Changeset 299

Timestamp:

03/19/09 15:38:55 (15 years ago)

Author:

smidl

Message:

merger - cull de sac :-(

Files:

• Doxyfile (modified) (5 diffs)
• bdm/estim/merger.cpp (modified) (1 diff)
• bdm/estim/merger.h (modified) (1 diff)
• bdm/stat/libEF.h (modified) (2 diffs)
• mpdm/CMakeLists.txt (modified) (1 diff)
• mpdm/TR2244/merger_iter_cond.cpp (modified) (4 diffs)

Doxyfile

@@ -1 @@
-# Doxyfile 1.5.6-KDevelop
+# 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           = mixpp
+
+# 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         = 1
+
+# 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       = ./doc
+
+# 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        = English
+
+# 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" \
@@ -23 +98 @@
                          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        = NO
+
+# 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        = /home/smidl/
+
+# 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      = NO
+
+# 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
-DETAILS_AT_TOP         = YES
+
+# 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               = 8
+
+# 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      = 
+
+# 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   = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to 
+# determine which symbols to keep in memory and which to flush to disk. 
+# When the cache is full, less often used symbols will be written to disk. 
+# For small to medium size projects (<1000 input files) the default value is 
+# probably good enough. For larger projects a too small cache size can cause 
+# doxygen to be busy swapping symbols to and from disk most of the time 
+# causing a significant performance 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            = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
+# will be included in the documentation.
+
 EXTRACT_PRIVATE        = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file 
+# will be included in the documentation.
+
 EXTRACT_STATIC         = NO
+
+# 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  = NO
+
+# 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       = YES
+
+# 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       = NO
+
+# 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        = NO
+
+# 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       = NO
+
+# 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                  = .
+
+# 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         = UTF-8
+
+# 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 \
@@ -108 +603 @@
                          *.m \
                          *.doc
+
+# 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                = win32 \
                          linux \
@@ -114 +619 @@
                          doprava \
                          bdm/libconfig
+
+# 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       = 
+
+# 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           = ./doc/tutorial/src \
                          ./tests \
@@ -122 +651 @@
                          ./library/tutorial \
                          ./library/mex
+
+# 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             = ./doc/images
+
+# 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        = 
+
+# 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 = YES
+
+# 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    = YES
+
+# 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     = YES
+
+# 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  = YES
+
+# 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
-GENERATE_DOCSET        = NO
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-HTML_DYNAMIC_SECTIONS  = YES
+
+# 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           = 
-QTHELP_FILE            = 
-QTHELP_CONFIG          = 
-DOXYGEN2QTHELP_LOC     = 
+
+# 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      = ALL
+
+# 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       = 11
+
 #---------------------------------------------------------------------------
 # 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.
+
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+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then 
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+
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+
+# 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.
+
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+
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+
+# 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) 
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+# is run, you must also specify the path to the tagfile here.
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+
+# 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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+
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+
+# The PERL_PATH should be the absolute path and name of the perl script 
+# interpreter (i.e. the result of `which perl').
+
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+
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+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will 
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+# powerful graphs.
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+
+# You can define message sequence charts within doxygen comments using the \msc 
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+# default search path.
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+# other documented files.
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+# doxygen will generate a call dependency graph for every global function 
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+# found. If left blank, it is assumed the dot tool can be found in the path.
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+# code bases. Also note that the size of a graph can be further restricted by 
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+# 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, 
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+# a graph (i.e. they become hard to read).
+
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+# support this, this feature is disabled by default.
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+# 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.
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+# remove the intermediate dot files that are used to generate 
+# the various graphs.
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-#---------------------------------------------------------------------------
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-#---------------------------------------------------------------------------
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+#---------------------------------------------------------------------------
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+# 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

bdm/estim/merger.cpp

@@ -3 +3 @@
 #include "arx.h"
 
