Field Detail

• GRAY8

  public static final int GRAY8
  8-bit grayscale (unsigned)
  See Also: Constant Field Values

• GRAY16

  public static final int GRAY16
  16-bit grayscale (unsigned)
  See Also: Constant Field Values

• GRAY32

  public static final int GRAY32
  32-bit floating-point grayscale
  See Also: Constant Field Values

• COLOR_256

  public static final int COLOR_256
  8-bit indexed color
  See Also: Constant Field Values

• COLOR_RGB

  public static final int COLOR_RGB
  32-bit RGB color
  See Also: Constant Field Values

• flattenTitle

  public static final java.lang.String flattenTitle
  Title of image used by Flatten command
  See Also: Constant Field Values

• changes

  public boolean changes
  True if any changes have been made to this image.

• img

  protected java.awt.Image img

• ip

  protected ImageProcessor ip

• win

  protected ImageWindow win

• roi

  protected Roi roi

• currentSlice

  protected int currentSlice

• OPENED

  protected static final int OPENED See Also: Constant Field Values

• CLOSED

  protected static final int CLOSED See Also: Constant Field Values

• UPDATED

  protected static final int UPDATED See Also: Constant Field Values

• SAVED

  protected static final int SAVED See Also: Constant Field Values

• compositeImage

  protected boolean compositeImage

• width

  protected int width

• height

  protected int height

• locked

  protected boolean locked

• nChannels

  protected int nChannels

• nSlices

  protected int nSlices

• nFrames

  protected int nFrames

• dimensionsSet

  protected boolean dimensionsSet

• setIJMenuBar

  public boolean setIJMenuBar

Constructor Detail

• ImagePlus

  public ImagePlus()
  Constructs an uninitialized ImagePlus.

• ImagePlus

  public ImagePlus​(java.lang.String title, java.awt.Image image)
  Constructs an ImagePlus from an Image or BufferedImage. The first argument will be used as the title of the window that displays the image. Throws an IllegalStateException if an error occurs while loading the image.

• ImagePlus

  public ImagePlus​(java.lang.String title, ImageProcessor ip)
  Constructs an ImagePlus from an ImageProcessor.

• ImagePlus

  public ImagePlus​(java.lang.String pathOrURL)
  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

  public ImagePlus​(java.lang.String title, ImageStack stack)
  Constructs an ImagePlus from a stack.

Method Detail

• setTemporary

  public void setTemporary()

• lock

  public boolean lock()
  Locks the image so other threads can test to see if it is in use. One thread can lock an image multiple times, then it has to unlock it as many times until it is unlocked. This allows nested locking within a thread. Returns true if the image was successfully locked. Beeps, displays a message in the status bar, and returns false if the image is already locked by another thread.

• lockSilently

  public boolean lockSilently()
  Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.

• unlock

  public void unlock()
  Unlocks the image. In case the image had been locked several times by the current thread, it gets unlocked only after as many unlock operations as there were previous lock operations.

• isLocked

  public boolean isLocked()
  Returns 'true' if the image is locked.

• isLockedByAnotherThread

  public boolean isLockedByAnotherThread()
  Returns 'true' if the image was locked on another thread.

• draw

  public void draw()
  Draws the image. If there is an ROI, its outline is also displayed. Does nothing if there is no window associated with this image (i.e. show() has not been called).

• draw

  public void draw​(int x, int y, int width, int height)
  Draws image and roi outline using a clip rect.

• updateAndDraw

  public void updateAndDraw()
  Updates this image from the pixel data in its associated ImageProcessor, then displays it. Does nothing if there is no window associated with this image (i.e. show() has not been called).

• updateVirtualSlice

  public void updateVirtualSlice()
  Use to update the image when the underlying virtual stack changes.

• setDisplayMode

  public void setDisplayMode​(int mode)
  Sets the display mode of composite color images, where 'mode' should be IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE.

• getDisplayMode

  public int getDisplayMode()
  Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a composite color image, or 0 if it not.

• setActiveChannels

  public void setActiveChannels​(java.lang.String channels)
  Controls which channels in a composite color image are displayed, where 'channels' is a list of ones and zeros that specify the channels to display. For example, "101" causes channels 1 and 3 to be displayed.

