Image5D (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ij.ImagePlus
- - sc.fiji.i5d.Image5D

All Implemented Interfaces:

ij.measure.Measurements, ImageObserver, Cloneable
```
public class Image5D
extends ij.ImagePlus
```
Extends ImagePlus to 5 dimensions: x, y, channel (color), slice (z), frame (t). Frame is last to minimize reordering during potential acquisition of time series.
An Image5D has a current "position", i.e. a currently active channel, slice and frame. The image belonging to this position is displayed. The stack returned by getStack() is a stack containing all slices belonging to the current channel and frame. In this way the Image5D is backward compatible to plugins, which work on image stacks.
When dealing with "position"s, indices range from 0 to dimensionSize-1 When dealing with "Channel", "Slice", "Frame", indices range from 1 to NChannels... This is to have the same behaviour as ImageJ has for Slices. The image data of an Image5D is stored in the imageStack (of type ij.ImageStack). Calibration data is stored in the ImagePlus.calibration field (type ij.measure.Calibration), the chCalibration array (components of type ChannelCalibration) and in the calibration5D field (of type Calibration5D) (TODO: will contain scaling of channel and time axes) The current display properties are stored in the array chDisplayProps (of type ChannelDisplayProperties). Working copies of the data are copied to the "channelIPs" array and to the ImagePlus.stack. To replace the "pixels" Object for the imageStack and the working copies, use the method: setPixels(Object pixels, int channel, int slice, int frame) Also, the display settings and calibration functions are copied to the "channelIPs" array. display settings and calibration functions can be brought to the same state by the methods: storeChannelProperties(), restoreChannelProperties(), storeCurrenChannelProperties(), and restoreCurrentChannelProperties().

Author:

Joachim Walter

Field Summary

Fields
Modifier and Type	Field and Description
`protected boolean`	`activated5d`
`protected ChannelImagePlus[]`	`channelImps`
`protected ij.process.ImageProcessor[]`	`channelIPs`
`protected int`	`colorDimension`
`protected int[]`	`currentPosition`
`protected boolean`	`displayAllGray`
`protected boolean`	`displayGrayInTiles`
`protected int`	`displayMode`
`protected ij.ImageStack`	`imageStack`
`protected int`	`imageStackSize`
`protected boolean`	`isInitialized`
`protected int`	`nDimensions`
`static String`	`VERSION`
`protected int`	`xSav`
`protected int`	`ySav`

Fields inherited from class ij.ImagePlus
changes, CLOSED, COLOR_256, COLOR_RGB, compositeImage, currentSlice, dimensionsSet, flattenTitle, GRAY16, GRAY32, GRAY8, height, img, ip, locked, nChannels, nFrames, nSlices, OPENED, roi, setIJMenuBar, UPDATED, width, win

