up to the first 60 characters or first newline and suffix removed) of the label of the specified slice.
getShortTitle() - Method in class ij.ImagePlus
Returns a shortened version of image name that does not include spaces or a file name extension.
getShowAllColor() - Static method in class ij.gui.ImageCanvas
Obsolete
getShowAllList() - Method in class ij.gui.ImageCanvas
 
getShowAllROIs() - Method in class ij.gui.ImageCanvas
Obsolete
getSingleWildcardChar() - Method in class ij.util.WildcardMatch
Returns the character used to specify exactly one character.
getSize() - Method in class com.jmatio.types.MLArray
 
getSize() - Static method in class ij.gui.TextRoi
Returns the global (default) font size.
getSize() - Method in class ij.ImageStack
Returns the number of slices in this stack.
getSize() - Method in class ij.macro.Program
 
getSize() - Method in class ij.plugin.AVI_Reader
Returns the number of images in this virtual stack (if it is one)
getSize() - Method in class ij.plugin.FileInfoVirtualStack
Returns the number of images in this stack.
getSize() - Method in class ij.plugin.ListVirtualStack
Returns the number of images in this stack.
getSize() - Method in class ij.VirtualStack
Returns the number of slices in this stack.
getSizeOfNumberInBytes() - Method in class org.javaabf.ABF
 
getSizeOfNumberInBytes() - Method in class org.javaabf.ABF18_parser
Returns 2 for integers && 4 for floating point, depending on the data format."""
getSizeOfNumberInBytes() - Method in class org.javaabf.ABF2_parser
Returns 2 for integers && 4 for floating point, depending on the data format."""
getSizeOfNumberInBytes() - Method in interface org.javaabf.ABF_parser
Returns 2 for integers && 4 for floating point, depending on the data format."""
getSizeOfNumberInBytes() - Method in class org.javaabf.AbstractABF_parser
Returns 2 for integers && 4 for floating point, depending on the data format."""
getSlice() - Method in class ij.ImagePlus
 
getSliceLabel(int) - Method in class ij.ImageStack
Returns the label of the specified slice, were 1<=n<=nslices.
getSliceLabel(int) - Method in class ij.plugin.AVI_Reader
Returns the label of the specified slice in this virtual stack (if it is one).
getSliceLabel(int) - Method in class ij.plugin.FileInfoVirtualStack
Returns the label of the Nth image.
getSliceLabel(int) - Method in class ij.plugin.ListVirtualStack
Returns the name of the specified image.
getSliceLabel(int) - Method in class ij.VirtualStack
Returns the label of the Nth image.
getSliceLabels() - Method in class ij.ImageStack
Returns the slice labels as an array of Strings.
getSliceNumber(String) - Method in class ij.gui.ImageCanvas
 
getSliceNumber() - Method in class ij.plugin.filter.PlugInFilterRunner
Return the slice number currently processed by the calling thread.
getSliceNumber(String) - Method in class ij.plugin.frame.RoiManager
Returns the slice number associated with the specified name, or -1 if the name does not include a slice number.
getSliceNumber() - Method in class ij.process.ImageProcessor
 
getSliders() - Method in class ij.gui.GenericDialog
Returns the Vector containing the sliders (Scrollbars).
getSmoothingPercent() - Static method in class org.jah.Configuration_
 
getSnapshotPixels() - Method in class ij.process.ByteProcessor
 
getSnapshotPixels() - Method in class ij.process.ColorProcessor
Returns a reference to the snapshot pixel array.
getSnapshotPixels() - Method in class ij.process.FloatProcessor
 
getSnapshotPixels() - Method in class ij.process.ImageProcessor
Returns a reference to the snapshot (undo) buffer, or null.
getSnapshotPixels() - Method in class ij.process.ShortProcessor
 
getSortedFitList() - Static method in class ij.measure.CurveFitter
Returns an array of fit names with nicer sorting
getSource() - Method in class ij.gui.LayoutComponent
 
getSourceImage() - Method in interface ij.gui.PlotMaker
Returns the ImagePlus that generates the profile plots.
getSourceImage() - Method in class ij.plugin.Profiler
 
getSourceImage() - Method in class ij.plugin.ZAxisProfiler
 
getSourceWidth(int) - Static method in class org.jah.HologConfiguration_
 
getSpikeUnits() - Method in class ij.wave.Wave
Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev where the stdevFactorAsThreshold defaults to 3.0.
getSpikeUnits(double) - Method in class ij.wave.Wave
Returns the spike units as a new wave -- this is defined as an absolute (value-median) > thresholdFactor*stdev.
getSplitPane() - Method in class ij.plugin.frame.ClusterFramePlugIn
 
getSrcRect() - Method in class ij.gui.ImageCanvas
 
getStack() - Method in class ij.ImagePlus
Returns the image stack.
getStackIndex(int, int, int) - Method in class ij.ImagePlus
Returns that stack index (one-based) corresponding to the specified position.
getStackSize() - Method in class ij.ImagePlus
If this is a stack, returns the number of slices, else returns 1.
getStackTrace(Exception) - Static method in class org.jah.JAH_Utils
Returns a String representing the stack trace of the Exception passed as argument.
getStart() - Method in class org.javaabf.Epoch
 
getStart_s() - Method in class org.javaabf.Epoch
 
getStartTime() - Method in class ij.ImagePlus
Returns the time in milliseconds when startTiming() was last called.
getStartTime() - Method in class org.javaabf.ABF
 
getStartTime() - Method in class org.javaabf.ABF18_parser
Returns the start of the file in milliseconds"""
getStartTime() - Method in class org.javaabf.ABF2_parser
Returns the start of the file in milliseconds"""
getStartTime() - Method in interface org.javaabf.ABF_parser
Returns the start of the file in milliseconds"""
getStartTime() - Method in class org.javaabf.ABFpClamp9_parser
Returns the start of the file in milliseconds"""
getStartTime() - Method in class org.javaabf.AbstractABF_parser
Returns the start of the file in milliseconds"""
getStartTime_s(String) - Method in class org.jah.ElectrophysManager
 
getState() - Method in class ij.gui.Roi
 
getStatistics() - Method in class ij.ImagePlus
Returns an ImageStatistics object generated using the standard measurement options (area, mean, mode, min and max).
getStatistics(int) - Method in class ij.ImagePlus
Returns an ImageStatistics object generated using the specified measurement options.
getStatistics(int, int) - Method in class ij.ImagePlus
Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.
getStatistics(int, int, double, double) - Method in class ij.ImagePlus
Returns an ImageStatistics object generated using the specified measurement options, histogram bin count and histogram range.
getStatistics() - Method in class ij.process.ImageProcessor
 
getStatistics(ImageProcessor, int, Calibration) - Static method in class ij.process.ImageStatistics
 
getStatus() - Method in class ij.measure.CurveFitter
 
getStatusBar() - Method in class ij.ImageJ
 
getStatusString() - Method in class ij.measure.CurveFitter
Get a short text with a short description of the status.
getStdevValue(double, double) - Method in class ij.wave.Wave
 
getStdevValue() - Method in class ij.wave.Wave
 
getStimulusMarkers() - Method in class ij.wave.Bursts
Returns a list of WaveMarkers (as stimulus markers) that can be added to the ChartFramePlugins.
getStimulusMarkers(ArrayList) - Static method in class ij.wave.WaveUtils
Returns the WaveMarkers of type STIMULUS in the list passed as argument.
getStorageClazz() - Method in interface com.jmatio.types.ByteStorageSupport
 
getStorageClazz() - Method in class com.jmatio.types.MLDouble
 
getStorageClazz() - Method in class com.jmatio.types.MLInt16
 
getStorageClazz() - Method in class com.jmatio.types.MLInt32
 
getStorageClazz() - Method in class com.jmatio.types.MLInt64
 
getStorageClazz() - Method in class com.jmatio.types.MLInt8
 
getStorageClazz() - Method in class com.jmatio.types.MLSingle
 
getStorageClazz() - Method in class com.jmatio.types.MLSparse
 
getStorageClazz() - Method in class com.jmatio.types.MLUInt64
 
getStorageClazz() - Method in class com.jmatio.types.MLUInt8
 
getStoredValue() - Method in class ij.wave.WaveMarker
 
getString(int) - Method in class com.jmatio.types.MLChar
Gets the m-th character matrix's row as String.
getString(String, String) - Static method in class ij.IJ
Allows the user to enter a string in a dialog box.
getString(String) - Static method in class ij.Prefs
Finds an string in IJ_Props or IJ_Prefs.txt.
getString(String, String) - Static method in class ij.Prefs
Finds an string in IJ_Props or IJ_Prefs.txt.
getStringFields() - Method in class ij.gui.GenericDialog
Returns the Vector containing the string TextFields.
getStringValue(String, int) - Method in class ij.measure.ResultsTable
Returns the string value of the given column and row, where row must be greater than or equal zero and less than the value returned by getCounter().
getStringValue(int, int) - Method in class ij.measure.ResultsTable
Returns the string value of the given column and row, where column must be less than or equal the value returned by getLastColumn() and row must be greater than or equal zero and less than the value returned by getCounter().
getStringVariable(String) - Method in class ij.macro.Interpreter
 
getStringWidth(String) - Method in class ij.process.ImageProcessor
Returns the width in pixels of the specified string.
getStringWidth(String, FontMetrics, Graphics) - Static method in class ij.util.Java2
 
getStroke() - Method in class ij.gui.Roi
Returns the Stroke used to draw this ROI, or null if no Stroke is used.
getStrokeColor() - Method in class ij.gui.Roi
Returns the the color used to draw the ROI outline or null if the default color is being used.
getStrokeWidth() - Method in class ij.gui.Roi
Returns the lineWidth.
getStubPath() - Static method in class ij.OtherInstance
 
getStyle() - Method in class ij.gui.Arrow
 
getStyle() - Static method in class ij.gui.TextRoi
Returns the global (default) font style.
getSumResidualsSqr() - Method in class ij.measure.CurveFitter
 
getSymbolTable() - Method in class ij.macro.Program
 
getT() - Method in class ij.ImagePlus
Returns the current hyperstack frame position.
getTableAsImage() - Method in class ij.measure.ResultsTable
Returns the contents of this ResultsTable as a FloatProcessor.
getTag(ImagePlus, String) - Static method in class ij.util.DicomTools
Returns the value (as a string) of the specified DICOM tag id (in the form "0018,0050") of the specified image or stack slice.
getTag() - Method in class org.javaabf.Comment
 
getTags() - Method in class org.javaabf.ABF
 
getTags() - Method in class org.javaabf.ABF18_parser
 
getTags() - Method in interface org.javaabf.ABF_parser
 
getTags() - Method in class org.javaabf.AbstractABF_parser
 
getTempCurrentImage() - Static method in class ij.WindowManager
Returns the temporary current image for this thread, or null.
getTemporalHistogram(double) - Method in class ij.wave.Wave
 
getText() - Method in class ij.gui.TextRoi
 
getText() - Method in class ij.plugin.frame.Editor
 
getText() - Method in class ij.plugin.frame.Jython_Console
 
getText() - Method in class ij.plugin.frame.Recorder
 
getText() - Method in class ij.text.TextPanel
Returns all the text as a string.
getText() - Method in class org.javaabf.Comment
 
getText() - Method in class org.javaabf.Tag
 
getTextArea() - Method in class ij.plugin.frame.Editor
 
getTextArea1() - Method in class ij.gui.GenericDialog
Returns a reference to textArea1.
getTextArea2() - Method in class ij.gui.GenericDialog
Returns a reference to textArea2.
getTextPanel() - Static method in class ij.IJ
Returns a reference to the "Results" window TextPanel.
getTextPanel() - Method in class ij.text.TextWindow
Returns a reference to this TextWindow's TextPanel.
getThickness() - Method in class ij.gui.LineLayoutComponent
 
getThread() - Method in class ij.macro.MacroRunner
 
getThreads() - Static method in class ij.Prefs
Returns the number of threads used by PlugInFilters to process images and stacks.
getThreshold(AutoThresholder.Method, int[]) - Method in class ij.process.AutoThresholder
 
getThreshold(String, int[]) - Method in class ij.process.AutoThresholder
 
getThresholdCrossingingIndex(double, int) - Method in class ij.wave.Burst
Returns the index of the burst data array corresponding to the first time the burst crosses the threshold relative to the burst array.
getThresholdCrossingTime(double, int) - Method in class ij.wave.Burst
Returns the first time the burst crosses the threshold (in seconds) relative to the reference wave.
getTiffInfo() - Method in class ij.io.TiffDecoder
 
getTime() - Method in class org.javaabf.Comment
 
getTime() - Method in class org.javaabf.Tag
 
getTimestamp() - Static method in class org.jah.JAH_Utils
 
getTimeUnit() - Method in class ij.measure.Calibration
Returns the distance unit (e.g.
getTitle() - Method in class ij.gui.LayoutComponent
 
getTitle() - Static method in class ij.IJ
 
getTitle() - Method in class ij.ImagePlus
Returns the image name.
getTolerance() - Static method in class ij.plugin.WandToolOptions
 
getToolIcon() - Method in class ij.plugin.tool.ArrowTool
 
getToolIcon() - Method in class ij.plugin.tool.BrushTool
 
getToolIcon() - Method in class ij.plugin.tool.OverlayBrushTool
 
getToolIcon() - Method in class ij.plugin.tool.PixelInspectionTool
 
getToolIcon() - Method in class ij.plugin.tool.PlugInTool
Return the string encoding of the tool icon.
getToolId() - Static method in class ij.gui.Toolbar
Returns the ID of the current tool (Toolbar.RECTANGLE, Toolbar.OVAL, etc.).
getToolId(String) - Method in class ij.gui.Toolbar
Returns the ID of the tool whose name (the description displayed in the status bar) starts with the specified string, or -1 if the tool is not found.
getToolName() - Static method in class ij.gui.Toolbar
Returns the name of the current tool.
getToolName() - Static method in class ij.IJ
Returns the name of the current tool.
getToolName() - Method in class ij.plugin.tool.ArrowTool
 
getToolName() - Method in class ij.plugin.tool.BrushTool
 
getToolName() - Method in class ij.plugin.tool.OverlayBrushTool
 
getToolName() - Method in class ij.plugin.tool.PixelInspectionTool
 
getToolName() - Method in class ij.plugin.tool.PlugInTool
Return the tool name.
getTopProgressBar() - Method in class ij.ImageJ
 
