Histopathology image classification: Highlighting the gap between manual analysis and AI automation

Developer(s)	Dimitri van Heesch
Initial release	26 October 1997; 27 years ago (1997-10-26)[1]
Stable release	1.12.0[2]  / 7 August 2024; 3 months ago (7 August 2024)
Repository	github.com/doxygen/doxygen
Written in	C++
Operating system	Cross-platform
Type	Documentation generator
License	GPLv2
Website	doxygen.nl

Doxygen (/ˈdɒksidʒən/ DOK-see-jən)^[3] is a documentation generator^[4][5][6][7] and static analysis tool for software source trees. When used as a documentation generator, Doxygen extracts information from specially-formatted comments within the code. When used for analysis, Doxygen uses its parse tree to generate diagrams and charts of the code structure. Doxygen can cross reference documentation and code, so that the reader of a document can easily refer to the actual code.

Doxygen is free software, released under the terms of the GNU General Public License version 2 (GPLv2).

Like Javadoc, Doxygen extracts documentation from source file comments. In addition to the Javadoc syntax, Doxygen supports the documentation tags used in the Qt toolkit and can generate output in HyperText Markup Language (HTML) as well as in Microsoft Compiled HTML Help (CHM), Rich Text Format (RTF), Portable Document Format (PDF), LaTeX, PostScript or man pages.

Programming languages supported by Doxygen include C,^[8] C++, C#, D, Fortran, IDL, Java, Objective-C,^[9] Perl,^[10] PHP,^[11] Python,^[12][13] and VHDL.^[11] Other languages can be supported with additional code.

Doxygen runs on most Unix-like systems, macOS, and Windows.

The first version of Doxygen borrowed code from an early version of DOC++, developed by Roland Wunderling and Malte Zöckler at Zuse Institute Berlin. Later, the Doxygen code was rewritten by Dimitri van Heesch.

Doxygen has built-in support to generate inheritance diagrams for C++ classes. For more advanced diagrams and graphs, Doxygen can use the "dot" tool from Graphviz.^[14]

The generic syntax of documentation comments is to start a comment with an extra asterisk (*) or exclamation (!) after the leading comment delimiter '/*':

/**
<A short one line description>

<Longer description>
<May span multiple lines or paragraphs as needed>

@param  someParameter  Description of method's or function's input or output parameter
@param  ...
@return Description of the return value
*/

All commands in the documentation start with a backslash (\) or an at-sign (@).^[15]

Many programmers like to mark the start of each line with space-asterisk-space, as follows, but that is not necessary.

/**
 * <A short one line description>
 *
 * <Longer description>
 * <May span multiple lines or paragraphs as needed>
 *
 * @param  someParameter  Description of method's or function's input or output parameter
 * @param  ...
 * @return Description of the return value
 */

Many programmers avoid using C-style comments and instead use C++ style single line comments. Doxygen accepts comments with an additional subsequent slash (/) or exclamation (!) as Doxygen comments.^[16]

/// <A short one line description>
///
/// <Longer description>
/// <May span multiple lines or paragraphs as needed>
///
/// @param  someParameter  Description of method's or function's input or output parameter
/// @param  ...
/// @return Description of the return value

//! <A short one line description>
//!
//! <Longer description>
//! <May span multiple lines or paragraphs as needed>
//!
//! @param  someParameter  Description of method's or function's input or output parameter
//! @param  ...
//! @return Description of the return value

The following illustrates how a C++ source file can be documented.

/**
 * @file
 * @brief  The header file of the Time class.
 * @author  John Doe <jdoe@example.com>
 * @version  1.0
 * @copyright  CC BY-SA or GFDL.
 * @sa  <a href="https://en.wikipedia.org/wiki/Wikipedia:Copyrights">Wikipedia:Copyrights - Wikipedia</a>
 */

/**
 * The time class represents a moment of time.
 *
 * @author John Doe
 */
class Time {
public:

    /**
     * Constructor that sets the time to a given value.
     *
     * @param timeMillis A number of milliseconds passed since Jan 1, 1970.
     */
    explicit Time(long long timeMillis) {
        // the code
    }

    /**
     * Get the current time.
     *
     * @return A time object set to the current time.
     */
    static Time now() {
        // the code
    }

private:
    long long m_timeMillis; ///< Milliseconds passed since Jan 1, 1970.
};

To put documentation after members, an additional < marker is required in the comment block.^[17]

An alternative approach for documenting parameters is shown below. It will produce the same documentation.

    /**
     * Constructor that sets the time to a given value.
     */
    explicit Time(long long timeMillis /**< A number of milliseconds passed since Jan 1, 1970. */
        )
    {
        // the code
    }

    /**
     * Constructor that sets the time to a given value.
     */
    explicit Time(long long timeMillis ///< A number of milliseconds passed since Jan 1, 1970.
        )
    {
        // the code
    }

Richer markup is also possible. For instance, add equations using LaTeX commands:

/**
 *
 * An inline equation @f$ e^{\pi i}+1 = 0 @f$
 *
 * A displayed equation: @f[ e^{\pi i}+1 = 0 @f]
 *
 */

The Doxygen sources are currently hosted at GitHub, where the main developer, Dimitri van Heesch, contributes under the user name "doxygen".^[18] Doxygen is written in C++, and consists of around 300,000 source lines of code. For lexical analysis, the standard tool Lex (or its replacement Flex) is run via approximately 35,000 lines of lex script. The parsing tool Yacc (or its replacement Bison) is also used, but only for minor tasks; the bulk of language parsing is done by native C++ code. The build process is based on CMake and also involves some Python scripts.

• Comparison of documentation generators
• API Writer
• Static program analysis

• Official website