• updateChannelAndDraw

  public void updateChannelAndDraw()
  Updates this image from the pixel data in its associated ImageProcessor, then displays it. The CompositeImage class overrides this method to only update the current channel.

• getChannelProcessor

  public ImageProcessor getChannelProcessor()
  Returns a reference to the current ImageProcessor. The CompositeImage class overrides this method to return the processor associated with the current channel.

• getLuts

  public LUT[] getLuts()
  Returns an array containing the lookup tables used by this image, one per channel, or an empty array if this is an RGB image.
  See Also: getNChannels(), isComposite(), Javascript example: luts = imp.getLuts(); for (i=0; iluts.length; i++) IJ.log((i+1)+“: “+luts[i].min+”-”+luts[i].max);

• repaintWindow

  public void repaintWindow()
  Calls draw to draw the image and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.

• updateAndRepaintWindow

  public void updateAndRepaintWindow()
  Calls updateAndDraw to update from the pixel data and draw the image, and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.

• updateImage

  public void updateImage()
  ImageCanvas.paint() calls this method when the ImageProcessor has generated a new image.

• hide

  public void hide()
  Closes the window, if any, that is displaying this image.

• close

  public void close()
  Closes this image and sets the ImageProcessor to null. To avoid the "Save changes?" dialog, first set the public 'changes' variable to false.

• show

  public void show()
  Opens a window to display this image and clears the status bar.

• show

  public void show​(java.lang.String statusMessage)
  Opens a window to display this image and displays 'statusMessage' in the status bar.

• waitTillActivated

  public void waitTillActivated()
  Waits until the image window becomes activated. This is necessary in macros or other programs if an ImagePlus is shown on the screen, because displaying the window is asynchronous (happens later) and will make the image the active one. Without waiting, in the meanwhile another window could be already the active one and would become deactivated. If the ImagePlus may have been displayed previously, first call setDeactivated(). ImagePlus.show() and new StackWindow(ImagePlus) call this method if IJ.isMacro() is true, i.e., when running a macro or executing an IJ.run(...) call.

• setActivated

  public void setActivated()
  Called by ImageWindow.windowActivated(); to end waiting in waitTillActivated.

• setDeactivated

  public void setDeactivated()
  Called by new StackWindow(ImagePlus) before showing the StackWindow, to prepare for waitTillActivated().

• getImage

  public java.awt.Image getImage()
  Returns this image as a AWT image.

• getBufferedImage

  public java.awt.image.BufferedImage getBufferedImage()
  Returns a copy of this image as an 8-bit or RGB BufferedImage.
  See Also: ShortProcessor.get16BitBufferedImage()

• getID

  public int getID()
  Returns this image's unique numeric ID.

• setImage

  public void setImage​(java.awt.Image image)
  Replaces the image, if any, with the one specified. Throws an IllegalStateException if an error occurs while loading the image.

• convertToImageProcessor

  public static ImageProcessor convertToImageProcessor​(java.awt.image.BufferedImage img, int band)
  Extract pixels as an ImageProcessor from a single band of a BufferedImage.
  Parameters: img - band - Returns:

• setImage

  public void setImage​(ImagePlus imp)
  Replaces this image with the specified ImagePlus. May not work as expected if 'imp' is a CompositeImage and this image is not.

• setProcessor

  public void setProcessor​(ImageProcessor ip)
  Replaces the ImageProcessor with the one specified and updates the display. With stacks, the ImageProcessor must be the same type as the other images in the stack and it must be the same width and height.

• setProcessor

  public void setProcessor​(java.lang.String title, ImageProcessor ip)
  Replaces the ImageProcessor with the one specified and updates the display. With stacks, the ImageProcessor must be the same type as other images in the stack and it must be the same width and height. Set 'title' to null to leave the title unchanged.

• setStack

  public void setStack​(ImageStack stack)
  Replaces the image with the specified stack and updates the display.

• setStack

  public void setStack​(java.lang.String title, ImageStack newStack)
  Replaces the image with the specified stack and updates the display. Set 'title' to null to leave the title unchanged.

