Module ij
Package ij

Class ImagePlus

java.lang.Object
ij.ImagePlus
All Implemented Interfaces:
Measurements, ImageObserver, Cloneable
Direct Known Subclasses:
BMP_Reader, CompositeImage, DICOM, FITS_Reader, GIF_Reader, HistogramPlot, LutLoader, PGM_Reader

public class ImagePlus extends Object implements ImageObserver, Measurements, Cloneable
An ImagePlus contain an ImageProcessor (2D image) or an ImageStack (3D, 4D or 5D image). It also includes metadata (spatial calibration and possibly the directory/file where it was read from). The ImageProcessor contains the pixel data (8-bit, 16-bit, float or RGB) of the 2D image and some basic methods to manipulate it. An ImageStack is essentually a list ImageProcessors of same type and size.
See Also:
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    boolean
    True if any changes have been made to this image.
    protected static final int
     
    static final int
    8-bit indexed color
    static final int
    32-bit RGB color
    protected boolean
     
    protected int
     
    protected boolean
     
    static final String
    Title of image used by Flatten command
    static final int
    16-bit grayscale (unsigned)
    static final int
    32-bit floating-point grayscale
    static final int
    8-bit grayscale (unsigned)
    protected int
     
    protected Image
     
    protected ImageProcessor
     
    protected boolean
     
    protected int
     
    protected int
     
    protected int
     
    protected static final int
     
    protected Roi
     
    protected static final int
     
    boolean
     
    protected static final int
     
    protected int
     
    protected ImageWindow
     

    Fields inherited from interface java.awt.image.ImageObserver

    ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
  • Constructor Summary

    Constructors
    Constructor
    Description
    Constructs an uninitialized ImagePlus.
    ImagePlus(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(String title, ImageStack stack)
    Constructs an ImagePlus from a stack.
    Constructs an ImagePlus from an ImageProcessor.
    ImagePlus(String title, Image image)
    Constructs an ImagePlus from an Image or BufferedImage.
  • Method Summary

    Modifier and Type
    Method
    Description
    static void
     
    Returns a shallow copy of this ImagePlus.
    void
    Closes this image and sets the ImageProcessor to null.
    int[]
    Converts the stack index 'n' (one-based) into a hyperstack position (channel, slice, frame).
    Extract pixels as an ImageProcessor from a single band of a BufferedImage.
    void
    Copies the contents of the current selection, or the entire image if there is no selection, to the internal clipboard.
    void
    copy(boolean cut)
    Copies the contents of the current selection to the internal clipboard.
    void
    Used internally.
    void
    Copies the calibration of the specified image to this image.
    void
    Copies the contents of the current selection, or the entire image if there is no selection, to the system clipboard.
    Returns an empty image stack that has the same width, height and color table as this image.
    createHyperStack(String title, int channels, int slices, int frames, int bitDepth)
    This method has been replaced by IJ.createHyperStack().
    Returns a new ImagePlus with this image's attributes (e.g.
    Creates a LookUpTable object that corresponds to this image.
    void
    createNewRoi(int sx, int sy)
    Starts the process of creating a new selection, where sx and sy are the starting screen coordinates.
    Returns an 8-bit binary (foreground=255, background=0) ROI or overlay mask that has the same dimensions as this image.
    Returns an 8-bit binary threshold mask (foreground=255, background=0) that has the same dimensions as this image.
    Returns a copy this image or stack slice, cropped if there is an ROI.
    crop(Roi[] rois)
    Multi-roi cropping with default "slice" option.
    crop(Roi[] rois, String options)
    Returns an array of cropped images based on the provided list of rois.
    crop(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").
    void
    cropAndSave(Roi[] rois, String directory, 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".
    void
    cut()
    Copies the contents of the current selection to the internal clipboard and then clears the selection.
    void
    Deletes the current region of interest.
    void
    Draws the image.
    void
    draw(int x, int y, int width, int height)
    Draws image and roi outline using a clip rect.
    Returns a copy of this image or stack.
    Returns a "flattened" version of this image, or stack slice, in RGB format.
    void
    Flattens all slices of this stack or HyperStack.
    void
    Sets the ImageProcessor, Roi, AWT Image and stack image arrays to null.
    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().
    int
    Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth is unknown.
    Returns a copy of this image as an 8-bit or RGB BufferedImage.
    int
    Returns the number of bytes per pixel.
    int
    Returns the current hyperstack channel position.
    Returns this image's calibration.
    Returns the ImageCanvas being used to display this image, or null.
    int
     