-namespace bdm{
-vec merger::lognorm_merge ( mat &lW ) {
-        int nu=lW.rows();
-        vec mu = sum ( lW ) /nu; //mean of logs
-        // vec lam = sum ( pow ( lW,2 ) )-nu*pow ( mu,2 ); ======= numerically unsafe!
-        vec lam = sum ( pow ( lW-outer_product ( ones ( lW.rows() ),mu ),2 ) );
-        double coef=0.0;
-        vec sq2bl=sqrt ( 2*beta*lam ); //this term is everywhere
-        switch ( nu ) {
-                case 2:
-                        coef= ( 1-0.5*sqrt ( ( 4.0*beta-3.0 ) /beta ) );
-                        return  coef*sq2bl + mu ;
-                        break;
-                case 3://Ratio of Bessel
-                        coef = sqrt ( ( 3*beta-2 ) /3*beta );
-                        return log ( besselk ( 0,sq2bl*coef ) ) - log ( besselk ( 0,sq2bl ) ) +  mu;
-                        break;
-                case 4:
-                        break;
-                default: // Approximate conditional density
-                        break;
+namespace bdm
+{
+        vec merger::lognorm_merge ( mat &lW )
+        {
+                int nu=lW.rows();
+                vec mu = sum ( lW ) /nu; //mean of logs
+                // vec lam = sum ( pow ( lW,2 ) )-nu*pow ( mu,2 ); ======= numerically unsafe!
+                vec lam = sum ( pow ( lW-outer_product ( ones ( lW.rows() ),mu ),2 ) );
+                double coef=0.0;
+                vec sq2bl=sqrt ( 2*beta*lam ); //this term is everywhere
+                switch ( nu )
+                {
+                        case 2:
+                                coef= ( 1-0.5*sqrt ( ( 4.0*beta-3.0 ) /beta ) );
+                                return  coef*sq2bl + mu ;
+                                break;
+                        case 3://Ratio of Bessel
+                                coef = sqrt ( ( 3*beta-2 ) /3*beta );
+                                return log ( besselk ( 0,sq2bl*coef ) ) - log ( besselk ( 0,sq2bl ) ) +  mu;
+                                break;
+                        case 4:
+                                break;
+                        default: // Approximate conditional density
+                                break;
+                }
+                return vec ( 0 );
         }
-        return vec ( 0 );
+
+        void merger::merge ( const epdf* g0 )
+        {
+
+                it_assert_debug ( rv.equal ( g0->_rv() ),"Incompatible g0" );
+                //Empirical density - samples
+                if (!fix_smp)
+                        eSmp.set_statistics ( ones ( Ns ), g0 );
+                
+                Array<vec> &Smp = eSmp._samples(); //aux
+                vec &w = eSmp._w(); //aux
+
+                mat Smp_ex =ones ( dim +1,Ns ); // Extended samples for the ARX model - the last row is ones
+                for ( int i=0;i<Ns;i++ ) {      set_col_part ( Smp_ex,i,Smp ( i ) );}
+
+                if ( DBG )      *dbg << Name ( "Smp_0" ) << Smp_ex;
+
+                // Stuff for merging
+                vec lw_src ( Ns );
+                vec lw_mix ( Ns );
+                vec lw ( Ns );
+                mat lW=zeros ( n,Ns );
+                vec vec0 ( 0 );
+
+                // Initial component in the mixture model
+                mat V0=1e-8*eye ( dim +1 );
+                ARX A0; A0.set_statistics ( dim, V0 ); //initial guess of Mix:
+
+                Mix.init ( &A0, Smp_ex, Nc );
+                //Preserve initial mixture for repetitive estimation via flattening
+                MixEF Mix_init ( Mix );
+
+                // ============= MAIN LOOP ==================
+                bool converged=false;
+                int niter = 0;
+                char str[100];
+
+                emix* Mpred=Mix.epredictor ( );
+                vec Mix_pdf ( Ns );
+                while ( !converged )
+                {
+                        //Re-estimate Mix
+                        //Re-Initialize Mixture model
+                        Mix.flatten ( &Mix_init );
+                        Mix.bayesB ( Smp_ex, w*Ns );
+                        delete Mpred;
+                        Mpred = Mix.epredictor ( ); // Allocation => must be deleted at the end!!
+                        Mpred->set_rv ( rv ); //the predictor predicts rv of this merger
+
+                        // This will be active only later in iterations!!!
+                        if ((!fix_smp)&( 1./sum_sqr ( w ) <0.5*Ns ))
+                        {
+                                // Generate new samples
+                                eSmp.set_samples ( Mpred );
+                                for ( int i=0;i<Ns;i++ )
+                                {
+                                        //////////// !!!!!!!!!!!!!
+                                        if ( Smp ( i ) ( 2 ) <0 ) {Smp ( i ) ( 2 ) = 0.01; }
+                                        set_col_part ( Smp_ex,i,Smp ( i ) );
+                                }
+                                if ( 0 )
+                                {
+                                        cout<<"Resampling =" << 1./sum_sqr ( w ) << endl;