• setStack

  public void setStack​(ImageStack newStack, int channels, int slices, int frames)

• setFileInfo

  public void setFileInfo​(FileInfo fi)
  Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo().

• getWindow

  public ImageWindow getWindow()
  Returns the ImageWindow that is being used to display this image. Returns null if show() has not be called or the ImageWindow has been closed.

• isVisible

  public boolean isVisible()
  Returns true if this image is currently being displayed in a window.

• setWindow

  public void setWindow​(ImageWindow win)
  This method should only be called from an ImageWindow.

• getCanvas

  public ImageCanvas getCanvas()
  Returns the ImageCanvas being used to display this image, or null.

• setColor

  public void setColor​(java.awt.Color c)
  Sets current foreground color.

• isProcessor

  public boolean isProcessor()

• getProcessor

  public ImageProcessor getProcessor()
  Returns a reference to the current ImageProcessor. If there is no ImageProcessor, it creates one. Returns null if this ImagePlus contains no ImageProcessor and no AWT Image. Sets the line width to the current line width and sets the calibration table if the image is density calibrated.

• trimProcessor

  public void trimProcessor()
  Frees RAM by setting the snapshot (undo) buffer in the current ImageProcessor to null.

• getMask

  public ImageProcessor getMask()
  For images with irregular ROIs, returns a byte mask, otherwise, returns null. Mask pixels have a non-zero value.and the dimensions of the mask are equal to the width and height of the ROI.
  See Also: createRoiMask(), createThresholdMask()

• createRoiMask

  public ByteProcessor createRoiMask()
  Returns an 8-bit binary (foreground=255, background=0) ROI or overlay mask that has the same dimensions as this image. Creates an ROI mask If the image has both both an ROI and an overlay. Set the threshold of the mask to 255.
  See Also: createThresholdMask(), Roi.getMask()

• createThresholdMask

  public ByteProcessor createThresholdMask()
  Returns an 8-bit binary threshold mask (foreground=255, background=0) that has the same dimensions as this image. The threshold of the mask is set to 255.
  See Also: Thresholder.createMask(ij.ImagePlus), ImageProcessor.createMask()

• getStatistics

  public ImageStatistics getStatistics()
  Get calibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation and mode. This code demonstrates how to get the area, mean max and median of the current image or selection: imp = IJ.getImage(); stats = imp.getStatistics(); IJ.log("Area: "+stats.area); IJ.log("Mean: "+stats.mean); IJ.log("Max: "+stats.max);
  Returns: an ImageStatistics object See Also: getAllStatistics(), getRawStatistics(), ImageProcessor.getStats()

• getAllStatistics

  public ImageStatistics getAllStatistics()
  This method returns complete calibrated statistics for this image or ROI (with "Limit to threshold"), but it is up to 70 times slower than getStatistics().
  Returns: an ImageStatistics object See Also: getStatistics(), ImageProcessor.getStatistics()

• getRawStatistics

  public ImageStatistics getRawStatistics()

• getStatistics

  public ImageStatistics getStatistics​(int mOptions)
  Returns an ImageStatistics object generated using the specified measurement options.
  See Also: Measurements

• getStatistics

  public ImageStatistics getStatistics​(int mOptions, int nBins)
  Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.

• getStatistics

  public ImageStatistics getStatistics​(int mOptions, int nBins, double histMin, double histMax)
  Returns an ImageStatistics object generated using the specified measurement options, histogram bin count and histogram range.

• getTitle

  public java.lang.String getTitle()
  Returns the image name.

• getShortTitle

  public java.lang.String getShortTitle()
  If the image title is a file name, returns the name without the extension and with spaces removed, otherwise returns the title shortened to the first space.

• setTitle

  public void setTitle​(java.lang.String title)
  Sets the image name.

• getWidth

  public int getWidth()
  Returns the width of this image in pixels.

• getHeight

  public int getHeight()
  Returns the height of this image in pixels.

• getSizeInBytes

  public double getSizeInBytes()
  Returns the size of this image in bytes.

• getStackSize

  public int getStackSize()
  Returns the number of stack images.

