1. A brief introduction to doxygen

2. What does a compiler do?
A compiler ignores comments and processes the code.
What does doxygen do?
It ignores the code and processes to comments.
Used to create HTML documentation.

3. Getting started with doxygen
Download from doxygen.org
Also on scott in /home/ggrevera/doxygen/bin
Do this only once in directory (folder) containing your source code:
doxygen –g
This creates a doxygen configuration file called Doxyfile which you may edit to change default options.
Edit Doxyfile and make sure all EXTRACTs are YES
For C (not C++) development, also set OPTIMIZE_OUTPUT_FOR_C = YES
Then whenever you change your code and wish to update the documentation:
doxygen
which updates all documentation in HTML subdirectory

4. Using doxygen: document every (source code) file
/**
* \file ImageData.java
* \brief contains ImageData class definition (note that this
* class is abstract) *
* <more verbose description here>
* \author George J. Grevera, Ph.D. */ .

5. Using doxygen: document every function//
/** \brief JImageViewer class. *
* Longer description goes here. */
public class JImageViewer extends JFrame implements ActionListener { .

6. Using doxygen: document every function//
/** \brief Main application entry point. *
* \param args Each image file name in args will cause that image
* to be displayed in a window.
* \returns nothing */
public static void main ( String[] args ) {
if (args.length==0) {
new JImageViewer();
} else {
for (int i = 0; i < args.length; i++)
new JImageViewer(args[i]); }

7. Using doxygen: document all class members (and global and static variables in C/C++)//
int mW; ///< image width
int mH; ///< image height
int mMin; ///< min image value
int mMax; ///< max image value
int[] mImage; ///< actual image data

8. Not every comment should be a doxygen comment.
Required:
every file
every function/method
every class member (data)
(in C/C++) every static and/or global variable
Use regular, plain comments in the body of a function/method. (One exception is the \todo.)

9. int mColorImageData[][][]; ///< should be mColorImageData[mH][mW][3]//
/** \brief Given a buffered image, this ctor reads the image data, stores
* the raw pixel data in an array, and creates a displayable version of
* the image. Note that this ctor is protected. The user should only
* use ImageData.load( fileName ) to instantiate an object of this type.
* \param bi buffered image used to construct this class instance
* \param w width of image
* \param h height of image
* \returns nothing (constructor) */
protected ColorImageData ( final BufferedImage bi, final int w, final int h ) {
mW = w;
mH = h;
mOriginalImage = bi;
mIsColor = true;
//format TYPE_INT_ARGB will be saved to mDisplayData
mDisplayData = mOriginalImage.getRGB(0, 0, mW, mH, null, 0, mW);
mImageData = new int[ mW * mH * 3 ];
mMin = mMax = mDisplayData[0] & 0xff;
for (int i=0,j=0; i<mDisplayData.length; i++) {
mDisplayData[i] &= 0xffffff; //just to insure that we only have 24-bit rgb
final int r = (mDisplayData[i] & 0xff0000) >> 16;
final int g = (mDisplayData[i] & 0xff00) >> 8;
final int b = mDisplayData[i] & 0xff;
if (r<mMin) mMin = r;
if (g<mMin) mMin = g; …

13. Summary of most useful tags
\file
\author
\brief
\param
\returns
\todo (not used in assignments)
And many, many others.