EE2E1. JAVA Programming

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ImageJ
EE4H, M.Sc 0407191 Computer Vision Dr. Mike
Spann m.spann_at_bham.ac.uk http//www.eee.bham.ac.uk
/spannm
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Contents

• About ImageJ
• Image representation in ImageJ
• Displaying images in ImageJ
• ImageJ utility class
• Regions of interest
• Writing plug-ins

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About ImageJ

• All of this material is taken from the ImageJ
  tutorial accessed from my web-site
• http//mtd.fh-hagenberg.at/depot/imaging/imagej/
  
• Also check out the ImageJ home page
• http//rsb.info.nih.gov/ij/
• ImageJ is a free image processing system allowing
  easy development of Java based image processing
  algorithms in the form of plug-ins

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About ImageJ

• It comes with a user-friendly GUI and can run
  either as an application or an applet
• http//rsb.info.nih.gov/ij/applet/

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About ImageJ

• It can handle 8,16,24 and 32 bit images
• It can handle most standard image formats
• TIFF
• GIF
• JPEG
• BMP
• DICOM
• It can handle stacks of images
• Also there are plug-ins allowing it to handle
  movie files
• It can also handle regions of interest (ROIs)

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About ImageJ

• The key point about ImageJ is that it is simple
  to add your own algorithms (written as plug-ins)
  callable from the front-end GUI
• File I/O taken care of by ImageJ
• Pixel access easy from image handles defined
  within ImageJ

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Image representation in ImageJ

• ImageJ has 5 built-in image classes
• 8 bit grayscale (byte)
• 8 bit colour (byte)
• 16 bit grayscale (short)
• RGB colour (int)
• 32 bit image (float)
• It also supports image stacks consisting of
  images (slices) of the same size

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Image representation in ImageJ

• ImageJ uses 2 classes to represent and manipulate
  images
• ImagePlus
• An image is represented by an ImagePlus object
• ImageProcessor
• This holds the pixel data and contains methods to
  access the pixel data

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Image representation in ImageJ

• Pixel access methods in ImageProcessor include
• Object getPixels() returns a reference to the
  pixel array (need to cast to appropriate type)
• int getHeight() returns height of pixel array
• int getWidth() returns width of pixel array

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Image representation in ImageJ

• A subclass of ImageProcessor is passed to the
  run() method of the plug-in filter (see later)
• ByteProcessor - 8 bit grayscale images
• ShortProcessor 16 bit grayscale images
• ColorProcessor RGB images
• FloatProcessor 32 bit floating point images

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Image representation in ImageJ

• Pixel representation in ImageJ uses the byte
  datatype for grayscale and colour images and
  short for 16-bit grayscale
• byte/short are signed data types
• byte ranges from 128 to 127
• short ranges from 32768 to 32767
• Obviously grayscale values are usually positive
  values

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Image representation in ImageJ

• To cast a byte to an integer, we need to
  eliminate the sign bit
• Can cast back the other way easily enough

byte pixels(byte) ip.getPixels() int
grey0xxff pixelsj
pixelsj(byte) grey
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Image representation in ImageJ

• The ColorProcessor return the pixels as int and
  the RGB values are packed into the one int
  variable

0 bit
31
int pixels(int) ip.getPixels() int
red(0xxff0000 pixelsj) gtgt 16 int
green(0xx00ff00 pixelsj) gtgt 8 int
blue(0xx0000ff pixelsj)
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Image representation in ImageJ

• Can reconstitute an RGB array by shifting the
  other way

pixelsj((red 0xff)ltlt16)((green
0xff)ltlt8)(blue 0xff)
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Displaying images in ImageJ

• A class ImageWindow is used to display ImagePlus
  objects
• We dont normally need to access methods of
  ImageWindow
• These are automatically called from ImagePlus
  methods show(), draw() and updateAndDraw()

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ImageJ utility class

• ImageJ contains a class called IJ which contains
  a number of useful static methods
• Error messages
• static void error(String message) displays an
  error message in a dialog box
• static boolean showMessageWithCancel(String
  title, String message) allows the user to
  cancel the plug in or continue

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ImageJ utility class

• Displaying text
• static void write(String s) - Outputs text in a
  window useful for displaying textual or
  numerical results of algorithms
• Displaying text in a status bar
• static void showStatus(String s)

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ImageJ utility class

• User input
• static double getNumber(String prompt, double
  default) Allows the user to input a number in a
  dialog box
• static String getString(String prompt, String
  default) Allows the user to input a string in a
  dialog box
• The GenericDialog class is a more sophisticated
  way of inputting more than a single number or
  string

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Regions of interest (ROIs)

• A plug in filter does not always have to work on
  the whole image
• ImageJ supports ROIs which can are usually
  rectangular but can be other shapes as well.
• We set/get the ROI using the following method of
  the ImageProcessor class
• void setROI(int x, int y, int w int h)
• Rectangle getROI()

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Writing plug-ins

• To write a plug in requires developing a class
  which implements either the PlugIn or
  PlugInFilter interfaces
• The second is more usual as this is used when the
  filter requires an input image

import ij. import ij.plugin.filter.PlugInFilter
import ij.process class myPlugin implements
PlugInFilter
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Writing plug-ins

• Methods setup() and run() must then be provided
• Method setup() sets up the plugin filter for use
• String arg allows input arguments to be passed to
  the plugin
• Argument imp handled automatically by ImageJ
• Its the currently active image

int setup(String arg, ImagePlus imp)
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Writing plug-ins

• Method setup() returns a flag word representing
  the capabilities of the plug-in filter (for
  example the types of images it can handle). For
  example
• static int DOES_8G
• static int DOES_RGB
• static int DOES_ALL
• static int NO_CHANGES (plug in doesnt change the
  image data)
• static int ROI_REQUIRED
• etc

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Writing plug-ins

• The run() method is called when the plugin is run
  from the ImageJ menu
• It contains the code to process individual pixels
• If no input image is required
• If an input image is required

void run(String arg)
void run(ImageProcessor ip)
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Writing plug-ins

• Once the Java program is written and compiled,
  the .class file is stored in the plug-in
  directory which is a sub-directory of the ImageJ
  home directory
• The class name should contain an underscore
  symbol (eg MyAlgorithm_ )
• It then appears under the plug-in sub-menu of the
  ImageJ gui

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Conclusions

• ImageJ is a useful and flexible environment for
  developing Java-based image processing algorithms
• User algorithms can be simply added to a GUI
  using the concept of a plug-in
• ImageJ allows easy access to image pixel data for
  a range of image types