ImagePlus (ImageJ API)

java.lang.Object
- ij.ImagePlus

All Implemented Interfaces:

Measurements, ImageObserver, Cloneable

Direct Known Subclasses:

BMP_Reader, CompositeImage, DICOM, FITS_Reader, GIF_Reader, 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:

ImageProcessor, ImageStack, ImageWindow, ImageCanvas

Field Summary

Fields
Modifier and Type	Field	Description
`boolean`	`changes`	True if any changes have been made to this image.
`protected static int`	`CLOSED`
`static int`	`COLOR_256`	8-bit indexed color
`static int`	`COLOR_RGB`	32-bit RGB color
`protected boolean`	`compositeImage`
`protected int`	`currentSlice`
`protected boolean`	`dimensionsSet`
`static String`	`flattenTitle`	Title of image used by Flatten command
`static int`	`GRAY16`	16-bit grayscale (unsigned)
`static int`	`GRAY32`	32-bit floating-point grayscale
`static int`	`GRAY8`	8-bit grayscale (unsigned)
`protected int`	`height`
`protected Image`	`img`
`protected ImageProcessor`	`ip`
`protected boolean`	`locked`
`protected int`	`nChannels`
`protected int`	`nFrames`
`protected int`	`nSlices`
`protected static int`	`OPENED`
`protected Roi`	`roi`
`boolean`	`setIJMenuBar`
`protected static int`	`UPDATED`
`protected int`	`width`
`protected ImageWindow`	`win`

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields inherited from interface ij.measure.Measurements
ADD_TO_OVERLAY, ALL_STATS, AREA, AREA_FRACTION, CENTER_OF_MASS, CENTROID, CIRCULARITY, ELLIPSE, FERET, INTEGRATED_DENSITY, INVERT_Y, KURTOSIS, LABELS, LIMIT, MAX_STANDARDS, MEAN, MEDIAN, MIN_MAX, MODE, NaN_EMPTY_CELLS, PERIMETER, RECT, SCIENTIFIC_NOTATION, SHAPE_DESCRIPTORS, SKEWNESS, SLICE, STACK_POSITION, STD_DEV

