java.lang.Object
ij.ImagePlus
- All Implemented Interfaces:
Measurements
,ImageObserver
,Cloneable
- Direct Known Subclasses:
BMP_Reader
,CompositeImage
,DICOM
,FITS_Reader
,GIF_Reader
,HistogramPlot
,LutLoader
,PGM_Reader
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:
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
True if any changes have been made to this image.protected static final int
static final int
8-bit indexed colorstatic final int
32-bit RGB colorprotected boolean
protected int
protected boolean
static final String
Title of image used by Flatten commandstatic final int
16-bit grayscale (unsigned)static final int
32-bit floating-point grayscalestatic final int
8-bit grayscale (unsigned)protected int
protected Image
protected ImageProcessor
protected boolean
protected int
protected int
protected int
protected static final int
protected Roi
protected static final int
boolean
protected static final int
protected int
protected ImageWindow
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
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
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Constructor Summary
ConstructorsConstructorDescriptionConstructs an uninitialized ImagePlus.Constructs an ImagePlus from a TIFF, BMP, DICOM, FITS, PGM, GIF or JPRG specified by a path or from a TIFF, DICOM, GIF or JPEG specified by a URL.ImagePlus
(String title, ImageStack stack) Constructs an ImagePlus from a stack.ImagePlus
(String title, ImageProcessor ip) Constructs an ImagePlus from an ImageProcessor.Constructs an ImagePlus from an Image or BufferedImage. -
Method Summary
Modifier and TypeMethodDescriptionstatic void
addImageListener
(ImageListener listener) 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).static ImageProcessor
convertToImageProcessor
(BufferedImage img, int band) Extract pixels as an an ImageProcessor from a single band of a BufferedImage.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) Used internally.void
Copies the calibration of the specified image to this image.void
Copies the contents of the current selection, or the entire image if there is no selection, to the system clipboard.Returns an empty image stack that has the same width, height and color table as this image.createHyperStack
(String title, int channels, int slices, int frames, int bitDepth) This method has been replaced by IJ.createHyperStack().Returns a new ImagePlus with this image's attributes (e.g.Creates a LookUpTable object that corresponds to this image.void
createNewRoi
(int sx, int sy) Starts the process of creating a new selection, where sx and sy are the starting screen coordinates.Returns an 8-bit binary (foreground=255, background=0) ROI or overlay mask that has the same dimensions as this image.Returns an 8-bit binary threshold mask (foreground=255, background=0) that has the same dimensions as this image.crop()
Returns a copy this image or stack slice, cropped if there is an ROI.Multi-roi cropping with default "slice" option.Returns an array of cropped images based on the provided list of rois.Returns a cropped copy this image or stack, where 'options' can be "stack", "slice", "whole-slice" or a range (e.g., "20-30").void
cropAndSave
(Roi[] rois, String directory, String format) Saves the contents of the ROIs in this overlay as separate images, where 'directory' is the directory path and 'format' is "tif", "png" or "jpg".void
cut()
Copies the contents of the current selection to the internal clipboard and then clears the selection.void
Deletes the current region of interest.void
draw()
Draws the image.void
draw
(int x, int y, int width, int height) Draws image and roi outline using a clip rect.Returns a copy of this image or stack.flatten()
Returns a "flattened" version of this image, or stack slice, in RGB format.void
Flattens all slices of this stack or HyperStack.void
flush()
Sets the ImageProcessor, Roi, AWT Image and stack image arrays to null.This method returns complete calibrated statistics for this image or ROI (with "Limit to threshold"), but it is up to 70 times slower than getStatistics().int
Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth is unknown.Returns a copy of this image as an 8-bit or RGB BufferedImage.int
Returns the number of bytes per pixel.int
getC()
Returns the current hyperstack channel position.Returns this image's calibration.Returns the ImageCanvas being used to display this image, or null.int
Returns a reference to the current ImageProcessor.static ImagePlus
Returns the internal clipboard or null if the internal clipboard is empty.int
Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1.int
Returns the current stack index (one-based) or 1 if this is a single image.static int
Returns the default 16-bit display range, 0 (auto-scaling), 8, 10, 12, 14, 15 or 16.int[]
Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array.int[]
getDimensions
(boolean varify) int
Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a composite color image, or 0 if it not.double
double
Returns a FileInfo object containing information, including the pixel array, needed to save this image.int
getFrame()
Returns the system-wide calibration, or null.int
Returns the height of this image in pixels.boolean
int
getID()
Returns this image's unique numeric ID.getImage()
Returns this image as a AWT image.Returns the base image stack.int