+                                        cout << sum ( Smp_ex,2 ) /Ns <<endl;
+                                        cout << Smp_ex*Smp_ex.T() /Ns << endl;
+                                }
+                        }
+                        if ( DBG )
+                        {
+                                sprintf ( str,"Mpred_mean%d",niter );
+                                *dbg << Name ( str ) << Mpred->mean();
+
+
+                                sprintf ( str,"Mpdf%d",niter );
+                                for ( int i=0;i<Ns;i++ ) {Mix_pdf ( i ) = Mix.logpred ( Smp_ex.get_col ( i ) );}
+                                *dbg << Name ( str ) << Mix_pdf;
+
+                                sprintf ( str,"Smp%d",niter );
+                                *dbg << Name ( str ) << Smp_ex;
+
+                        }
+                        //Importace weighting
+                        for ( int i=0;i<n;i++ )
+                        {
+                                lw_src=0.0;
+                                //======== Same RVs ===========
+                                //Split according to dependency in rvs
+                                if ( mpdfs ( i )->dimension() ==dim )
+                                {
+                                        // no need for conditioning or marginalization
+                                        for ( int j=0;j<Ns; j++ )   // Smp is Array<> => for cycle
+                                        {
+                                                lw_src ( j ) =mpdfs ( i )->_epdf().evallog ( Smp ( j ) );
+                                        }
+                                }
+                                else
+                                {
+                                        // compute likelihood of marginal on the conditional variable
+                                        if ( mpdfs ( i )->dimensionc() >0 )
+                                        {
+                                                // Make marginal on rvc_i
+                                                epdf* tmp_marg = Mpred->marginal ( mpdfs ( i )->_rvc() );
+                                                //compute vector of lw_src
+                                                for ( int k=0;k<Ns;k++ )
+                                                {
+                                                        // Here val of tmp_marg = cond of mpdfs(i) ==> calling dls->get_cond
+                                                        lw_src ( k ) += tmp_marg->evallog ( dls ( i )->get_cond ( Smp ( k ) ) );
+                                                }
+                                                delete tmp_marg;
+
+//                                      sprintf ( str,"marg%d",niter );
+//                                      *dbg << Name ( str ) << lw_src;
+
+                                        }
+                                        // Compute likelihood of the missing variable
+                                        if ( dim > ( mpdfs ( i )->dimension() + mpdfs ( i )->dimensionc() ) )
+                                        {
+                                                ///////////////
+                                                // There are variales unknown to mpdfs(i) : rvzs
+                                                mpdf* tmp_cond = Mpred->condition ( rvzs ( i ) );
+                                                // Compute likelihood
+                                                vec lw_dbg=lw_src;
+                                                for ( int k= 0; k<Ns; k++ )
+                                                {
+                                                        lw_src ( k ) += log (
+                                                                            tmp_cond->evallogcond (
+                                                                                zdls ( i )->pushdown ( Smp ( k ) ),
+                                                                                zdls ( i )->get_cond ( Smp ( k ) ) ) );
+                                                        if ( !std::isfinite ( lw_src ( k ) ) )
+                                                        {
+                                                                lw_src ( k ) = -1e16; cout << "!";
+                                                        }
+                                                }
+                                                delete tmp_cond;
+                                        }
+                                        // Compute likelihood of the partial source
+                                        for ( int k= 0; k<Ns; k++ )
+                                        {
+                                                mpdfs ( i )->condition ( dls ( i )->get_cond ( Smp ( k ) ) );
+                                                lw_src ( k ) += mpdfs ( i )->_epdf().evallog ( dls ( i )->pushdown ( Smp ( k ) ) );
+                                        }