Constructor Summary

Constructors
Constructor	Description
`ImagePlus()`	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.
`ImagePlus(String title, ImageProcessor ip)`	Constructs an ImagePlus from an ImageProcessor.
`ImagePlus(String title, Image image)`	Constructs an ImagePlus from an Image or BufferedImage.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`static void`	`addImageListener(ImageListener listener)`
`Object`	`clone()`	Returns a shallow copy of this ImagePlus.
`void`	`close()`	Closes this image and sets the ImageProcessor to null.
`int[]`	`convertIndexToPosition(int n)`	Converts the stack index 'n' (one-based) into a hyperstack position (channel, slice, frame).
`void`	`copy()`	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`	`copyAttributes(ImagePlus imp)`	Copies attributes (name, ID, calibration, path, plot) of the specified image to this image.
`void`	`copyScale(ImagePlus imp)`	Copies the calibration of the specified image to this image.
`ImageStack`	`createEmptyStack()`	Returns an empty image stack that has the same width, height and color table as this image.
`ImagePlus`	`createHyperStack(String title, int channels, int slices, int frames, int bitDepth)`	This method has been replaced by IJ.createHyperStack().
`ImagePlus`	`createImagePlus()`	Returns a new ImagePlus with this image's attributes (e.g.
`LookUpTable`	`createLut()`	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.
`ByteProcessor`	`createRoiMask()`	Returns an 8-bit binary (0 and 255) ROI or overlay mask that has the same dimensions as this image.
`ByteProcessor`	`createThresholdMask()`	Returns an 8-bit binary (0 and 255) threshold mask that has the same dimensions as this image.
`ImagePlus`	`crop()`	Returns a copy this image or stack slice, cropped if there is an ROI.
`void`	`deleteRoi()`	Deletes the current region of interest.
`void`	`draw()`	Draws the image.
`void`	`draw(int x, int y, int width, int height)`	Draws image and roi outline using a clip rect.
`ImagePlus`	`duplicate()`	Returns a copy of this image or stack, cropped if there is an ROI.
`ImagePlus`	`flatten()`	Returns a "flattened" version of this image, in RGB format.
`void`	`flattenStack()`	Flattens all slices of this stack or HyperStack.
`void`	`flush()`	Sets the ImageProcessor, Roi, AWT Image and stack image arrays to null.
`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().
`int`	`getBitDepth()`	Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth is unknown.
`BufferedImage`	`getBufferedImage()`	Returns a copy of this image as an 8-bit or RGB BufferedImage.
`int`	`getBytesPerPixel()`	Returns the number of bytes per pixel.
`int`	`getC()`	Returns the current hyperstack channel position.
`Calibration`	`getCalibration()`	Returns this image's calibration.
`ImageCanvas`	`getCanvas()`	Returns the ImageCanvas being used to display this image, or null.
`int`	`getChannel()`
`ImageProcessor`	`getChannelProcessor()`	Returns a reference to the current ImageProcessor.
`static ImagePlus`	`getClipboard()`	Returns the internal clipboard or null if the internal clipboard is empty.
`int`	`getCompositeMode()`	Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.
`int`	`getCurrentSlice()`	Returns the current stack index (one-based) or 1 if this is a single image.
`static int`	`getDefault16bitRange()`	Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 14, 15 or 16.
`int[]`	`getDimensions()`	Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.
`int[]`	`getDimensions(boolean varify)`
`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.
`double`	`getDisplayRangeMax()`
`double`	`getDisplayRangeMin()`
`FileInfo`	`getFileInfo()`	Returns a FileInfo object containing information, including the pixel array, needed to save this image.
`int`	`getFrame()`
`Calibration`	`getGlobalCalibration()`	Returns the system-wide calibration, or null.
`int`	`getHeight()`
`boolean`	`getHideOverlay()`
`int`	`getID()`	Returns this image's unique numeric ID.
`Image`	`getImage()`	Returns this image as a AWT image.
`ImageStack`	`getImageStack()`	Returns the base image stack.
`int`	`getImageStackSize()`	If this is a stack, returns the actual number of images in the stack, else returns 1.
`String`	`getInfoProperty()`	Returns the "Info" property string, or null if it is not found.
`Calibration`	`getLocalCalibration()`	Returns this image's local calibration, ignoring the "Global" calibration flag.
`String`	`getLocationAsString(int x, int y)`	Converts the current cursor location to a string.
`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.
`ImageProcessor`	`getMask()`	For images with irregular ROIs, returns a byte mask, otherwise, returns null.
`int`	`getNChannels()`	Returns the number of channels.
`int`	`getNDimensions()`	Returns the number of dimensions (2, 3, 4 or 5).
`int`	`getNFrames()`	Returns the number of frames (time-points).
`int`	`getNSlices()`	Returns the image depth (number of z-slices).
`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.
`boolean`	`getOpenAsHyperStack()`
`FileInfo`	`getOriginalFileInfo()`	Returns the FileInfo object that was used to open this image.
`Overlay`	`getOverlay()`	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.
`ImageProcessor`	`getProcessor()`	Returns a reference to the current ImageProcessor.
`String`	`getProp(String key)`	Deprecated.
`Properties`	`getProperties()`	Returns this image's Properties.
`Object`	`getProperty(String key)`	Returns the property associated with 'key', or null if it is not found.
`ImageStatistics`	`getRawStatistics()`
`Roi`	`getRoi()`	Returns the current selection, or null if there is no selection.
`String`	`getShortTitle()`	Returns a shortened version of image name that does not include spaces or a file name extension.
`int`	`getSlice()`
