Index: /applications/bdmtoolbox/doc/Doxyfile
===================================================================
--- /applications/bdmtoolbox/doc/Doxyfile (revision 1044)
+++ /applications/bdmtoolbox/doc/Doxyfile (revision 1044)
@@ -0,0 +1,1541 @@
+# Doxyfile 1.5.8
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+#       TAG = value [value, ...]
+# For lists items can also be appended using:
+#       TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file 
+# that follow. The default is UTF-8 which is also the encoding used for all 
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the 
+# iconv built into libc) for the transcoding. See 
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING      = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
+# by quotes) that should identify the project.
+
+PROJECT_NAME           = SCORPION
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number. 
+# This could be handy for archiving the generated documentation or 
+# if some version control system is used.
+
+PROJECT_NUMBER         =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) 
+# base path where the generated documentation will be put. 
+# If a relative path is entered, it will be relative to the location 
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY       = C:/testDoxygen
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
+# 4096 sub-directories (in 2 levels) under the output directory of each output 
+# format and will distribute the generated files over these directories. 
+# Enabling this option can be useful when feeding doxygen a huge amount of 
+# source files, where putting all generated files in the same directory would 
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS         = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all 
+# documentation generated by doxygen is written. Doxygen will use this 
+# information to generate all constant output in the proper language. 
+# The default language is English, other supported languages are: 
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional, 
+# Croatian, Czech, Danish, Dutch, 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-Cyrilic, Slovak, Slovene, 
+# Spanish, Swedish, and Ukrainian.
+
+OUTPUT_LANGUAGE        =
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will 
+# include brief member descriptions after the members that are listed in 
+# the file and class documentation (similar to JavaDoc). 
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC      = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend 
+# the brief description of a member or function before the detailed description. 
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the 
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF           = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator 
+# that is used to form the text in various listings. Each string 
+# in this list, if found as the leading text of the brief description, will be 
+# stripped from the text and the result after processing the whole list, is 
+# used as the annotated text. Otherwise, the brief description is used as-is. 
+# If left blank, the following values are used ("$name" is automatically 
+# replaced with the name of the entity): "The $name class" "The $name widget" 
+# "The $name file" "is" "provides" "specifies" "contains" 
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF       = "The $name class" \
+                         "The $name widget" \
+                         "The $name file" \
+                         is \
+                         provides \
+                         specifies \
+                         contains \
+                         represents \
+                         a \
+                         an \
+                         the
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then 
+# Doxygen will generate a detailed section even if there is only a brief 
+# description.
+
+ALWAYS_DETAILED_SEC    = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all 
+# inherited members of a class in the documentation of that class as if those 
+# members were ordinary class members. Constructors, destructors and assignment 
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB  = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full 
+# path before files name in the file list and in the header files. If set 
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES        = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag 
+# can be used to strip a user-defined part of the path. Stripping is 
+# only done if one of the specified strings matches the left-hand part of 
+# the path. The tag can be used to show relative paths in the file list. 
+# If left blank the directory from which doxygen is run is used as the 
+# path to strip.
+
+STRIP_FROM_PATH        = /Users/dimitri/doxygen/mail/1.5.7/doxywizard/
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of 
+# the path mentioned in the documentation of a class, which tells 
+# the reader which header file to include in order to use a class. 
+# If left blank only the name of the header file containing the class 
+# definition is used. Otherwise one should specify the include paths that 
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH    = 
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter 
+# (but less readable) file names. This can be useful is your file systems 
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES            = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen 
+# will interpret the first line (until the first dot) of a JavaDoc-style 
+# comment as the brief description. If set to NO, the JavaDoc 
+# comments will behave just like regular Qt-style comments 
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF      = YES
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will 
+# interpret the first line (until the first dot) of a Qt-style 
+# comment as the brief description. If set to NO, the comments 
+# will behave just like regular Qt-style comments (thus requiring 
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF           = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen 
+# treat a multi-line C++ special comment block (i.e. a block of //! or /// 
+# comments) as a brief description. This used to be the default behaviour. 
+# The new default is to treat a multi-line C++ comment block as a detailed 
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented 
+# member inherits the documentation from any documented member that it 
+# re-implements.
+
+INHERIT_DOCS           = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce 
+# a new page for each member. If set to NO, the documentation of a member will 
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES  = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab. 
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE               = 16
+
+# This tag can be used to specify a number of aliases that acts 
+# as commands in the documentation. An alias has the form "name=value". 
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to 
+# put the command \sideeffect (or @sideeffect) in the documentation, which 
+# will result in a user-defined paragraph with heading "Side Effects:". 
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES                = 
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C 
+# sources only. Doxygen will then generate output that is more tailored for C. 
+# For instance, some of the names that are used will be different. The list 
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C  = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java 
+# sources only. Doxygen will then generate output that is more tailored for 
+# Java. For instance, namespaces will be presented as packages, qualified 
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA   = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran 
+# sources only. Doxygen will then generate output that is more tailored for 
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN   = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL 
+# sources. Doxygen will then generate output that is tailored for 
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL   = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it parses. 
+# With this tag you can assign which parser to use for a given extension. 
+# Doxygen has a built-in mapping, but you can override or extend it using this tag. 
+# The format is ext=language, where ext is a file extension, and language is one of 
+# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP, 
+# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat 
+# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran), 
+# use: inc=Fortran f=C
+
+EXTENSION_MAPPING      = m=C++
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want 
+# to include (a tag file for) the STL sources as input, then you should 
+# set this tag to YES in order to let doxygen match functions declarations and 
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s. 
+# func(std::string) {}). This also make the inheritance and collaboration 
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT    = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to 
+# enable parsing support.
+
+CPP_CLI_SUPPORT        = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only. 
+# Doxygen will parse them like normal C++ but will assume all classes use public 
+# instead of private inheritance when no explicit protection keyword is present.
+
+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 to 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
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC 
+# tag is set to YES, then doxygen will reuse the documentation of the first 
+# member in the group (if any) for the other members of the group. By default 
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC   = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of 
+# the same type (for instance a group of public functions) to be put as a 
+# subgroup of that type (e.g. under the Public Functions section). Set it to 
+# NO to prevent subgrouping. Alternatively, this can be done per class using 
+# the \nosubgrouping command.
+
+SUBGROUPING            = YES
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
+# is documented as struct, union, or enum with the name of the typedef. So 
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct 
+# with name TypeT. When disabled the typedef will appear as a member of a file, 
+# namespace, or class. And the struct will be named TypeS. This can typically 
+# be useful for C code in case the coding convention dictates that all compound 
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT   = YES
+
+# 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 penality. 
+# 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 rougly 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
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# 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
+
+EXTRACT_ALL            = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
+# will be included in the documentation.
+
+EXTRACT_PRIVATE        = YES
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
+# will be included in the documentation.
+
+EXTRACT_STATIC         = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
+# defined locally in source files will be included in the documentation. 
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES  = YES
+
+# This flag is only useful for Objective-C code. When set to YES local 
+# methods, which are defined in the implementation section but not in 
+# the interface are included in the documentation. 
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS  = YES
+
+# If this flag is set to YES, the members of anonymous namespaces will be 
+# extracted and appear in the documentation as a namespace called 
+# 'anonymous_namespace{file}', where file will be replaced with the base 
+# name of the file that contains the anonymous namespace. By default 
+# anonymous namespace are hidden.
+
+EXTRACT_ANON_NSPACES   = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all 
+# undocumented members of documented classes, files or namespaces. 
+# If set to NO (the default) these members will be included in the 
+# various overviews, but no documentation section is generated. 
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS     = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all 
+# undocumented classes that are normally visible in the class hierarchy. 
+# If set to NO (the default) these classes will be included in the various 
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES     = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all 
+# friend (class|struct|union) declarations. 
+# If set to NO (the default) these declarations will be included in the 
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS  = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any 
+# documentation blocks found inside the body of a function. 
+# If set to NO (the default) these blocks will be appended to the 
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS      = NO
+
+# The INTERNAL_DOCS tag determines if documentation 
+# that is typed after a \internal command is included. If the tag is set 
+# to NO (the default) then the documentation will be excluded. 
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS          = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate 
+# file names in lower-case letters. If set to YES upper-case letters are also 
+# allowed. This is useful if you have classes or files whose names only differ 
+# in case and if your file system supports case sensitive file names. Windows 
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES       = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen 
+# will show members with their full class and namespace scopes in the 
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES       = YES
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen 
+# will put a list of the files that are included by a file in the documentation 
+# of that file.
+
+SHOW_INCLUDE_FILES     = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline] 
+# is inserted in the documentation for inline members.
+
+INLINE_INFO            = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen 
+# will sort the (detailed) documentation of file and class members 
+# alphabetically by member name. If set to NO the members will appear in 
+# declaration order.
+
+SORT_MEMBER_DOCS       = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the 
+# brief documentation of file, namespace and class members alphabetically 
+# by member name. If set to NO (the default) the members will appear in 
+# declaration order.
+
+SORT_BRIEF_DOCS        = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the 
+# hierarchy of group names into alphabetical order. If set to NO (the default) 
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES       = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be 
+# sorted by fully-qualified names, including namespaces. If set to 
+# NO (the default), the class list will be sorted only by class name, 
+# not including the namespace part. 
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. 
+# Note: This option applies only to the class list, not to the 
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME     = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or 
+# disable (NO) the todo list. This list is created by putting \todo 
+# commands in the documentation.
+
+GENERATE_TODOLIST      = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or 
+# disable (NO) the test list. This list is created by putting \test 
+# commands in the documentation.
+
+GENERATE_TESTLIST      = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or 
+# disable (NO) the bug list. This list is created by putting \bug 
+# commands in the documentation.
+
+GENERATE_BUGLIST       = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or 
+# disable (NO) the deprecated list. This list is created by putting 
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional 
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS       = 
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines 
+# the initial value of a variable or define consists of for it to appear in 
+# the documentation. If the initializer consists of more lines than specified 
+# here it will be hidden. Use a value of 0 to hide initializers completely. 
+# The appearance of the initializer of individual variables and defines in the 
+# documentation can be controlled using \showinitializer or \hideinitializer 
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES  = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated 
+# at the bottom of the documentation of classes and structs. If set to YES the 
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES        = YES
+
+# If the sources in your project are distributed over multiple directories 
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES       = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page. 
+# This will remove the Files entry from the Quick Index and from the 
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES             = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the 
+# Namespaces page.  This will remove the Namespaces entry from the Quick Index 
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES        = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that 
+# doxygen should invoke to get the current version for each file (typically from 
+# the version control system). Doxygen will invoke the program by executing (via 
+# popen()) the command <command> <input-file>, where <command> is the value of 
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file 
+# provided by doxygen. Whatever the program writes to standard output 
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER    = 
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by 
+# doxygen. The layout file controls the global structure of the generated output files 
+# in an output format independent way. The create the layout file that represents 
+# doxygen's defaults, run doxygen with the -l option. You can optionally specify a 
+# file name after the option, if omitted DoxygenLayout.xml will be used as the name 
+# of the layout file.