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

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

Constructor Summary

Constructors
Constructor and Description
`Image5D()`
`Image5D(String pathOrURL)`
`Image5D(String title, Image img)`
`Image5D(String title, ij.process.ImageProcessor ip)`
`Image5D(String title, ij.ImageStack stack)` Makes an Image5D (one channel and one frame) from an ImageStack.
`Image5D(String title, ij.ImageStack stack, int nChannels, int nSlices, int nFrames)` Makes an Image5D from an ImageStack and dimension sizes.
`Image5D(String title, int type, int[] dimensions, boolean fill)`
`Image5D(String title, int type, int width, int height, int nChannels, int nSlices, int nFrames, boolean fill)` Same as Image5D(String title, int type, int[] dimensions, boolean fill), but the array dimensions[] replaced by the individual elements width, height, nChannels, nSlices and nFrames.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`checkChannel(int channel)`
`protected void`	`checkFrame(int frame)`
`protected void`	`checkSlice(int slice)`
`static int`	`compareToVersion(String testVersion)` Compares the "testVersion" to the version of the installed class.
`void`	`copy(boolean cut)` Copies the active channel to the ImageJ clipboard, if only one channel is displayed.
`Object`	`createEmptyPixels()` Creates an empty pixels-array of size width*height and type of this image, and returns a reference to it.
`protected static ij.process.ImageProcessor`	`createProcessorFromDims(int type, int[] dimensionSizes)` Called from constructor Image5D(String title, int type, int[] dimensions, boolean fill) in call to super().
`protected static ij.ImageStack`	`createZStackFromImageStack(ij.ImageStack imageStack, int nChannels, int nSlices, int nFrames)` Called from constructor Image5D(String title, ImageStack stack, int nChannels, int nSlices, int nFrames) in call to super().
`void`	`draw()` Draws the image.
`Image5D`	`duplicate()`
`void`	`expandDimension(int dimension, int newSize, boolean fill)` Expands Image5D to larger size in one dimension.
`void`	`flush()` Sets the image arrays to null to help the garbage collector do its job.
`ChannelCalibration`	`getChannelCalibration(int channel)` Get reference to ChannelCalibration item of a channel.
`ChannelDisplayProperties`	`getChannelDisplayProperties(int channel)` Get reference to ChannelDisplayProperties item of a channel.
`ChannelImagePlus`	`getChannelImagePlus(int channel)` Get reference to ChannelImagePlus item of a channel.
`int`	`getColorDimension()`
`int`	`getCurrentChannel()`
`int`	`getCurrentFrame()`
`int`	`getCurrentImageStackIndex()` Returns the index in the imageStack corresponding to the current position.
`int[]`	`getCurrentPosition()`
`int`	`getCurrentPosition(int dimension)`
`int`	`getCurrentSlice()`
`protected int`	`getCurrentSliceOffset()`
`protected int`	`getCurrentStackIncrement()`
`protected int`	`getCurrentStackOffset()`
`String`	`getDimensionLabel(int dimension)`
`int`	`getDimensionSize(int dimension)` Returns the size of a dimension.
`int`	`getDisplayMode()`
`ij.io.FileInfo`	`getFileInfo()`
`String`	`getI5DMetaData()` Returns Image5D-specific metadata to be saved in TIFF-file.
`Image`	`getImage()`
`ij.ImageStack`	`getImageStack()` Returns a reference to the imageStack that contains all channels, slices and frames.
`int`	`getImageStackIndex(int channel, int slice, int frame)` Returns the index in the imageStack corresponding to the specified position.
`int`	`getImageStackSize()` Returns the full size of the ImageStack, not just that of the current channel/frame.
`int`	`getNDimensions()`
`Object`	`getPixels(int channel, int slice, int frame)` Returns a reference to the image data of the given channel, slice and frame: An object of type byte-array, short-array or float-array.
`ij.process.ImageProcessor`	`getProcessor(int channel)`
`protected String`	`getStatusString(int x, int y)`
`boolean`	`isDisplayAllGray()` true: all channels are displayed in gray
`boolean`	`isDisplayedGray(int channel)`
`boolean`	`isDisplayedInOverlay(int channel)`
`boolean`	`isDisplayGrayInTiles()`
`void`	`mouseMoved(int x, int y)`
`void`	`paste()` Inserts the contents of the internal clipboard into the active image.
`void`	`putRoi(Roi newRoi)` Assigns the specified ROI to this image and displays it without saving it as previousRoi as it is done by `setRoi()`.
`void`	`restoreChannelProperties(int channel)`
`void`	`restoreCurrentChannelProperties()`
`void`	`setActivated()` Called by ImageWindow.windowActivated().
`void`	`setChannel(int index)`
`void`	`setChannelCalibration(int channel, ChannelCalibration cal)` Sets the ChannelCalibration item of a channel.
`void`	`setChannelColorModel(int channel, ColorModel model)` Changes the color model of a channel to this one.
`void`	`setChannelDisplayProperties(int channel, ChannelDisplayProperties props)` Sets the ChannelDisplayProperties item of a channel.
`void`	`setChannelMinMax(int channel, double minValue, double maxValue)` Changes the min- and max-value of a channel to these ones.
`void`	`setCurrentPosition(int[] position)` THE method to set the current Position in the Image5D.
`void`	`setCurrentPosition(int dimension, int position)`
`void`	`setCurrentPosition(int x, int y, int ch, int z, int t)`
`void`	`setDefaultChannelNames()`
`void`	`setDefaultColors()`
`void`	`setDimensions(int nChannels, int nSlices, int nFrames)` Make setDimensions non-functional, so that no one messes up stack dimensions in the GUI.
`void`	`setDisplayedGray(int channel, boolean displayedGray)`
`void`	`setDisplayedInOverlay(int channel, boolean displayed)`
`void`	`setDisplayGrayInTiles(boolean displayGrayInTiles)` Sets, whether all channels in TILED mode are displayed with a grayscale colormap and updates the ChannelControl of the Image5DWindow.
`void`	`setDisplayMode(int displayMode)` Sets the displayMode of the Image5D to one of ChannelControl.ONE_CHANNEL_GRAY, ONE_CHANNEL_COLOR, OVERLAY or TILED and updates the ChannelControl of the Image5DWindow.
`void`	`setFrame(int index)`
`void`	`setImage(Image img)` Replaces the AWT image, if any, with the one specified.
`void`	`setPixels(Object pixels)` Assigns a pixel array to the current position,
`void`	`setPixels(Object pixels, int channel, int slice, int frame)` Assigns a pixel array to the specified position,
`void`	`setProcessor(String title, ij.process.ImageProcessor ip)` Replaces the ImageProcessor, if any, with the one specified.
`void`	`setSlice(int index)`
`void`	`setStack(String title, ij.ImageStack stack)` Replaces the current stack, with the one specified.
`protected void`	`setType(int type)`
`void`	`show(String statusMessage)`
`void`	`storeChannelProperties(int channel)`
`void`	`storeCurrentChannelProperties()`
`void`	`updateAndDraw()` 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`	`updateImageAndDraw()` Causes the AWT image returned by getImage() to be fully recalculated.
`void`	`updateStatusbarValue()`
`void`	`updateWindowControls()` Updates the window controls of the Image5DWindow.