• getImageStackSize

  public int getImageStackSize()
  If this is a stack, returns the actual number of images in the stack, else returns 1.

• setDimensions

  public void setDimensions​(int nChannels, int nSlices, int nFrames)
  Sets the 3rd, 4th and 5th dimensions, where nChannels*nSlices*nFrames must be equal to the stack size.

• isHyperStack

  public boolean isHyperStack()
  Returns 'true' if this image has more than three dimensions.

• getNDimensions

  public int getNDimensions()
  Returns the number of dimensions (2, 3, 4 or 5).

• isDisplayedHyperStack

  public boolean isDisplayedHyperStack()
  Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.

• getNChannels

  public int getNChannels()
  Returns the number of channels.

• getNSlices

  public int getNSlices()
  Returns the image depth (number of z-slices).

• getNFrames

  public int getNFrames()
  Returns the number of frames (time-points).

• getDimensions

  public int[] getDimensions()
  Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.

• getDimensions

  public int[] getDimensions​(boolean varify)

• getType

  public int getType()
  Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
  See Also: getBitDepth()

• getBitDepth

  public int getBitDepth()
  Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth is unknown. RGB images actually use 32 bits per pixel.

• getBytesPerPixel

  public int getBytesPerPixel()
  Returns the number of bytes per pixel.

• setType

  protected void setType​(int type)

• setTypeToColor256

  public void setTypeToColor256()

• getStringProperty

  public java.lang.String getStringProperty​(java.lang.String key)
  Returns the string value from the "Info" property string associated with 'key', or null if the key is not found. Works with DICOM tags and Bio-Formats metadata.
  See Also: getNumericProperty(java.lang.String), getInfoProperty(), getProp(java.lang.String), setProp(java.lang.String, java.lang.String)

• getNumericProperty

  public double getNumericProperty​(java.lang.String key)
  Returns the numeric value from the "Info" property string associated with 'key', or NaN if the key is not found or the value associated with the key is not numeric. Works with DICOM tags and Bio-Formats metadata.
  See Also: getStringProperty(java.lang.String), getInfoProperty()

• setProp

  public void setProp​(java.lang.String key, java.lang.String value)
  Adds a key-value pair to this image's string properties. The key-value pair is removed if 'value' is null. The properties persist if the image is saved in TIFF format. Add a "HideInfo" property (e.g. set("HideInfo","true")) to prevent the properties from being displayed by the Image/Show Info command.

• setProp

  public void setProp​(java.lang.String key, double value)
  Saves a persistent numeric propery. The property is removed if 'value' is NaN.
  See Also: getNumericProp(java.lang.String)

• getProp

  public java.lang.String getProp​(java.lang.String key)
  Returns as a string the image property associated with the specified key or null if the property is not found.
  See Also: setProp(java.lang.String, java.lang.String), getNumericProp(java.lang.String), getStringProperty(java.lang.String)

• getNumericProp

  public double getNumericProp​(java.lang.String key)
  Returns the numeric property associated with the specified key or NaN if the property is not found.
  See Also: setProp(String,double), getProp(java.lang.String)

• getPropertiesAsArray

  public java.lang.String[] getPropertiesAsArray()
  Used for saving string properties in TIFF header.

• getPropsInfo

  public java.lang.String getPropsInfo()
  Returns information displayed by Image/Show Info command.

• setProperties

  public void setProperties​(java.lang.String[] props)
  Creates a set of image properties from an array of strings.
  See Also: getPropertiesAsArray(), getProp(String), setProp(String,String)

• getInfoProperty

  public java.lang.String getInfoProperty()
  Returns the "Info" property string, or null if it is not found.
  See Also: getProp(java.lang.String), setProp(java.lang.String, java.lang.String)

• getProperty

  public java.lang.Object getProperty​(java.lang.String key)
  Returns the property associated with 'key', or null if it is not found.
  See Also: getProp(java.lang.String), setProp(java.lang.String, java.lang.String), getStringProperty(java.lang.String), getNumericProperty(java.lang.String), getInfoProperty()

• setProperty

  public void setProperty​(java.lang.String key, java.lang.Object value)
  Adds a key-value pair to this image's properties. The key is removed from the properties table if value is null.
  See Also: getProp(java.lang.String), setProp(java.lang.String, java.lang.String)

• getProperties

  public java.util.Properties getProperties()
  Returns this image's Properties. May return null.

