1. A brief introduction to javadoc and doxygen Cont’d.

2. DOXYGEN

3. “Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, Tcl, and to some extent D.” -http://www.stack.nl/~dimitri/doxygen/

4. Getting started with doxygen 1. Download from doxy 1. Download from doxygen.org Also on scott in /home/ggrevera/doxygen/bin 2. 2. 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 3. 3. Then whenever you change your code and wish to update the documentation: doxygen which updates all documentation in HTML subdirectory

5. Using doxygen: document every (source code) file /** * \fileImageData.java * \briefcontains ImageData class definition (note that this *class is abstract) * * \authorGeorge J. Grevera, Ph.D. */.

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

7. 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] ); }

8. Using doxygen: document every class member (and global and static variable 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 //----------------------------------------------------------------------

9. Not every comment should be a doxygen comment. Required: 1. every file 2. every function/method 3. every class member (data) 4. (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.)

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

14. Summary of most useful tags/commands \file\author\brief\param\returns\todo And many, many others (more than 150; see http://www.stack.nl/~dimitri/doxygen/manual /commands.html). http://www.stack.nl/~dimitri/doxygen/manual /commands.html http://www.stack.nl/~dimitri/doxygen/manual /commands.html

15. Language specific notes Tags may start with either \ or @ (important for PHP as it uses \ as part of the language so you must use @ for PHP). Tags may start with either \ or @ (important for PHP as it uses \ as part of the language so you must use @ for PHP). See http://search.cpan.org/~jordan/Doxygen- Filter-Perl-1.50/lib/Doxygen/Filter/Perl.pm for Perl and doxygen. See http://search.cpan.org/~jordan/Doxygen- Filter-Perl-1.50/lib/Doxygen/Filter/Perl.pm for Perl and doxygen.http://search.cpan.org/~jordan/Doxygen- Filter-Perl-1.50/lib/Doxygen/Filter/Perl.pmhttp://search.cpan.org/~jordan/Doxygen- Filter-Perl-1.50/lib/Doxygen/Filter/Perl.pm

16. Inheritance and collaboration diagrams Automatically generated by doxygen. Example is from ITK’s AbsImageFilter (see http://www.itk.org/Doxygen43/html/classitk_1_1Abs ImageFilter.html). Automatically generated by doxygen. Example is from ITK’s AbsImageFilter (see http://www.itk.org/Doxygen43/html/classitk_1_1Abs ImageFilter.html). http://www.itk.org/Doxygen43/html/classitk_1_1Abs ImageFilter.html http://www.itk.org/Doxygen43/html/classitk_1_1Abs ImageFilter.htmlInheritance:Collaboration: