updated documentation

Josh Klontz
1 parent cc68531f
Showing 4 changed files with 169 additions and 72 deletions
openbr/openbr.h
openbr/openbr_export.cpp
share/openbr/Doxyfile.in
share/openbr/openbr.bib
@@ -146,8 +146,8 @@ BR_EXPORT float br_eval(const char *simmat, const char *mask, const char *csv = 
  
 /*!
  * \brief Evaluates and prints classification accuracy to terminal.
- * \param predicted_input The predicted br::Gallery.
- * \param truth_input The ground truth br::Gallery.
+ * \param predicted_gallery The predicted br::Gallery.
+ * \param truth_gallery The ground truth br::Gallery.
  */
 BR_EXPORT void br_eval_classification(const char *predicted_gallery, const char *truth_gallery);
  
@@ -162,7 +162,7 @@ BR_EXPORT void br_eval_clustering(const char *csv, const char *gallery);
 /*!
  * \brief Evaluates and prints detection accuracy to terminal.
  * \param predicted_gallery The predicted br::Gallery.
- * \param truth_galery The ground truth br::Gallery.
+ * \param truth_gallery The ground truth br::Gallery.
  * \param csv Optional \c .csv file to contain performance metrics.
  * \return Average detection bounding box overlap.
  */
@@ -170,8 +170,8 @@ BR_EXPORT float br_eval_detection(const char *predicted_gallery, const char *tru
  
 /*!
  * \brief Evaluates regression accuracy to disk.
- * \param predicted_input The predicted br::Gallery.
- * \param truth_input The ground truth br::Gallery.
+ * \param predicted_gallery The predicted br::Gallery.
+ * \param truth_gallery The ground truth br::Gallery.
  */
 BR_EXPORT void br_eval_regression(const char *predicted_gallery, const char *truth_gallery);
  
@@ -17,7 +17,7 @@
 /*!
  * \mainpage
  * \section overview Overview
- * OpenBR \cite openbr is a framework for investigating new modalities, improving existing algorithms, interfacing with commercial systems, measuring recognition performance, and deploying automated biometric systems.
+ * OpenBR \cite klontz2013open is a framework for investigating new modalities, improving existing algorithms, interfacing with commercial systems, measuring recognition performance, and deploying automated biometric systems.
  * The project is designed to facilitate rapid algorithm prototyping, and features a mature core framework, flexible plugin system, and support for open and closed source development.
  * Off-the-shelf algorithms are also available for specific modalities including \ref cpp_face_recognition, \ref cpp_age_estimation, and \ref cpp_gender_estimation.
  *
@@ -27,14 +27,24 @@
  * \image html "abstraction.svg" "The two principal software artifacts are the shared library 'openbr' and command line application 'br'."
  *
  * \section get_started Get Started
- * - \ref installation - \copybrief installation
- * - \ref qmake_integration - \copybrief qmake_integration
+ * - \ref introduction - A high-level technical overview of OpenBR.
+ * - \ref installation - A hacker's guide to building, editing, and running OpenBR.
+ * - \ref qmake_integration - Add OpenBR to your Qt <tt>.pro</tt> project.
  *
  * \section learn_more Learn More
- * - \ref algorithm_grammar - \copybrief algorithm_grammar
- * - \ref cli - \copybrief cli
- * - \ref c_sdk - \copybrief c_sdk
- * - \ref cpp_plugin_sdk - \copybrief cpp_plugin_sdk
+ * - \ref algorithm_grammar - How algorithms are constructed from string descriptions.
+ * - \ref cli - Command line wrapper of the \ref c_sdk.
+ * - \ref c_sdk - High-level API for running algorithms and evaluating results.
+ * - \ref cpp_plugin_sdk - Plugin API for extending OpenBR functionality.
+ * - \ref bee - A <a href="http://www.nist.gov/index.html">NIST</a> standard for evaluating biometric algorithms.
+ */
+
+/*!
+ * \page introduction Introduction
+ * \brief A high-level technical overview of OpenBR.
+ *
+ * We strongly encourage users new to OpenBR to read our <a href="www.openbiometrics.org/publications/klontz2013open.pdf"><b>publication</b></a> for an introduction to the core concepts.
+ * Researchers incorporating OpenBR into their own work are kindly requested to cite this paper.
  */
  