getTPosition() - Method in class ij.gui.Roi
Returns the frame position of this ROI, or zero if this ROI is not associated with a particular frame.
getTrace(String, int) - Static method in class org.jah.JAH_Utils
 
getTransferData(DataFlavor) - Method in class ij.plugin.Clipboard
 
getTransferDataFlavors() - Method in class ij.plugin.Clipboard
 
getTransparentIndex() - Static method in class ij.Prefs
Returns the transparent index (0-255), or -1 if transparency is disabled.
getTriggerMarkers() - Method in class ij.plugin.frame.ChartFramePlugIn
Returns the list of trigger markers, but should only be used for read-only.
getTruncatedZscoredWave(boolean) - Method in class ij.wave.Wave
 
getTruncatedZscoredWave() - Method in class ij.wave.Wave
 
getTruncatedZscoredWaves() - Method in class ij.wave.Waves
 
getType() - Method in class com.jmatio.types.MLArray
 
getType() - Method in class ij.gui.LayoutComponent
 
getType() - Method in class ij.gui.Roi
 
getType() - Method in class ij.ImagePlus
Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
getType() - Method in class ij.wave.ABFWaveProxy
 
getType() - Method in class ij.wave.EpisodicWave
 
getType() - Method in class ij.wave.Wave
 
getType() - Method in class ij.wave.WaveMarker
 
getType() - Method in class ij.wave.WaveProxy
 
getType() - Method in class org.javaabf.Epoch
 
getTypeAsString() - Method in class ij.gui.Roi
Convenience method that converts Roi type to a human-readable form.
getTypeAsString() - Method in class ij.wave.Wave
 
getTypeAsString() - Method in class org.javaabf.Epoch
 
getTypeName(int) - Static method in class ij.macro.ExtensionDescriptor
 
getTypes() - Static method in class ij.wave.WaveMarker
 
getUMeans() - Static method in class ij.plugin.filter.Analyzer
Returns an array containing the first 20 uncalibrated means.
getUncalibratedLength() - Method in class ij.gui.PolygonRoi
 
getUniqueName() - Method in class ij.plugin.frame.Layout
 
getUniqueName() - Method in class ij.plugin.frame.LayoutPanel
 
getUniqueName(String) - Static method in class ij.WindowManager
Returns a unique name by adding, before the extension, -1, -2, etc. as needed.
getUniqueTitle(String) - Static method in class ij.util.PlotterUtils
 
getUnit() - Method in class ij.measure.Calibration
Returns the default length unit (e.g.
getUnitIncrement() - Method in class ij.gui.ScrollbarWithLabel
 
getUnits() - Method in class ij.measure.Calibration
Returns the plural form of the length unit (e.g.
getUnits() - Method in class ij.wave.Wave
 
getValue(String) - Method in class ij.gui.GenericDialog
 
getValue() - Method in class ij.gui.ScrollbarWithLabel
 
getValue(String, String, String) - Static method in class ij.Macro
 
getValue(int, int) - Method in class ij.measure.ResultsTable
Deprecated. replaced by getValueAsDouble
getValue(String, int) - Method in class ij.measure.ResultsTable
Returns the value of the specified column and row, where column is the column heading and row is a number greater than or equal zero and less than value returned by getCounter().
getValue(int, int, Vector) - Static method in class ij.wave.ClusterUtils
 
getValueAsDouble(int, int) - Method in class ij.measure.ResultsTable
Returns the value of the given column and row, where column must be less than or equal the value returned by getLastColumn() and row must be greater than or equal zero and less than the value returned by getCounter().
getValueAt(int, int) - Method in class ij.plugin.frame.table.EpochTableModel
 
getValueAt(double) - Method in class ij.wave.Wave
Returns the value of the wave at the specified time (in seconds).
getValues() - Method in class ij.wave.ABFWaveProxy
 
getValues(int) - Method in class ij.wave.ABFWaveProxy
 
getValues(double, double, int) - Method in class ij.wave.ABFWaveProxy
 
getValues() - Method in class ij.wave.Wave
Returns the values of this Wave.
getValues(double, double, int) - Method in class ij.wave.Wave
 
getValues(int) - Method in class ij.wave.Wave
Returns a decimated array corresponding to the waveform and picks out the max/min values for the decimation.
getValues(int) - Method in class ij.wave.WaveProxy
Returns the full set of values of this source but with the degree of decimation defined by the argument.
getValues() - Method in class ij.wave.WaveProxy
Returns the full set of values of this source.
getValueUnit() - Method in class ij.measure.Calibration
Returns the value unit.
getVariable(String) - Method in class ij.macro.Interpreter
 
getVariable2(String) - Method in class ij.macro.Interpreter
 
getVariableAsString(String) - Method in class ij.macro.Interpreter
 
getVariables() - Method in class ij.macro.Interpreter
 
getVariance() - Method in class ij.util.ArrayUtil
Variance value
getVersion() - Method in class com.jmatio.io.MatFileHeader
When creating a MAT-file, set version to 0x0100
getVersion() - Static method in class ij.IJ
Returns the ImageJ version number as a string.
getVersion() - Method in class ij.plugin.PlugInInterpreter
Returns the version of ImageJ at the time this plugin was created.
getViewFrame() - Static method in class ij.wave.ClusterUtils
 
getVisibleAmount() - Method in class ij.gui.ScrollbarWithLabel
 
getVoxel(int, int, int) - Method in class ij.ImageStack
Returns, as a double, the specified voxel.
getVoxelDepth(ImageStack) - Static method in class ij.util.DicomTools
Calculates the voxel depth of the specified DICOM stack based on the distance between the first and last slices.
getVoxels(int, int, int, int, int, int, float[]) - Method in class ij.ImageStack
Experimental
getVoxels(int, int, int, int, int, int, float[], int) - Method in class ij.ImageStack
Experimental
getWave(String) - Method in class ij.plugin.frame.ChartFramePlugIn
Returns the Wave from the chart with the given name.
getWave(String) - Method in class ij.plugin.frame.WaveManager
 
getWave(int) - Method in class ij.wave.Waves
Returns the Wave at the given index in the collection.
getWave(String) - Method in class ij.wave.Waves
 
getWave(ABF, String, int) - Method in class org.javaabf.Epoch
 
getWave1() - Method in class ij.wave.CrosscorrelationWave
 
getWave2() - Method in class ij.wave.CrosscorrelationWave
 
getWaveForBurstAnalysisFromLocalMaxima(double) - Method in class ij.wave.Wave
Returns a new Wave that has a moving average filter applied to it and then a central finite difference applied.
getWaveRange(int, int) - Method in class ij.wave.Wave
Returns a duplicate Wave from the startIndex to the startIndex+length index.
getWaveRange(double, double) - Method in class ij.wave.Wave
Returns a duplicate Wave from the startTime_s up to endTime_s.
getWaves() - Method in class ij.plugin.frame.ChartFramePlugIn
Returns all the Waves from the chart.
getWaves() - Method in class ij.plugin.frame.WaveManager
 
getWaves() - Method in class ij.wave.WaveXYDataset
 
getWaves() - Method in class ij.wave.WaveXYZDataset
 
getWaves() - Method in class org.javaabf.Epoch
 
getWavesAsArray() - Method in class ij.plugin.frame.WaveManager
Returns the Waves as an array.
getWavesAsArray() - Static method in class org.jah.JAH_Utils
A utility function for returning all the Waves in the WaveManager.
getWavesByName(File) - Method in class ij.wave.Waves
 
getWavesFromMatFile(String) - Static method in class ij.wave.WaveUtils
 
getWavesHashtable() - Method in class ij.plugin.frame.WaveManager
Returns the Wave Hashtable.
getWeightingFactors() - Static method in class ij.process.ColorProcessor
Returns the three weighting factors used by getPixelValue(), getHistogram() and convertToByte() to do color conversions.
getWfdSrcInputDirectory() - Static method in class org.jah.Configuration_
 
getWidth() - Method in class ij.gui.LayoutComponent
 
getWidth() - Static method in class ij.gui.Line
 
getWidth() - Method in class ij.ImagePlus
 
getWidth() - Method in class ij.ImageStack
 
getWidth() - Method in class ij.plugin.AVI_Reader
Returns the image width of the virtual stack
getWidth() - Method in class ij.plugin.FileInfoVirtualStack
 
getWidth() - Method in class ij.plugin.ListVirtualStack
 
getWidth() - Method in class ij.process.ImageProcessor
Returns the width of this image in pixels.
getWindow() - Method in class ij.ImagePlus
Returns the ImageWindow that is being used to display this image.
getWindow(String) - Static method in class ij.WindowManager
Returns the window (a Frame or a Dialog) with the specified title, or null if a window with that title is not found.
getWindowCount() - Static method in class ij.WindowManager
Returns the number of open image windows.
getX() - Method in class ij.gui.LayoutComponent
 
getX(double) - Method in class ij.measure.Calibration
Converts a x-coodinate in pixels to physical units (e.g. mm).
getX(int, int) - Method in class ij.wave.DynamicXYDataset
 
getX(int, int) - Method in class ij.wave.WaveXYDataset
 
getX(int, int) - Method in class ij.wave.WaveXYZDataset
 
getXBase() - Method in class ij.gui.Roi
 
getXCoordinates() - Method in class ij.gui.PolygonRoi
Obsolete; replaced by either getPolygon() or getFloatPolygon().
getXOffset(int) - Static method in class org.jah.HologConfiguration_
 
getXPoints() - Method in class ij.measure.CurveFitter
returns the array with the x data
getXStartOffset() - Method in class ij.wave.Wave
An offset for the first element in the wave.
getXUnit() - Method in class ij.measure.Calibration
Returns the X length unit.
getXVal() - Method in class ij.wave.WaveMarker
 
getXValues() - Method in class ij.gui.HistogramWindow
 
getXValues() - Method in class ij.gui.PlotWindow
 
getXWave() - Method in class ij.wave.WaveWaveSeries
 
getXYDatasetForWave(String) - Method in class ij.plugin.frame.ChartFramePlugIn
 
getXYPlot() - Method in class ij.plugin.frame.ChartFramePlugIn
 
getXYPlot(Wave, boolean, int, double, double) - Static method in class ij.util.PlotterUtils
 
getXYPlot(Waves, boolean, int, double, double) - Static method in class ij.util.PlotterUtils
 
getXYPlotForWave(String) - Method in class ij.plugin.frame.ChartFramePlugIn
 
getXYZAnnotations(Waves) - Static method in class ij.util.PlotterUtils
 
getXYZAnnotations(Waves, int) - Static method in class ij.util.PlotterUtils
 
getXYZAnnotations(Waves, int, Font) - Static method in class ij.util.PlotterUtils
 
getXYZDataset(Waves) - Static method in class ij.util.PlotterUtils
 
getXZImage() - Method in class ij.plugin.Orthogonal_Views
 
getY() - Method in class ij.gui.LayoutComponent
 
getY(double) - Method in class ij.measure.Calibration
Converts a y-coordinate in pixels to physical units (e.g. mm).
getY(double, int) - Method in class ij.measure.Calibration
Converts a y-coordinate in pixels to physical units (e.g. mm), taking into account the invertY and global "Invert Y Coordinates" flags.
getY(int, int) - Method in class ij.wave.DynamicXYDataset
 
getY(int, int) - Method in class ij.wave.WaveXYDataset
 
getY(int, int) - Method in class ij.wave.WaveXYZDataset
 
getYBase() - Method in class ij.gui.Roi
 
getYCoordinates() - Method in class ij.gui.PolygonRoi
Obsolete; replaced by either getPolygon() or getFloatPolygon().
getYOffset(int) - Static method in class org.jah.HologConfiguration_
 
getYPoints() - Method in class ij.measure.CurveFitter
returns the array with the y data
getYUnit() - Method in class ij.measure.Calibration
Returns the Y length unit, or the default unit if 'yunit' is null.
getYUV(ImageProcessor, byte[], byte[], byte[]) - Method in class ij.plugin.frame.ColorThresholder
 
getYValues() - Method in class ij.gui.PlotWindow
 
getYWave() - Method in class ij.wave.WaveWaveSeries
 
getYZImage() - Method in class ij.plugin.Orthogonal_Views
 
getZ() - Method in class ij.ImagePlus
Returns the current hyperstack slice position.
getZ(double) - Method in class ij.measure.Calibration
Converts a z-coordinate in pixels to physical units (e.g. mm).
getZ(int, int) - Method in class ij.wave.WaveXYZDataset
 
getZAxisProfile(Analyzer, Calibration, ImageStack, Roi) - Static method in class org.jah.JAH_Utils
 
getZeroLagCorrelation() - Method in class ij.wave.CrosscorrelationWave
 
getZPosition() - Method in class ij.gui.Roi
Returns the slice position of this ROI, or zero if this ROI is not associated with a particular slice.
getZProjection(ImagePlus, int) - Static method in class org.jah.JAH_Utils
A convenience function for projecting a time-series to one plane using the method specified in the argument.
getZscoredWave(boolean) - Method in class ij.wave.Wave
Returns a clone copy of this wave but where each value in the series has the z-scored value (i.e., the mean of the Wave should be 0 and stdev=1).
getZscoredWave() - Method in class ij.wave.Wave
 
getZUnit() - Method in class ij.measure.Calibration
Returns the Z length unit, or the default unit if 'zunit' is null.
GIF - Static variable in class ij.io.Opener
 
GIF_OR_JPG - Static variable in class ij.io.FileInfo
 
GifWriter - Class in ij.plugin
Writes a stack as an animated Gif
GifWriter() - Constructor for class ij.plugin.GifWriter
 
gLUT1 - Variable in class ij.process.ImageProcessor
 
gLUT2 - Variable in class ij.process.ImageProcessor
 
GRAY12_UNSIGNED - Static variable in class ij.io.FileInfo
12-bit unsigned integer (0-4095).
GRAY16 - Static variable in class ij.gui.NewImage
 
GRAY16 - Static variable in class ij.ImagePlus
16-bit grayscale (unsigned)
GRAY16_SIGNED - Static variable in class ij.io.FileInfo
16-bit signed integer (-32768-32767).
GRAY16_UNSIGNED - Static variable in class ij.io.FileInfo
16-bit unsigned integer (0-65535).
GRAY24_UNSIGNED - Static variable in class ij.io.FileInfo
24-bit unsigned integer.
GRAY32 - Static variable in class ij.gui.NewImage
 