    Returns a reference to the current ImageProcessor.
    static ImagePlus
    Returns the internal clipboard or null if the internal clipboard is empty.
    int
    Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.
    int
    Returns the current stack index (one-based) or 1 if this is a single image.
    static int
    Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 14, 15 or 16.
    int[]
    Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.
    int[]
    getDimensions(boolean varify)
     
    int
    Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a composite color image, or 0 if it not.
    double
    Returns the display range maximum of the current channel.
    double
    Returns the display range minimum of the current channel.
    Returns a FileInfo object containing information, including the pixel array, needed to save this image.
    int
     
    Returns the system-wide calibration, or null.
    int
    Returns the height of this image in pixels.
    boolean
     
    int
    Returns this image's unique numeric ID.
    Returns this image as a AWT image.
     
    Returns the base image stack.
    int
    If this is a stack, returns the actual number of images in the stack, else returns 1.
    Returns the "Info" property string, or null if it is not found.
    static Vector
     
    Returns this image's local calibration, ignoring the "Global" calibration flag.
    getLocationAsString(int x, int y)
    Converts the current cursor location to a string.
    LUT[]
    Returns an array containing the lookup tables used by this image, one per channel, or an empty array if this is an RGB image.
    For images with irregular ROIs, returns a byte mask, otherwise, returns null.
    int
    Returns the number of channels.
    int
    Returns the number of dimensions (2, 3, 4 or 5).
    int
    Returns the number of frames (time-points).
    int
    Returns the image depth (number of z-slices).
    double
    Returns the numeric property associated with the specified key or NaN if the property is not found.
    double
    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.
    boolean
     
    Returns the FileInfo object that was used to open this image.
    Returns the current overly, or null if this image does not have an overlay.
    int[]
    getPixel(int x, int y)
    Returns the pixel value at (x,y) as a 4 element array.
     
    Returns a reference to the current ImageProcessor.
    Returns as a string the image property associated with the specified key or null if the property is not found.
    Returns this image's Properties.
    Used for saving string properties in TIFF header.
    Returns the property associated with 'key', or null if it is not found.
    Returns information displayed by Image/Show Info command.
     
    Returns the current selection, or null if there is no selection.
    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.
    double
    Returns the size of this image in bytes.
    int
     
    Returns the image stack.
    int
    getStackIndex(int channel, int slice, int frame)
    Returns that stack index (one-based) corresponding to the specified position.
    int
    Returns the number of stack images.
    long
    Returns the time in milliseconds when startTiming() was last called.
    This is a version of getGlobalCalibration() that can be called from a static context.
    Get calibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation and mode.
    getStatistics(int mOptions)
    Returns an ImageStatistics object generated using the specified measurement options.
    getStatistics(int mOptions, int nBins)
    Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.
    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.
    Returns the string value from the "Info" property string associated with 'key', or null if the key is not found.
    int
    Returns the current hyperstack frame position.
    Returns the image name.
    int
    Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
    int
    Returns the width of this image in pixels.
    Returns the ImageWindow that is being used to display this image.
    int
    Returns the current hyperstack slice position.
    boolean
    Returns 'true' if this ImagePlus contains an ImageStack.
    void
    Closes the window, if any, that is displaying this image.
    boolean
    imageUpdate(Image img, int flags, int x, int y, int w, int h)
    Used by ImagePlus to monitor loading of images.
    boolean
    Returns true if this is a CompositeImage.
    boolean
    Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.
    boolean
    Returns 'true' if this image has more than three dimensions.
    boolean
    Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.
    boolean
    Returns 'true' if the image is locked.
    boolean
    Returns 'true' if the image was locked on another thread.
    boolean
     
    boolean
     
    boolean
    Deprecated.
    Replaced by ImagePlus.hasImageStack()
    boolean
    Returns 'true' if this image is thresholded.
    boolean
    Returns true if this image is currently being displayed in a window.
    void
    Deletes the current region of interest.
    void
     
    boolean
    Locks the image so other threads can test to see if it is in use.
    boolean
    Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.
    static void
    For debug purposes, writes all registered (and possibly, forgotten) ImageListeners to the log window
    void
    mouseMoved(int x, int y)
    Displays the cursor coordinates and pixel value in the status bar.
    protected void
     
    boolean
     
    void
    Inserts the contents of the internal clipboard into this image.
    void
    paste(int x, int y)
    Inserts the contents of the internal clipboard at the specified location, without updating the display.
    void
    paste(int x, int y, 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").
    Plots a 256 bin histogram of this image and returns the PlotWindow.
    plotHistogram(int bins)
    Plots a histogram of this image using the specified number of bins and returns the PlotWindow.
    static void
     