+
+                                }
+//                      it_assert_debug(std::isfinite(sum(lw_src)),"bad");
+                                lW.set_row ( i, lw_src ); // do not divide by mix
+                        }
+                        //Importance of the mixture
+                        for ( int j=0;j<Ns;j++ )
+                        {
+                                lw_mix ( j ) =Mix.logpred ( Smp_ex.get_col ( j ) );
+                        }
+                        lw = lognorm_merge ( lW ); //merge
+
+                        if ( DBG )
+                        {
+                                sprintf ( str,"lW%d",niter );
+                                *dbg << Name ( str ) << lW;
+                                sprintf ( str,"w%d",niter );
+                                *dbg << Name ( str ) << w;
+                                sprintf ( str,"lw_m%d",niter );
+                                *dbg << Name ( str ) << lw_mix;
+                        }
+                        //Importance weighting
+                        if (!fix_smp)
+                                lw -=  lw_mix; // hoping that it is not numerically sensitive...
+                        w = exp ( lw-max ( lw ) );
+                        //renormalize
+                        double sumw =sum ( w );
+                        if ( std::isfinite ( sumw ) )
+                        {
+                                w = w/sumw;
+                        }
+                        else
+                        {
+                                it_file itf ( "merg_err.it" );
+                                itf << Name ( "w" ) << w;
+                        }
+
+                        if ( DBG )
+                        {
+                                sprintf ( str,"w_is_%d",niter );
+                                *dbg << Name ( str ) << w;
+                        }
+                        // ==== stopping rule ===
+                        niter++;
+                        converged = ( niter>20 );
+                }
+                delete Mpred;
+//              cout << endl;
+
+        }
+
 }
-
-void merger::merge ( const epdf* g0 ) {
-//      it_file dbg ( "merger_debug.it" );
-
-        it_assert_debug ( rv.equal ( g0->_rv() ),"Incompatible g0" );
-        //Empirical density - samples
-        eSmp.set_statistics ( ones ( Ns ), g0 );
-        Array<vec> &Smp = eSmp._samples(); //aux
-        vec &w = eSmp._w(); //aux
-
-        mat Smp_ex =ones ( dim +1,Ns ); // Extended samples for the ARX model - the last row is ones
-        for ( int i=0;i<Ns;i++ ) {      set_col_part ( Smp_ex,i,Smp ( i ) );}
-
-//      dbg << Name ( "Smp_0" ) << Smp_ex;
-
-        // Stuff for merging
-        vec lw_src ( Ns );
-        vec lw_mix ( Ns );
-        vec lw ( Ns );
-        mat lW=zeros ( n,Ns );
-        vec vec0 ( 0 );
-
-        // Initial component in the mixture model
-        mat V0=1e-8*eye ( dim +1 );
-        ARX A0; A0.set_statistics(dim, V0); //initial guess of Mix: 
-
-        Mix.init ( &A0, Smp_ex, Nc );
-        //Preserve initial mixture for repetitive estimation via flattening
-        MixEF Mix_init ( Mix );
-
-        // ============= MAIN LOOP ==================
-        bool converged=false;
-        int niter = 0;
-        char str[100];
-
-        emix* Mpred=Mix.epredictor (  );
-        vec Mix_pdf ( Ns );
-        while ( !converged ) {
-                //Re-estimate Mix
-                //Re-Initialize Mixture model
-                Mix.flatten ( &Mix_init );
-                Mix.bayesB ( Smp_ex, w*Ns );
-                delete Mpred;
-                Mpred = Mix.epredictor ( ); // Allocation => must be deleted at the end!!
-                Mpred->set_rv(rv); //the predictor predicts rv of this merger
-
-                // This will be active only later in iterations!!!
-                if ( 1./sum_sqr ( w ) <0.5*Ns ) {
-                        // Generate new samples
-                        eSmp.set_samples ( Mpred );
-                        for ( int i=0;i<Ns;i++ ) {
-                                //////////// !!!!!!!!!!!!!
-                                if ( Smp ( i ) ( 2 ) <0 ) {Smp ( i ) ( 2 ) = 0.01; }
-                                set_col_part ( Smp_ex,i,Smp ( i ) );
-                        }
-                        if(0){cout<<"Resampling =" << 1./sum_sqr ( w ) << endl;
-                        cout << sum ( Smp_ex,2 ) /Ns <<endl;
-                        cout << Smp_ex*Smp_ex.T() /Ns << endl;}
-                }
-//              sprintf ( str,"Mpred_mean%d",niter );
-//              dbg << Name ( str ) << Mpred->mean();
-
-
-//              sprintf ( str,"Mpdf%d",niter );
-//              for ( int i=0;i<Ns;i++ ) {Mix_pdf ( i ) = Mix.logpred ( Smp_ex.get_col ( i ) );}
-//              dbg << Name ( str ) << Mix_pdf;
-
-//              sprintf ( str,"Smp%d",niter );
-//              dbg << Name ( str ) << Smp_ex;
-
-                //Importace weighting
-                for ( int i=0;i<n;i++ ) {
-                        lw_src=0.0;
-                        //======== Same RVs ===========
-                        //Split according to dependency in rvs
-                        if ( mpdfs ( i )->dimension() ==dim ) {
-                                // no need for conditioning or marginalization
-                                for ( int j=0;j<Ns; j++ ) { // Smp is Array<> => for cycle
-                                        lw_src ( j ) =mpdfs ( i )->_epdf().evallog ( Smp ( j ) );
-                                }
-                        }
-                        else {
-                                // compute likelihood of marginal on the conditional variable
-                                if ( mpdfs ( i )->dimensionc() >0 ) {
-                                        // Make marginal on rvc_i
-                                        epdf* tmp_marg = Mpred->marginal ( mpdfs ( i )->_rvc() );
-                                        //compute vector of lw_src
-                                        for ( int k=0;k<Ns;k++ ) {
-                                                // Here val of tmp_marg = cond of mpdfs(i) ==> calling dls->get_cond
-                                                lw_src ( k ) += tmp_marg->evallog ( dls ( i )->get_cond ( Smp ( k ) ) );
-                                        }
-                                        delete tmp_marg;
-
-//                                      sprintf ( str,"marg%d",niter );
-//                                      dbg << Name ( str ) << lw_src;
-
-                                }
-                                // Compute likelihood of the missing variable
-                                if ( dim > ( mpdfs ( i )->dimension() + mpdfs ( i )->dimensionc() ) ) {
-                                        ///////////////
-                                        // There are variales unknown to mpdfs(i) : rvzs
-                                        mpdf* tmp_cond = Mpred->condition ( rvzs ( i ) );
-                                        // Compute likelihood
-                                        vec lw_dbg=lw_src;
-                                        for ( int k= 0; k<Ns; k++ ) {
-                                                lw_src ( k ) += log (
-                                                                    tmp_cond->evallogcond (
-                                                                        zdls ( i )->pushdown ( Smp ( k ) ),
-                                                                        zdls ( i )->get_cond ( Smp ( k ) ) ) );
-                                                if ( !std::isfinite ( lw_src ( k ) ) ) {
-                                                        lw_src ( k ) = -1e16; cout << "!";
-                                                }
-                                        }
-                                        delete tmp_cond;
-                                }
-                                // Compute likelihood of the partial source
-                                for ( int k= 0; k<Ns; k++ ) {
-                                        mpdfs ( i )->condition ( dls ( i )->get_cond ( Smp ( k ) ) );
-                                        lw_src ( k ) += mpdfs ( i )->_epdf().evallog ( dls ( i )->pushdown ( Smp ( k ) ) );
-                                }
-
-                        }
-//                      it_assert_debug(std::isfinite(sum(lw_src)),"bad");
-                        lW.set_row ( i, lw_src ); // do not divide by mix
-                }
-                //Importance of the mixture
-                for ( int j=0;j<Ns;j++ ) {
-                        lw_mix ( j ) =Mix.logpred ( Smp_ex.get_col ( j ) );
-                }
-//              sprintf ( str,"lW%d",niter );
-//              dbg << Name ( str ) << lW;
-
-                lw = lognorm_merge ( lW ); //merge
-
-//              sprintf ( str,"w%d",niter );
-//              dbg << Name ( str ) << w;
-//              sprintf ( str,"lw_m%d",niter );
-//              dbg << Name ( str ) << lw_mix;
-
-                //Importance weighting
-                lw -=  lw_mix; // hoping that it is not numerically sensitive...
-                w = exp ( lw-max ( lw ) );
-                //renormalize
-                double sumw =sum ( w );
-                if ( std::isfinite ( sumw ) ) {
-                        w = w/sumw;
-                }
-                else {
-                        it_file itf ( "merg_err.it" );
-                        itf << Name ( "w" ) << w;
-                }
-
-//              sprintf ( str,"w_is_%d",niter );
-//              dbg << Name ( str ) << w;
-
-//              eSmp.resample(); // So that it can be used in bayes
-//              for ( int i=0;i<Ns;i++ ) {      set_col_part ( Smp_ex,i,Smp ( i ) );}
-
-//              sprintf ( str,"Smp_res%d",niter );
-//              dbg << Name ( str ) << Smp;
-
-                // ==== stopping rule ===
-                niter++;
-                converged = ( niter>20 );
-        }
-        delete Mpred;
-        cout << endl;
-
-}
-
-}

bdm/estim/merger.h

@@ -17 +17 @@
 #include "mixef.h"
 
-namespace bdm{
-using std::string;
-
-/*!
-@brief Function for general combination of pdfs
-
-Mixtures of Gaussian densities are used internally. Switching to other densities should be trivial.
-*/
-
-class merger : public compositepdf, public epdf {
-protected:
-        //!Internal mixture of EF models
-        MixEF Mix;
-        //! Data link for each mpdf in mpdfs
-        Array<datalink_m2e*> dls;
-        //! Array of rvs that are not modelled by mpdfs at all (aux)
-        Array<RV> rvzs;
-        //! Data Links of rv0 mpdfs - these will be conditioned the (rv,rvc) of mpdfs
-        Array<datalink_m2e*> zdls;
-
-        //!Number of samples used in approximation
-        int Ns;
-        //!Number of components in a mixture
-        int Nc;
-        //!Prior on the log-normal merging model
-        double beta;
-        //! Projection to empirical density
-        eEmp eSmp;
-
-public:
+namespace bdm
+{
+        using std::string;
+
+        /*!
+        @brief Function for general combination of pdfs
+
+        Mixtures of Gaussian densities are used internally. Switching to other densities should be trivial.
+        */
+
+        class merger : public compositepdf, public epdf
+        {
+                protected:
+                        //!Internal mixture of EF models
+                        MixEF Mix;
+                        //! Data link for each mpdf in mpdfs
+                        Array<datalink_m2e*> dls;
+                        //! Array of rvs that are not modelled by mpdfs at all (aux)
+                        Array<RV> rvzs;
+                        //! Data Links of rv0 mpdfs - these will be conditioned the (rv,rvc) of mpdfs
+                        Array<datalink_m2e*> zdls;
+
+                        //!Number of samples used in approximation
+                        int Ns;
+                        //!Number of components in a mixture
+                        int Nc;
+                        //!Prior on the log-normal merging model
+                        double beta;
+                        //! Projection to empirical density
+                        eEmp eSmp;
+
+                        //! debug or not debug
+                        bool DBG;
+                        //! debugging file
+                        it_file* dbg;
+                        //! Flag if the samples are fixed or not
+                        bool fix_smp;
+                public:
 //!Default constructor
-        merger ( const Array<mpdf*> &S ) :
-                        compositepdf ( S ), epdf ( ),
-                        Mix ( Array<BMEF*> ( 0 ),vec ( 0 ) ), dls ( n ), rvzs ( n ), zdls ( n ), eSmp() {
-                RV ztmp;
-                rv = getrv(false);
-                dim = rv._dsize();
-                // Extend rv by rvc!
-                RV rvc; setrvc ( rv,rvc );
-                rv.add ( rvc );
-                for ( int i=0;i<n;i++ ) {
-                        //Establich connection between mpdfs and merger
-                        dls ( i ) = new datalink_m2e;dls(i)->set_connection( mpdfs ( i )->_rv(), mpdfs ( i )->_rvc(), rv );
-                        // find out what is missing in each mpdf
-                        ztmp= mpdfs ( i )->_rv();
-                        ztmp.add ( mpdfs ( i )->_rvc() );
-                        rvzs ( i ) =rv.subt ( ztmp );
-                        zdls ( i ) = new datalink_m2e; zdls(i)->set_connection ( rvzs ( i ), ztmp, rv ) ;
-                };
-                //Set Default values of parameters
-                beta=2.0;
-                Ns=100;
-                Nc=10;
-                Mix.set_method ( EM );
-        }
+                        merger ( const Array<mpdf*> &S ) :
+                                        compositepdf ( S ), epdf ( ),
+                                        Mix ( Array<BMEF*> ( 0 ),vec ( 0 ) ), dls ( n ), rvzs ( n ), zdls ( n ), eSmp()
+                        {
+                                RV ztmp;
+                                rv = getrv ( false );
+                                RV rvc; setrvc ( rv,rvc ); // Extend rv by rvc!
+                                rv.add ( rvc );
+                                // get dimension
+                                dim = rv._dsize();
+
+                                for ( int i=0;i<n;i++ )