`ImageStack`	`getStack()`	Returns the image stack.
`int`	`getStackIndex(int channel, int slice, int frame)`	Returns that stack index (one-based) corresponding to the specified position.
`int`	`getStackSize()`	If this is a stack, returns the number of slices, else returns 1.
`long`	`getStartTime()`	Returns the time in milliseconds when startTiming() was last called.
`static Calibration`	`getStaticGlobalCalibration()`	This is a version of getGlobalCalibration() that can be called from a static context.
`ImageStatistics`	`getStatistics()`	Get calibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation and mode.
`ImageStatistics`	`getStatistics(int mOptions)`	Returns an ImageStatistics object generated using the specified measurement options.
`ImageStatistics`	`getStatistics(int mOptions, int nBins)`	Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.
`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.
`String`	`getStringProperty(String key)`	Returns the string value from the "Info" property string associated with 'key', or null if the key is not found.
`int`	`getT()`	Returns the current hyperstack frame position.
`String`	`getTitle()`	Returns the image name.
`int`	`getType()`	Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).
`int`	`getWidth()`
`ImageWindow`	`getWindow()`	Returns the ImageWindow that is being used to display this image.
`int`	`getZ()`	Returns the current hyperstack slice position.
`void`	`hide()`	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`	`isComposite()`	Returns true if this is a CompositeImage.
`boolean`	`isDisplayedHyperStack()`	Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.
`boolean`	`isHyperStack()`	Returns 'true' if this image is a hyperstack.
`boolean`	`isInvertedLut()`	Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.
`boolean`	`isLocked()`	Returns 'true' if the image is locked.
`boolean`	`isProcessor()`
`boolean`	`isStack()`
`boolean`	`isThreshold()`	Returns 'true' if this image is thresholded.
`boolean`	`isVisible()`	Returns true if this image is currently being displayed in a window.
`void`	`killRoi()`	Deletes the current region of interest.
`void`	`killStack()`
`boolean`	`lock()`	Locks the image so other threads can test to see if it is in use.
`boolean`	`lockSilently()`	Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.
`void`	`mouseMoved(int x, int y)`	Displays the cursor coordinates and pixel value in the status bar.
`protected void`	`notifyListeners(int id)`
`void`	`paste()`	Inserts the contents of the internal clipboard into the active image.
`static void`	`removeImageListener(ImageListener listener)`
`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.
`static void`	`resetClipboard()`	Clears the internal clipboard.
`void`	`resetDisplayRange()`
`void`	`resetStack()`
`void`	`restoreRoi()`
`void`	`revert()`	Implements the File/Revert command.
`void`	`saveRoi()`
`void`	`setActivated()`	Called by ImageWindow.windowActivated().
`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.
`void`	`setAntialiasRendering(boolean antialiasRendering)`	Enable/disable use of antialiasing by the flatten() method.
`void`	`setC(int channel)`	Sets the hyperstack channel position (one based).
`void`	`setCalibration(Calibration cal)`	Sets this image's calibration.
`void`	`setColor(Color c)`	Sets current foreground color.
`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`	`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`	`setFileInfo(FileInfo fi)`	Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo().
`void`	`setGlobalCalibration(Calibration global)`	Sets the system-wide calibration.
`void`	`setHideOverlay(boolean hide)`
`void`	`setIgnoreFlush(boolean ignoreFlush)`
`void`	`setIgnoreGlobalCalibration(boolean ignoreGlobalCalibration)`
`boolean`	`setIJMenuBar()`
`void`	`setIJMenuBar(boolean b)`
`void`	`setImage(ImagePlus imp)`	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`	`setOverlay(Overlay overlay)`	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`	`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`	`setProcessor(ImageProcessor ip)`	Replaces the ImageProcessor with the one specified and updates the display.
`void`	`setProcessor(String title, ImageProcessor ip)`	Replaces the ImageProcessor with the one specified and updates the display.
`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`	`setRoi(Rectangle r)`	Creates a rectangular selection.
`void`	`setSlice(int n)`	Displays the specified stack image, where 1<=n<=stackSize.
`void`	`setSliceWithoutUpdate(int n)`	Displays the specified stack image (1<=n<=stackSize) without updating the display.
`void`	`setStack(ImageStack stack)`	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`	`setTitle(String title)`	Sets the image name.
`protected void`	`setType(int type)`
`void`	`setWindow(ImageWindow win)`	This method should only be called from an ImageWindow.
`void`	`setZ(int slice)`	Sets the hyperstack slice position (one based).
`void`	`show()`	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`	`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.
`String`	`toString()`
`void`	`trimProcessor()`	Frees RAM by setting the snapshot (undo) buffer in the current ImageProcessor to null.
`void`	`unlock()`	Unlocks the image.
`void`	`updateAndDraw()`	Updates this image from the pixel data in its associated ImageProcessor, then displays it.
`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.
`void`	`updateChannelAndDraw()`	Updates this image from the pixel data in its associated ImageProcessor, then displays it.
`void`	`updateImage()`	ImageCanvas.paint() calls this method when the ImageProcessor has generated a new image.
`void`	`updatePosition(int c, int z, int t)`
`void`	`updateStatusbarValue()`	Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar.