• createLut

  public LookUpTable createLut()
  Creates a LookUpTable object that corresponds to this image.

• isInvertedLut

  public boolean isInvertedLut()
  Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.

• getPixel

  public int[] getPixel​(int x, int y)
  Returns the pixel value at (x,y) as a 4 element array. Grayscale values are retuned in the first element. RGB values are returned in the first 3 elements. For indexed color images, the RGB values are returned in the first 3 three elements and the index (0-255) is returned in the last.

• createEmptyStack

  public ImageStack createEmptyStack()
  Returns an empty image stack that has the same width, height and color table as this image.

• getStack

  public ImageStack getStack()
  Returns the image stack. The stack may have only one slice. After adding or removing slices, call setStack() to update the image and the window that is displaying it.
  See Also: setStack(ij.ImageStack)

• getImageStack

  public ImageStack getImageStack()
  Returns the base image stack.

• getCurrentSlice

  public int getCurrentSlice()
  Returns the current stack index (one-based) or 1 if this is a single image.

• getChannel

  public int getChannel()

• getSlice

  public int getSlice()

• getFrame

  public int getFrame()

• killStack

  public void killStack()

• setPosition

  public void setPosition​(int channel, int slice, int frame)
  Sets the current hyperstack position and updates the display, where 'channel', 'slice' and 'frame' are one-based indexes.

• setPositionWithoutUpdate

  public void setPositionWithoutUpdate​(int channel, int slice, int frame)
  Sets the current hyperstack position without updating the display, where 'channel', 'slice' and 'frame' are one-based indexes.

• setC

  public void setC​(int channel)
  Sets the hyperstack channel position (one based).

• setZ

  public void setZ​(int slice)
  Sets the hyperstack slice position (one based).

• setT

  public void setT​(int frame)
  Sets the hyperstack frame position (one based).

• getC

  public int getC()
  Returns the current hyperstack channel position.

• getZ

  public int getZ()
  Returns the current hyperstack slice position.

• getT

  public int getT()
  Returns the current hyperstack frame position.

• getStackIndex

  public int getStackIndex​(int channel, int slice, int frame)
  Returns that stack index (one-based) corresponding to the specified position.

• resetStack

  public void resetStack()

• setPosition

  public void setPosition​(int n)
  Set the current hyperstack position based on the stack index 'n' (one-based).

• convertIndexToPosition

  public int[] convertIndexToPosition​(int n)
  Converts the stack index 'n' (one-based) into a hyperstack position (channel, slice, frame).

• setSlice

  public void setSlice​(int n)
  Displays the specified stack image, where 1<=n<=stackSize. Does nothing if this image is not a stack.
  See Also: setPosition(int, int, int), setC(int), setZ(int), setT(int)

• setSliceWithoutUpdate

  public void setSliceWithoutUpdate​(int n)
  Displays the specified stack image (1<=n<=stackSize) without updating the display.

• getRoi

  public Roi getRoi()
  Returns the current selection, or null if there is no selection.

• setRoi

  public void setRoi​(Roi newRoi)
  Assigns the specified ROI to this image and displays it. Any existing ROI is deleted if roi is null or its width or height is zero.

• setRoi

  public void setRoi​(Roi newRoi, boolean updateDisplay)
  Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.

• setRoi

  public void setRoi​(int x, int y, int width, int height)
  Creates a rectangular selection.

• setRoi

  public void setRoi​(java.awt.Rectangle r)
  Creates a rectangular selection.

• createNewRoi

  public void createNewRoi​(int sx, int sy)
  Starts the process of creating a new selection, where sx and sy are the starting screen coordinates. The selection type is determined by which tool in the tool bar is active. The user interactively sets the selection size and shape.

• deleteRoi

  public void deleteRoi()
  Deletes the current region of interest. Makes a copy of the ROI so it can be recovered by Edit/Selection/Restore Selection.

• removeScale

  public void removeScale()
  Removes the spatial scaling of this image.