+
+LAYOUT_FILE            = 
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated 
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET                  = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are 
+# generated by doxygen. Possible values are YES and NO. If left blank 
+# NO is used.
+
+WARNINGS               = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED   = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for 
+# potential errors in the documentation, such as not documenting some 
+# parameters in a documented function, or documenting parameters that 
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR      = YES
+
+# This WARN_NO_PARAMDOC option can be abled to get warnings for 
+# functions that are documented, but have no documentation for their parameters 
+# or return value. If set to NO (the default) doxygen will only warn about 
+# wrong or incomplete parameter documentation, but not about the absence of 
+# documentation.
+
+WARN_NO_PARAMDOC       = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that 
+# doxygen can produce. The string should contain the $file, $line, and $text 
+# tags, which will be replaced by the file and line number from which the 
+# warning originated and the warning text. Optionally the format may contain 
+# $version, which will be replaced by the version of the file (if it could 
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT            = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning 
+# and error messages should be written. If left blank the output is written 
+# to stderr.
+
+WARN_LOGFILE           = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain 
+# documented source files. You may enter file names like "myfile.cpp" or 
+# directories like "/usr/src/myproject". Separate the files or directories 
+# with spaces.
+
+INPUT                  = C:/SPP_dev/Code/Librairie
+
+# This tag can be used to specify the character encoding of the source files 
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
+# also the default input encoding. Doxygen uses libiconv (or the iconv built 
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for 
+# the list of possible encodings.
+
+INPUT_ENCODING         = ISO-8859-1
+
+# If the value of the INPUT tag contains directories, you can use the 
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank the following patterns are tested: 
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+
+FILE_PATTERNS          = *.c \
+                         *.cc \
+                         *.cxx \
+                         *.cpp \
+                         *.c++ \
+                         *.d \
+                         *.java \
+                         *.ii \
+                         *.ixx \
+                         *.ipp \
+                         *.i++ \
+                         *.inl \
+                         *.h \
+                         *.hh \
+                         *.hxx \
+                         *.hpp \
+                         *.h++ \
+                         *.idl \
+                         *.odl \
+                         *.cs \
+                         *.php \
+                         *.php3 \
+                         *.inc \
+                         *.m \
+                         *.mm \
+                         *.dox \
+                         *.py \
+                         *.f90 \
+                         *.f \
+                         *.vhd \
+                         *.vhdl
+
+# 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. 
+# If left blank NO is used.
+
+RECURSIVE              = YES
+
+# The EXCLUDE tag can be used to specify files and/or directories that should 
+# excluded from the INPUT source files. This way you can easily exclude a 
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE                = 
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
+# directories that are symbolic links (a Unix filesystem feature) are excluded 
+# from the input.
+
+EXCLUDE_SYMLINKS       = NO
+
+# If the value of the INPUT tag contains directories, you can use the 
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
+# certain files from those directories. Note that the wildcards are matched 
+# against the file with absolute path, so to exclude all test directories 
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS       = *.py
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
+# (namespaces, classes, functions, etc.) that should be excluded from the 
+# output. The symbol name can be a fully qualified name, a word, or if the 
+# wildcard * is used, a substring. Examples: ANamespace, AClass, 
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS        = 
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or 
+# directories that contain example code fragments that are included (see 
+# the \include command).
+
+EXAMPLE_PATH           = 
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the 
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
+# and *.h) to filter out the source-files in the directories. If left 
+# blank all files are included.
+
+EXAMPLE_PATTERNS       = *
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be 
+# searched for input files to be used with the \include or \dontinclude 
+# commands irrespective of the value of the RECURSIVE tag. 
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE      = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or 
+# directories that contain image that are included in the documentation (see 
+# the \image command).
+
+IMAGE_PATH             = 
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should 
+# invoke to filter for each input file. Doxygen will invoke the filter program 
+# by executing (via popen()) the command <filter> <input-file>, where <filter> 
+# 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.
+
+INPUT_FILTER           = 
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern 
+# basis.  Doxygen will compare the file name with each pattern and apply the 
+# filter if there is a match.  The filters are a list of the form: 
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further 
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER 
+# is applied to all files.
+
+FILTER_PATTERNS        = *.m=C:/SPP_dev/Compilation/m2cpp.pl
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using 
+# INPUT_FILTER) will be used to filter the input files when producing source 
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES    = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will 
+# be generated. Documented entities will be cross-referenced with these sources. 
+# Note: To get rid of all source code in the generated output, make sure also 
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER         = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body 
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES         = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct 
+# doxygen to hide any special comment blocks from generated source code 
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS    = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES 
+# then for each documented function all documented 
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES 
+# then for each documented function all documented entities 
+# called/used by that function will be listed.
+
+REFERENCES_RELATION    = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default) 
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from 
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will 
+# link to the source code.  Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code 
+# will point to the HTML generated by the htags(1) tool instead of doxygen 
+# built-in source browser. The htags tool is part of GNU's global source 
+# tagging system (see http://www.gnu.org/software/global/global.html). You 
+# will need version 4.8.6 or higher.
+
+USE_HTAGS              = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen 
+# will generate a verbatim copy of the header file for each class for 
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS       = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index 
+# of all compounds will be generated. Enable this if the project 
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX     = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then 
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns 
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX    = 5
+
+# In case all classes in a project start with a common prefix, all 
+# classes will be put under the same header in the alphabetical index. 
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that 
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX          = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will 
+# generate HTML output.
+
+GENERATE_HTML          = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT            = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for 
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank 
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION    = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard header.
+
+HTML_HEADER            = 
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for 
+# each generated HTML page. If it is left blank doxygen will generate a 
+# standard footer.
+
+HTML_FOOTER            = 
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
+# style sheet that is used by each HTML page. It can be used to 
+# fine-tune the look of the HTML output. If the tag is left blank doxygen 
+# will generate a default style sheet. Note that doxygen will try to copy 
+# the style sheet file to the HTML output directory, so don't put your own 
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET        = 
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
+# files or namespaces will be aligned in HTML using tables. If set to 
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS     = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML 
+# documentation will contain sections that can be hidden and shown after the 
+# page has loaded. For this to work a browser that supports 
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox 
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS  = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files 
+# will be generated that can be used as input for Apple's Xcode 3 
+# integrated development environment, introduced with OSX 10.5 (Leopard). 
+# To create a documentation set, doxygen will generate a Makefile in the 
+# HTML output directory. Running make will produce the docset in that 
+# directory and running "make install" will install the docset in 
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find 
+# it at startup. 
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
+
+GENERATE_DOCSET        = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the 
+# feed. A documentation feed provides an umbrella under which multiple 
+# documentation sets from a single provider (such as a company or product suite) 
+# can be grouped.
+
+DOCSET_FEEDNAME        = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that 
+# should uniquely identify the documentation set bundle. This should be a 
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen 
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID       = org.doxygen.Project
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files 
+# will be generated that can be used as input for tools like the 
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP      = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can 
+# be used to specify the file name of the resulting .chm file. You 
+# can add a path in front of the file if the result should not be 
+# written to the html output directory.
+
+CHM_FILE               = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can 
+# be used to specify the location (absolute path including file name) of 
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run 
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION           = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag 
+# controls if a separate .chi index file is generated (YES) or that 
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI           = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING 
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file 
+# content.
+
+CHM_INDEX_ENCODING     = 
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag 
+# controls whether a binary table of contents is generated (YES) or a 
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC             = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members 
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND             = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER 
+# are set, an additional index file will be generated that can be used as input for 
+# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated 
+# HTML documentation.
+
+GENERATE_QHP           = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can 
+# be used to specify the file name of the resulting .qch file. 
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE               = 
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating 
+# Qt Help Project output. For more information please see 
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE          = 
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating 
+# Qt Help Project output. For more information please see 
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER     = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add. 
+# For more information please see 
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME   = 
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see 
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS  = 
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's 
+# filter section matches. 
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS  = 
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can 
+# be used to specify the location of Qt's qhelpgenerator. 
+# If non-empty doxygen will try to run qhelpgenerator on the generated 
+# .qhp file.
+
+QHG_LOCATION           = 
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at 
+# top of each HTML page. The value NO (the default) enables the index and 
+# the value YES disables it.
+
+DISABLE_INDEX          = NO
+
+# This tag can be used to set the number of enum values (range [1..20]) 
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE   = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index 
+# structure should be generated to display hierarchical information. 
+# If the tag value is set to FRAME, a side panel will be generated 
+# containing a tree-like index structure (just like the one that 
+# is generated for HTML Help). For this to work a browser that supports 
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+, 
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are 
+# probably better off using the HTML help feature. Other possible values 
+# for this tag are: HIERARCHIES, which will generate the Groups, Directories, 
+# and Class Hierarchy pages using a tree view instead of an ordered list; 
+# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which 
+# disables this behavior completely. For backwards compatibility with previous 
+# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE 
+# respectively.
+
+GENERATE_TREEVIEW      = NONE
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be 
+# used to set the initial width (in pixels) of the frame in which the tree 
+# is shown.
+
+TREEVIEW_WIDTH         = 250
+
+# Use this tag to change the font size of Latex formulas included 
+# as images in the HTML documentation. The default is 10. Note that 
+# when you change the font size after a successful doxygen run you need 
+# to manually remove any form_*.png images from the HTML output directory 
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE       = 10
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will 
+# generate Latex output.
+
+GENERATE_LATEX         = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT           = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be 
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME         = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to 
+# generate index for LaTeX. If left blank `makeindex' will be used as the 
+# default command name.
+
+MAKEINDEX_CMD_NAME     = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact 
+# LaTeX documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+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, a4wide, letter, legal and 
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE             = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX 
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES         = 
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for 
+# the generated latex document. The header should contain everything until 
+# the first chapter. If it is left blank doxygen will generate a 
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER           = 
+
+# 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 
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS         = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of 
+# plain latex in the generated Makefile. Set this option to YES to get a 
+# higher quality PDF documentation.
+
+USE_PDFLATEX           = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. 
+# command to the generated LaTeX files. This will instruct LaTeX to keep 
+# running if errors occur, instead of asking the user for help. 
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE        = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not 
+# include the index chapters (such as File Index, Compound Index, etc.) 
+# in the output.
+
+LATEX_HIDE_INDICES     = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output 
+# The RTF output is optimized for Word 97 and may not look very pretty with 
+# other RTF readers or editors.
+
+GENERATE_RTF           = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. 
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be 
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT             = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact 
+# RTF documents. This may be useful for small projects and may help to 
+# save some trees in general.
+
+COMPACT_RTF            = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated 
+# will contain hyperlink fields. The RTF file will 
+# contain links (just like the HTML output) instead of page references. 
+# This makes the output suitable for online browsing using WORD or other 
+# programs which support those fields. 
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS         = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's 
+# config file, i.e. a series of assignments. You only have to provide 
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE    = 
+
+# Set optional variables used in the generation of an rtf document. 