+                                {
+                                        //Establich connection between mpdfs and merger
+                                        dls ( i ) = new datalink_m2e;dls ( i )->set_connection ( mpdfs ( i )->_rv(), mpdfs ( i )->_rvc(), rv );
+                                        // find out what is missing in each mpdf
+                                        ztmp= mpdfs ( i )->_rv();
+                                        ztmp.add ( mpdfs ( i )->_rvc() );
+                                        rvzs ( i ) =rv.subt ( ztmp );
+                                        zdls ( i ) = new datalink_m2e; zdls ( i )->set_connection ( rvzs ( i ), ztmp, rv ) ;
+                                };
+                                //Set Default values of parameters
+                                beta=2.0;
+                                Ns=100;
+                                Nc=10;
+                                Mix.set_method ( EM );
+                                DBG = false;
+                                fix_smp = false;
+                        }
+                        //! set debug file
+                        void debug_file ( const string fname ) { if ( DBG ) delete dbg; dbg = new it_file ( fname ); if ( dbg ) DBG=true;}
 //! Set internal parameters used in approximation
-        void set_parameters ( double beta0, int Ns0, int Nc0 ) {beta=beta0;Ns=Ns0;Nc=Nc0;eSmp.set_parameters(Ns0,false);}
+                        void set_parameters ( double beta0, int Ns0, int Nc0 ) {beta=beta0;Ns=Ns0;Nc=Nc0;eSmp.set_parameters ( Ns0,false );}
+                        void set_grid ( Array<vec> &XYZ )
+                        {
+                                int dim=XYZ.length(); ivec szs ( dim );
+                                for(int i=0; i<dim;i++){szs=XYZ(i).length();}
+                                Ns=prod(szs);
+                                eSmp.set_parameters(Ns,false);
+                                Array<vec> &samples=eSmp._samples();
+                                eSmp._w()=ones(Ns)/Ns;
+                                                
+                                //set samples
+                                ivec is=zeros_i(dim);//indeces of dimensions in for cycle;
+                                vec smpi(dim);
+                                for(int i=0; i<Ns; i++){
+                                        for(int j=0; j<dim; j++){smpi(j)=XYZ(j)(is(j)); /* jty vector*/ }
+                                        samples(i)=smpi;
+                                        // shift indeces
+                                        for (int j=0;j<dim;j++){
+                                                if (is(j)==szs(j)-1) { //j-th index is full
+                                                        is(j)=0; //shift back
+                                                        is(j+1)++; //increase th next dimension;
+                                                        if (is(j+1)<szs(j+1)-1) break;
+                                                } else {
+                                                        is(j)++; break;
+                                                }
+                                        }
+                                }
+                                
+                                fix_smp = true;
+                        }
 //!Initialize the proposal density. This function must be called before merge()!
-        void init() { ////////////// NOT FINISHED
-                Array<vec> Smps ( n );
-                //Gibbs sampling
-                for ( int i=0;i<n;i++ ) {Smps ( i ) =zeros ( 0 );}
-        }
+                        void init()   ////////////// NOT FINISHED
+                        {
+                                Array<vec> Smps ( n );
+                                //Gibbs sampling
+                                for ( int i=0;i<n;i++ ) {Smps ( i ) =zeros ( 0 );}
+                        }
 //!Create a mixture density using known proposal
-        void merge ( const epdf* g0 );
+                        void merge ( const epdf* g0 );
 //!Create a mixture density, make sure to call init() before the first call
-        void merge () {merge ( & ( Mix.posterior() ) );};
+                        void merge () {merge ( & ( Mix.posterior() ) );};
 
