ImageStack (ImageJ API)

java.lang.Object
- ij.ImageStack

Direct Known Subclasses:

VirtualStack
```
public class ImageStack
extends Object
```
This class represents an expandable array of images.

See Also:

ImagePlus

Constructor Summary

Constructors
Constructor	Description
`ImageStack()`	Default constructor.
`ImageStack(int width, int height)`	Creates a new, empty image stack.
`ImageStack(int width, int height, int size)`	Creates a new, empty image stack with a capacity of 'size'.
`ImageStack(int width, int height, ColorModel cm)`	Creates a new, empty image stack using the specified color model.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`void`	`addSlice(ImageProcessor ip)`	Adds the image in 'ip' to the end of the stack.
`void`	`addSlice(String sliceLabel, ImageProcessor ip)`	Adds the image in 'ip' to the end of the stack, setting the string 'sliceLabel' as the slice metadata.
`void`	`addSlice(String sliceLabel, ImageProcessor ip, int n)`	Adds the image in 'ip' to the stack following slice 'n'.
`void`	`addSlice(String sliceLabel, Object pixels)`	Adds an image in the form of a pixel array to the end of the stack.
`void`	`addUnsignedShortSlice(String sliceLabel, Object pixels)`	Deprecated. Short images are always unsigned.
`ImageStack`	`convertToFloat()`	Creates a float version of this stack.
`static ImageStack`	`create(int width, int height, int depth, int bitdepth)`	Creates a new ImageStack.
`ImageStack`	`crop(int x, int y, int z, int width, int height, int depth)`	Creates a new stack by cropping this one.
`void`	`deleteLastSlice()`	Deletes the last slice in the stack.
`void`	`deleteSlice(int n)`	Deletes the specified slice, were 1<=n<=nslices.
`void`	`drawSphere(double radius, int xc, int yc, int zc)`	Experimental
`ImageStack`	`duplicate()`	Duplicates this stack.
`int`	`getBitDepth()`	Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).
`ColorModel`	`getColorModel()`	Returns this stack's color model.
`int`	`getHeight()`
`Object[]`	`getImageArray()`	Returns the stack as an array of 1D pixel arrays.
`Object`	`getPixels(int n)`	Returns the pixel array for the specified slice, were 1<=n<=nslices.
`ImageProcessor`	`getProcessor(int n)`	Returns an ImageProcessor for the specified slice, were 1<=n<=nslices.
`Rectangle`	`getRoi()`
`String`	`getShortSliceLabel(int n)`	Returns a shortened version (up to the first 60 characters or first newline and suffix removed) of the label of the specified slice.
`int`	`getSize()`	Returns the number of slices in this stack.
`String`	`getSliceLabel(int n)`	Returns the label of the specified slice, were 1<=n<=nslices.
`String[]`	`getSliceLabels()`	Returns the slice labels as an array of Strings.
`double`	`getVoxel(int x, int y, int z)`	Returns, as a double, the specified voxel.
`float[]`	`getVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels)`
`float[]`	`getVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel)`
`int`	`getWidth()`
`boolean`	`isHSB()`	Returns true if this is a 3-slice HSB stack.
`boolean`	`isLab()`	Returns true if this is a Lab stack.
`boolean`	`isRGB()`	Returns true if this is a 3-slice, 8-bit RGB stack.
`boolean`	`isVirtual()`	Returns true if this is a virtual (disk resident) stack.
`void`	`setColorModel(ColorModel cm)`	Assigns a new color model to this stack.
`void`	`setPixels(Object pixels, int n)`	Assigns a pixel array to the specified slice, were 1<=n<=nslices.
`void`	`setProcessor(ImageProcessor ip, int n)`	Assigns the pixel array of an ImageProcessor to the specified slice, were 1<=n<=nslices.
`void`	`setRoi(Rectangle roi)`
`void`	`setSliceLabel(String label, int n)`	Sets the label of the specified slice, were 1<=n<=nslices.
`void`	`setVoxel(int x, int y, int z, double value)`
`void`	`setVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels)`	Experimental
`void`	`setVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel)`	Experimental
`int`	`size()`	Returns the number of slices in this stack.
`String`	`toString()`
`void`	`trim()`	Frees memory by deleting a few slices from the end of the stack.
`void`	`update(ImageProcessor ip)`	Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.