GRAY32 - Static variable in class ij.ImagePlus
32-bit floating-point grayscale
GRAY32_FLOAT - Static variable in class ij.io.FileInfo
32-bit floating-point.
GRAY32_INT - Static variable in class ij.io.FileInfo
32-bit signed integer.
GRAY32_UNSIGNED - Static variable in class ij.io.FileInfo
32-bit unsigned integer.
GRAY64_FLOAT - Static variable in class ij.io.FileInfo
64-bit floating-point.
GRAY8 - Static variable in class ij.gui.NewImage
 
GRAY8 - Static variable in class ij.ImagePlus
8-bit grayscale (unsigned)
GRAY8 - Static variable in class ij.io.FileInfo
8-bit unsigned integer (0-255).
GRAYSCALE - Static variable in class ij.CompositeImage
Display modes (note: TRANSPARENT mode has not yet been implemented)
GRAYSCALE - Static variable in class ij.IJ
Image display modes
green - Variable in class ij.plugin.filter.RGBStackSplitter
 
greens - Variable in class ij.io.FileInfo
 
grow(int, int) - Method in class ij.gui.EllipseRoi
 
grow(int, int) - Method in class ij.gui.FreehandRoi
 
grow(int, int) - Method in class ij.gui.Line
 
grow(int, int) - Method in class ij.gui.PolygonRoi
 
grow(int, int) - Method in class ij.gui.Roi
 
GT - Static variable in interface ij.macro.MacroConstants
 
GTE - Static variable in interface ij.macro.MacroConstants
 
GUI - Class in ij.gui
This class consists of static GUI utility methods.
GUI() - Constructor for class ij.gui.GUI
 

H

HAND - Static variable in class ij.gui.Toolbar
 
handCursor - Static variable in class ij.gui.ImageCanvas
 
handle(Throwable) - Method in interface ij.IJ.ExceptionHandler
 
HANDLE_SIZE - Static variable in class ij.gui.Roi
 
handleColor - Variable in class ij.gui.Roi
 
handleException(Throwable) - Static method in class ij.IJ
Displays a stack trace.
handleExtension(String, Object[]) - Method in interface ij.macro.MacroExtension
 
handleMouseDown(int, int) - Method in class ij.gui.Arrow
 
handleMouseDown(int, int) - Method in class ij.gui.Line
 
handleMouseDown(int, int) - Method in class ij.gui.Roi
 
handleMouseDrag(int, int, int) - Method in class ij.gui.Roi
 
handleMouseUp(int, int) - Method in class ij.gui.EllipseRoi
 
handleMouseUp(int, int) - Method in class ij.gui.FreehandRoi
 
handleMouseUp(int, int) - Method in class ij.gui.Line
 
handleMouseUp(int, int) - Method in class ij.gui.PointRoi
 
handleMouseUp(int, int) - Method in class ij.gui.PolygonRoi
With segmented selections, ignore first mouse up and finalize when user double-clicks, control-clicks or clicks in start box.
handleMouseUp(int, int) - Method in class ij.gui.Roi
 
handleMouseUp(int, int) - Method in class ij.gui.TextRoi
 
handlePopupMenu(MouseEvent) - Method in class ij.gui.ImageCanvas
 
handler - Variable in class ij.macro.ExtensionDescriptor
 
handleRoiMouseDown(MouseEvent) - Method in class ij.gui.ImageCanvas
 
hasCustomLuts() - Method in class ij.CompositeImage
 
hasVars() - Method in class ij.macro.Program
 
hasWord(String) - Method in class ij.macro.Program
 
HEADER2_OFFSET - Static variable in class ij.io.RoiDecoder
 
HEADLESS - Static variable in class ij.gui.Arrow
 
HEAP_BYTE_BUFFER - Static variable in class com.jmatio.io.MatFileReader
 
HeapBufferDataOutputStream - Class in com.jmatio.io
 
HeapBufferDataOutputStream() - Constructor for class com.jmatio.io.HeapBufferDataOutputStream
 
height - Variable in class ij.ImagePlus
 
height - Variable in class ij.io.FileInfo
 
height - Variable in class ij.process.ImageProcessor
 
height - Variable in class ij.process.ImageStatistics
 
HEIGHT_KEY - Static variable in class ij.text.TextWindow
 
HEIGHTD - Static variable in class ij.io.RoiDecoder
 
hexDigits - Static variable in class ij.util.Tools
This array contains the 16 hex digits '0'-'F'.
hexToColor(String) - Static method in class ij.plugin.Colors
Converts a hex color (e.g., "ffff00") into "red", "green", "yellow", etc.
hexToColor2(String) - Static method in class ij.plugin.Colors
Converts a hex color (e.g., "ffff00") into "Red", "Green", "Yellow", etc.
hide() - Method in class ij.ImagePlus
Closes the window, if any, that is displaying this image.
hideCancelButton() - Method in class ij.gui.GenericDialog
No not display "Cancel" button.
hideDetails() - Method in class ij.plugin.frame.ChartFramePlugIn
 
hideErrorMessages() - Method in class ij.plugin.TextReader
 
hideMarker() - Method in class ij.wave.WaveMarker
 
hideOutputImage - Variable in class ij.plugin.filter.ParticleAnalyzer
 
hideProcessStackDialog - Static variable in class ij.IJ
 
hideProgress() - Method in class ij.process.ImageProcessor
Deprecated.  
histMax - Variable in class ij.process.ImageStatistics
 
histMin - Variable in class ij.process.ImageStatistics
 
histogram - Variable in class ij.gui.HistogramWindow
 
Histogram - Class in ij.plugin
This plugin implements the Analyze/Histogram command.
Histogram() - Constructor for class ij.plugin.Histogram
 
histogram - Variable in class ij.process.ImageStatistics
 
histogram16 - Variable in class ij.process.ImageStatistics
65536 element histogram (16-bit images only)
histogramMax - Variable in class ij.process.ImageProcessor
 
histogramMin - Variable in class ij.process.ImageProcessor
 
histogramSize - Variable in class ij.process.ImageProcessor
 
HistogramWindow - Class in ij.gui
This class is an extended ImageWindow that displays histograms.
HistogramWindow(ImagePlus) - Constructor for class ij.gui.HistogramWindow
Displays a histogram using the title "Histogram of ImageName".
HistogramWindow(String, ImagePlus, int) - Constructor for class ij.gui.HistogramWindow
Displays a histogram using the specified title and number of bins.
HistogramWindow(String, ImagePlus, int, double, double) - Constructor for class ij.gui.HistogramWindow
Displays a histogram using the specified title, number of bins and histogram range.
HistogramWindow(String, ImagePlus, int, double, double, int) - Constructor for class ij.gui.HistogramWindow
Displays a histogram using the specified title, number of bins, histogram range and yMax.
HistogramWindow(String, ImagePlus, ImageStatistics) - Constructor for class ij.gui.HistogramWindow
Displays a histogram using the specified title and ImageStatistics.
histYMax - Variable in class ij.process.ImageStatistics
 
HologConfiguration_ - Class in org.jah
 
HologConfiguration_() - Constructor for class org.jah.HologConfiguration_
 
HOST_COMPUTER - Static variable in class ij.io.TiffDecoder
 
Hotkeys - Class in ij.plugin
Implements the Plugins/Hotkeys/Install and Remove commands.
Hotkeys() - Constructor for class ij.plugin.Hotkeys
 
HTMLDialog - Class in ij.gui
This is modal dialog box that displays HTML formated text.
HTMLDialog(String, String) - Constructor for class ij.gui.HTMLDialog
 
HTMLDialog(Dialog, String, String) - Constructor for class ij.gui.HTMLDialog
 
hyperlinkUpdate(HyperlinkEvent) - Method in class ij.gui.HTMLDialog
 
HyperStackConverter - Class in ij.plugin
Implements the "Stack to HyperStack", "RGB to HyperStack" and "HyperStack to Stack" commands.
HyperStackConverter() - Constructor for class ij.plugin.HyperStackConverter
 
HyperStackMaker - Class in ij.plugin
This plugin implements the File/New/Hyperstack command.
HyperStackMaker() - Constructor for class ij.plugin.HyperStackMaker
 
HyperStackReducer - Class in ij.plugin
Implements the Image/HyperStacks/Reduce Dimensionality command.
HyperStackReducer() - Constructor for class ij.plugin.HyperStackReducer
Default constructor
HyperStackReducer(ImagePlus) - Constructor for class ij.plugin.HyperStackReducer
Constructs a HyperStackReducer using the specified source image.

I

ic - Variable in class ij.gui.ImageWindow
 
ic - Variable in class ij.gui.Roi
 
IF - Static variable in interface ij.macro.MacroConstants
 
ifile - Variable in class org.javaabf.AbstractABF_parser
 
ignoreClipRect - Variable in class ij.gui.Roi
 
ij - package ij
 
ij - Variable in class ij.gui.ImageCanvas
 
ij - Variable in class ij.gui.ImageWindow
 
IJ - Class in ij
This class consists of static utility methods.
IJ() - Constructor for class ij.IJ
 
ij - Variable in class ij.plugin.frame.ChartFramePlugIn
 
IJ.ExceptionHandler - Interface in ij
 
ij.gui - package ij.gui
 
ij.io - package ij.io
 
ij.macro - package ij.macro
 
ij.measure - package ij.measure
 
ij.plugin - package ij.plugin
 
ij.plugin.filter - package ij.plugin.filter
 
ij.plugin.frame - package ij.plugin.frame
 
ij.plugin.frame.table - package ij.plugin.frame.table
 
ij.plugin.tool - package ij.plugin.tool
 
ij.process - package ij.process
 
ij.text - package ij.text
 
ij.util - package ij.util
 
ij.wave - package ij.wave
 
IJ_CALL - Static variable in interface ij.macro.MacroConstants
 
IJEventListener - Interface in ij
Plugins that implement this interface are notified when the user changes the foreground color, changes the background color, closes the color picker, closes the Log window or switches to another tool.
ijInstance - Variable in class ij.plugin.frame.SyncWindows
reference to current instance of ImageJ (to avoid repeated IJ.getInstance() s)
IMAGE - Static variable in class ij.io.RoiDecoder
 
IMAGE - Static variable in class ij.plugin.frame.Layout
 
image - Variable in class ij.process.ImageProcessor
 
IMAGE_DESCRIPTION - Static variable in class ij.io.TiffDecoder
 
IMAGE_LENGTH - Static variable in class ij.io.TiffDecoder
 
IMAGE_OPACITY - Static variable in class ij.io.RoiDecoder
 
IMAGE_SIZE - Static variable in class ij.io.RoiDecoder
 
IMAGE_TYPE - Static variable in class ij.WindowManager
 
IMAGE_WIDTH - Static variable in class ij.io.TiffDecoder
 
ImageCalculator - Class in ij.plugin
This plugin implements the Process/Image Calculator command.
ImageCalculator() - Constructor for class ij.plugin.ImageCalculator
 
ImageCanvas - Class in ij.gui
This is a Canvas used to display images in a Window.
ImageCanvas(ImagePlus) - Constructor for class ij.gui.ImageCanvas
 
imageClosed(ImagePlus) - Method in class ij.gui.HistogramWindow
 
imageClosed(ImagePlus) - Method in class ij.gui.PlotWindow
 
imageClosed(ImagePlus) - Method in interface ij.ImageListener
 
imageClosed(ImagePlus) - Method in class ij.plugin.frame.Recorder
 
imageClosed(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
Implementation of ImageListener interface: update window list, if image is opened or closed
imageClosed(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
 
imageClosed(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
 
ImageConverter - Class in ij.process
This class converts an ImagePlus object to a different type.
ImageConverter(ImagePlus) - Constructor for class ij.process.ImageConverter
Constructs an ImageConverter based on an ImagePlus object.
imageHeight - Variable in class ij.gui.ImageCanvas
 
IMAGEIO - Static variable in class ij.io.FileInfo
 
ImageJ - Class in ij
This frame is the main ImageJ class.
ImageJ() - Constructor for class ij.ImageJ
Creates a new ImageJ frame that runs as an application.
ImageJ(int) - Constructor for class ij.ImageJ
Creates a new ImageJ frame that runs as an application in the specified mode.
ImageJ(Applet) - Constructor for class ij.ImageJ
Creates a new ImageJ frame that runs as an applet.
ImageJ(Applet, int) - Constructor for class ij.ImageJ
If 'applet' is not null, creates a new ImageJ frame that runs as an applet.
ImageJ_Updater - Class in ij.plugin
This plugin implements the Help/Update ImageJ command.
ImageJ_Updater() - Constructor for class ij.plugin.ImageJ_Updater
 
ImageJApplet - Class in ij
Runs ImageJ as an applet and optionally opens up to nine images using URLs passed as a parameters.
ImageJApplet() - Constructor for class ij.ImageJApplet
 
ImageLayout - Class in ij.gui
This is a custom layout manager that supports resizing of zoomed images.
ImageLayout(ImageCanvas) - Constructor for class ij.gui.ImageLayout
Creates a new ImageLayout with center alignment and 5 pixel horizontal and vertical gaps.
ImageListener - Interface in ij
Plugins that implement this interface are notified when an image is opened, closed or updated.
ImageMath - Class in ij.plugin.filter
This plugin implements ImageJ's Process/Math submenu.
ImageMath() - Constructor for class ij.plugin.filter.ImageMath
 
imageOpened(ImagePlus) - Method in class ij.gui.HistogramWindow
 
imageOpened(ImagePlus) - Method in class ij.gui.PlotWindow
 
imageOpened(ImagePlus) - Method in interface ij.ImageListener
 
imageOpened(ImagePlus) - Method in class ij.plugin.frame.Recorder
 
imageOpened(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
Implementation of ImageListener interface: update window list, if image is opened or closed
imageOpened(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
 
imageOpened(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
 
ImagePlus - Class in ij
An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image).
ImagePlus() - Constructor for class ij.ImagePlus
Constructs an uninitialized ImagePlus.
ImagePlus(String, Image) - Constructor for class ij.ImagePlus
Constructs an ImagePlus from an Image or BufferedImage.
ImagePlus(String, ImageProcessor) - Constructor for class ij.ImagePlus
Constructs an ImagePlus from an ImageProcessor.
ImagePlus(String) - Constructor for class ij.ImagePlus
Constructs an ImagePlus from a TIFF, BMP, DICOM, FITS, PGM, GIF or JPRG specified by a path or from a TIFF, DICOM, GIF or JPEG specified by a URL.
ImagePlus(String, ImageStack) - Constructor for class ij.ImagePlus
Constructs an ImagePlus from a stack.
ImageProcessor - Class in ij.process
This abstract class is the superclass for classes that process the four data types (byte, short, float and RGB) supported by ImageJ.
ImageProcessor() - Constructor for class ij.process.ImageProcessor
 
