Class ImageStack

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, where 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, where 1<=n<=nslices.

• setPixels

  public void setPixels(Object pixels, int n)

  Assigns a pixel array to the specified slice, where 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.

• size

  public int size()

  Returns the number of slices in this stack.

• getSize

  public int getSize()

• 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, where 1<=n<=nslices. Returns null if the slice does not have a label or 'n'; is out of range. 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), with the extension removed, of the specified slice label, or null if the slice does not have a label.

• getShortSliceLabel

  public String getShortSliceLabel(int n, int max)

  Returns a shortened version (up to the first 'max' characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label.

• setSliceLabel

  public void setSliceLabel(String label, int n)

  Sets the label of the specified slice, where 1<=n<=nslices.

• getProcessor

  public ImageProcessor getProcessor(int n)

  Returns an ImageProcessor for the specified slice, where 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, where 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.

• isHSB32

  public boolean isHSB32()

  Returns true if this is a 3-slice 32-bit 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).

• setBitDepth

  public void setBitDepth(int depth)

  Sets 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)

• create

  public static ImageStack create(ImagePlus[] images)

  Creates an ImageStack from an ImagePlus array.

• 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.

• setOptions

  public void setOptions(String options)