If this is a stack, returns the actual number of images in the stack, else returns 1.Returns the "Info" property string, or null if it is not found.static Vector
Returns this image's local calibration, ignoring the "Global" calibration flag.getLocationAsString
(int x, int y) Converts the current cursor location to a string.LUT[]
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.getMask()
For images with irregular ROIs, returns a byte mask, otherwise, returns null.int
Returns the number of channels.int
Returns the number of dimensions (2, 3, 4 or 5).int
Returns the number of frames (time-points).int
Returns the image depth (number of z-slices).double
getNumericProp
(String key) Returns the numeric property associated with the specified key or NaN if the property is not found.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
Returns the FileInfo object that was used to open this image.Returns the current overly, or null if this image does not have an overlay.int[]
getPixel
(int x, int y) Returns the pixel value at (x,y) as a 4 element array.getPlot()
Returns a reference to the current ImageProcessor.Returns as a string the image property associated with the specified key or null if the property is not found.Returns this image's Properties.String[]
Used for saving string properties in TIFF header.getProperty
(String key) Returns the property associated with 'key', or null if it is not found.Returns information displayed by Image/Show Info command.getRoi()
Returns the current selection, or null if there is no selection.If the image title is a file name, returns the name without the extension and with spaces removed, otherwise returns the title shortened to the first space.double
Returns the size of this image in bytes.int
getSlice()
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
Returns the number of stack images.long
Returns the time in milliseconds when startTiming() was last called.static Calibration
This is a version of getGlobalCalibration() that can be called from a static context.Get calibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation and mode.getStatistics
(int mOptions) Returns an ImageStatistics object generated using the specified measurement options.getStatistics
(int mOptions, int nBins) Returns an ImageStatistics object generated using the specified measurement options and histogram bin count.getStatistics
(int mOptions, int nBins, double histMin, double histMax) Returns an ImageStatistics object generated using the specified measurement options, histogram bin count and histogram range.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.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()
Returns the width of this image in pixels.Returns the ImageWindow that is being used to display this image.int
getZ()
Returns the current hyperstack slice position.boolean
Returns 'true' if this ImagePlus contains an ImageStack.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
Returns true if this is a CompositeImage.boolean
Returns 'true' if this is a hyperstack currently being displayed in a StackWindow.boolean
Returns 'true' if this image has more than three dimensions.boolean
Returns true is this image uses an inverting LUT that displays zero as white and 255 as black.boolean
isLocked()
Returns 'true' if the image is locked.boolean
Returns 'true' if the image was locked on another thread.boolean
boolean
isRGB()
boolean
isStack()
Deprecated.Replaced by ImagePlus.hasImageStack()boolean
Returns 'true' if this image is thresholded.boolean
Returns true if this image is currently being displayed in a window.void
killRoi()
Deletes the current region of interest.void
boolean
lock()
Locks the image so other threads can test to see if it is in use.boolean
Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails.static void
For debug purposes, writes all registered (and possibly, forgotten) ImageListeners to the log windowvoid
mouseMoved
(int x, int y) Displays the cursor coordinates and pixel value in the status bar.protected void
notifyListeners
(int id) boolean
void
paste()
Inserts the contents of the internal clipboard into this image.void
paste
(int x, int y) Inserts the contents of the internal clipboard at the specified location, without updating the display.void
Copies the contents of the internal clipboard to the specified location using the specified transfer mode ("Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide").Plots a 256 bin histogram of this image and returns the PlotWindow.plotHistogram
(int bins) Plots a histogram of this image using the specified number of bins and returns the PlotWindow.static void
removeImageListener
(ImageListener listener) void
Calls draw to draw the image and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.static void
Clears the internal clipboard.void
void
resetRoi()
Deletes the current region of interest.void
Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'.void
void
revert()
Implements the File/Revert command.void
saveRoi()
void
Called by ImageWindow.windowActivated(); to end waiting in waitTillActivated.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
setBorderColor
(Color borderColor) void
setC
(int channel) Sets the hyperstack channel position (one based).void
Sets this image's calibration.void
Sets current foreground color.void
Called bynew StackWindow(ImagePlus)