ImageProperties - Class in ij.plugin.filter
 
ImageProperties() - Constructor for class ij.plugin.filter.ImageProperties
 
ImageReader - Class in ij.io
Reads raw 8-bit, 16-bit or 32-bit (float or RGB) images from a stream or URL.
ImageReader(FileInfo) - Constructor for class ij.io.ImageReader
Constructs a new ImageReader using a FileInfo object to describe the file to be read.
ImageRoi - Class in ij.gui
An ImageRoi is an Roi that displays an image as an overlay.
ImageRoi(int, int, BufferedImage) - Constructor for class ij.gui.ImageRoi
Creates a new ImageRoi from a BufferedImage.
ImageRoi(int, int, ImageProcessor) - Constructor for class ij.gui.ImageRoi
Creates a new ImageRoi from a ImageProcessor.
ImageStack - Class in ij
This class represents an expandable array of images.
ImageStack() - Constructor for class ij.ImageStack
Default constructor.
ImageStack(int, int) - Constructor for class ij.ImageStack
Creates a new, empty image stack.
ImageStack(int, int, int) - Constructor for class ij.ImageStack
Creates a new, empty image stack with a capacity of 'size'.
ImageStack(int, int, ColorModel) - Constructor for class ij.ImageStack
Creates a new, empty image stack using the specified color model.
ImageStatistics - Class in ij.process
Statistics, including the histogram, of an image or selection.
ImageStatistics() - Constructor for class ij.process.ImageStatistics
 
ImagesToStack - Class in ij.plugin
Implements the Image/Stacks/Images to Stack" command.
ImagesToStack() - Constructor for class ij.plugin.ImagesToStack
 
imageUpdate(Image, int, int, int, int, int) - Method in class ij.ImagePlus
Used by ImagePlus to monitor loading of images.
imageUpdated(ImagePlus) - Method in class ij.gui.HistogramWindow
 
imageUpdated - Variable in class ij.gui.ImageCanvas
 
imageUpdated(ImagePlus) - Method in class ij.gui.PlotWindow
 
imageUpdated(ImagePlus) - Method in interface ij.ImageListener
 
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.Recorder
 
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.SyncWindows
 
imageUpdated(ImagePlus) - Method in class ij.plugin.frame.ThresholdAdjuster
 
imageUpdated(ImagePlus) - Method in class ij.plugin.Orthogonal_Views
 
imageWidth - Variable in class ij.gui.ImageCanvas
 
ImageWindow - Class in ij.gui
A frame for displaying images.
ImageWindow(String) - Constructor for class ij.gui.ImageWindow
 
ImageWindow(ImagePlus) - Constructor for class ij.gui.ImageWindow
 
ImageWindow(ImagePlus, ImageCanvas) - Constructor for class ij.gui.ImageWindow
 
ImageWriter - Class in ij.io
Writes a raw image described by a FileInfo object to an OutputStream.
ImageWriter(FileInfo) - Constructor for class ij.io.ImageWriter
 
IMAGING - Static variable in class org.javaabf.Epoch
 
IMAGING_TYPE - Static variable in class ij.wave.Wave
 
img - Variable in class ij.ImagePlus
 
img - Variable in class ij.process.ImageProcessor
 
imp - Variable in class ij.gui.ImageCanvas
 
imp - Variable in class ij.gui.ImageWindow
 
imp - Variable in class ij.gui.ProfilePlot
 
imp - Variable in class ij.gui.Roi
 
imp - Variable in class ij.plugin.filter.ParticleAnalyzer
 
IMPORT_MENU - Static variable in class ij.Menus
 
ImportDialog - Class in ij.io
This is a dialog box used to imports raw 8, 16, 24 and 32-bit images.
ImportDialog(String, String) - Constructor for class ij.io.ImportDialog
 
ImportDialog() - Constructor for class ij.io.ImportDialog
 
importWaves() - Method in class ij.plugin.frame.WaveManager
 
importWaves(ImagePlus) - Method in class ij.plugin.frame.WaveManager
 
in - Variable in class ij.io.TiffDecoder
 
in - Static variable in class org.jah.PhysImageServerProxy
 
IN_PLACE - Static variable in class ij.plugin.Resizer
 
IN_SITU_SHOW - Static variable in class ij.plugin.filter.ParticleAnalyzer
Replace original image with masks.
IN_TOLERANCE - Static variable in class ij.plugin.filter.MaximumFinder
Output type all points around the maximum within the tolerance
inBigTextString - Variable in class ij.plugin.frame.Jython_Console
 
INCLUDE_HOLES - Static variable in class ij.plugin.filter.ParticleAnalyzer
Flood fill to ignore interior holes.
incrementCounter() - Method in class ij.measure.ResultsTable
Increments the measurement counter by one.
INDEX_OF - Static variable in interface ij.macro.MacroConstants
 
indices - Variable in class ij.process.DownsizeTable
For each source point between srcStart and srcEnd, indices of destination points where the data should be added.
info - Variable in class ij.io.FileInfo
 
info - Variable in class ij.measure.Calibration
Plugin writers can use this string to store information about the image.
Info - Class in ij.plugin.filter
This plugin implements the Image/Show Info command.
Info() - Constructor for class ij.plugin.filter.Info
 
info() - Static method in class ij.plugin.frame.WaveManager
 
init() - Method in class ij.ImageJApplet
Starts ImageJ if it's not already running.
INITIALIZATION_FAILURE - Static variable in class ij.measure.Minimizer
Status returned: Could not initialize the simplex because either the initialParams resulted in the target function returning NaN or all attempts to find starting parameters for the other simplex points resulted in the target function returning NaN.
initialize() - Method in class ij.plugin.frame.Jython_Console
 
initializeLJ() - Method in interface org.jah.Labjack
 
initializeLJ() - Method in class org.jah.Labjack32bit
 
initializeLJ() - Method in class org.jah.SimpleLabjackControl
 
inputStream - Variable in class ij.io.FileInfo
 
insert(ImageProcessor, int, int) - Method in class ij.process.ImageProcessor
Inserts the image contained in 'ip' at (xloc, yloc).
insertComment(int, String) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
insertComment(int, Comment) - Method in class org.javaabf.Comments
 
insertComment(int, String) - Method in class org.javaabf.Comments
 
insertComment(int, String, String) - Method in class org.javaabf.Comments
 
insertCommentAbove(int) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
insertCommentBelow(int) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
inSituShow - Variable in class ij.plugin.filter.ParticleAnalyzer
 
install(String) - Method in class ij.plugin.MacroInstaller
 
install(String, Menu) - Method in class ij.plugin.MacroInstaller
 
install(String) - Method in class ij.plugin.PluginInstaller
 
Installer - Class in ij.plugin
Implements the Plugins/Shortcuts/Install... command.
Installer() - Constructor for class ij.plugin.Installer
 
installFile(String) - Method in class ij.plugin.MacroInstaller
 
installFromIJJar(String) - Method in class ij.plugin.MacroInstaller
Installs a macro set contained in ij.jar.
installLibrary(String) - Method in class ij.plugin.MacroInstaller
 
installPlugin(String, char, String, String, ImageJ) - Static method in class ij.Menus
Adds a plugin based command to the end of a specified menu.
installSingleTool(String) - Method in class ij.plugin.MacroInstaller
 
installStartupMacrosTools() - Static method in class ij.gui.Toolbar
 
installStartupTools() - Method in class ij.gui.Toolbar
 
installTool(String) - Method in class ij.plugin.MacroInstaller
 
installUserPlugin(String, boolean) - Method in class ij.Menus
 
instance - Static variable in class org.jah.ElectrophysManager
 
instanceColor - Variable in class ij.gui.Roi
 
integrate() - Method in class ij.wave.Wave
 
integrate() - Method in class ij.wave.Waves
Integrates each Wave in this instance.
INTEGRATED_DENSITY - Static variable in interface ij.measure.Measurements
 
INTEGRATED_DENSITY - Static variable in class ij.measure.ResultsTable
 
intelByteOrder - Variable in class ij.io.FileInfo
 
intelByteOrder - Static variable in class ij.Prefs
Export TIFF and Raw using little-endian byte order.
interpolate - Static variable in class ij.gui.PlotWindow
Interpolate line profiles.
interpolate - Variable in class ij.process.ImageProcessor
 
interpolateScaledImages - Static variable in class ij.Prefs
Display images scaled <100% using bilinear interpolation
interpolationMethod - Variable in class ij.process.ImageProcessor
 
Interpreter - Class in ij.macro
This is the recursive descent parser/interpreter for the ImageJ macro language.
Interpreter() - Constructor for class ij.macro.Interpreter
 
intersection(Waves) - Method in class ij.wave.Waves
Returns only the waves that are in both this instance's Waves and waves2 where the return Waves are from this list.
intersection(Waves, Waves) - Static method in class ij.wave.WaveUtils
Returns only the waves that are in both waves1 and waves2 from the waves2 list.
INV_RODBARD - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
INVALID_SHORTCUT - Static variable in class ij.Menus
 
invalidNumber() - Method in class ij.gui.GenericDialog
Returns true if one or more of the numeric fields contained an invalid number.
inverseTransform() - Method in class ij.process.FHT
Performs an inverse transform, converting this image into the space domain.
inversionTested - Variable in class ij.process.ImageProcessor
 
INVERT - Static variable in interface ij.macro.MacroConstants
 
invert() - Method in class ij.process.FloatProcessor
 
invert() - Method in class ij.process.ImageProcessor
Inverts the image or ROI.
invert() - Method in class ij.process.ShortProcessor
 
invert() - Method in class ij.process.StackProcessor
 
invert() - Method in class ij.wave.Wave
Inverts the sign of the wave.
INVERT_Y - Static variable in interface ij.measure.Measurements
 
invertedLut - Variable in class ij.process.ImageProcessor
 
invertLut() - Method in class ij.process.ColorProcessor
Does nothing since RGB images do not use LUTs.
invertLut() - Method in class ij.process.ImageProcessor
Inverts the values in this image's LUT (indexed color model).
ip - Variable in class ij.ImagePlus
 
IPLAB - Static variable in class ij.io.TiffDecoder
 
IS - Static variable in interface ij.macro.MacroConstants
 
is64Bit() - Static method in class ij.IJ
Returns true if ImageJ is running a 64-bit version of Java.
IS_ACTIVE - Static variable in interface ij.macro.MacroConstants
 
IS_KEY_DOWN - Static variable in interface ij.macro.MacroConstants
 
IS_NAN - Static variable in interface ij.macro.MacroConstants
 
IS_OPEN - Static variable in interface ij.macro.MacroConstants
 
isActiveOverlayRoi() - Method in class ij.gui.Roi
 
isAntialiased() - Static method in class ij.gui.TextRoi
Returns the state of global 'antialiasedText' variable, which is used by the "Fonts" widget.
isArea() - Method in class ij.gui.Roi
Returns 'true' if this is an area selection.
isAutoloadingLayoutTemplates() - Static method in class org.jah.Configuration_
 
isAutonamingStreams() - Static method in class org.jah.Configuration_
 
isAutoRunAndHide() - Method in class ij.plugin.MacroInstaller
Returns true if an "AutoRunAndHide" macro was run/installed.
isAutosaving() - Static method in class org.jah.Configuration_
 
isAutosavingHistory() - Static method in class org.jah.Configuration_
 
isAutoSendingTemplatesToWfdIV() - Static method in class org.jah.Configuration_
 
isBatchMode() - Static method in class ij.macro.Interpreter
 
isBatchModeRoiManager() - Static method in class ij.macro.Interpreter
Returns true if there is an internal batch mode RoiManager.
isBinary() - Method in class ij.process.ByteProcessor
Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isBinary() - Method in class ij.process.ImageProcessor
Returns 'true' if this is a binary image (8-bit-image with only 0 and 255).
isCalibrationBar() - Method in class ij.gui.Overlay
 
isCell() - Method in class com.jmatio.types.MLArray
 
isCellEditable(int, int) - Method in class ij.plugin.frame.table.EpochTableModel
 
isChar() - Method in class com.jmatio.types.MLArray
 
isClosed() - Method in class ij.gui.ImageWindow
Has this window been closed?
isColorLut() - Method in class ij.process.ImageProcessor
Returns true if this image uses a color LUT.
isComplex() - Method in class com.jmatio.types.MLArray
 
isComposite() - Method in class ij.ImagePlus
Returns true if this is a CompositeImage.
isDataFlavorSupported(DataFlavor) - Method in class ij.plugin.Clipboard
 
isDefaultLut() - Method in class ij.process.ImageProcessor
Returns true if the image is using the default grayscale LUT.
isDisplayedHyperStack() - Method in class ij.ImagePlus
Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.
isDouble() - Method in class com.jmatio.types.MLArray
 
isDrawingTool() - Method in class ij.gui.Arrow
 
isDrawingTool() - Method in class ij.gui.Roi
Returns 'true' if this is an ROI primarily used from drawing (e.g., TextRoi or Arrow).
isDrawingTool() - Method in class ij.gui.TextRoi
 
isElectrophysType() - Method in class ij.wave.Wave
 
isEmpty() - Method in class com.jmatio.types.MLArray
 
isFunctionObject() - Method in class com.jmatio.types.MLArray
 
isGrayscale() - Method in class ij.LookUpTable
Returns true if this is a 256 entry grayscale LUT.
isGrayscale() - Method in class ij.process.ColorProcessor
Returns 'true' if this is a grayscale image.
isGrayscale() - Method in class ij.process.ImageProcessor
Returns 'true' if this is an image with a grayscale LUT or an RGB image with identical red, green and blue channels.
isHandle(int, int) - Method in class ij.gui.EllipseRoi
 
isHandle(int, int) - Method in class ij.gui.Line
Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.OvalRoi
Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.PolygonRoi
Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.Roi
Returns a handle number if the specified screen coordinates are inside or near a handle, otherwise returns -1.
isHandle(int, int) - Method in class ij.gui.ShapeRoi
Always returns -1 since ShapeRois do not have handles.
isHSB() - Method in class ij.ImageStack
Returns true if this is a 3-slice HSB stack.
isHyperStack() - Method in class ij.gui.StackWindow
 
isHyperStack() - Method in class ij.ImagePlus
Returns 'true' if this image is a hyperstack.
isImagingType() - Method in class ij.wave.Wave
 