    void
    Removes the spatial scaling of this image.
    void
    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.
    static void
    Clears the internal clipboard.
    void
     
    void
    Deletes the current region of interest.
    void
     
    resize(int dstWidth, int dstHeight, int dstDepth, String options)
    Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
    resize(int dstWidth, int dstHeight, String options)
    Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.
    void
     
    void
    Implements the File/Revert command.
    void
     
    void
    Called by ImageWindow.windowActivated(); to end waiting in waitTillActivated.
    void
    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.
    void
    setAntialiasRendering(boolean antialiasRendering)
    Enable/disable use of antialiasing by the flatten() method.
    void
    Uses the specified method to set the threshold levels of this image.
    void
    setBorderColor(Color borderColor)
     
    void
    setC(int channel)
    Sets the hyperstack channel position (one based).
    void
    Sets this image's calibration.
    void
    Sets current foreground color.
    void
    Called by new StackWindow(ImagePlus) before showing the StackWindow, to prepare for waitTillActivated().
    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).
    void
    setDefaultDisplayRange(double min, double max)
     
    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.
    void
    setDisplayMode(int mode)
    Sets the display mode of composite color images, where 'mode' should be IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE.
    void
    setDisplayRange(double min, double max)
    Sets the display range of the current channel.
    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.
    void
    Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo().
    void
    Sets the system-wide calibration.
    void
    setHideOverlay(boolean hide)
     
    void
    setIgnoreFlush(boolean ignoreFlush)
     
    void
    setIgnoreGlobalCalibration(boolean ignoreGlobalCalibration)
     
    boolean
     
    void
    setIJMenuBar(boolean b)
     
    void
    Replaces this image with the specified ImagePlus.
    void
    setImage(Image image)
    Replaces the image, if any, with the one specified.
    void
    setLut(LUT lut)
    Assigns a LUT (lookup table) to this image.
    void
    setOpenAsHyperStack(boolean openAsHyperStack)
     
    void
    Installs a list of ROIs that will be drawn on this image as a non-destructive overlay.
    void
    setOverlay(Roi roi, Color strokeColor, int strokeWidth, Color fillColor)
    Creates an Overlay from the specified ROI, and assigns it to this image.
    void
    setOverlay(Shape shape, Color color, BasicStroke stroke)
    Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image.
    void
    setPlot(Plot plot)
     
    void
    setPosition(int n)
    Set the current hyperstack position based on the stack index 'n' (one-based).
    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.
    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.
    void
    Replaces the ImageProcessor with the one specified and updates the display.
    void
    Replaces the ImageProcessor with the one specified and updates the display.
    void
    setProp(String key, double value)
    Saves a persistent numeric propery.
    void
    setProp(String key, String value)
    Adds a key-value pair to this image's string properties.
    void
    Creates a set of image properties from an array of strings.
    void
    setProperty(String key, Object value)
    Adds a key-value pair to this image's properties.
    void
    setRoi(int x, int y, int width, int height)
    Creates a rectangular selection.
    void
    setRoi(Roi newRoi)
    Assigns the specified ROI to this image and displays it.
    void
    setRoi(Roi newRoi, boolean updateDisplay)
    Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.
    void
    Creates a rectangular selection.
    void
    setSlice(int n)
    Displays the specified stack image, where 1<=n<=stackSize.
    void
    Displays the specified stack image (1<=n<=stackSize) without updating the display.
    void
    Replaces the image with the specified stack and updates the display.
    void
    setStack(ImageStack newStack, int channels, int slices, int frames)
     
    void
    setStack(String title, ImageStack newStack)
    Replaces the image with the specified stack and updates the display.
    void
    setT(int frame)
    Sets the hyperstack frame position (one based).
    void
     
    void
    Sets the image name.
    protected void
    setType(int type)
     
    void
     
    void
    This method should only be called from an ImageWindow.
    void
    setZ(int slice)
    Sets the hyperstack slice position (one based).
    void
    Opens a window to display this image and clears the status bar.
    void
    show(String statusMessage)
    Opens a window to display this image and displays 'statusMessage' in the status bar.
    void
    Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation.
    boolean
     
    boolean
     
     
    void
    Frees RAM by setting the snapshot (undo) buffer in the current ImageProcessor to null.
    void
    Unlocks the image.
    void
    Updates this image from the pixel data in its associated ImageProcessor, then displays it.
    void
    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.
    void
    Updates this image from the pixel data in its associated ImageProcessor, then displays it.
    void
    ImageCanvas.paint() calls this method when the ImageProcessor has generated a new image.
    void
    updatePosition(int c, int z, int t)
     
    void
    Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar.
    void
    Use to update the image when the underlying virtual stack changes.
    void
    Waits until the image window becomes activated.
    boolean
     