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

- Constructor Detail
  - ImageStack
```
public ImageStack()
```
    Default constructor.
  - ImageStack
```
public ImageStack(int width,
                  int height)
```
    Creates a new, empty image stack.
  - ImageStack
```
public ImageStack(int width,
                  int height,
                  int size)
```
    Creates a new, empty image stack with a capacity of 'size'. All 'size' slices and labels of this image stack are initially null.
  - ImageStack
```
public ImageStack(int width,
                  int height,
                  ColorModel cm)
```
    Creates a new, empty image stack using the specified color model.
- Method Detail
  - addSlice
```
public void addSlice(String sliceLabel,
                     Object pixels)
```
    Adds an image in the form of a pixel array to the end of the stack.
  - addUnsignedShortSlice
```
public void addUnsignedShortSlice(String sliceLabel,
                                  Object pixels)
```
    Deprecated.
    Short images are always unsigned.
  - addSlice
```
public void addSlice(ImageProcessor ip)
```
    Adds the image in 'ip' to the end of the stack.
  - addSlice
```
public void addSlice(String sliceLabel,
                     ImageProcessor ip)
```
    Adds the image in 'ip' to the end of the stack, setting the string 'sliceLabel' as the slice metadata.
  - addSlice
```
public void addSlice(String sliceLabel,
                     ImageProcessor ip,
                     int n)
```
    Adds the image in 'ip' to the stack following slice 'n'. Adds the slice to the beginning of the stack if 'n' is zero.
  - deleteSlice
```
public void deleteSlice(int n)
```
    Deletes the specified slice, were 1<=n<=nslices.
  - deleteLastSlice
```
public void deleteLastSlice()
```
    Deletes the last slice in the stack.
  - getWidth
```
public int getWidth()
```
  - getHeight
```
public int getHeight()
```
  - setRoi
```
public void setRoi(Rectangle roi)
```
  - getRoi
```
public Rectangle getRoi()
```
  - update
```
public void update(ImageProcessor ip)
```
    Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.
  - getPixels
```
public Object getPixels(int n)
```
    Returns the pixel array for the specified slice, were 1<=n<=nslices.
  - setPixels
```
public void setPixels(Object pixels,
                      int n)
```
    Assigns a pixel array to the specified slice, were 1<=n<=nslices.
  - getImageArray
```
public Object[] getImageArray()
```
    Returns the stack as an array of 1D pixel arrays. Note that the size of the returned array may be greater than the number of slices currently in the stack, with unused elements set to null.
  - getSize
```
public int getSize()
```
    Returns the number of slices in this stack.
  - size
```
public int size()
```
    Returns the number of slices in this stack.
  - getSliceLabels
```
public String[] getSliceLabels()
```
    Returns the slice labels as an array of Strings. Note that the size of the returned array may be greater than the number of slices currently in the stack. Returns null if the stack is empty or the label of the first slice is null.
  - getSliceLabel
```
public String getSliceLabel(int n)
```
    Returns the label of the specified slice, were 1<=n<=nslices. Returns null if the slice does not have a label. For DICOM and FITS stacks, labels may contain header information.
  - getShortSliceLabel
```
public String getShortSliceLabel(int n)
```
    Returns a shortened version (up to the first 60 characters or first newline and suffix removed) of the label of the specified slice. Returns null if the slice does not have a label.
  - setSliceLabel
```
public void setSliceLabel(String label,
                          int n)
```
    Sets the label of the specified slice, were 1<=n<=nslices.
  - getProcessor
```
public ImageProcessor getProcessor(int n)
```
    Returns an ImageProcessor for the specified slice, were 1<=n<=nslices. Returns null if the stack is empty.
  - setProcessor
```
public void setProcessor(ImageProcessor ip,
                         int n)
```
    Assigns the pixel array of an ImageProcessor to the specified slice, were 1<=n<=nslices.
  - setColorModel
```
public void setColorModel(ColorModel cm)
```
    Assigns a new color model to this stack.
  - getColorModel
```
public ColorModel getColorModel()
```
    Returns this stack's color model. May return null.
  - isRGB
```
public boolean isRGB()
```
    Returns true if this is a 3-slice, 8-bit RGB stack.
  - isHSB
```
public boolean isHSB()
```
    Returns true if this is a 3-slice HSB stack.
  - isLab
```
public boolean isLab()
```
    Returns true if this is a Lab stack.
  - isVirtual
```
public boolean isVirtual()
```
    Returns true if this is a virtual (disk resident) stack. This method is overridden by the VirtualStack subclass.
  - trim
```
public void trim()
```
    Frees memory by deleting a few slices from the end of the stack.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - getVoxel
```
public final double getVoxel(int x,
                             int y,
                             int z)
```
    Returns, as a double, the specified voxel. Returns NaN if x, y or z are beyond the stack limits. Use the ImagePlus.getStackIndex() method to convert a C,Z,T hyperstack position (one-based) into a z index (zero-based).
    