isInt16() - Method in class com.jmatio.types.MLArray
 
isInt32() - Method in class com.jmatio.types.MLArray
 
isInt64() - Method in class com.jmatio.types.MLArray
 
isInt8() - Method in class com.jmatio.types.MLArray
 
isInvertedLut() - Method in class ij.ImagePlus
Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.
isInvertedLut() - Method in class ij.process.ColorProcessor
Always returns false since RGB images do not use LUTs.
isInvertedLut() - Method in class ij.process.ImageProcessor
Returns true if this image uses an inverting LUT that displays zero as white and 255 as black.
isJava14() - Static method in class ij.IJ
Returns true if ImageJ is running on a Java 1.4 or greater JVM.
isJava15() - Static method in class ij.IJ
Returns true if ImageJ is running on a Java 1.5 or greater JVM.
isJava16() - Static method in class ij.IJ
Returns true if ImageJ is running on a Java 1.6 or greater JVM.
isJava17() - Static method in class ij.IJ
Returns true if ImageJ is running on a Java 1.7 or greater JVM.
isJava2() - Static method in class ij.IJ
Always returns true.
isKillable() - Method in class ij.process.ImageProcessor
Deprecated.  
isLine() - Method in class ij.gui.Roi
Returns 'true' if this is a line selection.
isLinux() - Static method in class ij.IJ
Returns true if ImageJ is running on Linux.
isLocked() - Method in class ij.ImagePlus
Returns 'true' if the image is locked.
isLocked() - Method in class ij.plugin.frame.Layout
 
isLocked() - Method in class ij.plugin.frame.LayoutPanel
 
isLogging() - Static method in class org.jah.Configuration_
 
isLogical() - Method in class com.jmatio.types.MLArray
 
isMacintosh() - Static method in class ij.IJ
Returns true if this machine is a Macintosh.
isMacOSX() - Static method in class ij.IJ
Returns true if this machine is a Macintosh running OS X.
isMacro() - Static method in class ij.IJ
Returns true if a macro is running, or if the run(), open() or newImage() method is executing.
isMaximum(double) - Method in class ij.util.ArrayUtil
 
isObject() - Method in class com.jmatio.types.MLArray
 
ISODATA - Static variable in class ij.process.ImageProcessor
Isodata thresholding method
ISODATA2 - Static variable in class ij.process.ImageProcessor
Modified isodata method used in Image/Adjust/Threshold tool
isOpaque() - Method in class com.jmatio.types.MLArray
 
isOptionalArg(int) - Static method in class ij.macro.ExtensionDescriptor
 
isOrthoViewsImage(ImagePlus) - Static method in class ij.plugin.Orthogonal_Views
 
isOutputArg(int) - Static method in class ij.macro.ExtensionDescriptor
 
isProcessor() - Method in class ij.ImagePlus
 
isProxy() - Method in class ij.wave.Wave
Returns false unless a class extends WaveProxy.
isProxy() - Method in class ij.wave.WaveProxy
Always returns true.
isPseudoColorLut() - Method in class ij.process.ImageProcessor
Returns true if this image uses a pseudocolor or grayscale LUT, in other words, is this an image that can be filtered.
isRedirectImage() - Static method in class ij.plugin.filter.Analyzer
Returns true if an image is selected in the "Redirect To:" popup menu of the Analyze/Set Measurements dialog box.
isResultsWindow() - Static method in class ij.IJ
Returns true if the "Results" window is open.
isRGB() - Method in class ij.ImageStack
Returns true if this is a 3-slice RGB stack.
isRMIEnabled() - Static method in class ij.OtherInstance
 
isScriptExecuting() - Method in class ij.plugin.frame.Jython_Console
 
isSelected(LayoutComponent) - Method in class ij.plugin.frame.LayoutPanel
 
isSigned16Bit() - Method in class ij.measure.Calibration
Returns true if this is a signed 16-bit image.
isSingle() - Method in class com.jmatio.types.MLArray
 
isSparse() - Method in class com.jmatio.types.MLArray
 
isSplineFit() - Method in class ij.gui.PolygonRoi
Returns 'true' if this selection has been fitted with a spline.
isStruct() - Method in class com.jmatio.types.MLArray
 
isUint16() - Method in class com.jmatio.types.MLArray
 
isUint32() - Method in class com.jmatio.types.MLArray
 
isUint64() - Method in class com.jmatio.types.MLArray
 
isUint8() - Method in class com.jmatio.types.MLArray
 
isUnknown() - Method in class com.jmatio.types.MLArray
 
isUnknownType() - Method in class ij.wave.Wave
 
isVirtual() - Method in class ij.ImageStack
Returns true if this is a virtual (disk resident) stack.
isVirtual() - Method in class ij.VirtualStack
Always return true.
isVisible() - Method in class ij.gui.Roi
Returns true if this ROI is currently displayed on an image.
isVisible() - Method in class ij.ImagePlus
Returns true if this image is currently being displayed in a window.
isVista() - Static method in class ij.IJ
Obsolete; always returns false.
isWindows() - Static method in class ij.IJ
Returns true if this machine is running Windows.
itemStateChanged(ItemEvent) - Method in class ij.gui.GenericDialog
 
itemStateChanged(ItemEvent) - Method in class ij.gui.Toolbar
 
itemStateChanged(ItemEvent) - Method in class ij.ImageJ
Handles CheckboxMenuItem state changes.
itemStateChanged(ItemEvent) - Method in class ij.macro.FunctionFinder
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.BatchProcesser
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Colors
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.CommandFinder
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Concatenator
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Channels
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ColorThresholder
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ContrastAdjuster
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Editor
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Fitter
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Fonts
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.LineWidthAdjuster
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.PasteController
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.Recorder
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.RoiManager
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.SyncWindows
Item Listener method
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.ThresholdAdjuster
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.frame.WaveManager
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Resizer
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Slicer
 
itemStateChanged(ItemEvent) - Method in class ij.plugin.Thresholder
 
itemStateChanged(ItemEvent) - Method in class ij.text.TextWindow
 
IterFactor - Static variable in class ij.measure.CurveFitter
Deprecated. now in the Minimizer class (since ImageJ 1.46f). (probably of not much value for anyone anyhow?)

J

JAH_Utils - Class in org.jah
 
JAH_Utils() - Constructor for class org.jah.JAH_Utils
 
JAHMenuItem - Class in ij
 
JAHMenuItem() - Constructor for class ij.JAHMenuItem
 
JAHMenuItem(String) - Constructor for class ij.JAHMenuItem
 
JAHMenuItem(String, String) - Constructor for class ij.JAHMenuItem
 
JAHMenuItem(String, MenuShortcut) - Constructor for class ij.JAHMenuItem
 
Java2 - Class in ij.util
This class contains static methods that use the Java 2 API.
Java2() - Constructor for class ij.util.Java2
 
JAVA_OR_TEXT - Static variable in class ij.io.Opener
 
JavaProperties - Class in ij.plugin
Displays the Java system properties in a text window.
JavaProperties() - Constructor for class ij.plugin.JavaProperties
 
JAVASCRIPT - Static variable in class ij.plugin.NewPlugin
 
JavaScriptIncludes - Static variable in class ij.plugin.frame.Editor
ImportPackage statements added in front of scripts.
JPEG - Static variable in class ij.io.FileInfo
 
JPEG - Static variable in class ij.io.Opener
 
JPEG - Static variable in class ij.Prefs
 
JPEG_COMPRESSION - Static variable in class ij.plugin.filter.AVI_Writer
 
JPEG_TABLES - Static variable in class ij.io.TiffDecoder
 
JpegWriter - Class in ij.plugin
The File/Save As/Jpeg command (FileSaver.saveAsJpeg() method) uses this plugin to save images in JPEG format.
JpegWriter() - Constructor for class ij.plugin.JpegWriter
 
justification - Variable in class ij.process.ImageProcessor
 
JyRecorder - Class in ij.util
 
JyRecorder() - Constructor for class ij.util.JyRecorder
 
Jython_Console - Class in ij.plugin.frame
 
Jython_Console() - Constructor for class ij.plugin.frame.Jython_Console
 
jythonConsole - Static variable in class ij.IJ
 

K

KEEP_PREVIEW - Static variable in interface ij.plugin.filter.ExtendedPlugInFilter
Set this flag if the last preview image may be kept as a result.
KEEP_THRESHOLD - Static variable in interface ij.plugin.filter.PlugInFilter
Set this flag to keep the invisible binary threshold from being reset.
keepArrowSelections - Static variable in class ij.Prefs
Keep arrow selection after adding to overlay
keepUndoBuffers - Static variable in class ij.Prefs
Preserve undo (snapshot) buffers when switching images
kernel(double) - Method in class ij.process.DownsizeTable
 
kernelSize - Variable in class ij.process.DownsizeTable
Number of kernel points per source data point
KEY_PREFIX - Static variable in class ij.Prefs
 
keyPressed(KeyEvent) - Method in class ij.gui.GenericDialog
 
keyPressed(KeyEvent) - Method in class ij.gui.HistogramWindow
 
keyPressed(KeyEvent) - Method in class ij.gui.HTMLDialog
 
keyPressed(KeyEvent) - Method in class ij.gui.MessageDialog
 
keyPressed(KeyEvent) - Method in class ij.gui.NonBlockingGenericDialog
 
keyPressed(KeyEvent) - Method in class ij.gui.PlotWindow
 
keyPressed(KeyEvent) - Method in class ij.gui.SaveChangesDialog
 
keyPressed(KeyEvent) - Method in class ij.gui.WaitForUserDialog
 
keyPressed(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
 
keyPressed(KeyEvent) - Method in class ij.ImageJ
 
keyPressed(KeyEvent) - Method in class ij.macro.FunctionFinder
 
keyPressed(KeyEvent) - Method in class ij.plugin.CommandFinder
 
keyPressed(KeyEvent) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
keyPressed(KeyEvent) - Method in class ij.plugin.frame.Fitter
 
keyPressed(KeyEvent) - Method in class ij.plugin.frame.Jython_Console
 
keyPressed(KeyEvent) - Method in class ij.plugin.frame.LayoutPanel
 
keyPressed(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
 
keyPressed(KeyEvent) - Method in class ij.text.TextPanel
 
keyReleased(KeyEvent) - Method in class ij.gui.GenericDialog
 
keyReleased(KeyEvent) - Method in class ij.gui.HistogramWindow
 
keyReleased(KeyEvent) - Method in class ij.gui.HTMLDialog
 
keyReleased(KeyEvent) - Method in class ij.gui.MessageDialog
 
keyReleased(KeyEvent) - Method in class ij.gui.PlotWindow
 
keyReleased(KeyEvent) - Method in class ij.gui.SaveChangesDialog
 
keyReleased(KeyEvent) - Method in class ij.gui.WaitForUserDialog
 
keyReleased(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
 
keyReleased(KeyEvent) - Method in class ij.ImageJ
 
keyReleased(KeyEvent) - Method in class ij.macro.FunctionFinder
 
keyReleased(KeyEvent) - Method in class ij.plugin.CommandFinder
 
keyReleased(KeyEvent) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
keyReleased(KeyEvent) - Method in class ij.plugin.frame.Fitter
 
keyReleased(KeyEvent) - Method in class ij.plugin.frame.Jython_Console
 
keyReleased(KeyEvent) - Method in class ij.plugin.frame.LayoutPanel
 
keyReleased(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
 
keyReleased(KeyEvent) - Method in class ij.text.TextPanel
 
keyTyped(KeyEvent) - Method in class ij.gui.GenericDialog
 
keyTyped(KeyEvent) - Method in class ij.gui.HistogramWindow
 
keyTyped(KeyEvent) - Method in class ij.gui.HTMLDialog
 
keyTyped(KeyEvent) - Method in class ij.gui.MessageDialog
 
keyTyped(KeyEvent) - Method in class ij.gui.PlotWindow
 
keyTyped(KeyEvent) - Method in class ij.gui.SaveChangesDialog
 
keyTyped(KeyEvent) - Method in class ij.gui.WaitForUserDialog
 
keyTyped(KeyEvent) - Method in class ij.gui.YesNoCancelDialog
 
keyTyped(KeyEvent) - Method in class ij.ImageJ
 
keyTyped(KeyEvent) - Method in class ij.macro.FunctionFinder
 
keyTyped(KeyEvent) - Method in class ij.plugin.CommandFinder
 
keyTyped(KeyEvent) - Method in class ij.plugin.frame.ElectrophysManager_Frame
 
keyTyped(KeyEvent) - Method in class ij.plugin.frame.Fitter
 
keyTyped(KeyEvent) - Method in class ij.plugin.frame.Jython_Console
 
keyTyped(KeyEvent) - Method in class ij.plugin.frame.LayoutPanel
 
keyTyped(KeyEvent) - Method in class ij.plugin.Orthogonal_Views
 
keyTyped(KeyEvent) - Method in class ij.text.TextPanel
 
keywordIDs - Static variable in interface ij.macro.MacroConstants
 
keywords - Static variable in interface ij.macro.MacroConstants
 
killRoi() - Method in class ij.ImagePlus
Deletes the current region of interest.
killStack() - Method in class ij.ImagePlus
 
KURTOSIS - Static variable in interface ij.measure.Measurements
 
KURTOSIS - Static variable in class ij.measure.ResultsTable
 
kurtosis - Variable in class ij.process.ImageStatistics
 

L

label - Variable in class ij.gui.MessageDialog
 
label - Variable in class ij.gui.WaitForUserDialog
 
label(ImageProcessor) - Method in class ij.plugin.filter.Filler
 
LABEL - Static variable in class ij.plugin.frame.Layout
 
labelHyperstack(ImagePlus) - Static method in class ij.plugin.HyperStackMaker
 
LABELS - Static variable in interface ij.measure.Measurements
 
LABELS - Static variable in class ij.plugin.frame.RoiManager
 
Labjack - Interface in org.jah
 
Labjack32bit - Class in org.jah
 
Labjack32bit() - Constructor for class org.jah.Labjack32bit
 
LabjackFactory - Class in org.jah
 
LabjackFactory() - Constructor for class org.jah.LabjackFactory
 
LANDSCAPE_MODE - Static variable in class ij.plugin.frame.Layout
 
LAST_HEADING - Static variable in class ij.measure.ResultsTable
 
LAST_INDEX_OF - Static variable in interface ij.macro.MacroConstants
 
LAYOUT - Static variable in class ij.io.Opener
 
Layout - Class in ij.plugin.frame
 
Layout() - Constructor for class ij.plugin.frame.Layout
 
Layout(int) - Constructor for class ij.plugin.frame.Layout
 
Layout(String) - Constructor for class ij.plugin.frame.Layout
 
Layout(File) - Constructor for class ij.plugin.frame.Layout
 
LayoutComponent - Class in ij.gui
 
LayoutComponent() - Constructor for class ij.gui.LayoutComponent
 
LayoutComponent(Object) - Constructor for class ij.gui.LayoutComponent
 
LayoutComponent(Object, String, int, int, ImageObserver) - Constructor for class ij.gui.LayoutComponent
 
layoutContainer(Container) - Method in class ij.gui.ImageLayout
Lays out the container and calls ImageCanvas.resizeCanvas() to adjust the image canvas size as needed.
LayoutPanel - Class in ij.plugin.frame
 
