Package ij

Class ImageStack

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

    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 value of 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 Details

    • 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 Details

    • 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 value of the specified voxel. Throws an IndexOutOfBoundsException 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.