before showing the StackWindow, to prepare for waitTillActivated().static void
setDefault16bitRange
(int bitDepth) Set the default 16-bit display range, where 'bitDepth' must be 0 (auto-scaling), 8 (0-255), 10 (0-1023), 12 (0-4095, 14 (0-16383), 15 (0-32767) or 16 (0-65535).void
setDefaultDisplayRange
(double min, double max) void
setDimensions
(int nChannels, int nSlices, int nFrames) Sets the 3rd, 4th and 5th dimensions, wherenChannels
*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
void
setIJMenuBar
(boolean b) void
Replaces this image with the specified ImagePlus.void
Replaces the image, if any, with the one specified.void
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
void
setPosition
(int n) Set the current hyperstack position based on the stack index 'n' (one-based).void
setPosition
(int channel, int slice, int frame) Sets the current hyperstack position and updates the display, where 'channel', 'slice' and 'frame' are one-based indexes.void
setPositionWithoutUpdate
(int channel, int slice, int frame) Sets the current hyperstack position without updating the display, where 'channel', 'slice' and 'frame' are one-based indexes.void
Replaces the ImageProcessor with the one specified and updates the display.void
setProcessor
(String title, ImageProcessor ip) Replaces the ImageProcessor with the one specified and updates the display.void
Saves a persistent numeric propery.void
Adds a key-value pair to this image's string properties.void
setProperties
(String[] props) Creates a set of image properties from an array of strings.void
setProperty
(String key, Object value) Adds a key-value pair to this image's properties.void
setRoi
(int x, int y, int width, int height) Creates a rectangular selection.void
Assigns the specified ROI to this image and displays it.void
Assigns 'newRoi' to this image and displays it if 'updateDisplay' is true.void
Creates a rectangular selection.void
setSlice
(int n) Displays the specified stack image, where 1<=n<=stackSize.void
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
void
Sets the image name.protected void
setType
(int type) void
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
Opens a window to display this image and displays 'statusMessage' in the status bar.void
Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation.boolean
toString()
void
Frees RAM by setting the snapshot (undo) buffer in the current ImageProcessor to null.void
unlock()
Unlocks the image.void
Updates this image from the pixel data in its associated ImageProcessor, then displays it.void
Calls updateAndDraw to update from the pixel data and draw the image, and also repaints the image window to force the information displayed above the image (dimension, type, size) to be updated.void
Updates this image from the pixel data in its associated ImageProcessor, then displays it.void
ImageCanvas.paint() calls this method when the ImageProcessor has generated a new image.void
updatePosition
(int c, int z, int t) void
Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar.void
Use to update the image when the underlying virtual stack changes.void
Waits until the image window becomes activated.boolean
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Field Details
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GRAY8
public static final int GRAY88-bit grayscale (unsigned)- See Also:
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GRAY16
public static final int GRAY1616-bit grayscale (unsigned)- See Also:
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GRAY32
public static final int GRAY3232-bit floating-point grayscale- See Also:
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COLOR_256
public static final int COLOR_2568-bit indexed color- See Also:
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COLOR_RGB
public static final int COLOR_RGB32-bit RGB color- See Also:
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flattenTitle
Title of image used by Flatten command- See Also:
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changes
public boolean changesTrue if any changes have been made to this image. -
img
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ip
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win
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roi
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currentSlice
protected int currentSlice -
OPENED
protected static final int OPENED- See Also:
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CLOSED
protected static final int CLOSED- See Also:
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UPDATED
protected static final int UPDATED- See Also:
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SAVED
protected static final int SAVED- See Also:
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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
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Constructor Details
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ImagePlus
public ImagePlus()Constructs an uninitialized ImagePlus. -
ImagePlus
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
Constructs an ImagePlus from an ImageProcessor. -
ImagePlus
Constructs an ImagePlus from a TIFF, BMP, DICOM, FITS, PGM, GIF or JPRG specified by a path or from a TIFF, DICOM, GIF or JPEG specified by a URL. -
ImagePlus
Constructs an ImagePlus from a stack.