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE    = 
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will 
+# generate man pages
+
+GENERATE_MAN           = NO
+
+# The MAN_OUTPUT tag is used to specify where the man 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 `man' will be used as the default path.
+
+MAN_OUTPUT             = man
+
+# The MAN_EXTENSION tag determines the extension that is added to 
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION          = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output, 
+# then it will generate one additional man file for each entity 
+# documented in the real man page(s). These additional files 
+# only source the real man page, but without them the man command 
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS              = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will 
+# generate an XML file that captures the structure of 
+# the code including all documentation.
+
+GENERATE_XML           = NO
+
+# The XML_OUTPUT tag is used to specify where the XML 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 `xml' will be used as the default path.
+
+XML_OUTPUT             = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_SCHEMA             = 
+
+# The XML_DTD tag can be used to specify an XML DTD, 
+# which can be used by a validating XML parser to check the 
+# syntax of the XML files.
+
+XML_DTD                = 
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
+# dump the program listings (including syntax highlighting 
+# and cross-referencing information) to the XML output. Note that 
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING     = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will 
+# generate an AutoGen Definitions (see autogen.sf.net) file 
+# that captures the structure of the code including all 
+# documentation. Note that this feature is still experimental 
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF   = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will 
+# generate a Perl module file that captures the structure of 
+# the code including all documentation. Note that this 
+# feature is still experimental and incomplete at the 
+# moment.
+
+GENERATE_PERLMOD       = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate 
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able 
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX          = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be 
+# nicely formatted so it can be parsed by a human reader.  This is useful 
+# if you want to understand what is going on.  On the other hand, if this 
+# tag is set to NO the size of the Perl module output will be much smaller 
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY         = YES
+
+# The names of the make variables in the generated doxyrules.make file 
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. 
+# This is useful so different doxyrules.make files included by the same 
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX = 
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor   
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will 
+# evaluate all C-preprocessor directives found in the sources and include 
+# files.
+
+ENABLE_PREPROCESSING   = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro 
+# names in the source code. If set to NO (the default) only conditional 
+# compilation will be performed. Macro expansion can be done in a controlled 
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION        = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES 
+# then the macro expansion is limited to the macros specified with the 
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF     = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files 
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES        = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that 
+# contain include files that are not input files but should be processed by 
+# the preprocessor.
+
+INCLUDE_PATH           = 
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
+# patterns (like *.h and *.hpp) to filter out the header-files in the 
+# directories. If left blank, the patterns specified with FILE_PATTERNS will 
+# be used.
+
+INCLUDE_FILE_PATTERNS  = 
+
+# The PREDEFINED tag can be used to specify one or more macro names that 
+# are defined before the preprocessor is started (similar to the -D option of 
+# gcc). The argument of the tag is a list of macros of the form: name 
+# or name=definition (no spaces). If the definition and the = are 
+# omitted =1 is assumed. To prevent a macro definition from being 
+# undefined via #undef or recursively expanded use the := operator 
+# instead of the = operator.
+
+PREDEFINED             = 
+
+# 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. 
+# The macro definition that is found in the sources will be used. 
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED      = 
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then 
+# doxygen's preprocessor will remove all function-like macros that are alone 
+# on a line, have an all uppercase name, and do not end with a semicolon. Such 
+# function macros are typically used for boiler-plate code, and will confuse 
+# the parser if not removed.
+
+SKIP_FUNCTION_MACROS   = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references   
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles. 
+# Optionally an initial location of the external documentation 
+# can be added for each tagfile. The format of a tag file without 
+# this location is as follows: 
+#   TAGFILES = file1 file2 ... 
+# Adding location for the tag files is done as follows: 
+#   TAGFILES = file1=loc1 "file2 = loc2" ... 
+# where "loc1" and "loc2" can be relative or absolute paths or 
+# URLs. If a location is present for each tag, the installdox tool 
+# does not have to be run to correct the links. 
+# Note that each tag file must have a unique name 
+# (where the name does NOT include the path) 
+# If a tag file is not located in the directory in which doxygen 
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES               = BDM.tag=../../library
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create 
+# a tag file that is based on the input files it reads.
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+GENERATE_TAGFILE       = 
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed 
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+ALLEXTERNALS           = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed 
+# in the modules index. If set to NO, only the current project's groups will 
+# be listed.
+
+EXTERNAL_GROUPS        = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script 
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH              = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool   
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base 
+# or super classes. Setting the tag to NO turns the diagrams off. Note that 
+# this option is superseded by the HAVE_DOT option below. This is only a 
+# fallback. It is recommended to install and use dot, since it yields more 
+# powerful graphs.
+
+CLASS_DIAGRAMS         = YES
+
+# You can define message sequence charts within doxygen comments using the \msc 
+# command. Doxygen will then run the mscgen tool (see 
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the 
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where 
+# the mscgen tool resides. If left empty the tool is assumed to be found in the 
+# default search path.
+
+MSCGEN_PATH            = 
+
+# If set to YES, the inheritance and collaboration graphs will hide 
+# inheritance and usage relations if the target is undocumented 
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS   = NO
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is 
+# available from the path. This tool is part of Graphviz, a graph visualization 
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section 
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+
+HAVE_DOT               = YES
+
+# By default doxygen will write a font called FreeSans.ttf to the output 
+# directory and reference it in all dot files that doxygen generates. This 
+# font does not include all possible unicode characters however, so when you need 
+# these (or just want a differently looking font) you can specify the font name 
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+# which can be done by putting it in a standard location or by setting the 
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
+# containing the font.
+
+DOT_FONTNAME           = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs. 
+# The default size is 10pt.
+
+DOT_FONTSIZE           = 10
+
+# By default doxygen will tell dot to use the output directory to look for the 
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a 
+# different font using DOT_FONTNAME you can set the path where dot 
+# can find it using this tag.
+
+DOT_FONTPATH           = 
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+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect inheritance relations. Setting this tag to YES will force the 
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH            = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for each documented class showing the direct and 
+# indirect implementation dependencies (inheritance, containment, and 
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+COLLABORATION_GRAPH    = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen 
+# will generate a graph for groups, showing the direct groups dependencies
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+GROUP_GRAPHS           = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and 
+# collaboration diagrams in a style similar to the OMG's Unified Modeling 
+# Language.
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+UML_LOOK               = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the 
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS     = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT 
+# tags are set to YES then doxygen will generate a graph for each documented 
+# file showing the direct and indirect include dependencies of the file with 
+# other documented files.
+
+INCLUDE_GRAPH          = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and 
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each 
+# documented header file showing the documented files that directly or 
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+INCLUDED_BY_GRAPH      = YES
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+# If the CALL_GRAPH and HAVE_DOT options are set to YES then 
+# doxygen will generate a call dependency graph for every global function 
+# or class method. Note that enabling this option will significantly increase 
+# the time of a run. So in most cases it will be better to enable call graphs 
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH             = YES
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then 
+# doxygen will generate a caller dependency graph for every global function 
+# or class method. Note that enabling this option will significantly increase 
+# the time of a run. So in most cases it will be better to enable caller 
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH           = YES
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen 
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY    = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES 
+# then doxygen will show the dependencies a directory has on other directories 
+# in a graphical way. The dependency relations are determined by the #include 
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH        = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
+# generated by dot. Possible values are png, jpg, or gif 
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT       = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be 
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH               = "C:/Program Files/Graphviz2.22/bin"
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that 
+# contain dot files that are included in the documentation (see the 
+# \dotfile command).
+
+DOTFILE_DIRS           = 
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of 
+# nodes that will be shown in the graph. If the number of nodes in a graph 
+# becomes larger than this value, doxygen will truncate the graph, which is 
+# visualized by representing a node as a red box. Note that doxygen if the 
+# number of direct children of the root node in a graph is already larger than 
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note 
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES    = 54
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the 
+# graphs generated by dot. A depth value of 3 means that only nodes reachable 
+# from the root by following a path via at most 3 edges will be shown. Nodes 
+# that lay further from the root node will be omitted. Note that setting this 
+# option to 1 or 2 may greatly reduce the computation time needed for large 
+# code bases. Also note that the size of a graph can be further restricted by 
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH    = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent 
+# background. This is disabled by default, because dot on Windows does not 
+# seem to support this out of the box. Warning: Depending on the platform used, 
+# enabling this option may lead to badly anti-aliased labels on the edges of 
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT        = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output 
+# files in one run (i.e. multiple -o and -T options on the command line). This 
+# makes dot run faster, but since only newer versions of dot (>1.8.10) 
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS      = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will 
+# generate a legend page explaining the meaning of the various boxes and 
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND        = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will 
+# remove the intermediate dot files that are used to generate 
+# the various graphs.
+
+DOT_CLEANUP            = YES
+
+#---------------------------------------------------------------------------
+# Options related to the search engine
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be 
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE           = NO
Index: /applications/bdmtoolbox/doc/local/000install.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/000install.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/000install.dox (revision 1044)
@@ -0,0 +1,103 @@
+/*!
+\page install BDM Toolbox - Installation
+
+\section in_bin Binaries for BDMtoolbox
+Binaries for the matlab BDMtoolbox are available only for windows (win32) platform, compiled against matlab 7.1 for compatibility.
+
+Installation:
+ - svn checkout http://mys.utia.cas.cz:1800/svn/mixpp/applications/bdmtoolbox/ into your local directory of your choice (this will be denoted \<toolbox_dir\>)
+ - or download a prepared zip file from http://staff.utia.cas.cz/smidl/Public/bdmtoolbox_win32.zip and extract it to any directory (will be denoted \<toolbox_dir\>)
+ - open matlab and type:
+\code 
+>> addpath <toolbox_dir>/mex; 
+>> addpath <toolbox_dir>/mexw32
+>> addpath <toolbox_dir>/mex_classes
+\endcode
+for downloaded win32 version of the toolbox. When compiling from sources, the mex files may be located in Debug of Release directories. Check where 
+	the latest compiled files are and add apropriate path. E.g. for Windown and Mac:
+\code 
+>> addpath <toolbox_dir>/mex; 
+>> addpath <toolbox_dir>/mex/Debug; 
+>> addpath <toolbox_dir>/mex_classes
+\endcode
+For linux, the default build dir is \<toolbox_dir\>/mex, hence only me and mex_classes need to be in the path.
+ - the toolbox is ready to be used, test it e.g. by: 
+\code >> cd tutorial/userguide; 
+>> pdfds_example \endcode
+ - if no error is given, the toolbox is installed correctly
+ - proceed to tutorial at http://mys.utia.cas.cz:1800/trac/bdm/doxygen/pages.html to learn how to use it
+
+\section src Source code
+
+is available from svn repository:
+http://mys.utia.cas.cz:1800/svn/mixpp using guest/guest as login/password.
+
+For download use an appropriate SVN client http://subversion.tigris.org/links.html#clients
+
+Download the source files to any directory of your choise, this directory will be refered to as \<bdm_dir\>.
+
+\subsection pre Prerequisities
+
+You need to have the following tools available on your system:
+ - working C++ compiler, e.g. gcc on Linux, or Visual Studio on windows
+ - CMake, a cross-platform build system, http://www.cmake.org
+ 
+\section lin Linux
+
+All prerequisities are available as binary packages for most distribution. E.g. for debian-based distributions, use
+\code
+apt-get install g++ cmake 
+\endcode
+
+Compile the BDM library and its applications using 
+\code
+$ cd <bdm_dir>/library/
+$ cmake .
+$ make
+$ cd <bdm_dir>/applications/bdmtoolbox/
+$ cmake .
+$ make
+\endcode
+
+
+\section win Windows
+
+The following approach was tested on the Microsoft Visual Studio 9. 
+
+Make sure you have cmake installed.
+
+We are including latest stable code from IT++ which requires a implementation of BLAS and LAPACK routines. 
+The most convenient library is ACML which can be downloaded from AMD.
+
+For convenience of the beginners, DLLS of the ACML and lib+include files for ITPP and ACML are
+provided at: http://staff.utia.cas.cz/smidl/Public/mixpp_win32lib.zip
+If you want to use them copy the content of the zip file to \<bdm_dir\>/library/system/win32/ directory and
+make sure to set your PATH environment variable:
+\code
+ Path = %PATH%; <bdm_dir>\library\system\win32\dll
+\endcode
+
+Be sure to set system variable globally, i.e., through the dialog box "System Properties", 
+tab "Advanced" and button "Environment Variables". Otherwise you will not be able to run 
+any programs.
+
+
+Compilation of BDM for the first time:
+
+ -# Run CMake GUI and specify address to your \<bdm_dir\>/library, press "Configure" and then "Generate"
+ -# It should generate build files for your compiler in the main BDM  directory, open then in Visual Studio and press Build
+ -# Run CMake GUI and specify address to your \<bdm_dir\>/applications/bdmtoolbox/, press "Configure" and then "Generate"
+ -# It should generate build files for your compiler in the application/bdmtoolbox directory, open then in Visual Studio and press Build
+ 
+Once the CMake files are created, there is no need to run it again. Th Visual Studio will call cmake itself.
+
+\section mac Mac OS X
+
+All prerequisities for Mac OS X are avaliable, make sure you have them installed.
+
+Right now, Cmake configuration is hard-coded for one testing machine. Look for the paths in SetBDMEnv.cmake and correct them.
+Open CMake GUI, click Configure followed by Create.
+
+Compilation is the same as for Windows, with Visual Studio replaced by XCode
+
+*/
Index: /applications/bdmtoolbox/doc/local/00scenarios.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/00scenarios.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/00scenarios.dox (revision 1044)
@@ -0,0 +1,29 @@
+/*!
+\page bdt_scenarios Basic Scenarios of BDMToolbox
+
+The basic elements of BDM are:
+ -# probability density functions, (bdm::pdf), both conditional and unconditional 
+ -# functions, (bdm::fnc), of vector arguments
+ -# Bayesian estimators (bdm::BM), providing variaous exact and approximate algorithms for Bayesian inference
+ -# Data Sources (bdm::DS), providing access to various form of recursive data
+ -# Controllers (bdm::Controller), generating control strategies, both feedback, or feedforward
+ -# Loggers (bdm::logger), for storing results of experiments
+
+The objects are designed to allow mutual combination of these. Distinction of what needs to be connected where is provided by class RV which stands for random variable.
+
+Predefined scenarios implemented in mex are:
+
+ - Simulation, see \ref simulator.cpp
+ - Estimation, see \ref estimator.cpp
+ - Controll Loop, see \ref controlloop.cpp
+ - Multiple-Participant Decision-Making, see \ref arena.cpp
+
+For details of their use, see tutorials:
+ - \ref userguide_pdf
+ - \ref userguide_sim
+ - \ref userguide_estim
+ - \ref userguide_ctrl
+ 
+ 
+
+ */
Index: /applications/bdmtoolbox/doc/local/01userguide_pdf.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/01userguide_pdf.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/01userguide_pdf.dox (revision 1044)
@@ -0,0 +1,122 @@
+/*!
+\page userguide_pdf BDM Use - Probability density functions
+
+This section serves as an introduction to basic elements of the BDM: probability density functions, pdfs.
+
+Table of content:
+ - \ref ug_pdf_create 
+ - \ref ug_pdf_marg 
+ - \ref ug_pdf_cond 
+ - \ref ug_pdf_fnc 
+ - \ref ug_pdf_mex 
+
+\section ug_pdf_create Using built-in pdfs
+
+In BDM toolbox, a pdf is specified by matlab structure, e.g.
+\code
+Nab.class= 'enorm<ldmat>';
+Nab.mu   = [3,2];
+Nab.R    = eye(2);
+Nab.rv   = RV({'a','b'});
+\endcode
+Which encodes information \f$ f(a,b) = \mathcal{N}(mu=[3;2],R=eye(2))\f$.
+\li the keyword "enorm\<ldmat\>" means "Unconditional Normal distribution with covariance matrix in L'DL form", other possibilities are: 
+"enorm\<chmat\>" for Choleski decomposition, and "enorm\<fsqmat\>" for full (non-decomposed) matrices.
+\li mu denotes mean value
+\li R denotes variance (written in full matrix regardles of the used decomposition),
+\li parameters mu and R are vector and matrix, respectively. They can be given directly (as in Nab.mu) or as a result of arbitrary matlab function, (as in Nab.R)
+\li rv denotes names assigned to the variables. RV is more complicated structure, but here it is sufficient to use default values.
+\li rv is an optional parameter, some operations do not need it, such as sampling or evaluation of moments
+
+For generating samples try:
+\code
+>> M=epdf_sample_mat(Nab,4);
+\endcode
+which should return 4 samples of the Nab distribution.
+
+For evaluation of mean and variance:
+\code
+>> Nab_m=epdf_mean(Nab);
+>> Nab_v=epdf_variance(Nab);
+\endcode
+
+Other distributions are created analogously, see \ref bdm_doc/annotated_epdf.html
+
+\section ug_pdf_marg Marginalization and conditioning
+
+Basic operations on pdfs are marginalization and conditioning, which are provided by mex functions edpf_marginal and epdf_condition, respectively.
+
+This operation does require the rv parametetr to be fully specified. If it isn't, it will fail with the following message
+\code
+--- fill in the message ----
+\endcode
+
+If rv is correctly specified, marginal pdf of Nab on variable "a" is obtained by:
+\code
+Na = epdf_marginal(Nab,RV('a'));
+\endcode
+
+Similarly for conditional:
+\code
+Na_b = epdf_condition(Nab,RV('a'));
+Nb_a = epdf_condition(Nab,RV('b'));
+\endcode
+
+\section ug_pdf_cond Conditioned densities
+Note that the result of conditioning is of type "mlnorm\<ldmat\>" which is a special case of pdf with variables in condition, specifically 
+\f[ f(a|b) = \mathcal{N}(A*b+const, R)\f] 
+i.e. "Normal distributed pdf with mean value as linear function of variable b".
+
+This type of pdfs differ from previously used type is the way of use. For example, it is not possible to sample directly form such density, 
+it is necessary to specify what is the value of variable in condition. 
+
+That is why a different function is used:
+\code
+Smp=pdf_samplecond_mat(Na_b, 10)
+\endcode
+
+The conditioned and Unconditioned pdf may be combined together in the chain rule. The chain rule can be of two different types: conditioned or unconditioned, i.e.:
+\f[ f(a,b)=f(a|b)f(b), OR, f(a,b|c)=f(a|b)f(b|c)\f]
+Thus it is differently encoded as:
+\code
+fab.class = 'eprod';         % result is unconditioned pdf
+fab.pdfs  = {fa_b, fb};
+
+fab_c.class = 'mprod';       % result is conditioned pdf
+fab_c.pdfs  = {fa_b, fb_c};
+\endcode
+
+\section ug_pdf_fnc Pdfs with functional transformation
+
+In more general type of pdfs, variables in condition may be transformed by a function. 
+For example Gaussian density with nonlinear transformation of mean value, \f$ f(x|y) = \mathcal{N}(g(y), R)\f$, is represented by class \c mgnorm
+
+\code
+fx.class  = 'mgnorm<ldmat>';             
+fx.g      = 'mexFunction';              % function is evaluated in matlab
+fx.g.function = 'test_function';         % name of the matlab function to evaluate
+fx.g.dim  = 2;                          % expected dimension of output
+fx.g.dimc = 2;                          % expected dimension of input
+fx.R      = eye(2);                     % variance R
+\endcode
+
+This example is using generic function specified by name of Matlab .m file. 
+Compulsory fields \c g.dim and \c g.dimc are used to check correct dimension of inputs and outputs of the function. 
+
+List of functions is in \ref bdm_doc/annotated_fnc
+
+\section ug_pdf_mex Using Matlab classes of pdfs
+
+Access to Matlab defined classe of pdfs is provided via structure:
+\code 
+class = 'mexEpdf';
+object = any_object_of_mexEpdf;
+\endcode
+where object can be created by any offspring of mexEpdf.
+
+See \ref mex_bdm, and files: mex/mex_classes/mexEpdf.m
+
+If you wish to write your own Matlab classes see \ref ug_dev_mat.
+
+For list of all available pdf objects, see \ref annotated_epdf.html , \ref annotated_pdf.html and \ref annotated.html
+*/
Index: /applications/bdmtoolbox/doc/local/02userguide_sim.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/02userguide_sim.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/02userguide_sim.dox (revision 1044)
@@ -0,0 +1,253 @@
+/*!
+\page userguide_sim BDM Use - System, Data, Simulation
+
+This section serves as introduction to the scenario of data simulation. Since it is the simplest of all scenarios defined in \ref userguide0 it also serves as introduction to configuration of an experiment (see \ref ui) and basic decision making objects (bdm::RV and bdm::DS).
+
+All experiments are demonstrated on mex file \c simulator, which is also available as a standalone application.
+
+Table of contents:
+\ref ug_sim_config 
+\ref ug_sim 
+\ref ug_memds 
+\ref ug_rvs 
+\ref ug_rv_connect 
+\ref ug_pdfds 
+\ref ug_arx_sim 
+\ref ug_ini 
+\ref ug_store 
+
+
+\section ug_sim_config Configuration of an experiment
+
+Configuration file (or config structure) is organized as a tree of information. High levels represent complex structures, leafs of the tree are basic data elements such as strings, numbers or vectors.
+
+Specific treatment was developed for objects. Since BDM is designed as object oriented library, the configuration was designed to honor the rule of inheritance. That is, offspring of a class can be used in place of its predecessor. Hence, objects (instances of classes) are configured by a structure  with compulsory field \c class. This is a string variable corresponding to the name of the class to be used. This information is stored in Matlab structures (or objects, see section on Matlab extensions).
+
+Advanced users can find more information in (\ref ui).
+
+\subsection ug_first First experiment
+
+The first experiment that can be performed is:
+\code
+DS.class='MemDS';
+DS.Data =[1 2 3 4 5 6];
+\endcode
+which can be found in file bdmtoolbox/tutorials/userguide/memds_example.m.
+
+The code above is the minimum necessary information to run scenario \c simulator in Matlab. 
+To actually do so, make sure that Matlab paths are correctly set, as described in \ref install.
+
+The expected result for Matlab is:
+\code
+>> M=simulator(DS)
+
+M = 
+
+    ch0: [6x1 double]
+\endcode
+
+All that the simulator did was actually copying \c DS.Data to \c M.ch0. Explanation of the experiment and the logic used there follows.
+
+\section ug_sim Systems and DataSources
+
+In standard system theory, the system is typically illustrated graphically as:
+\dot 
+digraph sys{
+	node [shape=box];
+	{"System"}
+	node [shape=plaintext]
+	{rank="same"; "u"; "System"; "y"}
+	"u" -> "System" -> "y" [nodesep=2];
+}
+\enddot
+Where \c u typically denotes input and \c y denotes output of the system. A causal dependence between input and output is typically presumed.
+
+We are predominantly concerned with discrete-time systems, hence, we will add indices \f$ _t \f$ to both input and output, \f$ u_t \f$ and \f$ y_t \f$. We presume that the causal dependence is \f$ u_t \f$ comes before \f$ y_t \f$.
+
+One of the definition of a system is that system is a "set of variables observed on a part of the world". Under this definition system is understood as generator of data. This definition may be a considered too simplistic, but it serves well as a description of what software object \c DataSource is.
+
+DataSource is an object that is essentially able to:
+ -# return data observed at time \f$ t \f$, 
+ -# perform one a time step.
+ -# describe what these data are, via class RV, introduced in ref \ref ug_pdf_marg,
+ -# store log of its activity into dedicated logger.
+
+No further specification, e.g. if the data are pre-recorded or computed on-the-fly, are given.
+For a list of available DataSources, see ...
+
+
+\section ug_memds DataSource of pre-recorded data -- MemDS
+
+The first experiment run in \ref ug_first was actually an instance of DataSource of pre-recorded data that were stored in memory, i.e. the bdm::MemDS class.
+
+Operation of such object is trivial, the data are stored as a matrix and the general operations defined above are specialized as follows:
+ -# data observed at time \f$ t \f$  are columns of the matrix, getdata() returns current column,
+ -# time step itself is performed by increasing the column index,
+ -# each row is named as "ch0","ch1",...
+
+This is the default behavior. It can be customized using the UI mechanism. Full list of options is:
+\code
+DS.class = 'MemDS';
+DS.Data = (...);            // Data matrix or data vector
+	--- optional ---
+DS.drv = RV({"ch0",...} ); // Identification how rows of the matrix Data will be known to others
+DS.time = 0;               // Index of the first column to user_info,
+\endcode
+The compulsory fields are listed at the beginning; the optional fields are separated by string "--- optional ---".
+
+Fields \c time denotes the first record to start counting from. Field \c drv is a the one that specifies identification of the data elements, (point 3. of the general requirements of a DataSource). 
+
+All optionals fields will be filled by default values, it this case:
+\code
+DS.drv  = RV({'ch0'},1,0);
+DS.time = 0;
+\endcode
+Where the first line specifies a universal identification structure: random variable (bdm::RV).
+
+\section ug_rvs What is RV and how to use it
+
+RV stands for \c random \c variable which is a description of random variable or its realization. However, this object serves as general descriptor of fields in vectors of data. 
+
+It is used for:
+ - description of RV in pdfs, ways how to define marginalization and conditioning,
+ - connection between source of data and computational objects that use them,
+ - connection <b>time</b>, more exactly time shift from \f$ t \f$, defaults to 0.
+
+For example, the estimators will request the data from the above mentioned data source by asking for rv 'ch0'. If a more meaningful names are available, the fields drv can be added to read:
+\code
+DS.class='MemDS';
+DS.Data =[1 2 3 4 5 6];
+DS.drv = RV('y');
+\endcode
+Data from this data source will be available when estimators ask for rv 'y'.
+
+\subsection ug_rv_connect Storing results
+
+results of an experiment can be stored in many ways. This functionality was abstracted into a class called logger. Exact form of the stored results is chosen by choosing appropriate class.
+For example, \c stdlog writes all output in the console, \c dirfilelog writes all data in the dirfilelog format for high-speed data processing, \c mexlog writes data into Matlab structure. 
+The \c mexlog is the default option in bdmtoolbox.
+
+Connection between computational blocks and loggers is controlled by structure called \c log_level which governs the level of details to be logged.
+A standard Data source has two levels, \c logdt and \c logut which means "log all outputs, dt" and "log all inputs, ut".
+Readers familiar with Simulink environment may look at the RV as being unique identifiers of inputs and outputs of simulation blocks. The inputs are connected automatically with the outputs with matching RV. This view is however, very incomplete, RV have more roles than this.
+
+\section ug_pdfds How to create a simulator from pdfs 
+For example, we would like to simulate a random Uniform distributed noise on interval <-1,1>. 
+This is achieved by plugging an object representing uniform pdf into general simulator of independent random samples, pdfDS. Uniform density is implemented as class bdm::euni, which is created from the following structure:
+\code
+U.class='euni';
+U.rv   = RV({'a'});
+U.high = 1.0;
+U.low  = -1.0;
+\endcode
+which encodes information:\f[
+f(a) = \mathcal{U}(-1,1)
+\f]
+  
+The datasource itself, i.e. the instance of \c EpdfDS can be then configured via:
+\code
+DS.class = 'pdfDS';
+DS.pdf  = U;
+\endcode
+where \c U is the structure defined above.
+
+Contrary to the previous example, we need to tell to algorithm \c simulator how many samples from the data source we need. This is configured by variable \c experiment.ndat. The configuration has to be finalized by:
+\code 
+experiment.ndat = 10;
+M=simulator(DS,experiment);
+\endcode
+
+The result is as expected in field \c M.DS_dt_a the name of which corresponds to results form "datasouce" / "output_dt" / "name given in U.rv".
+
+If the task was only to generate random realizations, this would indeed be a very clumsy way of doing it. 
+However, the power of the proposed approach will be revealed in more demanding examples, one of which follows next.
+
+By default, data from this datasouce will be named after the rvs in given by the pdfs. When pdf with no rv is used, drv of the data source is set again to 'ch0'.
+
+\section ug_arx_sim Simulating autoregressive model
+
+Consider the following autoregressive model: 
+\f[
+f(y_t|y_{t-3},u_{t-1}) = \mathcal{N}( a y_{t-3} + b u_{t-1}, r)
+\f]
+where \f$ a,b \f$ are known constants, and \f$ r \f$ is known variance.
+
+We need to handle two issues:
+ -# extra unsimulated variable \f$ u \f$,
+ -# time delays of the values.
+
+The first issue can be handled in two ways. First, \f$ u \f$ can be considered as input and as such it could be externally given to the datasource. This solution is used in scenario \c closedloop.
+However, for the \c simulator scenario we will apply the second option, that is we complement \f$ f(y_{t}|y_{t-3},u_{t-1})\f$ by extra pdf:\f[
+f(u_t) = \mathcal{N}(0, r_u)
+\f]
+where \f$ r_u \f$ is another known constant.
+Thus, the joint density is now:\f[
+f(y_{t},u_{t}|y_{t-3},u_{t-1}) = f(y_{t}|y_{t-3},u_{t-1})f(u_{t})
+\f]
+and we have no need for input since the datasource have all necessary information inside. All that is required is to store them and copy their values to appropriate places.
+
+That is done in automatic way (via bdm::datalink_buffered). The only issue a user may need to take care about is the missing initial conditions for simulation.
+By default these are set to zeros. Using the default values, the full configuration of this system is:
+\code
+y = RV({'y'});
+u = RV({'u'});
+
+fy.class = 'mlnorm\<ldmat\>';
+fy.rv    = y;
+fy.rvc   = RV({'y','u'}, [1 1], [-3, -1]);
+fy.A     = [0.5, -0.9];
+fy.const = 0;
+fy.R     = 0.1;
+
+
+fu.class = 'enorm\<ldmat\>';
+fu.rv    = u;
+fu.mu    = 0;
+fu.R     = 0.2;
+
+DS.class = 'pdfDS';
+DS.pdf.class  = 'mprod';
+DS.pdf.pdfs  = {fy, fu};
+\endcode
+
+Explanation of this example will require few remarks:
+ - class of the \c fy object is 'mlnorm\<ldmat\>' which is Normal pdf with mean value given by linear function, and covariance matrix stored in LD decomposition, see bdm::mlnorm for details.
+ - naming convention 'mlnorm\<ldmat\>' relates to the concept of templates in C++. For those unfamiliar with this concept, it is basically a way how to share code for different flavors of the same object. Note that mlnorm exist in three versions: mlnorm\<ldmat\>, mlnorm<chmat>, mlnorm<fsqmat>. Those classes act identically the only difference is that the internal data are stored either in LD decomposition, choleski decomposition or full matrices, respectively. 
+ - the same concept is used for enorm, where enorm<chmat> and enorm<fsqmat> are also possible. In this particular use, these objects are equivalent. In specific situation, e.g. Kalman filter implemented on Choleski decomposition (bdm::KalmanCh), only enorm<chmat> is approprate.
+ - class 'mprod' represents the chain rule of probability, see \ref ug_pdf_cond.
+ 
+The code above can be immediately run, using the same execution sequence of \c estimator as above. 
+
+\subsection ug_ini Initializing simulation
+
+When zeros are not appropriate initial conditions, the correct conditions can be set using additional commands:
+\code
+DS.init_rv = RV({'y','y','y'}, [1,1,1], [-1,-2,-3]);
+DS.init_values = [0.1, 0.2, 0.3];
+\endcode
+
+The values of \c init_values will be copied to places in history identified by corresponding values of \c init_rv.
+Initial data is not checked for completeness, i.e. values of random variables missing from \c init_rv (in this case all occurrences of \f$ u \f$) are still initialized to 0.
+
+\section ug_store Storing results of simulation
+
+If the simulated data are to be analyzed off-line it may be advantageous to store them and use later on. 
+This operation is straightforward if the class of logger used in the \c simulator is compatible with some datasource class.
+
+For example, the output of \c MemDS can be stored as an .it file (filename is specified in configuration structure) which can be later read by bdm::ITppFileDS.
+
+In Matlab, the output of mexlog is a structure of vectors or matrices. The results can be saved in a Matlab file using:
+\code
+Data=[M.y; M.u];
+drv = RVjoin({y,u});
+save pdfds_results Data drv
+\endcode
+Such data can be later provided e.g. by MemDS
+\code
+mxDS.class   = 'MemDS';
+mxDS.Data    = 'Data';
+mxDS.drv     = drv;
+\endcode
+
+For list of all DataSources and loggers, see \ref app_base
+*/
Index: /applications/bdmtoolbox/doc/local/20devguide_matlab.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/20devguide_matlab.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/20devguide_matlab.dox (revision 1044)
@@ -0,0 +1,240 @@
+/*!
+\page devguide_mat  BDMToolbox Development - your first bdm class in Matlab
+
+bdmtoolbox provides a prodefined points of extensions in directory applications/bdmtoolbox/mex/mex_classes.
+
+The easiest way to extend bdmtoolbox is to use clasess starting with "mex". The simplies class of this type is mexFnc, which just contains name of an arbitrary matlab function to call.
+See \ref ug_pdf_fnc example.
+
+This tutorial assumes you are familiar with basic classes of BDM: pdfs, random variables (\ref userguide_pdf) and estimators (\ref userguide_estim).
+
+Previous part of the tutorial introduced ways how to use existing classes. If no premade class is suitable for your mneeds, you can create your own class in Matlab via predefined interfaces to class epdf (mexEpdf) and BM (mexBM).
+These classes are treated as regular C++ classes in prepared mex files. Creation of a new estimator (offspring of class BM) can be achieved by inheriting from class mexBM.
+
+In practice this means creation of a new file, e.g. my_bm.m, with header:
+\code
+class my_bm < mexBM
+\endcode
+This file must be located in directories known to matlab (must be in its path). This can be any directory if you use addpath command. 
+See relevant documentation in Matlab.
+
+For list of existing mex* classes see \ref annotated.html
+
+\section dev_mat_pdf Creating your own probability density
+
+Creation of your own density is achieved by inheriting from mexEpdf:
+\code
+class my_pdf < mexEpdf
+\endcode
+in a file called my_pdf.m. 
+
+Calling methods from mexEpdf will result in an error that tells you which functionality is missing.
+It is necessary to give them a meaning.
+
+Epdf is a class representing probability density function of a multivariate (vector) variable.
+
+The easiest example of a density is dirac Delta function 
+\f[
+f(x_t) = \delta( x_t - \bar{x}_t )
+\f]
+with properties:
+ - \f$ \bar{x}_t \f$ is the statistics of this density.
+ - dimension of the density is dimension of the vector \f$ \bar{x}_t \f$
+ - the mean value of the density is \f$ E(x_t) = \bar{x}_t \f$
+ - the variance value of the density is \f$ var(x_t) = zeros() \f$
+ - all samples from this density are equal to \f$ \bar{x}_t \f$
+ 
+ These properties are encoded in software as follows:
+ 
+\code
+classdef mexDirac < mexEpdf
+    % Dirac delta probability distribution
+    properties                                                 % DATA structures
+        point                                                  % point of the support, \bar{x}_t
+    end
+    methods
+        function m=mean(obj)                                   % compute mean values of the density
+            m = obj.point;
+        end
+        function obj=validate(obj)                             % check if data structures are consistent
+            % point should be a column
+            if (size(obj.point,2)>1)
+                if (size(obj.point,1)==1) % it is row
+                    obj.point = obj.point';
+                end
+            else
+                error('Point in mexDirac is not a vector');
+            end
+        end
+        function dim=dimension(obj)                            % inform others about your dimensions
+            dim = size(obj.point,1);
+        end
+        function v=variance(obj)                               % compute variance
+            v=zeros(size(obj.point));
+        end
+        function l=evallog(obj,x)                              % return logarithm of your density at point x
+            if obj.point==x
+                l = inf;
+            else
+                l=0;
+            end
+        end
+        function s=sample(obj);                                % return random sample from your density
+            s = obj.point;
+        end
+    end
+end
+\endcode
+
+An additional compulsory function is called \c validate which is called always before use of the class in an algorithm. The task of this function is to detect any inconsistency in the object and give the user an appropriate warning. 
+For example, in this case, the function checks if the property point is indeed a vector and not a matrix or other structure.
+
+Once you define the methdos above, this object can be plugged into (almost) an arbitrary algoritm, such as simulator, etc.
+
+For seamless use with other objects, you need to define its random variables - via attribute rv, \ref ug_pdf_create.
+
+For inspiration see example class mexLaplace.m and its use in simulation in tutorial/userguide/epdfds_example.m
+
+\section dev_mat_bm Defining your own Bayesian Estimator (BM)
+If you look into the mexBM.m file you see the basic attributes and default functions. mexBM as such will not work as a valid estimator.
+In order to make it work, you need to re-define at least functions <b>dimensions</b> and <b>bayes</b>, and attribute <b>apost_pdf</b>:
+  
+This function announces sizes of random variables to other objects. 
+
+These sizes can be fixed for a specific problem, or derived from size of internal objects. E.g. for a Kalman filter, the function would be:
+\code
+function dims=dimensions(p)
+   %please fill
+   %dims = [size_of_posterior size_of_data size_of_condition]
+   dims = [size(A,1), size(C,1), size(B,2)] %
+end
+\endcode
+Which indicates that dimension of \f$x_t\f$ is the rows of matrix A, size of \f$y_t\f$ is the rows of matrix C and the size of \f$u_t\f$ is given by columns of matrix B.
+  
+The argument apost_pdf should be a valid object of class mexEpdf, see previous section how to achieve it.
+
+The second function to extend is
+\code
+function obj=bayes(obj,dt,cond)
+   % transform old estimate into new estimate
+end
+\endcode
+
+Here, you need to define an update (both time- and data-update) of your Bayesian filter.
+
+Note, that statistics of the posterior are stored in attribute apost_pdf. So, the task of this function is to update fileds in apost_pdf. 
+
+Any additional attributes needed for this task shoul be added to properties of the object.
+
+
+\section dev_exa Example task: Laplace estimation
+
+Consider a systems, where data are generated by a Laplace model 
+\f[
+f(y_t|a,b) = \frac{1}{2b} \exp \left( -\frac{x-a}{b} \right)
+\f]
+with unknown time-varying parameters \f$ a \f$ and \f$ b \f$. 
+
+We decided to estimate parameters of the system using ML estimates of parameters on a sliding window. The estimates are then:
+\f{eqnarray}
+\hat{a}& =& \mathrm{median}([y_{t},y_{t-1},\ldots , y_{t-d}),\\
+\hat{b}& = & \frac{1}{d} \sum_{\tau=t-d}^{t} | y_\tau - \hat{a} |
+\f}
+
+Implementing this system in BDM requires the following steps:
+ - realize that ML estimation is an extreme approximation of Bayes rule with posterior in the form of Dirac delat pdf, this pdf is ready from the previous step.
+ - under this choice, the posterior is a 2-dimensional dirac, which is encoded as:
+ \code
+ apost_pdf = mexDirac;
+ apost_pdf.point = [0;0];
+ \endcode 
+ - the class mexDirac as introduced has only one attribute: point, which is a vector of the support. If we wish to distinguish the meaning of these values, we use attribute rv. For example, 
+ \code
+ apost_pdf.rv = RV({'a','b'});
+ \endcode
+ - the class representing an estimator of this type, needs to remember internal statistics in the form window of data, which will be stored in properties of the class
+
+ - dimensionality of the estimator is then: 2-dimensional parameters, 1-dimensional observation, 0-dimensional conditioning variables. It is encoded as:
+ \code
+  function dims=dimensions(p)
+      %please fill
+      %dims = [size_of_posterior size_of_data size_of_condition]
+      dims = [2,1,0] %
+  end
+  \endcode
+ - the method \c bayes then copies the obtained data into the window and updates estimates \f$ \hat{a}, \hat{b}\f$
+
+This estimator has been implemented as class mexLaplaceBM as follows:
+ 
+This is implemented as follows:
+\code
+classdef mexLaplaceBM < mexBM
+    % Approximate Bayesian estimator of parameters of Laplace distributed observation.
+    % Maximum likelihood approximation of the Bayes rule is used, posterior is in the form of dirac.
+    properties
+        max_window_length = 10;                               % max window length (default = 10)
+        data_window =[];                                      % sliding window of data 
+    end
+    methods
+        function obj=validate(obj)                            % prepare all internal objects for use
+            obj.apost_pdf = mexDirac;
+            obj.apost_pdf.point = [0;0];
+            obj.log_evidence = 0;                             % evidence is not computed!
+        end
+
+        function dims=dimensions(obj)
+            %please fill: dims = [size_of_posterior size_of_data size_of_condition]
+            dims = [2,1,0]                                    % we have: [2d parameters, 1d observations, 0d condition]
+        end
+        function obj=bayes(obj,dt,cond)                       % approximate bayes rule
+            if size(obj.data_window,2)>=obj.max_window_length
+                obj.data_window = [dt obj.data_window(1:end-1)];
+            else
+                obj.data_window = [dt obj.data_window];
+            end
+            % transform old estimate into new estimate
+            m_hat = mean(obj.data_window);
+            b_hat = sum(abs(obj.data_window-m_hat))/ size(obj.data_window,2);
+            obj.apost_pdf.point = [m_hat; b_hat];             % store result in psoterior pdf
+        end
+    end
+
+end
+\endcode
+
+\section dev_mat_alt Alternative representations of this estimator
+
+Note, that the estimator above is rather coarse approximation of the Bayes rule. Indeed, in this case, the sliding window represnts a statistics on the posterior parameters, 
+and thus it should be part of the posterior, which can thus evaluate more moments that the current Dirac density.
+
+Such a design is certainly possible, however, it would result in much more complex calculations and more complex coding. If that is the aim, a new class can be designed.
+
+\section dev_mat_pred Predictors and simulation
+
+Note, that the Laplacian likelihood model of the example is not needed for its estimation. The very basic estimator introduced above does not need to know about existence of the likelihood function.
+
+However, existence of this distribution is required by related tasks of data simulation and data prediction.
+Therefore, a class mexLaplace was designed, which implements all operations of pdf in the same manner as the in \ref dev_mat_pdf.
+
+This pdf is then used in the mexLaplaceBM in function that creates predictors:
+\code 
+function p=epredictor(obj,cond)                       % when predictive density is needed approximate it by Laplace with point estimates
+   % return predictive density (max likelihood)
+   p = mexLaplace;
+   p.mu = obj.apost_pdf.point(1);
+   p.b  = obj.apost_pdf.point(2);
+	% do not forget to validate
+   p=p.validate;
+	% assign descriptions
+	p.rv = yrv;
+	% rvc is empty be default
+end
+\endcode
+  
+Also, the class mexLaplace can be used to generate data, see bdmtoolbox/mex/epdfds_example.m
+
+Since it provides all required methods, it can be combined with other pdfs in chain rules, as in pdfds_example.m
+
+Similar extensions to mexEpdf and mexBM can be made to other classes. See library/mex/mex_Epdf.h and library/mex/mex_BM.h how it is done.
+As always, feel free to contact the maintainer for help.
+*/
Index: /applications/bdmtoolbox/doc/local/21mex_bdm.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/21mex_bdm.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/21mex_bdm.dox (revision 1044)
@@ -0,0 +1,39 @@
+/*!
+\page mex_bdm  BDMToolbox Development - combining Matlab classes and BDM classes
+
+The classes written in Matlab can be combined with standard BDM classes via corresponding C++ classes with equal names, i.e. mexBM.m is accepted by C++ class mexBM
+
+The class bdm::mexEpdf has the following Matlab structure:
+\code
+class = 'mexEpdf';
+object = any_mexEpdf_object;
+\endcode
+
+This clas acts as an interface between BDM objects of type bdm::epdf and Matlab objects of type mexEpdf.
+
+Example:
+\code
+clear all
+
+f.class = 'mexEpdf';
+f.object = mexLaplace;
+f.object.mu =12;
+f.object.b = 1;
+f.object.rv = RV('b',1);
+
+
+DS.class='EpdfDS';
+DS.epdf =f; %U
+
+experiment.ndat=10;
+
+M=simulator(DS,experiment);
+
+M.DS_dt_b
+\endcode
+
+Here, Matlab class mexLaplace is created and plugged in as attribute \c object of bdm class 'mexEpdf'.
+Class bdm::EpdfDS accepts this kind of object and perfroms its task, i.e. it generates samples from the density.
+
+
+*/
Index: /applications/bdmtoolbox/doc/local/03userguide_estim.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/03userguide_estim.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/03userguide_estim.dox (revision 1044)
@@ -0,0 +1,188 @@
+/*!
+\page userguide_estim BDM Use - Estimation and Bayes Rule
+
+Bayesian theory is predominantly used in system identification, or estimation problems. 
+This section is concerned with recursive estimation, as implemented in prepared scenario \c estimator.
+
+Table of contents:
+\ref ug2_theory 
+\ref ug2_arx_basic 
+\ref ug2_model_sel 
+\ref ug2_bm_composition 
+\ref ug_est_ext 
+
+The function of the \c estimator is graphically illustrated:
+\dot
+digraph estimation{
+	node [shape=box];
+	{rank="same"; "Data Source"; "Bayesian Model"}
+	"Data Source" -> "Bayesian Model" [label="data"];
+	"Bayesian Model" -> "Result Logger" [label="estimation\n result"];
+	"Data Source" -> "Result Logger" [label="Simulated\n data"];
+}
+\enddot
+
+Here,
+\li Data Source is an object (class DS) providing sequential data, \f$ [d_1, d_2, \ldots d_t] \f$.
+\li Bayesian Model is an object (class BM) performing Bayesian filtering,
+\li Result Logger is an object (class logger) dedicated to storing important data from the experiment.
+
+Since objects  datasource and the logger has already been introduced in section \ref userguide_sim, it remains to introduce 
+object \c Bayesian \c Model (bdm::BM).
+
+\section ug2_theory Bayes rule and estimation
+The object bdm::BM is basic software image of the Bayes rule:
+\f[ f(x_t|d_1\ldots d_t) \propto f(d_t|x_t,d_1\ldots d_{t-1}) f(x_t| d_1\ldots d_{t-1}) \f]
+
+Since this operation can not be defined universally, the object is defined as abstract class with methods for:
+ - <b> Bayes rule </b> as defined above, operation bdm::BM::bayes() which expects to get the current data record \c dt, \f$ d_t \f$
+ - <b> evidence </b> i.e. numerical value of \f$ f(d_t|d_1\ldots d_{t-1})\f$ as a typical side-product, since it is required in denominator of the above formula.
+   For some models, computation of this value may require extra effort, and can be switched off.
+ - <b> prediction </b> the object has enough information to create the one-step ahead predictor, i.e. \f[ f(d_{t+1}| d_1 \ldots d_{t}), \f] 
+	
+Implementation of these operations is heavily dependent on the specific class of prior pdf, or its approximations. We can identify only a few principal approaches to this problem. For example, analytical estimation which is possible within sufficient the Exponential Family, or estimation when both prior and posterior are approximated by empirical densities. 
+These approaches are first level of descendants of class \c BM, classes bdm::BMEF and bdm::PF, respectively.
+
+\section ug2_arx_basic Estimation of ARX models
+
+Autoregressive models has already been introduced in \ref ug_arx_sim where their simulator has been presented.
+We will use results of simulation of the ARX datasource defined there to provide data for estimation using MemDS.
+
+The following code is from bdmtoolbox/tutorial/userguide/arx_basic_example.m
+\code
+A1.class = 'ARX';
+A1.rv = y;
+A1.rgr = RVtimes([y,y],[-3,-1]) ;
+A1.log_level = 'logbounds,logevidence';
+\endcode 
+This is the minimal configuration of an ARX estimator. 
+
+The first three fields are self explanatory, they identify which data are predicted (field \c rv) and which are in regresor (field \c rgr).
+The field \c log_level is a string of options passed to the object. In particular, class \c BM understand only options related to storing results:
+ - logbounds - store also lower and upper bounds on estimates (obtained by calling BM::posterior().qbounds()),
+ - logevidence - store also evidence of each step of the Bayes rule.
+These values are stored in given logger (\ref ug_store). By default, only mean values of the estimate are stored.
+
+Storing of the evidence is useful, e.g. in model selection task when two models are compared.
+
+The bounds are useful e.g. for visualization of the results. Run of the example should provide result like the following:
+\image latex arx_basic_example.png "Typical run of tutorial/userguide/arx_basic_example.m" width=\linewidth
+
+\section ug2_model_sel Model selection
+
+In Bayesian framework, model selection is done via comparison of evidence (marginal likelihood) of the recorded data. See [some theory].
+
+A trivial example how this can be done is presented in file bdmtoolbox/tutorial/userguide/arx_selection_example.m. The code extends the basic A1 object as follows:
+\code
+A2=A1;
+A2.constant = 0;
+
+A3=A2;
+A3.frg = 0.95;
+\endcode
+That is, two other ARX estimators are created, 
+ - A2 which is the same as A1 except it does not model constant term in the linear regression. Note that if the constant was set to zero, then this is the correct model.
+ - A3 which is the same as A2, but assumes time-variant parameters with forgetting factor 0.95.
+ 
+Since all estimator were configured to store values of marginal log-likelihood, we can easily compare them by computing total log-likelihood for each of them and converting them to probabilities. Typically, the results should look like:
+\code
+Model_probabilities =
+
+    0.0002    0.7318    0.2680
+\endcode
+Hence, the true model A2 was correctly identified as the most likely to produce this data. 
+
+For this task, additional technical adjustments were needed:
+\code
+A1.name='A1';
+A2.name='A2';
+A2.rv_param = RV({'a2th', 'r'},[2,1],[0,0]);
+A3.name='A3';
+A3.rv_param = RV({'a3th', 'r'},[2,1],[0,0]);
+\endcode
+First, in order to distinguish the estimators from each other, the estimators were given names. Hence, the results will be logged with prefix given by the name, such as M.A1_evidence.
+
+Second, if the parameters of a ARX model are not specified, they are automatically named \c theta and \c r. However, in this case, \c A1 and \c A2 differ in size, hence their random variables differ and can not use the same name. Therefore, we have explicitly used another names (RVs) of the parameters.
+
+\section ug2_bm_composition Composition of estimators
+
+Similarly to pdfs which could be composed via \c mprod, the Bayesian models can be composed together. However, justification of this step is less clear than in the case of epdfs.
+
+One possible theoretical base of composition is the Marginalized particle filter, which splits the prior and the posterior in two parts:
+\f[ f(x_t|d_1\ldots d_t)=f(x_{1,t}|x_{2,t},d_1\ldots d_t)f(x_{2,t}|d_1\ldots d_t) \f]
+each of these parts is estimated using different approach. The first part is assumed to be analytically tractable, while the second is approximated using empirical approximation.
+
+The whole algorithm runs by parallel evaluation of many \c BMs for estimation of \f$ x_{1,t}\f$, each of them conditioned on value of a sample of \f$ x_{2,t}\f$.
+
+For example, the forgetting factor, \f$ \phi \f$ of an ARX model can be considered to be unknown. Then, the whole parameter space is \f$ [\theta_t, r_t, \phi_t]\f$ decomposed as follows:
+\f[ f(\theta_t, r_t, \phi_t) = f(\theta_t, r_t| \phi_t) f(\phi_t) \f]
+Note that for known trajectory of \f$ \phi_t \f$ the standard ARX estimator can be used if we find a way how to feed the changing \f$ \phi_t \f$ into it.
+This is achieved by a trivial extension using inheritance method bdm::BM::condition().
+
+Extension of standard ARX estimator to conditional estimator is implemented as class bdm::ARXfrg. The only difference from standard ARX is that this object will obtain its forgetting factor externally as a conditioning variable. 
+Informally, the name 'ARXfrg' means: "if anybody calls your condition(0.9), it tells you new value of forgetting factor".
+
+The MPF estimator for this case is specified as follows:
+\code
+%%%%%% ARX estimator conditioned on frg
+
+A1.class = 'ARXfrg';
+A1.rv = y;
+A1.rgr = RVtimes([y,u],[-3,-1]) ; 
+A1.log_level ='logbounds,logevidence';
+A1.frg = 0.9;
+A1.name = 'A1';
+
+%%%%%% Random walk on frg - Dirichlet 
+phi_pdf.class = 'mDirich';         % random walk on coefficient phi
+phi_pdf.rv    = RV('phi',2);       % 2D random walk - frg is the first element
+phi_pdf.k     = 0.01;              % width of the random walk
+phi_pdf.betac = [0.01 0.01];       % stabilizing elememnt of random walk
+
+%%%%%% Particle
+p.class = 'MarginalizedParticle';
+p.parameter_pdf = phi_pdf;         % Random walk is the parameter evolution model
+p.bm    = A1;
+
+% prior on ARX
+%%%%%% Combining estimators in Marginalized particle filter
+E.class = 'PF';
+E.particle = p;                    % ARX is the analytical part
+E.res_threshold = 1.0;             % resampling parameter
+E.n = 100;                         % number of particles
+E.prior.class = 'eDirich';         % prior on non-linear part
+E.prior.beta  = [2 1]; % 
+E.log_level = 'logbounds';
+E.name = 'MPF';
+
+M=estimator(DS,{E});
+
+\endcode
+ 
+Here, the configuration structure \c A1 is a description of an ARX model, as used in previous examples, the only difference is in its name 'ARXfrg'. 
+
+The configuration structure \c phi_pdf defines random walk on the forgetting factor. It was chosen as Dirichlet, hence it will produce 2-dimensional vector of \f$[\phi, 1-\phi]\f$. The class \c ARXfrg was designed to read only the first element of its condition.
+The random walk of type mDirich is:
+\f[ f(\phi_t|\phi_{t-1}) = Di (\phi_{t-1}/k + \beta_c) \f]
+where \f$ k \f$ influences the spread of the walk and \f$ \beta_c \f$ has the role of stabilizing, to avoid traps of corner cases such as [0,1] and [1,0].
+Its influence on the results is quite important.
+
+This example is implemented as bdmtoolbox/tutorial/userguide/frg_example.m
+Its typical run should look like the following:
+\image html frg_example_small.png 
+\image latex frg_example.png "Typical run of tutorial/userguide/frg_example.m" width=\linewidth
+
+Note: error bars in this case are not directly comparable with those of previous examples. The MPF class implements the qbounds function as minimum and maximum of bounds in the considered set (even if its weight is extremely small). Hence, the bounds of the MPF are probably larger than it should be. Nevertheless, they provide great help when designing and tuning algorithms.
+
+\section ug_est_ext Matlab extensions of the Bayesian estimators
+
+Similarly to the extension of pdf, the estimators (or filters) can be extended via prepared class \c mexBM in directory bdmtoolbox/mex/mex_classes.
+
+An example of such class is mexLaplaceBM in \<toolbox_dir\>/tutorial/userguide/laplace_example.m
+
+Note that matlab-extended classes of mexEpdf, specifically, mexDirac and mexLaplace are used as outputs of methods posterior and epredictor, respectively.
+
+In order to create a new extension of an estimator, copy file with class mexLaplaceBM.m and redefine the methods therein. If needed create new classes for pdfs by inheriting from mexEpdf, it the same way as in the mexLaplace.m example class.
+
+For list of all estimators, see \ref app_base.
+*/
Index: /applications/bdmtoolbox/doc/local/mainpage.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/mainpage.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/mainpage.dox (revision 1044)
@@ -0,0 +1,28 @@
+/*!
+\mainpage Matlab toolbox using BDM library (BDMToolbox)
+
+\version 0.1
+
+\author Vaclav Smidl
+
+BDMToolbox is a high-level frontend to low level C++ routines of BDM.
+
+It has three main categories of usecases:
+ -# Easy access to ready solutions of typical decision-making scenarios:
+ 
+  For example simulation, estimation, feedback control. These objects are described by matlab structures.
+  See \ref bdt_scenarios
+ -# Wrappers for selected C++ functions 
+ 
+   Taking matlab structures as inputs and retunring matlab structures as outputs, see \ref bdt_wrappers
+ 
+ -# Native Matlab classes that reflect the basic classes of BDM. 
+ 
+   These classes are pure Matlab classes and can be used without BDM. 
+  
+   However, their main advantage is that BDM attach to these calsses and use them via C++ classes (e.g. mexEpdf and mexBM). Hence, these calsses can be used as building blocks in advances 
+   algorithms implemnetyed in BDM, see \ref bdt_mex_classes
+
+For tutorial on the above scenarios see \ref pages.html
+
+ */
Index: /applications/bdmtoolbox/doc/local/04userguide_ctrl.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/04userguide_ctrl.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/04userguide_ctrl.dox (revision 1044)
@@ -0,0 +1,64 @@
+/*!
+\page userguide_ctrl BDM Use - Control and Design of Decision Making Strategy
+
+Bayesian estimation as introduced in Section \ref userguide_estim is a special case of Decision Strategy, see. ....
+A more demanding scenario is to design a control strategy that will influence the system operating under uncertainty, this is implemented as scenario \c closedloop.
+
+Table of content:
+\ref ug3_theory 
+\ref ug3_arx_basic 
+\ref ug3_arx_distributed 
+
+The function of the \c closedloop is graphically illustrated:
+\dot
+digraph estimation{
+	node [shape=box];
+	"Data Source" -> "Controller 1" [label="data"];
+	"Data Source" -> "Controller 2" [label="data"];
+	"Controller 1" -> "Data Source" [label="actions"];
+	"Controller 2" -> "Data Source" [label="actions"];
+	
+	"Data Source" -> "Result Logger" [label="Simulated\n data"];
+	"Controller 1" -> "Result Logger" [label="Internal \n variables"];
+	"Controller 2" -> "Result Logger" [label="Internal \n variables"];
+}
+\enddot
+The numer of controllers in not limited, however, they can not influence the same variable. Thus, it is limited by the number of available actions.
+
+Here,
+\li Data Source is an object (class DS) providing sequential data, \f$ [d_1, d_2, \ldots d_t] \f$ and accepting input actions \f$[u_{1,t},\ldots u_{m,t}]\f$
+\li Controller is an object (class Controller) performing adaptive control. Typically is has some internal Bayesian Estimator.
+\li Result Logger is an object (class logger) dedicated to storing important data from the experiment.
+
+Since objects  datasource and the logger has already been introduced in section \ref userguide_sim, it remains to introduce 
+object \c Controller (bdm::Controller).
+
+\section ug3_theory Design of DM strategy
+The object bdm::Contoller has two principal methods: 
+ * redesign, which (re)designs the control strategy - this may be computationally costly operation,
+ * ctrlaction, which evaluates the current decision strategy and returns a numerical value of the action variable.
+ 
+At the most general class, we do not prescribe any technique how to design the strategy in \c redesign(). Most of the implemented techniques are, however, 
+variants and approximations of dynamic programming (or optimal control), see [].
+
+TODO...
+
+\section ug3_arx_basic Control of ARX models
+
+Autoregressive models has already been introduced in \ref ug_arx_sim and \ref ug2_arx_basic where their simulator and estimator has been presented.
+Control of an ARX model under the qudratic loss function is known as LQG control. This is implemented in object bdm::LQG_ARX.
+
+The following code is from bdmtoolbox/tutorial/userguide/lqg_arx_example.m
+\code
+\endcode 
+This is the minimal configuration of an LQG_ARX estimator. Optional elements of bdm::ARX::from_setting() were set using their default values:
+
+\section ug3_arx_distributed Naive distributed control 
+
+In the example above, only one controller was influencing the system. We extend this approach to a scenario where more controllers is acting independently. 
+
+A trivial example how this can be done is presented in file bdmtoolbox/tutorial/userguide/lqg_arx_distrib_example.m. The code extends previous example as follows:
+\code
+\endcode
+
+*/
Index: /applications/bdmtoolbox/doc/local/10wrappers.dox
===================================================================
--- /applications/bdmtoolbox/doc/local/10wrappers.dox (revision 1044)
+++ /applications/bdmtoolbox/doc/local/10wrappers.dox (revision 1044)
@@ -0,0 +1,131 @@
+/*!
+\page bdt_wrappers Elementary functions operating on descriptive matlab structures
+
+A wrapper is a mex file that does the following:
+ -# reads its arguments from Matlab structures and translates them into C++ structures
+ -# calls the corresponding function in C++,
+ -# converts the results into Matlab structures and passes them to the output
+ 
+The use of these functions is inefficient, however, it is very usefull for:
+ - operations on parts of the experiment configurations for scenarios, see example in \ref some_ref
+ - insight into the results, e.g. mean values of non-standard densities 
+ - algorithms written in Matlab using these functions can be trivially re-written into C++
+ 
+ 
+General notation of wrappers is: <b> \<class\>_\<function\>.m </b>
+
+For example, function \b epdf_mean.m  represents function \b mean  of class \b epdf  and any it its offsprings.
+
+For full list of available wrappers see content of directory /bdmtoolbox/mex
+
+\section bdt_wr_conv Convenience wrappers
+
+A useful wrapper is called \b class_defaults which takes the input matlab structure tries to copy it into BDM class and returns a structure how BDM interprets it.
+
+This is useful for:
+ - checking if the fields are correctly named: fields of input structure that are not in the output are not understood
+ - seeing what defaults the BDM assigns to fields that are optional
+ 
+Example:
+\code
+>> CLS.class='RV'
+
+CLS = 
+
+    class: 'RV'
+
+>> CLSout=class_defaults(CLS)
+
+CLSout = 
+
+    class: 'RV'
+    names: {1x0 cell}
+    sizes: [1x0 double]
+    times: [1x0 double]
+\endcode
+
+The fields that are understood and accepted were filled.
+
+\code
+>> CLS.class='egauss'
+
+CLS = 
+
+    class: 'egauss'
+
+>> CLSout=class_defaults(CLS)
+??? Unexpected Standard exception from MEX file.
+What() is:UIException: the compulsory Setting named
+"mu" is missing. Check path "".
+\endcode
+
+In this case, empty class of type 'egauss' is not allowed, the fields named "mu" is compulsory. The next step would be to add define CLS.mu.
+
+
+\section bdt_wrp_epdf Wrappers for pdfs
+
+The follwing wrappers are provided:
+ - \b epdf_mean returning mean value of any epdf function in \ref annotated_epdf.
+ \code 
+ >> G.class='egamma';
+ >> G.alpha = 3;
+ >> G.beta = 4;
+ >> epdf_mean(G) 
+
+ ans =
+
+    0.7500 
+ \endcode
+ - \b epdf_variance returning variance of any epdf function in \ref annotated_epdf.
+ \code
+ >> epdf_variance(G)
+
+ ans =
+
+    0.1875
+ \endcode
+ - \b epdf_evallog_mat returns logarithm of the values in argument,
+ - \b epdf_sample_mat sample given number of independent samples for this density,
+ - \b epdf_marginal sample given number of independent samples for this density,
+ - \b epdf_condition sample given number of independent samples for this density,
+ - \b epdf_sample_mat sample given number of independent samples for this density,
+
+List of arguments of each function can be obtained by running the function with no argument:
+\code
+>> epdf_mean
+??? Error using ==> epdf_mean
+Usage:
+vec=pdf_mean(pdf_struct)
+  pdf_struct = struct('class','pdf_offspring',...);  %
+  description of pdf
+output:
+  vec mean value of given pdf.
+\endcode
+
+For up-to-date list of wrappers see files in \ref files.html
+ 
+ \section bdt_wrp_off Wrappers of offsprings
+ 
+ When a new class defines its private function, its wrapper starts with the name of the class that defines it.
+ An example is function \b enorm_bhattacharyya.m  which id defined only for normal distributed densities (enorm\<sqmat\>)
+
+\section bdt_wrp_bm Wrappers for Bayesian Models (BMs)
+
+Wrappers for BM correspond to the main functions of BM, that is:
+ - \b bayes recursive update of posterior statistics by currently observed data and data in conditions, function \b bm_bayes
+ - \b bayesweighted recursive update of posterior statistics by currently observed data and data in conditions, when data are generated from this class only with probability w, function \b bm_bayesweighted
+ - \b epredictor returns unconditional predictor of the next data observation (if such density is available) \b bm_epredictor
+
+Example:
+\code
+>> CLS.class='multiBM'                % Estimator of multinomial density
+>> CLS.prior.beta = [1,2];            % Prior is Dirichlet with statistics beta
+
+>> CLSapost=bm_bayes(CLS, [0.5 0.5])  % update posterior, using data [0.5, 0.5]
+>> CLSapost.prior.beta
+
+ans =
+
+    1.5000    2.5000
+\endcode 
+ */
Index: /applications/bdmtoolbox/build_doc.sh
===================================================================
--- /applications/bdmtoolbox/build_doc.sh (revision 1044)
+++ /applications/bdmtoolbox/build_doc.sh (revision 1044)
@@ -0,0 +1,16 @@
+#!/bin/sh
+
+# filter source from BDM
+
+$this_dir=pwd
+cd doc/from_bdm
+./make_all
+
+cd $this_dir
+
+# create doc for this documentation
+doxygen
+
+# correct links in the referenced documentation from bdm
+cd doc/html/
+./installdox -l BDM.tag@bdm_doc