    See Also:
    
    ImagePlus.getStackIndex(int, int, int)
  - setVoxel
```
public final void setVoxel(int x,
                           int y,
                           int z,
                           double value)
```
  - getVoxels
```
public float[] getVoxels(int x0,
                         int y0,
                         int z0,
                         int w,
                         int h,
                         int d,
                         float[] voxels)
```
  - getVoxels
```
public float[] getVoxels(int x0,
                         int y0,
                         int z0,
                         int w,
                         int h,
                         int d,
                         float[] voxels,
                         int channel)
```
  - setVoxels
```
public void setVoxels(int x0,
                      int y0,
                      int z0,
                      int w,
                      int h,
                      int d,
                      float[] voxels)
```
    Experimental
  - setVoxels
```
public void setVoxels(int x0,
                      int y0,
                      int z0,
                      int w,
                      int h,
                      int d,
                      float[] voxels,
                      int channel)
```
    Experimental
  - drawSphere
```
public void drawSphere(double radius,
                       int xc,
                       int yc,
                       int zc)
```
    Experimental
  - getBitDepth
```
public int getBitDepth()
```
    Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).
  - create
```
public static ImageStack create(int width,
                                int height,
                                int depth,
                                int bitdepth)
```
    Creates a new ImageStack.
    
    Parameters:
    
    width - width in pixels
    
    height - height in pixels
    
    depth - number of images
    
    bitdepth - 8, 16, 32 (float) or 24 (RGB)
  - duplicate
```
public ImageStack duplicate()
```
    Duplicates this stack.
  - crop
```
public ImageStack crop(int x,
                       int y,
                       int z,
                       int width,
                       int height,
                       int depth)
```
    Creates a new stack by cropping this one.
  - convertToFloat
```
public ImageStack convertToFloat()
```
    Creates a float version of this stack.

Class ImageStack

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ImageStack

ImageStack

ImageStack

ImageStack

Method Detail

addSlice

addUnsignedShortSlice

addSlice

addSlice

addSlice

deleteSlice

deleteLastSlice

getWidth

getHeight

setRoi

getRoi

update

getPixels

setPixels

getImageArray

getSize

size

getSliceLabels

getSliceLabel

getShortSliceLabel

setSliceLabel

getProcessor

setProcessor

setColorModel

getColorModel

isRGB

isHSB

isLab

isVirtual

trim

toString

getVoxel

setVoxel

getVoxels

getVoxels

setVoxels

setVoxels

drawSphere

getBitDepth

create

duplicate

crop

convertToFloat