• okToDeleteRoi

  public boolean okToDeleteRoi()

• killRoi

  public void killRoi()
  Deletes the current region of interest.

• resetRoi

  public void resetRoi()
  Deletes the current region of interest.

• saveRoi

  public void saveRoi()

• restoreRoi

  public void restoreRoi()

• revert

  public void revert()
  Implements the File/Revert command.

• getFileInfo

  public FileInfo getFileInfo()
  Returns a FileInfo object containing information, including the pixel array, needed to save this image. Use getOriginalFileInfo() to get a copy of the FileInfo object used to open the image.
  See Also: FileInfo, getOriginalFileInfo(), setFileInfo(ij.io.FileInfo)

• getOriginalFileInfo

  public FileInfo getOriginalFileInfo()
  Returns the FileInfo object that was used to open this image. Returns null for images created using the File/New command.
  See Also: FileInfo, getFileInfo()

• imageUpdate

  public boolean imageUpdate​(java.awt.Image img, int flags, int x, int y, int w, int h)
  Used by ImagePlus to monitor loading of images.
  Specified by: imageUpdate in interface java.awt.image.ImageObserver

• flush

  public void flush()
  Sets the ImageProcessor, Roi, AWT Image and stack image arrays to null. Does nothing if the image is locked.

• setIgnoreFlush

  public void setIgnoreFlush​(boolean ignoreFlush)

• duplicate

  public ImagePlus duplicate()
  Returns a copy of this image or stack.
  See Also: crop(), Duplicator.run(java.lang.String)

• resize

  public ImagePlus resize​(int dstWidth, int dstHeight, java.lang.String options)
  Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'. 'bicubic', 'average' and 'constrain'.

• resize

  public ImagePlus resize​(int dstWidth, int dstHeight, int dstDepth, java.lang.String options)
  Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'. 'bicubic', 'average' and 'constrain'.

• crop

  public ImagePlus crop()
  Returns a copy this image or stack slice, cropped if there is an ROI.
  See Also: duplicate(), Duplicator.crop(ij.ImagePlus)

• crop

  public ImagePlus crop​(java.lang.String options)
  Returns a cropped copy this image or stack, where 'options' can be "stack", "slice", "whole-slice" or a range (e.g., "20-30").
  See Also: duplicate(), crop(), Duplicator.crop(ij.ImagePlus)

• crop

  public ImagePlus[] crop​(Roi[] rois, java.lang.String options)
  Returns an array of cropped images based on the provided list of rois. 'options' applies with stacks and can be "stack", "slice" or a range (e.g., "20-30").
  See Also: crop(ij.gui.Roi[])

• crop

  public ImagePlus[] crop​(Roi[] rois)
  Multi-roi cropping with default "slice" option.

• cropAndSave

  public void cropAndSave​(Roi[] rois, java.lang.String directory, java.lang.String format)
  Saves the contents of the ROIs in this overlay as separate images, where 'directory' is the directory path and 'format' is "tif", "png" or "jpg". Set 'format' to "show" and the images will be displayed in a stack and not saved.

• createImagePlus

  public ImagePlus createImagePlus()
  Returns a new ImagePlus with this image's attributes (e.g. spatial scale), but no image.

• createHyperStack

  public ImagePlus createHyperStack​(java.lang.String title, int channels, int slices, int frames, int bitDepth)
  This method has been replaced by IJ.createHyperStack().

• copyScale

  public void copyScale​(ImagePlus imp)
  Copies the calibration of the specified image to this image.

• copyAttributes

  public void copyAttributes​(ImagePlus imp)
  Used internally.

• startTiming

  public void startTiming()
  Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation.

• getStartTime

  public long getStartTime()
  Returns the time in milliseconds when startTiming() was last called.

• getCalibration

  public Calibration getCalibration()
  Returns this image's calibration.

• setCalibration

  public void setCalibration​(Calibration cal)
  Sets this image's calibration.

• setGlobalCalibration

  public void setGlobalCalibration​(Calibration global)
  Sets the system-wide calibration.

• getGlobalCalibration

  public Calibration getGlobalCalibration()
  Returns the system-wide calibration, or null.