Methods inherited from class ij.ImagePlus
addImageListener, clone, close, convertIndexToPosition, copy, copyAttributes, copyScale, copyToSystem, createEmptyStack, createHyperStack, createImagePlus, createLut, createNewRoi, createRoiMask, createThresholdMask, crop, crop, crop, crop, cropAndSave, cut, deleteRoi, draw, flatten, flattenStack, getAllStatistics, getBitDepth, getBufferedImage, getBytesPerPixel, getC, getCalibration, getCanvas, getChannel, getChannelProcessor, getClipboard, getCompositeMode, getDefault16bitRange, getDimensions, getDimensions, getDisplayRangeMax, getDisplayRangeMin, getFrame, getGlobalCalibration, getHeight, getHideOverlay, getID, getImageProperties, getInfoProperty, getLocalCalibration, getLocationAsString, getLuts, getMask, getNChannels, getNFrames, getNSlices, getNumericProp, getNumericProperty, getOpenAsHyperStack, getOriginalFileInfo, getOverlay, getPixel, getPlot, getProcessor, getProp, getProperties, getPropertiesAsArray, getProperty, getPropsInfo, getRawStatistics, getRoi, getShortTitle, getSizeInBytes, getSlice, getStack, getStackIndex, getStackSize, getStartTime, getStaticGlobalCalibration, getStatistics, getStatistics, getStatistics, getStatistics, getStringProperty, getT, getTitle, getType, getWidth, getWindow, getZ, hide, imageUpdate, isComposite, isDisplayedHyperStack, isHyperStack, isInvertedLut, isLocked, isLockedByAnotherThread, isProcessor, isStack, isThreshold, isVisible, killRoi, killStack, lock, lockSilently, logImageListeners, notifyListeners, okToDeleteRoi, paste, plotHistogram, plotHistogram, removeImageListener, repaintWindow, resetClipboard, resetDisplayRange, resetStack, resize, resize, restoreRoi, revert, saveRoi, setActiveChannels, setAntialiasRendering, setC, setCalibration, setColor, setDefault16bitRange, setDisplayRange, setDisplayRange, setFileInfo, setGlobalCalibration, setHideOverlay, setIgnoreFlush, setIgnoreGlobalCalibration, setIJMenuBar, setIJMenuBar, setImage, setLut, setOpenAsHyperStack, setOverlay, setOverlay, setOverlay, setPlot, setPosition, setPosition, setPositionWithoutUpdate, setProcessor, setProp, setProp, setProperties, setProperty, setRoi, setRoi, setRoi, setRoi, setSliceWithoutUpdate, setStack, setStack, setT, setTitle, setTypeToColor256, setWindow, setZ, show, startTiming, tempOverlay, toString, trimProcessor, unlock, updateAndRepaintWindow, updateChannelAndDraw, updatePosition, updateVirtualSlice