LayoutPanel(Layout) - Constructor for class ij.plugin.frame.LayoutPanel
 
LayoutPanel(Layout, String) - Constructor for class ij.plugin.frame.LayoutPanel
 
LayoutPanel(Layout, File) - Constructor for class ij.plugin.frame.LayoutPanel
 
LayoutWriter - Class in ij.plugin
This plugin implements the File/Save As/Layout command.
LayoutWriter() - Constructor for class ij.plugin.LayoutWriter
 
LEFT - Static variable in class ij.gui.Plot
Text justification.
LEFT - Static variable in class ij.gui.TextRoi
 
LEFT - Static variable in class ij.io.RoiDecoder
 
LEFT_JUSTIFY - Static variable in class ij.process.ImageProcessor
Left justify text.
LEFT_MARGIN - Static variable in class ij.gui.Plot
the margin width left of the plot frame (enough for 5-digit numbers such as unscaled 16-bit
leftPad(String, int) - Static method in class org.jah.JAH_Utils
Pads a string with 0's on the left side of the String passed as argument to the number of digits passed.
LEGACY_MODE - Static variable in class ij.gui.Wand
Wand operation type similar to that of ImageJ 1.42p and before; for backwards compatibility.
LENGTH_OF - Static variable in interface ij.macro.MacroConstants
 
length_s - Variable in class ij.wave.SimulatedUniformPulseWave
 
LIMIT - Static variable in interface ij.measure.Measurements
 
Line - Class in ij.gui
This class represents a straight line selection.
Line(int, int, int, int) - Constructor for class ij.gui.Line
Creates a new straight line selection using the specified starting and ending offscreen integer coordinates.
Line(double, double, double, double) - Constructor for class ij.gui.Line
Creates a new straight line selection using the specified starting and ending offscreen double coordinates.
Line(int, int, ImagePlus) - Constructor for class ij.gui.Line
Starts the process of creating a new user-generated straight line selection.
Line(int, int, int, int, ImagePlus) - Constructor for class ij.gui.Line
Deprecated. replaced by Line(int, int, int, int)
LINE - Static variable in class ij.gui.Plot
Connect points with solid lines.
LINE - Static variable in class ij.gui.PlotWindow
Connect points with solid lines.
LINE - Static variable in class ij.gui.Roi
 
LINE - Static variable in class ij.gui.Toolbar
 
LINE_TO - Static variable in interface ij.macro.MacroConstants
 
linearFit() - Method in class ij.wave.Wave
Applies a linear fit to the contents of this Wave and fires a waveChanged event.
linearFit() - Method in class ij.wave.Waves
Scales each Wave in this instance with respect to its own pattern by a linear fit.
LineGraphAnalyzer - Class in ij.plugin.filter
Implements ImageJ's Analyze/Tools/Analyze Line Graph command.
LineGraphAnalyzer() - Constructor for class ij.plugin.filter.LineGraphAnalyzer
 
LineLayoutComponent - Class in ij.gui
 
LineLayoutComponent(int, int, int, int, Color, int) - Constructor for class ij.gui.LineLayoutComponent
 
lineSeparator - Static variable in class ij.plugin.frame.Jython_Console
 
lineTo(int, int) - Method in class ij.process.ImageProcessor
Draws a line from the current drawing location to (x2,y2).
lineWidth - Static variable in class ij.gui.Roi
 
lineWidth - Variable in class ij.process.ImageProcessor
 
LineWidthAdjuster - Class in ij.plugin.frame
Adjusts the width of line selections.
LineWidthAdjuster() - Constructor for class ij.plugin.frame.LineWidthAdjuster
 
list - Variable in class ij.gui.HistogramWindow
 
LIST - Static variable in interface ij.macro.MacroConstants
 
LIST - Static variable in class ij.plugin.filter.MaximumFinder
Do not create an image, just list x, y of maxima in the Results table
list - Variable in class ij.plugin.frame.WaveManager
 
list() - Method in class org.jah.PhysImage_Properties
Returns a string showing the contents of this properties object.
listAllThreads(PrintWriter) - Static method in class ij.plugin.ThreadLister
 
listCommands() - Method in class ij.plugin.CommandLister
 
listeners - Variable in class ij.wave.Wave
 
listRois(Roi[]) - Static method in class ij.plugin.OverlayCommands
 
listShortcuts() - Method in class ij.plugin.CommandLister
 
listValues - Static variable in class ij.gui.PlotWindow
Display the XY coordinates in a separate window.
ListVirtualStack - Class in ij.plugin
This plugin opens images specified by list of file paths as a virtual stack.
ListVirtualStack() - Constructor for class ij.plugin.ListVirtualStack
 
live - Variable in class ij.gui.HistogramWindow
 
ln() - Method in class ij.process.ImageProcessor
Does a natural logarithmic (base e) transform of the image or ROI.
load(Object, Applet) - Static method in class ij.Prefs
Finds and loads the ImageJ configuration file, "IJ_Props.txt".
load(BufferedReader) - Method in class ij.text.TextWindow
Appends the text in the specified file to the end of this TextWindow.
load(String) - Method in class ij.wave.ABFWaveProxy
 
load(String) - Method in class ij.wave.Wave
 
load(String) - Method in class ij.wave.WaveProxy
 
load(String) - Method in class ij.wave.Waves
Loads either .txt, .zip, or individual .wave files into the current collection.
load() - Static method in class org.jah.HologConfiguration_
 
load(String) - Static method in class org.jah.HologConfiguration_
 
load(String) - Method in class org.javaabf.ABF
 
load(String) - Static method in class org.javaabf.Comments
 
load(String) - Static method in class org.javaabf.Epoch
 
load(File) - Static method in class org.javaabf.Epoch
 
loadChartComponents() - Method in class ij.plugin.Reorder_Components
 
loadComments() - Static method in class org.javaabf.Comments
 
loadComments(boolean) - Static method in class org.javaabf.Comments
 
loadEpochTables() - Static method in class org.jah.ElectrophysManager
 
loadEpochTables() - Static method in class org.javaabf.EpochUtils
 
loadFromText(String, int) - Method in class ij.wave.Wave
 
loadHints() - Method in class ij.wave.ClusterHints
 
loadImageComponents() - Method in class ij.plugin.Reorder_Components
 
loadInfo(String) - Method in class ij.JAHMenuItem
 
loadInitialCache() - Method in class org.javaabf.ABF18_parser
 
loadInitialCache() - Method in class org.javaabf.AbstractABF_parser
 
loadLayout(File) - Method in class ij.plugin.frame.Layout
 
loadLayout() - Method in class ij.plugin.frame.Layout
 
loadLayout(File) - Method in class ij.plugin.frame.LayoutPanel
 
loadLayout() - Method in class ij.plugin.frame.LayoutPanel
 
loadLut(String) - Static method in class ij.Executer
Opens a .lut file from the ImageJ/luts directory and returns 'true' if successful.
loadMarkers(String) - Method in class ij.plugin.frame.ChartFramePlugIn
Loads the WaveMarkers from the file into the chart.
loadMarkers(String) - Static method in class ij.wave.WaveUtils
 
loadMatrixFromMat(String, String) - Static method in class ij.wave.WaveUtils
 
loadMetaData() - Method in class org.javaabf.ABF18_parser
 
loadMetaData() - Method in class org.javaabf.ABF2_parser
 
loadMetaData() - Method in class org.javaabf.ABFpClamp9_parser
 
loadPreferences() - Static method in class ij.Prefs
Opens the IJ_Prefs.txt file.
loadPrefs() - Static method in class ij.OtherInstance
 
loadRoisFromZip(String) - Method in class ij.plugin.frame.RoiZipLoader
 
LOC_KEY - Static variable in class ij.plugin.frame.ContrastAdjuster
 
LOC_KEY - Static variable in class ij.plugin.frame.Fonts
 
LOC_KEY - Static variable in class ij.plugin.frame.Jython_Console
 
LOC_KEY - Static variable in class ij.plugin.frame.LineWidthAdjuster
 
LOC_KEY - Static variable in class ij.plugin.frame.RoiManager
 
LOC_KEY - Static variable in class ij.plugin.frame.ThresholdAdjuster
 
LOC_KEY - Static variable in class ij.plugin.frame.WaveManager
 
LOC_KEY - Static variable in class ij.text.TextWindow
 
lock() - Method in class ij.ImagePlus
Locks the image so other threads can test to see if it is in use.
locked - Variable in class ij.ImagePlus
 
lockSilently() - Method in class ij.ImagePlus
Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.
log - Variable in class ij.gui.HistogramWindow
 
log(String) - Static method in class ij.IJ
 
LOG - Static variable in interface ij.macro.MacroConstants
 
LOG - Static variable in class ij.measure.Calibration
 
LOG - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
log() - Method in class ij.process.FloatProcessor
 
log() - Method in class ij.process.ImageProcessor
Does a natural logarithmic (base e) transform of the image or ROI.
log() - Method in class ij.process.ShortProcessor
 
log(String) - Method in class org.jah.ElectrophysManager
 
log(String) - Static method in class org.jah.Logger
 
log(String, boolean) - Static method in class org.jah.Logger
 
LOG2 - Static variable in class ij.measure.Calibration
 
LOG2 - Static variable in class ij.measure.CurveFitter
Constants for the built-in fit functions
LOG_HEIGHT_KEY - Static variable in class ij.text.TextWindow
 
LOG_LOC_KEY - Static variable in class ij.text.TextWindow
 
LOG_WIDTH_KEY - Static variable in class ij.text.TextWindow
 
LOG_WINDOW_CLOSED - Static variable in interface ij.IJEventListener
 
logException(Exception) - Method in class org.jah.ElectrophysManager
 
Logger - Class in org.jah
 
Logger() - Constructor for class org.jah.Logger
 
LOGICAL_AND - Static variable in interface ij.macro.MacroConstants
 
LOGICAL_OR - Static variable in interface ij.macro.MacroConstants
 
logProperties() - Method in class ij.plugin.ProxySettings
 
logScale - Variable in class ij.gui.HistogramWindow
 
LogStream - Class in ij.io
This class provides the functionality to divert output sent to the System.out and System.err streams to ImageJ's log console.
LogStream() - Constructor for class ij.io.LogStream
 
LONG - Static variable in interface org.javaabf.ABF_parser
 
longHistogram - Variable in class ij.process.ImageStatistics
Long histogram; use getHIstogram() to retrieve.
LONGLONG - Static variable in interface org.javaabf.ABF_parser
 
longOffset - Variable in class ij.io.FileInfo
 
longPixelCount - Variable in class ij.process.ImageStatistics
 
lookupPathVariable(String) - Static method in class ij.io.OpenDialog
 
LookUpTable - Class in ij
This class represents a color look-up table.
LookUpTable(Image) - Constructor for class ij.LookUpTable
Constructs a LookUpTable object from an AWT Image.
LookUpTable(ColorModel) - Constructor for class ij.LookUpTable
Constructs a LookUpTable object from a ColorModel.
loop - Variable in class ij.measure.Calibration
 
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.HistogramWindow
 
lostOwnership(Clipboard, Transferable) - Method in class ij.gui.PlotWindow
 
lostOwnership(Clipboard, Transferable) - Method in class ij.plugin.frame.Editor
 
lostOwnership(Clipboard, Transferable) - Method in class ij.text.TextPanel
 
LT - Static variable in interface ij.macro.MacroConstants
 
LTE - Static variable in interface ij.macro.MacroConstants
 
ltrim(String) - Static method in class org.jah.JAH_Utils
From http://stackoverflow.com/questions/15567010/what-is-a-good-alternative-of-ltrim-and-rtrim-in-java
lut - Variable in class ij.gui.HistogramWindow
 
LUT - Static variable in class ij.io.Opener
 
LUT - Class in ij.process
This is an indexed color model that allows an lower and upper bound to be specified.
LUT(byte[], byte[], byte[]) - Constructor for class ij.process.LUT
Constructs a LUT from red, green and blue byte arrays, which must have a length of 256.
LUT(int, int, byte[], byte[], byte[]) - Constructor for class ij.process.LUT
Constructs a LUT from red, green and blue byte arrays, where 'bits' must be 8 and 'size' must be less than or equal to 256.
LUT(IndexColorModel, double, double) - Constructor for class ij.process.LUT
 
LUT_Editor - Class in ij.plugin
 
LUT_Editor() - Constructor for class ij.plugin.LUT_Editor
 
lutAnimation - Variable in class ij.process.ImageProcessor
 
LutApplier - Class in ij.plugin.filter
This plugin implements the Image/Lookup Tables/Apply LUT command.
LutApplier() - Constructor for class ij.plugin.filter.LutApplier
 
LutLoader - Class in ij.plugin
Opens NIH Image look-up tables (LUTs), 768 byte binary LUTs (256 reds, 256 greens and 256 blues), LUTs in text format, or generates the LUT specified by the string argument passed to the run() method.
LutLoader() - Constructor for class ij.plugin.LutLoader
 
lutMessage - Static variable in class ij.plugin.ZProjector
 
lutSize - Variable in class ij.io.FileInfo
 
lutUpdateMode - Variable in class ij.process.ImageProcessor
 
LutViewer - Class in ij.plugin.filter
Displays the active image's look-up table.
LutViewer() - Constructor for class ij.plugin.filter.LutViewer
 
LZW - Static variable in class ij.io.FileInfo
 
LZW_WITH_DIFFERENCING - Static variable in class ij.io.FileInfo
 
lzwUncompress(byte[]) - Method in class ij.io.ImageReader
Utility method for decoding an LZW-compressed image strip.