    Methods inherited from class java.lang.Object

    equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
  • Field Details

    • GRAY8

      public static final int GRAY8
      8-bit grayscale (unsigned)
      See Also:
    • GRAY16

      public static final int GRAY16
      16-bit grayscale (unsigned)
      See Also:
    • GRAY32

      public static final int GRAY32
      32-bit floating-point grayscale
      See Also:
    • COLOR_256

      public static final int COLOR_256
      8-bit indexed color
      See Also:
    • COLOR_RGB

      public static final int COLOR_RGB
      32-bit RGB color
      See Also:
    • flattenTitle

      public static final String flattenTitle
      Title of image used by Flatten command
      See Also:
    • changes

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

      protected 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:
    • CLOSED

      protected static final int CLOSED
      See Also:
    • UPDATED

      protected static final int UPDATED
      See Also:
    • SAVED

      protected static final int SAVED
      See Also:
    • 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 Details

    • ImagePlus

      public ImagePlus()
      Constructs an uninitialized ImagePlus.
    • ImagePlus

      public ImagePlus(String title, 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(String title, ImageProcessor ip)
      Constructs an ImagePlus from an ImageProcessor.
    • ImagePlus

      public ImagePlus(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(String title, ImageStack stack)
      Constructs an ImagePlus from a stack.
  • Method Details

    • 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(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:
    • 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(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 Image getImage()
      Returns this image as a AWT image.
    • getBufferedImage

      public BufferedImage getBufferedImage()
      Returns a copy of this image as an 8-bit or RGB BufferedImage.
      See Also:
    • getID

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

      public void setImage(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(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(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(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(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

      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

      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:
    • 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

      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:
    • getRawStatistics

      public ImageStatistics getRawStatistics()
    • getStatistics

      public ImageStatistics getStatistics(int mOptions)
      Returns an ImageStatistics object generated using the specified measurement options.
      See Also:
    • 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 String getTitle()
      Returns the image name.
    • getShortTitle

      public 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(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

      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 String getStringProperty(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

      public double getNumericProperty(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:
    • setProp

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

      public String getProp(String key)
      Returns as a string the image property associated with the specified key or null if the property is not found.
      See Also:
    • getNumericProp

      public double getNumericProp(String key)
      Returns the numeric property associated with the specified key or NaN if the property is not found.
      See Also:
    • getPropertiesAsArray

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

      public String getPropsInfo()
      Returns information displayed by Image/Show Info command.
    • setProperties

      public void setProperties(String[] props)
      Creates a set of image properties from an array of strings.
      See Also:
    • getInfoProperty

      public String getInfoProperty()
      Returns the "Info" property string, or null if it is not found.
      See Also:
    • getProperty

      public Object getProperty(String key)
      Returns the property associated with 'key', or null if it is not found.
      See Also:
    • setProperty

      public void setProperty(String key, 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:
    • getProperties

      public 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:
    • 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:
    • 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(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:
    • 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:
    • imageUpdate

      public boolean imageUpdate(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 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:
    • resize

      public ImagePlus resize(int dstWidth, int dstHeight, 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, 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:
    • crop

      public ImagePlus crop(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:
    • crop

      public ImagePlus[] crop(Roi[] rois, 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

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

      public void cropAndSave(Roi[] rois, String directory, 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(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 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, 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 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:
    • getDisplayRangeMax

      public double getDisplayRangeMax()
      Returns the display range maximum of the current channel.
      See Also:
    • 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(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:
    • 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:
      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:
    • 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:
    • setOverlay

      public void setOverlay(Shape shape, Color color, BasicStroke stroke)
      Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image.
      See Also:
    • setOverlay

      public void setOverlay(Roi roi, Color strokeColor, int strokeWidth, Color fillColor)
      Creates an Overlay from the specified ROI, and assigns it to this image.
      See Also:
    • 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 Object clone()
      Returns a shallow copy of this ImagePlus.
      Overrides:
      clone in class 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 String toString()
      Overrides:
      toString in class 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:
    • isStack

      public boolean isStack()
      Deprecated.
      Replaced by ImagePlus.hasImageStack()
    • setPlot

      public void setPlot(Plot plot)
    • getPlot

      public Plot getPlot()
    • getImageProperties

      public Properties getImageProperties()
    • isRGB

      public boolean isRGB()
    • setBorderColor

      public void setBorderColor(Color borderColor)
    • windowActivated

      public boolean windowActivated()