Differences between revisions 7 and 8 - No differences found!

Doxygen

Basics

This page is for notes on using Doxygen to document the Freesurfer source code.

Doxygen, http://www.stack.nl/~dimitri/doxygen/index.html, is a documentation system for C++, C, Java, and some other weird languages. It can generate html docs documenting a projects source code, by either extracting special tags from the source code (put there by people wanting to make use of doxygen), or doxygen attempts to build documentation from existing source.

Doxygen seems to be installed on the NMR systems, type:

doxygen --version

Step 1 in using doxygen is the creation of a config file. A default is created by typing:

doxygen -g

which creates a file called Doxygen.

For Freesurfer, a config file called Doxygen has been created and commited to CVS, and appears at the root directory after a CVS update.

The defaults that have been changed are the following:

20c20
< PROJECT_NAME           = FreeSurfer
---
> PROJECT_NAME           =
33c33
< OUTPUT_DIRECTORY       = ./doxygen
---
> OUTPUT_DIRECTORY       =
189c189
< OPTIMIZE_OUTPUT_FOR_C  = YES
---
> OPTIMIZE_OUTPUT_FOR_C  = NO
462c462
< INPUT                  = utils
---
> INPUT                  =
471c471
< FILE_PATTERNS          = *.c *.cpp *.h
---
> FILE_PATTERNS          =
477c477
< RECURSIVE              = YES
---
> RECURSIVE              = NO
489c489
< EXCLUDE_SYMLINKS       = YES
---
> EXCLUDE_SYMLINKS       = NO

These changes are preliminary. Notice just the utils directory is marked to be processed. Because virtually none of the freesurfer source files have any doxygen tags, the html output produced by doxygen is mostly useless junk, or missing vast numbers of file.

To generate the html and latex docs, where $FSDEV is your CVS dev dir, type:

cd $FSDEV
doxygen

The docs are put in the ./doxygen directory. See ./doxygen/html/index.html

Default file header

header could/should contain:

filename
module (see next section)
brief description
original author, or file owner (to contact in case of need for major changes)
last edit author
open-source license blrub with link
?
?

Modules

doxygen supports grouping things together: http://www.stack.nl/~dimitri/doxygen/grouping.html

what modules should be created for freesurfer? group by utility type? ie volume, surface, display

Comments and Suggestions

Doesnt seem to allow documenting csh scripts
What special commands, http://www.stack.nl/~dimitri/doxygen/commands.html, are useful?
- \file
- \addtogroup
Support for open-source community: example of well-documented source (using doxygen) that community can follow if they want to document the source (not making code changes)
best approach is probably to build one file at a time, not try to 'auto-document' the whole code-base (resulting in useless documentation). start with, say, utils.h and the mri struct.

Status

8 March 2006 - the next step is to devise a basic header, and also to create a config file that generates docs for a few core files, with the intent to add files to be 'doygenated' as they are completed.