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Method Details
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setTemporary
public void setTemporary() -
lock
public boolean lock()Locks the image so other threads can test to see if it is in use. One thread can lock an image multiple times, then it has to unlock it as many times until it is unlocked. This allows nested locking within a thread. Returns true if the image was successfully locked. Beeps, displays a message in the status bar, and returns false if the image is already locked by another thread. -
lockSilently
public boolean lockSilently()Similar to lock, but doesn't beep and display an error message if the attempt to lock the image fails. -
unlock
public void unlock()Unlocks the image. In case the image had been locked several times by the current thread, it gets unlocked only after as many unlock operations as there were previous lock operations. -
isLocked
public boolean isLocked()Returns 'true' if the image is locked. -
isLockedByAnotherThread
public boolean isLockedByAnotherThread()Returns 'true' if the image was locked on another thread. -
draw
public void draw()Draws the image. If there is an ROI, its outline is also displayed. Does nothing if there is no window associated with this image (i.e. show() has not been called). -
draw
public void draw(int x, int y, int width, int height) Draws image and roi outline using a clip rect. -
updateAndDraw
public void updateAndDraw()Updates this image from the pixel data in its associated ImageProcessor, then displays it. Does nothing if there is no window associated with this image (i.e. show() has not been called). -
updateVirtualSlice
public void updateVirtualSlice()Use to update the image when the underlying virtual stack changes. -
setDisplayMode
public void setDisplayMode(int mode) Sets the display mode of composite color images, where 'mode' should be IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE. -
getDisplayMode
public int getDisplayMode()Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a composite color image, or 0 if it not. -
setActiveChannels
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
Returns a reference to the current ImageProcessor. The CompositeImage class overrides this method to return the processor associated with the current channel. -
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:
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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
Opens a window to display this image and displays 'statusMessage' in the status bar. -
waitTillActivated
public void waitTillActivated()Waits until the image window becomes activated. This is necessary in macros or other programs if an ImagePlus is shown on the screen, because displaying the window is asynchronous (happens later) and will make the image the active one. Without waiting, in the meanwhile another window could be already the active one and would become deactivated. If the ImagePlus may have been displayed previously, first call setDeactivated().ImagePlus.show()
andnew StackWindow(ImagePlus)
call this method if IJ.isMacro() is true, i.e., when running a macro or executing an IJ.run(...) call. -
setActivated
public void setActivated()Called by ImageWindow.windowActivated(); to end waiting in waitTillActivated. -
setDeactivated
public void setDeactivated()Called bynew StackWindow(ImagePlus)
before showing the StackWindow, to prepare for waitTillActivated(). -
getImage
Returns this image as a AWT image. -
getBufferedImage
Returns a copy of this image as an 8-bit or RGB BufferedImage.- See Also:
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getID
public int getID()Returns this image's unique numeric ID. -
setImage
Replaces the image, if any, with the one specified. Throws an IllegalStateException if an error occurs while loading the image. -
convertToImageProcessor
Extract pixels as an an ImageProcessor from a single band of a BufferedImage.- Parameters:
img
-band
-- Returns:
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setImage
Replaces this image with the specified ImagePlus. May not work as expected if 'imp' is a CompositeImage and this image is not. -
setProcessor
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
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
Replaces the image with the specified stack and updates the display. -
setStack
Replaces the image with the specified stack and updates the display. Set 'title' to null to leave the title unchanged. -
setStack
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setFileInfo
Saves this image's FileInfo so it can be later retieved using getOriginalFileInfo(). -