• getStaticGlobalCalibration

  public static Calibration getStaticGlobalCalibration()
  This is a version of getGlobalCalibration() that can be called from a static context.

• getLocalCalibration

  public Calibration getLocalCalibration()
  Returns this image's local calibration, ignoring the "Global" calibration flag.

• setIgnoreGlobalCalibration

  public void setIgnoreGlobalCalibration​(boolean ignoreGlobalCalibration)

• mouseMoved

  public void mouseMoved​(int x, int y)
  Displays the cursor coordinates and pixel value in the status bar. Called by ImageCanvas when the mouse moves.

• updateStatusbarValue

  public void updateStatusbarValue()
  Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar. Called by the Next Slice and Previous Slice commands to update the z-coordinate and pixel value.

• getLocationAsString

  public java.lang.String getLocationAsString​(int x, int y)
  Converts the current cursor location to a string.

• cut

  public void cut()
  Copies the contents of the current selection to the internal clipboard and then clears the selection.

• copy

  public void copy()
  Copies the contents of the current selection, or the entire image if there is no selection, to the internal clipboard.

• copy

  public void copy​(boolean cut)
  Copies the contents of the current selection to the internal clipboard. Copies the entire image if there is no selection. Also clears the selection if cut is true.

• paste

  public void paste()
  Inserts the contents of the internal clipboard into this image. If there is a selection the same size as the image on the clipboard, the image is inserted into that selection, otherwise the selection is inserted into the center of the image.

• paste

  public void paste​(int x, int y)
  Inserts the contents of the internal clipboard at the specified location, without updating the display.

• paste

  public void paste​(int x, int y, java.lang.String mode)
  Copies the contents of the internal clipboard to the specified location using the specified transfer mode ("Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide"). The display is not updating.

• getClipboard

  public static ImagePlus getClipboard()
  Returns the internal clipboard or null if the internal clipboard is empty.

• resetClipboard

  public static void resetClipboard()
  Clears the internal clipboard.

• copyToSystem

  public void copyToSystem()
  Copies the contents of the current selection, or the entire image if there is no selection, to the system clipboard.

• notifyListeners

  protected void notifyListeners​(int id)

• addImageListener

  public static void addImageListener​(ImageListener listener)

• removeImageListener

  public static void removeImageListener​(ImageListener listener)

• getListeners

  public static java.util.Vector getListeners()

• logImageListeners

  public static void logImageListeners()
  For debug purposes, writes all registered (and possibly, forgotten) ImageListeners to the log window

• setOpenAsHyperStack

  public void setOpenAsHyperStack​(boolean openAsHyperStack)

• getOpenAsHyperStack

  public boolean getOpenAsHyperStack()

• isComposite

  public boolean isComposite()
  Returns true if this is a CompositeImage.

• getCompositeMode

  public int getCompositeMode()
  Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.

• setDisplayRange

  public void setDisplayRange​(double min, double max)
  Sets the display range of the current channel. With non-composite images it is identical to ip.setMinAndMax(min, max). Call updateAndDraw() to update the display.

• getDisplayRangeMin

  public double getDisplayRangeMin()
  Returns the display range minimum of the current channel.
  See Also: ImageProcessor.getMin(), getLuts()

• getDisplayRangeMax

  public double getDisplayRangeMax()
  Returns the display range maximum of the current channel.
  See Also: ImageProcessor.getMax(), getLuts()

• setDisplayRange

  public void setDisplayRange​(double min, double max, int channels)
  Sets the display range of specified channels in an RGB image, where 4=red, 2=green, 1=blue, 6=red+green, etc. With non-RGB images, this method is identical to setDisplayRange(min, max). This method is used by the Image/Adjust/Color Balance tool .

• resetDisplayRange

  public void resetDisplayRange()

• setDefaultDisplayRange

  public void setDefaultDisplayRange​(double min, double max)

• setAutoThreshold

  public void setAutoThreshold​(java.lang.String method)
  Uses the specified method to set the threshold levels of this image. Use AutoThresholder.getMethods() to get a list of the available methods. Add " dark" to the method name if the image has a dark background. Add " 16-bit" to use the full 16-bit histogram when calculating the threshold of 16-bit images. Add " stack" to use the histogram of the entire stack when calculating the threshold.

