ImagePlus (ImageJ 1.51r API)

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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, LutLoader, MacClipboard, PGM_Reader

public class ImagePlus
extends Object
implements ImageObserver, Measurements, Cloneable
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
`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`
`boolean`	`typeSet`
`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
`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, Image img)` Constructs an ImagePlus from an Image or BufferedImage.
`ImagePlus(String title, ImageProcessor ip)` Constructs an ImagePlus from an ImageProcessor.
`ImagePlus(String title, ImageStack stack)` Constructs an ImagePlus from a stack.

Method Summary
`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.
`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`	`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(Image img)` Replaces the image, if any, with the one specified.
`void`	`setImage(ImagePlus imp)` Replaces this image with the specified ImagePlus.
`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(Rectangle r)` 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`	`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

typeSet

public boolean typeSet

Constructor Detail

ImagePlus

public ImagePlus()

Constructs an uninitialized ImagePlus.

ImagePlus

public ImagePlus(String title,
                 Image img)

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 img)

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.

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()

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ij Class ImagePlus

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lock

lockSilently

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draw

draw

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setActiveChannels

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getLuts

repaintWindow

updateAndRepaintWindow

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hide

close

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show

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getRawStatistics

getStatistics

getStatistics

getStatistics

getTitle

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setTitle

ij
Class ImagePlus