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

- Field Detail
  - VERSION
```
public static final String VERSION
```
    See Also:
    
    Constant Field Values
  - nDimensions
```
protected int nDimensions
```
  - isInitialized
```
protected boolean isInitialized
```
  - imageStack
```
protected ij.ImageStack imageStack
```
  - imageStackSize
```
protected int imageStackSize
```
  - currentPosition
```
protected int[] currentPosition
```
  - channelImps
```
protected ChannelImagePlus[] channelImps
```
  - channelIPs
```
protected ij.process.ImageProcessor[] channelIPs
```
  - colorDimension
```
protected int colorDimension
```
  - displayMode
```
protected int displayMode
```
  - displayAllGray
```
protected boolean displayAllGray
```
  - displayGrayInTiles
```
protected boolean displayGrayInTiles
```
  - activated5d
```
protected boolean activated5d
```
  - xSav
```
protected int xSav
```
  - ySav
```
protected int ySav
```
- Constructor Detail
  - Image5D
```
public Image5D(String title,
               int type,
               int[] dimensions,
               boolean fill)
```
    Parameters:
    
    title -
    
    type -
    
    dimensions - array containing width, height, nChannels, nSlices and nFrames.
    
    fill - If true, data is allocated for each combination of <ch, z, t> ("position"). If false, only references to one and the same pixel array will be created. This is much faster, but changes to one position will apply to all positions.
  - Image5D
```
public Image5D(String title,
               int type,
               int width,
               int height,
               int nChannels,
               int nSlices,
               int nFrames,
               boolean fill)
```
    Same as Image5D(String title, int type, int[] dimensions, boolean fill), but the array dimensions[] replaced by the individual elements width, height, nChannels, nSlices and nFrames.
  - Image5D
```
public Image5D(String title,
               ij.process.ImageProcessor ip)
```
    Parameters:
    
    title -
    
    ip -
  - Image5D
```
public Image5D(String title,
               ij.ImageStack stack)
```
    Makes an Image5D (one channel and one frame) from an ImageStack.
    
    Parameters:
    
    title - title of the image
    
    stack - stack containing the image data
  - Image5D
```
public Image5D(String title,
               ij.ImageStack stack,
               int nChannels,
               int nSlices,
               int nFrames)
```
    Makes an Image5D from an ImageStack and dimension sizes. All other constructors of Image5D eventually call this one. So changes that apply to all constructors should go here.
    
    Parameters:
    
    title - title of the image
    
    stack - stack containing the image data. Changes first by channel, then by slice then by frame.
    
    nChannels -
    
    nSlices -
    
    nFrames -
  - Image5D
```
public Image5D()
```
  - Image5D
```
public Image5D(String title,
               Image img)
```
  - Image5D
```
public Image5D(String pathOrURL)
```
- Method Detail
  - compareToVersion
```
public static int compareToVersion(String testVersion)
```
    Compares the "testVersion" to the version of the installed class. The class must specify its version in a static field "VERSION". Result is -1, if testVersion < VERSION, +1, if testVersion > VERSION and 0 if both are the same. Version numbering is expected in the format x.y.z where x, y and z are positive integer numbers. E.g. this method was introduced in Image5D version 1.1.6. If z is not specified, it is counted as 0. No letters are allowed in the version, only digits.
  - setStack
```
public void setStack(String title,
                     ij.ImageStack stack)
```
    Replaces the current stack, with the one specified. Set 'title' to null to leave the title unchanged. Type ColorRGB is not permitted. If the Image5D is initialized, stack type and dimensions have to match to current type/dims.
    
    Overrides:
    
    setStack in class ij.ImagePlus
  - updateWindowControls
```
public void updateWindowControls()
```
    Updates the window controls of the Image5DWindow. Right now only the Channel selector
  - updateImageAndDraw
```
public void updateImageAndDraw()
```
    Causes the AWT image returned by getImage() to be fully recalculated.
  - mouseMoved
```
public void mouseMoved(int x,
                       int y)
```
    Overrides:
    
    mouseMoved in class ij.ImagePlus
  - updateStatusbarValue
```
public void updateStatusbarValue()
```
    Overrides:
    
    updateStatusbarValue in class ij.ImagePlus
  - getStatusString
```
protected String getStatusString(int x,
                                 int y)
```
  - setImage
```
public void setImage(Image img)
```
    Replaces the AWT image, if any, with the one specified. Throws an IllegalStateException if an error occurs while loading the image. Use of this method is untested.
    