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- 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 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 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
  - 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(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 Detail
  - lock
```
public boolean lock()
```
    Locks the image so other threads can test to see if it is in use. 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.
  - 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.
  - 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).
  - 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:
    
    getNChannels(), isComposite(), getCompositeMode()
  - 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.
  - setActivated
```
public void setActivated()
```
    Called by ImageWindow.windowActivated().
  - 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:
    
    ShortProcessor.get16BitBufferedImage()
  - 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.
  - 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(), createThresholdMask()
  - createRoiMask
```
public ByteProcessor createRoiMask()
```
    Returns an 8-bit binary (0 and 255) ROI or overlay mask that has the same dimensions as this image.
    
    See Also:
    
    Roi.getMask()
  - createThresholdMask
```
public ByteProcessor createThresholdMask()
```
    Returns an 8-bit binary (0 and 255) threshold mask that has the same dimensions as this image.
    
    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);
                
```
    See Also:
    
    getAllStatistics(), getRawStatistics(), ImageProcessor.getStats(), ImageStatistics, ImageStatistics.getStatistics(ij.process.ImageProcessor)
  - 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().
  - getRawStatistics
```
public ImageStatistics getRawStatistics()
```
  - getStatistics
```
public ImageStatistics getStatistics(int mOptions)
```
    Returns an ImageStatistics object generated using the specified measurement options.
    
    See Also:
    
    ImageStatistics, Measurements
  - getStatistics
```
public ImageStatistics getStatistics(int mOptions,
                                     int nBins)
```
    Returns an ImageStatistics object generated using the specified measurement options and histogram bin count. Note: except for float images, the number of bins is currently fixed at 256.
  - 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. Note: for 8-bit and RGB images, the number of bins is fixed at 256 and the histogram range is always 0-255.
  - getTitle
```
public String getTitle()
```
    Returns the image name.
  - getShortTitle
```
public String getShortTitle()
```
    Returns a shortened version of image name that does not include spaces or a file name extension.
  - setTitle
```
public void setTitle(String title)
```
    Sets the image name.
  - getWidth
```
public int getWidth()
```
  - getHeight
```
public int getHeight()
```
  - getStackSize
```
public int getStackSize()
```
    If this is a stack, returns the number of slices, else returns 1.
  - 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 is a hyperstack.
  - 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)
```
  - 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(java.lang.String), getInfoProperty()
  - 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:
    
    getStringProperty(java.lang.String), getInfoProperty()
  - getProp
```
public String getProp(String key)
```
    Deprecated.
    
    See Also:
    
    getStringProperty(java.lang.String)
  - getInfoProperty
```
public String getInfoProperty()
```
    Returns the "Info" property string, or null if it is not found.
  - getProperty
```
public Object getProperty(String key)
```
    Returns the property associated with 'key', or null if it is not found.
    
    See Also:
    
    getStringProperty(java.lang.String), getNumericProperty(java.lang.String), getInfoProperty()
  - 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.
  - 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:
    
    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(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.
  - killRoi
```
public void killRoi()
```
    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(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, cropped if there is an ROI.
    
    See Also:
    
    crop(), Duplicator.run(java.lang.String)
  - 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)
  - 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)
```
    Copies attributes (name, ID, calibration, path, plot) of the specified image to this image.
  - 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. Can be overridden by ImagePlus subclasses.
  - 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.
  - 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 the active 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.
  - 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.
  - notifyListeners
```
protected void notifyListeners(int id)
```
  - addImageListener
```
public static void addImageListener(ImageListener listener)
```
  - removeImageListener
```
public static void removeImageListener(ImageListener listener)
```
  - isLocked
```
public boolean isLocked()
```
    Returns 'true' if the image is locked.
  - 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).
  - getDisplayRangeMin
```
public double getDisplayRangeMin()
```
  - getDisplayRangeMax
```
public double getDisplayRangeMax()
```
  - 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()
```
  - isThreshold
```
public boolean isThreshold()
```
    Returns 'true' if this image is thresholded.
  - 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, 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
    or Java version is less than 1.6. Copied from OverlayCommands and modified by Marcel Boeglin on 2014.01.08 to work with HyperStacks.
  - 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(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(ij.gui.Overlay), Roi.setStrokeColor(java.awt.Color), Roi.setStrokeWidth(float)
  - 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:
    
    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()
```
  - 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
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - setIJMenuBar
```
public void setIJMenuBar(boolean b)
```
  - setIJMenuBar
```
public boolean setIJMenuBar()
```
  - isStack
```
public boolean isStack()
```

Class ImagePlus

Field Summary

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface ij.measure.Measurements

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

GRAY8

GRAY16

GRAY32

COLOR_256

COLOR_RGB

flattenTitle

changes

img

ip

win

roi

currentSlice

OPENED

CLOSED

UPDATED

compositeImage

width

height

locked

nChannels

nSlices

nFrames

dimensionsSet

setIJMenuBar

Constructor Detail

ImagePlus

ImagePlus

ImagePlus

ImagePlus

ImagePlus

Method Detail

lock

lockSilently

unlock

draw

draw

updateAndDraw

setDisplayMode

getDisplayMode

setActiveChannels

updateChannelAndDraw

getChannelProcessor

getLuts

repaintWindow

updateAndRepaintWindow

updateImage

hide

close

show

show

setActivated

getImage

getBufferedImage

getID

setImage

setImage

setProcessor

setProcessor

setStack

setStack

setStack

setFileInfo

getWindow

isVisible

setWindow

getCanvas

setColor

isProcessor

getProcessor

trimProcessor

getMask

createRoiMask