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
This method should only be called from an ImageWindow. -
getCanvas
Returns the ImageCanvas being used to display this image, or null. -
setColor
Sets current foreground color. -
isProcessor
public boolean isProcessor() -
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
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:
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createRoiMask
Returns an 8-bit binary (foreground=255, background=0) ROI or overlay mask that has the same dimensions as this image. Creates an ROI mask If the image has both both an ROI and an overlay. Set the threshold of the mask to 255.- See Also:
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createThresholdMask
Returns an 8-bit binary threshold mask (foreground=255, background=0) that has the same dimensions as this image. The threshold of the mask is set to 255. -
getStatistics
Get calibrated statistics for this image or ROI, including histogram, area, mean, min and max, standard deviation and mode. This code demonstrates how to get the area, mean max and median of the current image or selection:imp = IJ.getImage(); stats = imp.getStatistics(); IJ.log("Area: "+stats.area); IJ.log("Mean: "+stats.mean); IJ.log("Max: "+stats.max);
- Returns:
- an
ImageStatistics
object - See Also:
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getAllStatistics
This method returns complete calibrated statistics for this image or ROI (with "Limit to threshold"), but it is up to 70 times slower than getStatistics().- Returns:
- an
ImageStatistics
object - See Also:
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getRawStatistics
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getStatistics
Returns an ImageStatistics object generated using the specified measurement options.- See Also:
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getStatistics
Returns an ImageStatistics object generated using the specified measurement options and histogram bin count. -
getStatistics
Returns an ImageStatistics object generated using the specified measurement options, histogram bin count and histogram range. -
getTitle
Returns the image name. -
getShortTitle
If the image title is a file name, returns the name without the extension and with spaces removed, otherwise returns the title shortened to the first space. -
setTitle
Sets the image name. -
getWidth
public int getWidth()Returns the width of this image in pixels. -
getHeight
public int getHeight()Returns the height of this image in pixels. -
getSizeInBytes
public double getSizeInBytes()Returns the size of this image in bytes. -
getStackSize
public int getStackSize()Returns the number of stack images. -
getImageStackSize
public int getImageStackSize()If this is a stack, returns the actual number of images in the stack, else returns 1. -
setDimensions
public void setDimensions(int nChannels, int nSlices, int nFrames) Sets the 3rd, 4th and 5th dimensions, wherenChannels
*nSlices
*nFrames
must be equal to the stack size. -
isHyperStack
public boolean isHyperStack()Returns 'true' if this image has more than three dimensions. -
getNDimensions
public int getNDimensions()Returns the number of dimensions (2, 3, 4 or 5). -
isDisplayedHyperStack
public boolean isDisplayedHyperStack()Returns 'true' if this is a hyperstack currently being displayed in a StackWindow. -
getNChannels
public int getNChannels()Returns the number of channels. -
getNSlices
public int getNSlices()Returns the image depth (number of z-slices). -
getNFrames
public int getNFrames()Returns the number of frames (time-points). -
getDimensions
public int[] getDimensions()Returns the dimensions of this image (width, height, nChannels, nSlices, nFrames) as a 5 element int array. -
getDimensions
public int[] getDimensions(boolean varify) -
getType
public int getType()Returns the current image type (ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB).- See Also:
-
getBitDepth
public int getBitDepth()Returns the bit depth, 8, 16, 24 (RGB) or 32, or 0 if the bit depth is unknown. RGB images actually use 32 bits per pixel. -
getBytesPerPixel
public int getBytesPerPixel()Returns the number of bytes per pixel. -
setType
protected void setType(int type) -
setTypeToColor256
public void setTypeToColor256() -
getStringProperty
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. -
getNumericProperty
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. -
setProp
Adds a key-value pair to this image's string properties. The key-value pair is removed if 'value' is null. The properties persist if the image is saved in TIFF format. Add a "HideInfo" property (e.g. set("HideInfo","true")) to prevent the properties from being displayed by the Image/Show Info command. -