    Overrides:
    
    setImage in class ij.ImagePlus
  - setProcessor
```
public void setProcessor(String title,
                         ij.process.ImageProcessor ip)
```
    Replaces the ImageProcessor, if any, with the one specified. Set 'title' to null to leave the image title unchanged.
    
    Overrides:
    
    setProcessor in class ij.ImagePlus
  - setType
```
protected void setType(int type)
```
    Overrides:
    
    setType in class ij.ImagePlus
  - setChannel
```
public void setChannel(int index)
```
  - setSlice
```
public void setSlice(int index)
```
    Overrides:
    
    setSlice in class ij.ImagePlus
  - setFrame
```
public void setFrame(int index)
```
  - setCurrentPosition
```
public void setCurrentPosition(int dimension,
                               int position)
```
  - setCurrentPosition
```
public void setCurrentPosition(int x,
                               int y,
                               int ch,
                               int z,
                               int t)
```
  - setCurrentPosition
```
public void setCurrentPosition(int[] position)
```
    THE method to set the current Position in the Image5D. All other setCurrentPosition methods with different signature call this one.
    
    Parameters:
    
    position -
  - getNDimensions
```
public int getNDimensions()
```
    Overrides:
    
    getNDimensions in class ij.ImagePlus
  - getDimensionLabel
```
public String getDimensionLabel(int dimension)
```
  - getDimensionSize
```
public int getDimensionSize(int dimension)
```
    Returns the size of a dimension. Dimensions go from 0 to 4 (width, height, nChannels, nSlices, nFrames).
  - getImageStackSize
```
public int getImageStackSize()
```
    Returns the full size of the ImageStack, not just that of the current channel/frame. Overrides method in ImagePlus.
    
    Overrides:
    
    getImageStackSize in class ij.ImagePlus
  - getImageStack
```
public ij.ImageStack getImageStack()
```
    Returns a reference to the imageStack that contains all channels, slices and frames.
    
    Overrides:
    
    getImageStack in class ij.ImagePlus
  - getI5DMetaData
```
public String getI5DMetaData()
```
    Returns Image5D-specific metadata to be saved in TIFF-file.
  - getFileInfo
```
public ij.io.FileInfo getFileInfo()
```
    Overrides:
    
    getFileInfo in class ij.ImagePlus
  - getPixels
```
public Object getPixels(int channel,
                        int slice,
                        int frame)
```
    Returns a reference to the image data of the given channel, slice and frame: An object of type byte-array, short-array or float-array.
  - setPixels
```
public void setPixels(Object pixels)
```
    Assigns a pixel array to the current position,
    
    Parameters:
    
    pixels -
  - setPixels
```
public void setPixels(Object pixels,
                      int channel,
                      int slice,
                      int frame)
```
    Assigns a pixel array to the specified position,
    
    Parameters:
    
    pixels -
  - createEmptyPixels
```
public Object createEmptyPixels()
```
    Creates an empty pixels-array of size width*height and type of this image, and returns a reference to it.
  - getColorDimension
```
public int getColorDimension()
```
  - getCurrentImageStackIndex
```
public int getCurrentImageStackIndex()
```
    Returns the index in the imageStack corresponding to the current position.
  - getImageStackIndex
```
public int getImageStackIndex(int channel,
                              int slice,
                              int frame)
```
    Returns the index in the imageStack corresponding to the specified position.
  - getCurrentPosition
```
public int[] getCurrentPosition()
```
  - getCurrentPosition
```
public int getCurrentPosition(int dimension)
```
  - getCurrentChannel
```
public int getCurrentChannel()
```
  - getCurrentSlice
```
public int getCurrentSlice()
```
    Overrides:
    
    getCurrentSlice in class ij.ImagePlus
  - getCurrentFrame
```
public int getCurrentFrame()
```
  - setChannelColorModel
```
public void setChannelColorModel(int channel,
                                 ColorModel model)
```
    Changes the color model of a channel to this one.
    