M

Macro - Class in ij
The class contains static methods that perform macro operations.
Macro() - Constructor for class ij.Macro
 
MACRO - Static variable in interface ij.macro.MacroConstants
 
MACRO - Static variable in class ij.plugin.NewPlugin
 
MACRO_CANCELED - Static variable in class ij.Macro
 
MACRO_KEY - Static variable in class ij.plugin.filter.ImageMath
 
Macro_Runner - Class in ij.plugin
This class runs macros and scripts installed in the Plugins menu as well as macros and scripts opened using the Plugins/Macros/Run command.
Macro_Runner() - Constructor for class ij.plugin.Macro_Runner
 
MACRO_TOOL - Static variable in class ij.plugin.NewPlugin
 
MacroConstants - Interface in ij.macro
 
macroCount() - Method in class ij.macro.Program
 
MacroExtension - Interface in ij.macro
 
MacroInstaller - Class in ij.plugin
This plugin implements the Plugins/Macros/Install Macros command.
MacroInstaller() - Constructor for class ij.plugin.MacroInstaller
 
MacroRunner - Class in ij.macro
This class runs macros in a separate thread.
MacroRunner() - Constructor for class ij.macro.MacroRunner
Create a MacrRunner.
MacroRunner(String) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets macro source in a separate thread.
MacroRunner(String, Editor) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets macro source in debug mode if 'editor' is not null.
MacroRunner(String, String) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets macro source in a separate thread, and also passing a string argument.
MacroRunner(File) - Constructor for class ij.macro.MacroRunner
Create a new object that interprets a macro file using a separate thread.
MacroRunner(Program, int, String) - Constructor for class ij.macro.MacroRunner
Create a new object that runs a tokenized macro in a separate thread.
MacroRunner(Program, int, String, String) - Constructor for class ij.macro.MacroRunner
Create a new object that runs a tokenized macro in a separate thread, passing a string argument.
MacroRunner(Program, int, String, Editor) - Constructor for class ij.macro.MacroRunner
Create a new object that runs a tokenized macro in debug mode if 'editor' is not null.
macroRunning() - Static method in class ij.IJ
Returns true if the run(), open() or newImage() method is executing.
MACROS_MENU_ITEMS - Static variable in class ij.plugin.frame.Editor
 
MacroToolRunner - Class in ij.plugin.tool
 
MacroToolRunner(MacroInstaller) - Constructor for class ij.plugin.tool.MacroToolRunner
 
mag - Variable in class ij.gui.Roi
 
magnification - Variable in class ij.gui.ImageCanvas
 
magnification - Variable in class ij.gui.ProfilePlot
 
MAGNIFIER - Static variable in class ij.gui.Toolbar
 
main(String[]) - Static method in class ij.ImageJ
 
main(String[]) - Static method in class ij.wave.ClusterUtils
 
main(String[]) - Static method in class org.jah.PhysImageServerProxy
 
main(String[]) - Static method in class org.jah.SimpleLabjackControl
 
MAJOR - Static variable in class ij.measure.ResultsTable
 
major - Variable in class ij.process.EllipseFitter
Length of major axis
major - Variable in class ij.process.ImageStatistics
Length of major axis of fitted ellipse
make16bitEDM(ImageProcessor) - Method in class ij.plugin.filter.EDM
Calculates a 16-bit grayscale Euclidean Distance Map for a binary 8-bit image.
MAKE_ELLIPSE - Static variable in interface ij.macro.MacroConstants
 
MAKE_LINE - Static variable in interface ij.macro.MacroConstants
 
MAKE_OVAL - Static variable in interface ij.macro.MacroConstants
 
MAKE_POINT - Static variable in interface ij.macro.MacroConstants
 
MAKE_POLYGON - Static variable in interface ij.macro.MacroConstants
 
MAKE_RECTANGLE - Static variable in interface ij.macro.MacroConstants
 
MAKE_SELECTION - Static variable in interface ij.macro.MacroConstants
 
MAKE_TEXT - Static variable in interface ij.macro.MacroConstants
 
makeBackgroundImage(ImageStack, ImagePlus, ImagePlus, int, int, double) - Static method in class org.jah.JAH_Utils
 
makeBackgroundImageRolling(ImageStack, ImagePlus, ImagePlus, int, int, int) - Static method in class org.jah.JAH_Utils
 
makeBackgroundImageRolling(ImageStack, ImagePlus, ImagePlus, int, int, int, double) - Static method in class org.jah.JAH_Utils
 
makeBackgroundImageRolling(ImageStack, ImagePlus, ImagePlus, int, int, int, double, boolean) - Static method in class org.jah.JAH_Utils
 
makeComments(ABF, String, Epoch) - Static method in class org.jah.ElectrophysManager
 
makeComments(Comments, ABF, String) - Static method in class org.jah.ElectrophysManager
 
makeComposite(ImagePlus) - Static method in class ij.plugin.CompositeConverter
 
makeCTAs(Waves, String, double, double, double, boolean, Bursts) - Static method in class ij.wave.CTA_Utils
 
makeCTAs(Wave[], String, double, double, double, boolean, Bursts) - Static method in class ij.wave.CTA_Utils
 
makeCTAs(Wave[], String, double, double, boolean, Vector) - Static method in class ij.wave.CTA_Utils
 
makeDefaultColorModel() - Method in class ij.process.ImageProcessor
 
makeFilePrivate(String) - Static method in class ij.OtherInstance
 
makeFloatEDM(ImageProcessor, int, boolean) - Method in class ij.plugin.filter.EDM
Creates the Euclidian Distance Map of a (binary) byte image.
makeGaussianKernel(double, double, int) - Method in class ij.plugin.filter.GaussianBlur
Create a 1-dimensional normalized Gaussian kernel with standard deviation sigma and the running sum over the kernel Note: this is one side of the kernel only, not the full kernel as used by the Convolver class of ImageJ.
makeKernel(double) - Method in class ij.plugin.filter.RankFilters
Deprecated. Not needed any more, use the rank(ip, ...) method, which creates the kernel
makeLine(int, int, int, int) - Static method in class ij.IJ
Creates a straight line selection.
makeLine(double, double, double, double) - Static method in class ij.IJ
Creates a straight line selection using floating point coordinates.
makeLineRadii(double) - Method in class ij.plugin.filter.RankFilters
Create a circular kernel (structuring element) of a given radius.
makeListLabel(String, CommandFinder.CommandAction, boolean) - Method in class ij.plugin.CommandFinder
 
makeMask(ImageProcessor, Rectangle) - Method in class ij.plugin.filter.Filler
 
makeMaskFromRois(int, int, Color, Roi[]) - Static method in class ij.plugin.frame.RoiManager
 
makeMaskFromRois(int, int, String, Color, Roi[], boolean) - Static method in class ij.plugin.frame.RoiManager
 
makeMaskFromSelectedRois(int, int, String, Color, boolean) - Method in class ij.plugin.frame.RoiManager
 
makeMaskFromWaves(int, int, String, Color, Waves, boolean) - Static method in class ij.plugin.frame.RoiManager
 
makeMasksFromWaves(int, int, String, Color[], Waves[], boolean) - Static method in class ij.plugin.frame.RoiManager
 
makeMontage(ImagePlus) - Method in class ij.plugin.MontageMaker
 
makeMontage(ImagePlus, int, int, double, int, int, int, int, boolean) - Method in class ij.plugin.MontageMaker
Creates a montage and displays it.
makeMontage2(ImagePlus, int, int, double, int, int, int, int, boolean) - Method in class ij.plugin.MontageMaker
Creates a montage and returns it as an ImagePlus.
makeOval(int, int, int, int) - Static method in class ij.IJ
Creates an oval selection.
makeOval(double, double, double, double) - Static method in class ij.IJ
Creates an subpixel resolution oval selection.
makePoint(int, int) - Static method in class ij.IJ
Creates a point selection.
makeRectangle(int, int, int, int) - Static method in class ij.IJ
Creates a rectangular selection.
makeRectangle(double, double, double, double) - Static method in class ij.IJ
Creates a subpixel resolution rectangular selection.
makeRoi(ImageProcessor) - Method in class ij.process.EllipseFitter
Generates the xCoordinates, yCoordinates public arrays that can be used to create an ROI.
makeSimulatedWave() - Method in class ij.plugin.frame.WaveManager
 
makeSimulatedWave(Wave) - Method in class ij.plugin.frame.WaveManager
 
makeStack(String, int, int, boolean, boolean, boolean) - Method in class ij.plugin.AVI_Reader
Create an ImageStack from an avi file with given path.
makeSurfacePlot(ImageProcessor) - Method in class ij.plugin.SurfacePlotter
 
makeThumbnail(int, int, double) - Method in class ij.process.ColorProcessor
Uses averaging to creates a new ColorProcessor containing a downsized copy of this image or selection.
makeUniqueName(String) - Static method in class ij.WindowManager
If 'name' is not unique, adds -1, -2, etc. as needed to make it unique.
markWidth - Static variable in class ij.plugin.filter.Analyzer
 
MASKS - Static variable in class ij.plugin.filter.ParticleAnalyzer
 
maskSizeError(ImageProcessor) - Method in class ij.process.ImageProcessor
 
match(String, String) - Method in class ij.util.WildcardMatch
Matches a string against a pattern with wildcards.
matches(String) - Method in class com.jmatio.io.MatFileFilter
Test if given name matches the filter.
MATCHES - Static variable in interface ij.macro.MacroConstants
 
MatDataTypes - Class in com.jmatio.common
MAT-file data types
MatDataTypes() - Constructor for class com.jmatio.common.MatDataTypes
 
MatFileFilter - Class in com.jmatio.io
File filter.
MatFileFilter() - Constructor for class com.jmatio.io.MatFileFilter
Creates empty filter intance.
MatFileFilter(String[]) - Constructor for class com.jmatio.io.MatFileFilter
Create filter intance and add array names.
MatFileHeader - Class in com.jmatio.io
MAT-file header Level 5 MAT-files begin with a 128-byte header made up of a 124 byte text field and two, 16-bit flag fields
MatFileHeader(String, int, byte[]) - Constructor for class com.jmatio.io.MatFileHeader
New MAT-file header
MatFileIncrementalWriter - Class in com.jmatio.io
MAT-file Incremental writer.
MatFileIncrementalWriter(String) - Constructor for class com.jmatio.io.MatFileIncrementalWriter
Creates a writer to a file given the filename.
MatFileIncrementalWriter(File) - Constructor for class com.jmatio.io.MatFileIncrementalWriter
Creats a writer to a file given the File object.
MatFileIncrementalWriter(WritableByteChannel) - Constructor for class com.jmatio.io.MatFileIncrementalWriter
Creates a writer for a file, given an output channel to the file..
MatFileReader - Class in com.jmatio.io
 
MatFileReader(String) - Constructor for class com.jmatio.io.MatFileReader
Creates instance of MatFileReader and reads MAT-file from location given as fileName.
MatFileReader(String, MatFileFilter) - Constructor for class com.jmatio.io.MatFileReader
Creates instance of MatFileReader and reads MAT-file from location given as fileName.
MatFileReader(File) - Constructor for class com.jmatio.io.MatFileReader
Creates instance of MatFileReader and reads MAT-file from file.
MatFileReader(File, MatFileFilter) - Constructor for class com.jmatio.io.MatFileReader
Creates instance of MatFileReader and reads MAT-file from file.
MatFileReader() - Constructor for class com.jmatio.io.MatFileReader
 
MatFileWriter - Class in com.jmatio.io
MAT-file writer.
MatFileWriter() - Constructor for class com.jmatio.io.MatFileWriter
Creates the new MatFileWriter instance
MatFileWriter(String, Collection<MLArray>) - Constructor for class com.jmatio.io.MatFileWriter
Writes MLArrays into file given by fileName.
MatFileWriter(File, Collection<MLArray>) - Constructor for class com.jmatio.io.MatFileWriter
Writes MLArrays into File.
MatFileWriter(WritableByteChannel, Collection<MLArray>) - Constructor for class com.jmatio.io.MatFileWriter
Writes MLArrays into OuputSteram.
MatlabIOException - Exception in com.jmatio.io
MAT-file reader/writer exception
MatlabIOException(String) - Constructor for exception com.jmatio.io.MatlabIOException
 
max - Variable in class ij.io.ImageReader
 
MAX - Static variable in class ij.measure.ResultsTable
 
MAX - Static variable in class ij.plugin.Binner
 
MAX - Static variable in class ij.plugin.filter.RankFilters
 
MAX - Static variable in class ij.plugin.Filters3D
 
MAX - Static variable in interface ij.process.Blitter
dst=max(dst,src)
max(double) - Method in class ij.process.FloatProcessor
 
MAX - Static variable in class ij.process.ImageProcessor
 
max(double) - Method in class ij.process.ImageProcessor
Pixels greater than 'value' are set to 'value'.
max - Variable in class ij.process.ImageStatistics
 
max - Variable in class ij.process.LUT
 
max(double) - Method in class ij.process.ShortProcessor
 
max - Static variable in class ij.wave.Burst
 
max - Static variable in class ij.wave.Wave
 
MAX_CHANNELS - Static variable in class ij.CompositeImage
 
MAX_COLUMNS - Static variable in class ij.measure.ResultsTable
Obsolete; use getLastColumn().
MAX_ITERATIONS_EXCEEDED - Static variable in class ij.measure.Minimizer
Status returned: no convergence detected after maximum iteration count
MAX_MACROS - Static variable in class ij.plugin.MacroInstaller
 
MAX_METHOD - Static variable in class ij.plugin.ZProjector
 
MAX_OF - Static variable in interface ij.macro.MacroConstants
 
MAX_OPEN_RECENT_ITEMS - Static variable in class ij.Menus
 
MAX_RESTARTS_EXCEEDED - Static variable in class ij.measure.Minimizer
Status returned: not two equal solutions after maximum number of restarts
MAX_SIZE - Static variable in class ij.plugin.frame.Editor
 
MAX_SIZE - Static variable in class ij.plugin.MacroInstaller
 
MAX_SLIDERS - Static variable in class ij.gui.GenericDialog
 
MAX_STANDARDS - Static variable in interface ij.measure.Measurements
Maximum number of calibration standard (20)
maxCount - Variable in class ij.process.ImageStatistics
 
maxEntries - Variable in class ij.plugin.Concatenator
 
maximize() - Method in class ij.gui.ImageWindow
 
MaximumFinder - Class in ij.plugin.filter
This ImageJ plug-in filter finds the maxima (or minima) of an image.
MaximumFinder() - Constructor for class ij.plugin.filter.MaximumFinder
 