setProp
Saves a persistent numeric propery. The property is removed if 'value' is NaN.- See Also:
-
getProp
Returns as a string the image property associated with the specified key or null if the property is not found. -
getNumericProp
Returns the numeric property associated with the specified key or NaN if the property is not found. -
getPropertiesAsArray
Used for saving string properties in TIFF header. -
getPropsInfo
Returns information displayed by Image/Show Info command. -
setProperties
Creates a set of image properties from an array of strings. -
getInfoProperty
Returns the "Info" property string, or null if it is not found. -
getProperty
Returns the property associated with 'key', or null if it is not found. -
setProperty
Adds a key-value pair to this image's properties. The key is removed from the properties table if value is null. -
getProperties
Returns this image's Properties. May return null. -
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
Returns an empty image stack that has the same width, height and color table as this image. -
getStack
Returns the image stack. The stack may have only one slice. After adding or removing slices, callsetStack()
to update the image and the window that is displaying it.- See Also:
-
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. -
setSliceWithoutUpdate
public void setSliceWithoutUpdate(int n) Displays the specified stack image (1<=n<=stackSize) without updating the display. -
getRoi
Returns the current selection, or null if there is no selection. -
setRoi
Assigns the specified ROI to this image and displays it. Any existing ROI is deleted ifroi
is null or its width or height is zero. -
setRoi
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
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. -
okToDeleteRoi
public boolean okToDeleteRoi() -
killRoi
public void killRoi()Deletes the current region of interest. -
resetRoi
public void resetRoi()Deletes the current region of interest. -
saveRoi
public void saveRoi() -
restoreRoi
public void restoreRoi() -
revert
public void revert()Implements the File/Revert command. -
getFileInfo
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. -
getOriginalFileInfo
Returns the FileInfo object that was used to open this image. Returns null for images created using the File/New command.- See Also:
-
imageUpdate
Used by ImagePlus to monitor loading of images.- Specified by:
imageUpdate
in interfaceImageObserver
-
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
Returns a copy of this image or stack.- See Also:
-
resize
Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'. 'bicubic', 'average' and 'constrain'. -
resize
Returns a scaled copy of this image or ROI, where the 'options' string can contain 'none', 'bilinear'. 'bicubic', 'average' and 'constrain'. -
crop
Returns a copy this image or stack slice, cropped if there is an ROI.- See Also:
-
crop
Returns a cropped copy this image or stack, where 'options' can be "stack", "slice", "whole-slice" or a range (e.g., "20-30").- See Also:
-
crop
Returns an array of cropped images based on the provided list of rois. 'options' applies with stacks and can be "stack", "slice" or a range (e.g., "20-30").- See Also:
-
crop
Multi-roi cropping with default "slice" option. -
cropAndSave
Saves the contents of the ROIs in this overlay as separate images, where 'directory' is the directory path and 'format' is "tif", "png" or "jpg". Set 'format' to "show" and the images will be displayed in a stack and not saved. -
createImagePlus
Returns a new ImagePlus with this image's attributes (e.g. spatial scale), but no image. -
createHyperStack
This method has been replaced by IJ.createHyperStack(). -
copyScale
Copies the calibration of the specified image to this image. -
copyAttributes
Used internally. -
startTiming
public void startTiming()Calls System.currentTimeMillis() to save the current time so it can be retrieved later using getStartTime() to calculate the elapsed time of an operation. -
getStartTime
public long getStartTime()Returns the time in milliseconds when startTiming() was last called. -
getCalibration
Returns this image's calibration. -
setCalibration
Sets this image's calibration. -
setGlobalCalibration
Sets the system-wide calibration. -
getGlobalCalibration
Returns the system-wide calibration, or null. -
getStaticGlobalCalibration
This is a version of getGlobalCalibration() that can be called from a static context. -
getLocalCalibration
Returns this image's local calibration, ignoring the "Global" calibration flag. -
setIgnoreGlobalCalibration