• isThreshold

  public boolean isThreshold()
  Returns 'true' if this image is thresholded.
  See Also: ImageProcessor.isThreshold()

• setDefault16bitRange

  public static void setDefault16bitRange​(int bitDepth)
  Set the default 16-bit display range, where 'bitDepth' must be 0 (auto-scaling), 8 (0-255), 10 (0-1023), 12 (0-4095, 14 (0-16383), 15 (0-32767) or 16 (0-65535).

• getDefault16bitRange

  public static int getDefault16bitRange()
  Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 14, 15 or 16.

• updatePosition

  public void updatePosition​(int c, int z, int t)

• flatten

  public ImagePlus flatten()
  Returns a "flattened" version of this image, or stack slice, in RGB format.

• flattenStack

  public void flattenStack()
  Flattens all slices of this stack or HyperStack.
  
  Throws: java.lang.UnsupportedOperationException - if this image
  does not have an overlay and the RoiManager overlay is null.
  Non-RGB stacks are converted to RGB.
  Copied from OverlayCommands and modified by Marcel Boeglin on 2014.01.08 to work with HyperStacks.

• tempOverlay

  public boolean tempOverlay()

• setLut

  public void setLut​(LUT lut)
  Assigns a LUT (lookup table) to this image.
  See Also: Opener.openLut(java.lang.String)

• setOverlay

  public void setOverlay​(Overlay overlay)
  Installs a list of ROIs that will be drawn on this image as a non-destructive overlay.
  See Also: Roi.setStrokeColor(java.awt.Color), Roi.setStrokeWidth(float), Roi.setFillColor(java.awt.Color), Roi.setLocation(int, int), Roi.setNonScalable(boolean)

• setOverlay

  public void setOverlay​(java.awt.Shape shape, java.awt.Color color, java.awt.BasicStroke stroke)
  Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image.
  See Also: setOverlay(ij.gui.Overlay), Roi.setStrokeColor(java.awt.Color), Roi.setStrokeWidth(float)

• setOverlay

  public void setOverlay​(Roi roi, java.awt.Color strokeColor, int strokeWidth, java.awt.Color fillColor)
  Creates an Overlay from the specified ROI, and assigns it to this image.
  See Also: setOverlay(ij.gui.Overlay)

• getOverlay

  public Overlay getOverlay()
  Returns the current overly, or null if this image does not have an overlay.

• setHideOverlay

  public void setHideOverlay​(boolean hide)

• getHideOverlay

  public boolean getHideOverlay()

• toggleOverlay

  public boolean toggleOverlay()

• setAntialiasRendering

  public void setAntialiasRendering​(boolean antialiasRendering)
  Enable/disable use of antialiasing by the flatten() method.

• clone

  public java.lang.Object clone()
  Returns a shallow copy of this ImagePlus.
  Overrides: clone in class java.lang.Object

• plotHistogram

  public PlotWindow plotHistogram()
  Plots a 256 bin histogram of this image and returns the PlotWindow.

• plotHistogram

  public PlotWindow plotHistogram​(int bins)
  Plots a histogram of this image using the specified number of bins and returns the PlotWindow.

• toString

  public java.lang.String toString() Overrides: toString in class java.lang.Object

• setIJMenuBar

  public void setIJMenuBar​(boolean b)

• setIJMenuBar

  public boolean setIJMenuBar()

• hasImageStack

  public boolean hasImageStack()
  Returns 'true' if this ImagePlus contains an ImageStack.
  See Also: getStackSize(), getNChannels(), getNSlices(), getNFrames(), getNDimensions()

• isStack

  public boolean isStack()
  Deprecated.

  Replaced by ImagePlus.hasImageStack()

• setPlot

  public void setPlot​(Plot plot)

• getPlot

  public Plot getPlot()

• getImageProperties

  public java.util.Properties getImageProperties()

• isRGB

  public boolean isRGB()

• setBorderColor

  public void setBorderColor​(java.awt.Color borderColor)

• windowActivated

  public boolean windowActivated()