MAXLOCAL - Static variable in class ij.plugin.Filters3D
 
maxMemory() - Static method in class ij.IJ
Returns the maximum amount of memory available to ImageJ or zero if ImageJ is unable to determine this limit.
maxMemory() - Method in class ij.plugin.Memory
Returns the maximum amount of memory this JVM will attempt to use.
maxPoints - Variable in class ij.gui.PolygonRoi
 
maxThreshold - Variable in class ij.process.ImageProcessor
 
maxValue() - Method in class ij.process.FloatProcessor
Returns the largest possible positive finite pixel value.
maxValue() - Method in class ij.process.ImageProcessor
Returns the maximum possible pixel value.
maxValue() - Method in class ij.process.ShortProcessor
Returns the maximum possible pixel value.
maxX - Variable in class ij.plugin.frame.ChartFramePlugIn
 
MEAN - Static variable in interface ij.measure.Measurements
 
MEAN - Static variable in class ij.measure.ResultsTable
 
MEAN - Static variable in class ij.plugin.filter.RankFilters
 
MEAN - Static variable in class ij.plugin.Filters3D
 
mean - Variable in class ij.process.ImageStatistics
 
mean - Static variable in class ij.wave.Bursts
 
mean - Static variable in class ij.wave.Wave
 
measure() - Method in class ij.gui.MultiLineLabel
 
measure() - Method in class ij.plugin.filter.Analyzer
Measures the image or selection and adds the results to the default results table.
measureFrom(int, int) - Method in class ij.plugin.frame.ChartFramePlugIn
 
Measurements - Interface in ij.measure
 
MeasurementsWriter - Class in ij.plugin
Writes measurements to a csv or tab-delimited text file.
MeasurementsWriter() - Constructor for class ij.plugin.MeasurementsWriter
 
MEDIAN - Static variable in interface ij.measure.Measurements
 
MEDIAN - Static variable in class ij.measure.ResultsTable
 
MEDIAN - Static variable in class ij.plugin.Binner
 
MEDIAN - Static variable in class ij.plugin.filter.RankFilters
 
MEDIAN - Static variable in class ij.plugin.Filters3D
 
median - Variable in class ij.process.ImageStatistics
 
median - Static variable in class ij.wave.Wave
 
MEDIAN_FILTER - Static variable in class ij.process.ImageProcessor
 
MEDIAN_METHOD - Static variable in class ij.plugin.ZProjector
 
MedianCut - Class in ij.process
Converts an RGB image to 8-bit index color using Heckbert's median-cut color quantization algorithm.
MedianCut(int[], int, int) - Constructor for class ij.process.MedianCut
 
MedianCut(ColorProcessor) - Constructor for class ij.process.MedianCut
 
medianFilter() - Method in class ij.process.ByteProcessor
 
medianFilter() - Method in class ij.process.ColorProcessor
 
medianFilter() - Method in class ij.process.FloatProcessor
Not implemented.
medianFilter() - Method in class ij.process.ImageProcessor
A 3x3 median filter.
medianFilter() - Method in class ij.process.ShortProcessor
Not implemented.
medianSort() - Method in class ij.util.ArrayUtil
The median (sorted array)
Memory - Class in ij.plugin
This plugin implements the Edit/Options/Memory command.
Memory() - Constructor for class ij.plugin.Memory
 
MEMORY_MAPPED_FILE - Static variable in class com.jmatio.io.MatFileReader
 
MemoryMonitor - Class in ij.plugin
This plugin continuously plots ImageJ's memory utilization.
MemoryMonitor() - Constructor for class ij.plugin.MemoryMonitor
 
MENU_BAR - Static variable in class ij.plugin.frame.Editor
 
MENU_SIZE - Static variable in class ij.Prefs
 
Menus - Class in ij
This class installs and updates ImageJ's menus.
mergeChannels(ImagePlus[], boolean) - Static method in class ij.plugin.RGBStackMerge
 
mergeComments(Comments) - Method in class org.javaabf.Comments
 
mergeHyperstacks(ImagePlus[], boolean) - Method in class ij.plugin.RGBStackMerge
 
mergeStacks() - Method in class ij.plugin.RGBStackMerge
Combines up to seven grayscale stacks into one RGB or composite stack.
mergeStacks(ImageStack, ImageStack, ImageStack, boolean) - Static method in class ij.plugin.RGBStackMerge
 
mergeStacks(int, int, int, ImageStack, ImageStack, ImageStack, boolean) - Method in class ij.plugin.RGBStackMerge
 
MessageDialog - Class in ij.gui
A modal dialog box that displays information.
MessageDialog(Frame, String, String) - Constructor for class ij.gui.MessageDialog
 
META_DATA - Static variable in class ij.io.TiffDecoder
 
META_DATA_BYTE_COUNTS - Static variable in class ij.io.TiffDecoder
 
metaData - Variable in class ij.io.FileInfo
 
metaDataTypes - Variable in class ij.io.FileInfo
 
METAMORPH1 - Static variable in class ij.io.TiffDecoder
 
METAMORPH2 - Static variable in class ij.io.TiffDecoder
 
methods - Static variable in class ij.plugin.Thresholder
 
METHODS - Static variable in class ij.plugin.ZProjector
 
miCOMPRESSED - Static variable in class com.jmatio.common.MatDataTypes
 
micronSymbol - Static variable in class ij.IJ
 
miDOUBLE - Static variable in class com.jmatio.common.MatDataTypes
 
miINT16 - Static variable in class com.jmatio.common.MatDataTypes
 
miINT32 - Static variable in class com.jmatio.common.MatDataTypes
 
miINT64 - Static variable in class com.jmatio.common.MatDataTypes
 
miINT8 - Static variable in class com.jmatio.common.MatDataTypes
 
miMATRIX - Static variable in class com.jmatio.common.MatDataTypes
 
min - Variable in class ij.io.ImageReader
 
MIN - Static variable in class ij.measure.ResultsTable
 
MIN - Static variable in class ij.plugin.Binner
 
MIN - Static variable in class ij.plugin.filter.RankFilters
 
MIN - Static variable in class ij.plugin.Filters3D
 
MIN - Static variable in interface ij.process.Blitter
dst=min(dst,src)
min(double) - Method in class ij.process.FloatProcessor
 
MIN - Static variable in class ij.process.ImageProcessor
 
min(double) - Method in class ij.process.ImageProcessor
Pixels less than 'value' are set to 'value'.
min - Variable in class ij.process.ImageStatistics
 
min - Variable in class ij.process.LUT
 
min(double) - Method in class ij.process.ShortProcessor
 
min - Static variable in class ij.wave.Burst
 
min - Static variable in class ij.wave.Wave
 
MIN_FERET - Static variable in class ij.measure.ResultsTable
 
MIN_HEIGHT - Static variable in class ij.gui.ImageWindow
 
MIN_MAX - Static variable in interface ij.measure.Measurements
 
MIN_METHOD - Static variable in class ij.plugin.ZProjector
 
MIN_OF - Static variable in interface ij.macro.MacroConstants
 
MIN_WIDTH - Static variable in class ij.gui.ImageWindow
 
minimize() - Method in class ij.gui.ImageWindow
 
minimize(double[], double[]) - Method in class ij.measure.Minimizer
Perform minimization with the gradient-enhanced simplex method once or a few times, depending on the value of 'restarts'.
minimizeOnce(double[], double[]) - Method in class ij.measure.Minimizer
Perform minimization with the simplex method once, including re-initialization until we have a stable solution.
Minimizer - Class in ij.measure
Minimizer based on Nelder-Mead simplex method (also known as polytope method), including the 'outside contraction' as described in: J.C.
Minimizer() - Constructor for class ij.measure.Minimizer
 
minimumLayoutSize(Container) - Method in class ij.gui.ImageLayout
Returns the minimum dimensions for this layout.
minMaxSet - Variable in class ij.process.ImageProcessor
 
MINOR - Static variable in class ij.measure.ResultsTable
 
minor - Variable in class ij.process.EllipseFitter
Length of minor axis
minor - Variable in class ij.process.ImageStatistics
Length of minor axis of fitted ellipse
minThreshold - Variable in class ij.process.ImageProcessor
 
MINUS_EQUAL - Static variable in interface ij.macro.MacroConstants
 
MINUS_MINUS - Static variable in interface ij.macro.MacroConstants
 
minValue() - Method in class ij.process.FloatProcessor
Returns the smallest possible positive nonzero pixel value.
minValue() - Method in class ij.process.ImageProcessor
Returns the minimum possible pixel value.
minX - Variable in class ij.plugin.frame.ChartFramePlugIn
 
MISC - Static variable in class ij.wave.WaveMarker
 
miSINGLE - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_CHAR - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_DOUBLE - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_INT16 - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_INT32 - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_INT64 - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_INT8 - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_UINT16 - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_UINT32 - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_UINT64 - Static variable in class com.jmatio.common.MatDataTypes
 
miSIZE_UINT8 - Static variable in class com.jmatio.common.MatDataTypes
 
miUINT16 - Static variable in class com.jmatio.common.MatDataTypes
 
miUINT32 - Static variable in class com.jmatio.common.MatDataTypes
 
miUINT64 - Static variable in class com.jmatio.common.MatDataTypes
 
miUINT8 - Static variable in class com.jmatio.common.MatDataTypes
 
miUNKNOWN - Static variable in class com.jmatio.common.MatDataTypes
 
miUTF16 - Static variable in class com.jmatio.common.MatDataTypes
 
miUTF32 - Static variable in class com.jmatio.common.MatDataTypes
 
miUTF8 - Static variable in class com.jmatio.common.MatDataTypes
 
MLArray - Class in com.jmatio.types
 
MLArray(String, int[], int, int) - Constructor for class com.jmatio.types.MLArray
 
MLCell - Class in com.jmatio.types
 
MLCell(String, int[]) - Constructor for class com.jmatio.types.MLCell
 
MLCell(String, int[], int, int) - Constructor for class com.jmatio.types.MLCell
 
MLChar - Class in com.jmatio.types
 
MLChar(String, String) - Constructor for class com.jmatio.types.MLChar
Creates the 1 x String.length() MLChar from the given String.
MLChar(String, String[]) - Constructor for class com.jmatio.types.MLChar
Create the MLChar from array of Strings.
MLChar(String, String[], int) - Constructor for class com.jmatio.types.MLChar
Added method to allow initialization of a char array representing an array of strings.
MLChar(String, int[], int, int) - Constructor for class com.jmatio.types.MLChar
 
MLDouble - Class in com.jmatio.types
Class represents Double array (matrix)
MLDouble(String, int[], int, int) - Constructor for class com.jmatio.types.MLDouble
Normally this constructor is used only by MatFileReader and MatFileWriter
MLDouble(String, int[]) - Constructor for class com.jmatio.types.MLDouble
Create a MLDouble array with given name, and dimensions.
MLDouble(String, Double[], int) - Constructor for class com.jmatio.types.MLDouble
Jama [math.nist.gov] style: construct a 2D real matrix from a one-dimensional packed array
MLDouble(String, double[][]) - Constructor for class com.jmatio.types.MLDouble
Jama [math.nist.gov] style: construct a 2D real matrix from double[][] Note: array is converted to Double[]
MLDouble(String, double[], int) - Constructor for class com.jmatio.types.MLDouble
Jama [math.nist.gov] style: construct a matrix from a one-dimensional packed array
MLEmptyArray - Class in com.jmatio.types
 
MLEmptyArray() - Constructor for class com.jmatio.types.MLEmptyArray
 
MLEmptyArray(String) - Constructor for class com.jmatio.types.MLEmptyArray
 
MLEmptyArray(String, int[], int, int) - Constructor for class com.jmatio.types.MLEmptyArray
 
MLInt16 - Class in com.jmatio.types
Class represents Int16 array (matrix)
MLInt16(String, int[], int, int) - Constructor for class com.jmatio.types.MLInt16
Normally this constructor is used only by MatFileReader and MatFileWriter
MLInt16(String, int[]) - Constructor for class com.jmatio.types.MLInt16
Create a MLSingle array with given name, and dimensions.
MLInt16(String, Short[], int) - Constructor for class com.jmatio.types.MLInt16
Jama [math.nist.gov] style: construct a 2D real matrix from a one-dimensional packed array
MLInt16(String, short[][]) - Constructor for class com.jmatio.types.MLInt16
Jama [math.nist.gov] style: construct a 2D real matrix from double[][] Note: array is converted to Short[]
MLInt16(String, short[], int) - Constructor for class com.jmatio.types.MLInt16
Jama [math.nist.gov] style: construct a matrix from a one-dimensional packed array
MLInt32 - Class in com.jmatio.types
 
MLInt32(String, int[], int, int) - Constructor for class com.jmatio.types.MLInt32
Normally this constructor is used only by MatFileReader and MatFileWriter
MLInt32(String, int[]) - Constructor for class com.jmatio.types.MLInt32
Create a MLInt64 array with given name, and dimensions.
MLInt32(String, Integer[], int) - Constructor for class com.jmatio.types.MLInt32
Jama [math.nist.gov] style: construct a 2D real matrix from a one-dimensional packed array
MLInt32(String, int[][]) - Constructor for class com.jmatio.types.MLInt32
Jama [math.nist.gov] style: construct a 2D real matrix from byte[][] Note: array is converted to Byte[]
MLInt32(String, int[], int) - Constructor for class com.jmatio.types.MLInt32
Jama [math.nist.gov] style: construct a matrix from a one-dimensional packed array
MLInt64 - Class in com.jmatio.types
Class represents Int64 (long) array (matrix)
MLInt64(String, int[], int, int) - Constructor for class com.jmatio.types.MLInt64
Normally this constructor is used only by MatFileReader and MatFileWriter
MLInt64(String, int[]) - Constructor for class com.jmatio.types.MLInt64
Create a MLInt64 array with given name, and dimensions.
MLInt64(String, Long[], int) - Constructor for class com.jmatio.types.MLInt64
Jama [math.nist.gov] style: construct a 2D real matrix from a one-dimensional packed array
MLInt64(String, long[][]) - Constructor for class com.jmatio.types.MLInt64
Jama [math.nist.gov] style: construct a 2D real matrix from byte[][] Note: array is converted to Byte[]
MLInt64(String, long[], int) - Constructor for class com.jmatio.types.MLInt64
Jama [math.nist.gov] style: construct a matrix from a one-dimensional packed array
MLInt8 - Class in com.jmatio.types
 
MLInt8(String, int[], int, int) - Constructor for class com.jmatio.types.MLInt8
Normally this constructor is used only by MatFileReader and MatFileWriter
MLInt8(String, int[]) - Constructor for class com.jmatio.types.MLInt8
Create a MLUInt8 array with given name, and dimensions.
MLInt8(String, Byte[], int) - Constructor for class com.jmatio.types.MLInt8
Jama [math.nist.gov] style: construct a 2D re