ij
Class ImageStack

java.lang.Object
  extended by ij.ImageStack
Direct Known Subclasses:
VirtualStack

public class ImageStack
extends java.lang.Object

This class represents an expandable array of images.

See Also:
ImagePlus

Constructor Summary
ImageStack()
          Default constructor.
ImageStack(int width, int height)
          Creates a new, empty image stack.
ImageStack(int width, int height, java.awt.image.ColorModel cm)
          Creates a new, empty image stack using the specified color model.
ImageStack(int width, int height, int size)
          Creates a new, empty image stack with a capacity of 'size'.
 
Method Summary
 void addSlice(ImageProcessor ip)
          Adds the image in 'ip' to the end of the stack.
 void addSlice(java.lang.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(java.lang.String sliceLabel, ImageProcessor ip, int n)
          Adds the image in 'ip' to the stack following slice 'n'.
 void addSlice(java.lang.String sliceLabel, java.lang.Object pixels)
          Adds an image in the form of a pixel array to the end of the stack.
 void addUnsignedShortSlice(java.lang.String sliceLabel, java.lang.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).
 java.awt.image.ColorModel getColorModel()
          Returns this stack's color model.
 int getHeight()
           
 java.lang.Object[] getImageArray()
          Returns the stack as an array of 1D pixel arrays.
 java.lang.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.
 java.awt.Rectangle getRoi()
           
 java.lang.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.
 java.lang.String getSliceLabel(int n)
          Returns the label of the specified slice, were 1<=n<=nslices.
 java.lang.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)
          Experimental
 float[] getVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel)
          Experimental
 int getWidth()
           
 boolean isHSB()
          Returns true if this is a 3-slice HSB stack.
 boolean isRGB()
          Returns true if this is a 3-slice RGB stack.
 boolean isVirtual()
          Returns true if this is a virtual (disk resident) stack.
 void setColorModel(java.awt.image.ColorModel cm)
          Assigns a new color model to this stack.
 void setPixels(java.lang.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(java.awt.Rectangle roi)
           
 void setSliceLabel(java.lang.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
 java.lang.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,
                  java.awt.image.ColorModel cm)
Creates a new, empty image stack using the specified color model.

Method Detail

addSlice

public void addSlice(java.lang.String sliceLabel,
                     java.lang.Object pixels)
Adds an image in the form of a pixel array to the end of the stack.


addUnsignedShortSlice

public void addUnsignedShortSlice(java.lang.String sliceLabel,
                                  java.lang.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(java.lang.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(java.lang.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(java.awt.Rectangle roi)

getRoi

public java.awt.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 java.lang.Object getPixels(int n)
Returns the pixel array for the specified slice, were 1<=n<=nslices.


setPixels

public void setPixels(java.lang.Object pixels,
                      int n)
Assigns a pixel array to the specified slice, were 1<=n<=nslices.


getImageArray

public java.lang.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.


getSliceLabels

public java.lang.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 java.lang.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 java.lang.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(java.lang.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(java.awt.image.ColorModel cm)
Assigns a new color model to this stack.


getColorModel

public java.awt.image.ColorModel getColorModel()
Returns this stack's color model. May return null.


isRGB

public boolean isRGB()
Returns true if this is a 3-slice RGB stack.


isHSB

public boolean isHSB()
Returns true if this is a 3-slice HSB 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 java.lang.String toString()
Overrides:
toString in class java.lang.Object

getVoxel

public final double getVoxel(int x,
                             int y,
                             int z)
Returns, as a double, the specified voxel.


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)
Experimental


getVoxels

public float[] getVoxels(int x0,
                         int y0,
                         int z0,
                         int w,
                         int h,
                         int d,
                         float[] voxels,
                         int channel)
Experimental


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.