    Parameters:
    
    channel -
    
    model -
  - setChannelMinMax
```
public void setChannelMinMax(int channel,
                             double minValue,
                             double maxValue)
```
    Changes the min- and max-value of a channel to these ones.
  - getDisplayMode
```
public int getDisplayMode()
```
    Overrides:
    
    getDisplayMode in class ij.ImagePlus
  - setDisplayMode
```
public void setDisplayMode(int displayMode)
```
    Sets the displayMode of the Image5D to one of ChannelControl.ONE_CHANNEL_GRAY, ONE_CHANNEL_COLOR, OVERLAY or TILED and updates the ChannelControl of the Image5DWindow. This is the method to be called from external code, not the one in ChannelControl. In fact, the ChannelControl calls this method, when the displayMode is changed in the GUI. TODO: move all code to Image5DWindow. Display functions should not be in Image5D. Keep this method for legacy reasons: TransformJ and probably other plugins use it.
    
    Overrides:
    
    setDisplayMode in class ij.ImagePlus
  - setDisplayGrayInTiles
```
public void setDisplayGrayInTiles(boolean displayGrayInTiles)
```
    Sets, whether all channels in TILED mode are displayed with a grayscale colormap and updates the ChannelControl of the Image5DWindow. This is the method to be called from external code, not the one in ChannelControl. In fact, the ChannelControl calls this method, when the displayMode is changed in the GUI.
  - isDisplayGrayInTiles
```
public boolean isDisplayGrayInTiles()
```
  - isDisplayedInOverlay
```
public boolean isDisplayedInOverlay(int channel)
```
  - setDisplayedInOverlay
```
public void setDisplayedInOverlay(int channel,
                                  boolean displayed)
```
  - isDisplayedGray
```
public boolean isDisplayedGray(int channel)
```
  - setDisplayedGray
```
public void setDisplayedGray(int channel,
                             boolean displayedGray)
```
  - isDisplayAllGray
```
public boolean isDisplayAllGray()
```
    true: all channels are displayed in gray
  - setActivated
```
public void setActivated()
```
    Called by ImageWindow.windowActivated().
    
    Overrides:
    
    setActivated in class ij.ImagePlus
  - show
```
public void show(String statusMessage)
```
    Overrides:
    
    show in class ij.ImagePlus
  - getImage
```
public Image getImage()
```
    Overrides:
    
    getImage in class ij.ImagePlus
  - updateImage
```
public void updateImage()
```
    ImageCanvas.paint() calls this method when the ImageProcessor has generated a new image. Calculates the AWT Image displayed in the Image5DWindow. For ONE_CHANNEL_GRAY and ONE_CHANNEL_COLOR this uses the method from ImageProcessor. For OVERLAY this method has to calculate a lot.
    
    Overrides:
    
    updateImage in class ij.ImagePlus
  - 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).
    
    Overrides:
    
    draw in class ij.ImagePlus
  - 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).
    
    Overrides:
    
    updateAndDraw in class ij.ImagePlus
  - setDefaultColors
```
public void setDefaultColors()
```
  - setDefaultChannelNames
```
public void setDefaultChannelNames()
```
  - flush
```
public void flush()
```
    Sets the image arrays to null to help the garbage collector do its job. In addition to ImagePlus.flush() also sets the imageStack to null. Does nothing if the image is locked or a setIgnoreFlush(true) call has been made.
    
    Overrides:
    
    flush in class ij.ImagePlus
  - paste
```
public void paste()
```
    Inserts the contents of the internal clipboard into the active image. For tiled mode: also copies the pasted ROI to all satellite canvasses.
    
    Overrides:
    
    paste in class ij.ImagePlus
  - copy
```
public void copy(boolean cut)
```
    Copies the active channel to the ImageJ clipboard, if only one channel is displayed. In OVERLAY mode copy the currently displayed image as an RGB image.
    
    Overrides:
    
    copy in class ij.ImagePlus
  - putRoi
```
public void putRoi(Roi newRoi)
```
    Assigns the specified ROI to this image and displays it without saving it as previousRoi as it is done by setRoi().
  - expandDimension
```
public void expandDimension(int dimension,
                            int newSize,
                            boolean fill)
```
    Expands Image5D to larger size in one dimension. Does nothing, if newSize <= current size. Works only for dimension >=2 (i.e. channel, slice, frame) at present.
    
    Parameters:
    
    dimension -
    
    newSize -
    
    fill - if true, create black image for each position, if false, link a common dummy image to each position
  - setDimensions
```
public void setDimensions(int nChannels,
                          int nSlices,
                          int nFrames)
```
    Make setDimensions non-functional, so that no one messes up stack dimensions in the GUI.
    