public void setIgnoreGlobalCalibration(boolean ignoreGlobalCalibration) -
mouseMoved
public void mouseMoved(int x, int y) Displays the cursor coordinates and pixel value in the status bar. Called by ImageCanvas when the mouse moves. -
updateStatusbarValue
public void updateStatusbarValue()Redisplays the (x,y) coordinates and pixel value (which may have changed) in the status bar. Called by the Next Slice and Previous Slice commands to update the z-coordinate and pixel value. -
getLocationAsString
Converts the current cursor location to a string. -
cut
public void cut()Copies the contents of the current selection to the internal clipboard and then clears the selection. -
copy
public void copy()Copies the contents of the current selection, or the entire image if there is no selection, to the internal clipboard. -
copy
public void copy(boolean cut) Copies the contents of the current selection to the internal clipboard. Copies the entire image if there is no selection. Also clears the selection ifcut
is true. -
paste
public void paste()Inserts the contents of the internal clipboard into this image. If there is a selection the same size as the image on the clipboard, the image is inserted into that selection, otherwise the selection is inserted into the center of the image. -
paste
public void paste(int x, int y) Inserts the contents of the internal clipboard at the specified location, without updating the display. -
paste
Copies the contents of the internal clipboard to the specified location using the specified transfer mode ("Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide"). The display is not updating. -
getClipboard
Returns the internal clipboard or null if the internal clipboard is empty. -
resetClipboard
public static void resetClipboard()Clears the internal clipboard. -
copyToSystem
public void copyToSystem()Copies the contents of the current selection, or the entire image if there is no selection, to the system clipboard. -
notifyListeners
protected void notifyListeners(int id) -
addImageListener
-
removeImageListener
-
getListeners
-
logImageListeners
public static void logImageListeners()For debug purposes, writes all registered (and possibly, forgotten) ImageListeners to the log window -
setOpenAsHyperStack
public void setOpenAsHyperStack(boolean openAsHyperStack) -
getOpenAsHyperStack
public boolean getOpenAsHyperStack() -
isComposite
public boolean isComposite()Returns true if this is a CompositeImage. -
getCompositeMode
public int getCompositeMode()Returns the display mode (IJ.COMPOSITE, IJ.COLOR or IJ.GRAYSCALE) if this is a CompositeImage, otherwise returns -1. -
setDisplayRange
public void setDisplayRange(double min, double max) Sets the display range of the current channel. With non-composite images it is identical to ip.setMinAndMax(min, max). Call updateAndDraw() to update the display. -
getDisplayRangeMin
public double getDisplayRangeMin() -
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() -
setDefaultDisplayRange
public void setDefaultDisplayRange(double min, double max) -
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
Returns a "flattened" version of this image, or stack slice, in RGB format. -
flattenStack
public void flattenStack()Flattens all slices of this stack or HyperStack.- Throws:
UnsupportedOperationException
- if this image
does not have an overlay and the RoiManager overlay is null.
Non-RGB stacks are converted to RGB.
Copied from OverlayCommands and modified by Marcel Boeglin on 2014.01.08 to work with HyperStacks.
-
tempOverlay
public boolean tempOverlay() -
setLut
Assigns a LUT (lookup table) to this image.- See Also:
-
setOverlay
Installs a list of ROIs that will be drawn on this image as a non-destructive overlay. -
setOverlay
Creates an Overlay from the specified Shape, Color and BasicStroke, and assigns it to this image. -
setOverlay
Creates an Overlay from the specified ROI, and assigns it to this image.- See Also:
-
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
Returns a shallow copy of this ImagePlus. -
plotHistogram
Plots a 256 bin histogram of this image and returns the PlotWindow. -
plotHistogram
Plots a histogram of this image using the specified number of bins and returns the PlotWindow. -
toString
-
setIJMenuBar
public void setIJMenuBar(boolean b) -
setIJMenuBar
public boolean setIJMenuBar() -
hasImageStack
public boolean hasImageStack()Returns 'true' if this ImagePlus contains an ImageStack. -
isStack
public boolean isStack()Deprecated.Replaced by ImagePlus.hasImageStack() -
setPlot
-
getPlot
-
getImageProperties
-
isRGB
public boolean isRGB() -
setBorderColor
-
windowActivated
public boolean windowActivated()
-