 /*!
-# Doxyfile 1.8.2
+# Doxyfile 1.8.4
  
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
 #
+# All text after a double hash (##) is considered a comment and is placed
+# in front of the TAG it is preceding .
 # All text after a hash (#) is considered a comment and will be ignored.
 # The format is:
 #       TAG = value [value, ...]
@@ -70,9 +72,9 @@ CREATE_SUBDIRS         = NO
 # Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
 # Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
 # Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# messages), Korean, Korean-en, Latvian, Lithuanian, Norwegian, Macedonian,
+# Persian, Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic,
+# Slovak, Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
  
 OUTPUT_LANGUAGE        = English
  
@@ -252,10 +254,10 @@ EXTENSION_MAPPING      =
  
 MARKDOWN_SUPPORT       = YES
  
-# When enabled doxygen tries to link words that correspond to documented classes,
-# or namespaces to their corresponding documentation. Such a link can be
-# prevented in individual cases by by putting a % sign in front of the word or
-# globally by setting AUTOLINK_SUPPORT to NO.
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by by putting a % sign in front of the word
+# or globally by setting AUTOLINK_SUPPORT to NO.
  
 AUTOLINK_SUPPORT       = YES
  
@@ -279,7 +281,12 @@ CPP_CLI_SUPPORT        = NO
  
 SIP_SUPPORT            = NO
  
-# For Microsoft's IDL there are propget and propput attributes to indicate getter and setter methods for a property. Setting this option to YES (the default) will make doxygen replace the get and set methods by a property in the documentation. This will only work if the methods are indeed getting or setting a simple type. If this is not the case, or you want to show the methods anyway, you should set this option to NO.
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES (the
+# default) will make doxygen replace the get and set methods by a property in
+# the documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
  
 IDL_PROPERTY_SUPPORT   = YES
  
@@ -306,11 +313,11 @@ SUBGROUPING            = YES
 INLINE_GROUPED_CLASSES = NO
  
 # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
-# unions with only public data fields will be shown inline in the documentation
-# of the scope in which they are defined (i.e. file, namespace, or group
-# documentation), provided this scope is documented. If set to NO (the default),
-# structs, classes, and unions are shown on a separate page (for HTML and Man
-# pages) or section (for LaTeX and RTF).
+# unions with only public data fields or simple typedef fields will be shown
+# inline in the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO (the default), structs, classes, and unions are shown on a separate
+# page (for HTML and Man pages) or section (for LaTeX and RTF).
  
 INLINE_SIMPLE_STRUCTS  = NO
  
@@ -324,30 +331,14 @@ INLINE_SIMPLE_STRUCTS  = NO
  
 TYPEDEF_HIDES_STRUCT   = NO
  
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penalty.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will roughly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
-
-SYMBOL_CACHE_SIZE      = 0
-
-# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
-# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
-# their name and scope. Since this can be an expensive process and often the
-# same symbol appear multiple times in the code, doxygen keeps a cache of
-# pre-resolved symbols. If the cache is too small doxygen will become slower.
-# If the cache is too large, memory is wasted. The cache size is given by this
-# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can
+# be an expensive process and often the same symbol appear multiple times in
+# the code, doxygen keeps a cache of pre-resolved symbols. If the cache is too
+# small doxygen will become slower. If the cache is too large, memory is wasted.
+# The cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid
+# range is 0..9, the default is 0, corresponding to a cache size of 2^16 = 65536
+# symbols.
  