    Overrides:
    
    setDimensions in class ij.ImagePlus
  - getCurrentSliceOffset
```
protected int getCurrentSliceOffset()
```
  - getCurrentStackOffset
```
protected int getCurrentStackOffset()
```
  - getCurrentStackIncrement
```
protected int getCurrentStackIncrement()
```
  - checkChannel
```
protected void checkChannel(int channel)
```
  - checkSlice
```
protected void checkSlice(int slice)
```
  - checkFrame
```
protected void checkFrame(int frame)
```
  - getChannelImagePlus
```
public ChannelImagePlus getChannelImagePlus(int channel)
```
    Get reference to ChannelImagePlus item of a channel.
  - getChannelCalibration
```
public ChannelCalibration getChannelCalibration(int channel)
```
    Get reference to ChannelCalibration item of a channel.
  - setChannelCalibration
```
public void setChannelCalibration(int channel,
                                  ChannelCalibration cal)
```
    Sets the ChannelCalibration item of a channel.
  - getChannelDisplayProperties
```
public ChannelDisplayProperties getChannelDisplayProperties(int channel)
```
    Get reference to ChannelDisplayProperties item of a channel.
  - setChannelDisplayProperties
```
public void setChannelDisplayProperties(int channel,
                                        ChannelDisplayProperties props)
```
    Sets the ChannelDisplayProperties item of a channel.
  - storeCurrentChannelProperties
```
public void storeCurrentChannelProperties()
```
  - restoreCurrentChannelProperties
```
public void restoreCurrentChannelProperties()
```
  - storeChannelProperties
```
public void storeChannelProperties(int channel)
```
  - restoreChannelProperties
```
public void restoreChannelProperties(int channel)
```
  - getProcessor
```
public ij.process.ImageProcessor getProcessor(int channel)
```
  - duplicate
```
public Image5D duplicate()
```
    Overrides:
    
    duplicate in class ij.ImagePlus
  - createProcessorFromDims
```
protected static ij.process.ImageProcessor createProcessorFromDims(int type,
                                                                   int[] dimensionSizes)
```
    Called from constructor Image5D(String title, int type, int[] dimensions, boolean fill) in call to super(). Checks the number of dimensions and creates an ImageProcessor.
  - createZStackFromImageStack
```
protected static ij.ImageStack createZStackFromImageStack(ij.ImageStack imageStack,
                                                          int nChannels,
                                                          int nSlices,
                                                          int nFrames)
```
    Called from constructor Image5D(String title, ImageStack stack, int nChannels, int nSlices, int nFrames) in call to super(). Checks the dimensions and creates the z-stack at first channel/frame.

Class Image5D

Field Summary

Fields inherited from class ij.ImagePlus

Fields inherited from interface java.awt.image.ImageObserver

Fields inherited from interface ij.measure.Measurements

Constructor Summary

Method Summary

Methods inherited from class ij.ImagePlus

Methods inherited from class java.lang.Object

Field Detail

VERSION

nDimensions

isInitialized

imageStack

imageStackSize

currentPosition

channelImps

channelIPs

colorDimension

displayMode

displayAllGray

displayGrayInTiles

activated5d

xSav

ySav

Constructor Detail

Image5D

Image5D

Image5D

Image5D

Image5D

Image5D

Image5D

Image5D

Method Detail

compareToVersion

setStack

updateWindowControls

updateImageAndDraw

mouseMoved

updateStatusbarValue

getStatusString

setImage

setProcessor

setType

setChannel

setSlice

setFrame

setCurrentPosition

setCurrentPosition

setCurrentPosition

getNDimensions

getDimensionLabel

getDimensionSize

getImageStackSize

getImageStack

getI5DMetaData

getFileInfo

getPixels

setPixels

setPixels

createEmptyPixels

getColorDimension

getCurrentImageStackIndex

getImageStackIndex

getCurrentPosition

getCurrentPosition

getCurrentChannel

getCurrentSlice

getCurrentFrame

setChannelColorModel

setChannelMinMax

getDisplayMode

setDisplayMode

setDisplayGrayInTiles

isDisplayGrayInTiles

isDisplayedInOverlay

setDisplayedInOverlay

isDisplayedGray

setDisplayedGray