 LOOKUP_CACHE_SIZE      = 0
  
@@ -358,7 +349,7 @@ LOOKUP_CACHE_SIZE      = 0
 # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
 # documentation are documented, even if no documentation was available.
 # Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+# the EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES
  
 EXTRACT_ALL            = YES
  
@@ -539,7 +530,8 @@ GENERATE_BUGLIST       = YES
 GENERATE_DEPRECATEDLIST= YES
  
 # The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
+# documentation sections, marked by \if section-label ... \endif
+# and \cond section-label ... \endcond blocks.
  
 ENABLED_SECTIONS       =
  
@@ -597,7 +589,8 @@ LAYOUT_FILE            =
 # requires the bibtex tool to be installed. See also
 # http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
 # of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path.
+# feature you need bibtex and perl available in the search path. Do not use
+# file names with spaces, bibtex cannot handle them.
  
 CITE_BIB_FILES         = ${BR_SHARE_DIR}/openbr.bib
  
@@ -680,7 +673,8 @@ INPUT_ENCODING         = UTF-8
 # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
 # *.f90 *.f *.for *.vhd *.vhdl
  
-FILE_PATTERNS          = *.h *.cpp
+FILE_PATTERNS          = *.h \
+                         *.cpp
  
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories
 # should be searched for input files as well. Possible values are YES and NO.
@@ -763,8 +757,10 @@ IMAGE_PATH             = ${CMAKE_SOURCE_DIR}/share/openbr
 # is the value of the INPUT_FILTER tag, and <input-file> is the name of an
 # input file. Doxygen will then use the output that the filter program writes
 # to standard output.
-# If FILTER_PATTERNS is specified, this tag will be
-# ignored.
+# If FILTER_PATTERNS is specified, this tag will be ignored.
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
  
 INPUT_FILTER           =
  
@@ -793,6 +789,13 @@ FILTER_SOURCE_FILES    = NO
  
 FILTER_SOURCE_PATTERNS =
  
+# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -934,7 +937,7 @@ HTML_EXTRA_STYLESHEET  =
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
 # that these files will be copied to the base HTML output directory. Use the
-# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
 # files. In the HTML_STYLESHEET file, use the file name only. Also note that
 # the files will be copied as-is; there are no commands or markers available.
  
@@ -1202,6 +1205,13 @@ FORMULA_TRANSPARENT    = YES
  
 USE_MATHJAX            = NO
  
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and
+# SVG. The default value is HTML-CSS, which is slower, but has the best
+# compatibility.
+
+MATHJAX_FORMAT         = HTML-CSS
+
 # When MathJax is enabled you need to specify the location relative to the
 # HTML output directory using the MATHJAX_RELPATH option. The destination
 # directory should contain the MathJax.js script. For instance, if the mathjax
@@ -1219,6 +1229,11 @@ MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
  
 MATHJAX_EXTENSIONS     =
  
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript
+# pieces of code that will be used on startup of the MathJax code.
+
+MATHJAX_CODEFILE       =
+
 # When the SEARCHENGINE tag is enabled doxygen will generate a search box
 # for the HTML output. The underlying search engine uses javascript
 # and DHTML and should work on any modern browser. Note that when using
@@ -1230,15 +1245,55 @@ MATHJAX_EXTENSIONS     =
 SEARCHENGINE           = YES
  
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
+# implemented using a web server instead of a web client using Javascript.
+# There are two flavours of web server based search depending on the
+# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
+# searching and an index file used by the script. When EXTERNAL_SEARCH is
+# enabled the indexing and searching needs to be provided by external tools.
+# See the manual for details.
  
 SERVER_BASED_SEARCH    = NO
  
+# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain
+# the search results. Doxygen ships with an example indexer (doxyindexer) and
+# search engine (doxysearch.cgi) which are based on the open source search
+# engine library Xapian. See the manual for configuration details.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will returned the search results when EXTERNAL_SEARCH is enabled.
+# Doxygen ships with an example search engine (doxysearch) which is based on
+# the open source search engine library Xapian. See the manual for configuration
+# details.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id
+# of to a relative location where the documentation can be found.
+# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ...
+
+EXTRA_SEARCH_MAPPINGS  =
+
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
@@ -1276,7 +1331,7 @@ COMPACT_LATEX          = NO
  
 # The PAPER_TYPE tag can be used to set the paper type that is used
 # by the printer. Possible values are: a4, letter, legal and
-# executive. If left blank a4wide will be used.
+# executive. If left blank a4 will be used.
  
 PAPER_TYPE             = a4
  
@@ -1299,6 +1354,13 @@ LATEX_HEADER           =
  
 LATEX_FOOTER           =
  
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images
+# or other source files which should be copied to the LaTeX output directory.
+# Note that the files will be copied as-is; there are no commands or markers
+# available.
+
+LATEX_EXTRA_FILES      =
+
 # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
 # is prepared for conversion to pdf (using ps2pdf). The pdf file will
 # contain links (just like the HTML output) instead of page references
@@ -1444,6 +1506,21 @@ XML_DTD                =
 XML_PROGRAMLISTING     = YES
  
 #---------------------------------------------------------------------------
+# configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files
+# that can be used to generate PDF.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it. If left blank docbook will be used as the default path.
+
+DOCBOOK_OUTPUT         = docbook
+
+#---------------------------------------------------------------------------
 # configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
  
@@ -1539,7 +1616,8 @@ INCLUDE_FILE_PATTERNS  =
 # undefined via #undef or recursively expanded use the := operator
 # instead of the = operator.
  
-PREDEFINED             = BR_EXPORT= __cplusplus
+PREDEFINED             = BR_EXPORT= \
+                         __cplusplus
  
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
 # this tag can be used to specify a list of macro names that should be expanded.
@@ -1592,6 +1670,12 @@ ALLEXTERNALS           = NO
  
 EXTERNAL_GROUPS        = YES
  
+# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed
+# in the related pages index. If set to NO, only the current project's
+# pages will be listed.
+
+EXTERNAL_PAGES         = YES
+
 # The PERL_PATH should be the absolute path and name of the perl script
 # interpreter (i.e. the result of `which perl').
  
@@ -1688,7 +1772,7 @@ UML_LOOK               = NO
 # the class node. If there are many fields or methods and many nodes the
 # graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
 # threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
+# manageable. Set this to 0 for no limit. Note that the threshold may be
 # exceeded by 50% before the limit is enforced.
  
 UML_LIMIT_NUM_FIELDS   = 10
@@ -30,16 +30,11 @@
 	Title = {ottochar at gmail.com}}
  
 @misc{lbestrowden,
-	Author = {Lacey S. Best-Rowden},
+	Author = {{Lacey S. Best-Rowden}},
 	Howpublished = {https://github.com/lbestrowden},
 	Title = {bestrow1 at msu.edu}}
  
 % Software
-@misc{OpenBR,
-	Author = {Joshua C. Klontz and Dr. Mark J. Burge},
-	Title = {{OpenBR} - {Open} {Biometric} {Recognition}},
-	Year = {2012}}
-
 @misc{libface,
 	Howpublished = {http://libface.sourceforge.net/file/Home.html},
 	Title = {libface},
@@ -227,6 +222,14 @@
   pages={1--8},
 }
  
+@inproceedings{klontz2013open,
+  title={{Open Source Biometric Recognition}},
+  author={Klontz et al.},
+  booktitle={Biometrics: Theory, Applications and Systems (BTAS), 2013 IEEE Sixth International Conference on},
+  year={2013},
+  organization={IEEE}
+}
+
 @inproceedings{li2009hfb,
   title={The {HFB} face database for heterogeneous face biometrics research},
   author={Li, Stan Z and Lei, Zhen and Ao, Meng},