 //! Merge log-likelihood values
-        vec lognorm_merge ( mat &lW );
+                        vec lognorm_merge ( mat &lW );
 //! sample from merged density
 //! weight w is a
-        vec sample ( ) const { return Mix.posterior().sample();}
-        double evallog ( const vec &dt ) const {
-                vec dtf=ones ( dt.length() +1 );
-                dtf.set_subvector ( 0,dt );
-                return Mix.logpred ( dtf );
-        }
-        vec mean() const {
-                const Vec<double> &w = eSmp._w();
-                const Array<vec> &S = eSmp._samples();
-                vec tmp=zeros ( dim); 
-                for ( int i=0; i<Ns; i++ ) {
-                        tmp+=w ( i ) *S ( i );
-                }
-                return tmp;
-        }
-        mat covariance() const {
-                const vec &w = eSmp._w();
-                const Array<vec> &S = eSmp._samples();
-                
-                vec mea = mean(); 
-                
-                cout << sum(w) << "," << w*w <<endl;
-                
-                mat Tmp=zeros(dim, dim);
-                for ( int i=0; i<Ns; i++ ) {
-                        Tmp+=w ( i ) *outer_product(S ( i ), S(i));
-                }
-                return Tmp-outer_product(mea,mea);
-        }
-        vec variance() const {
-                const vec &w = eSmp._w();
-                const Array<vec> &S = eSmp._samples();
-                
-                vec tmp=zeros(dim);
-                for ( int i=0; i<Ns; i++ ) {
-                        tmp+=w ( i ) *pow(S ( i ),2);
-                }
-                return tmp-pow(mean(),2);
-        }
+                        vec sample ( ) const { return Mix.posterior().sample();}
+                        double evallog ( const vec &dt ) const
+                        {
+                                vec dtf=ones ( dt.length() +1 );
+                                dtf.set_subvector ( 0,dt );
+                                return Mix.logpred ( dtf );
+                        }
+                        vec mean() const
+                        {
+                                const Vec<double> &w = eSmp._w();
+                                const Array<vec> &S = eSmp._samples();
+                                vec tmp=zeros ( dim );
+                                for ( int i=0; i<Ns; i++ )
+                                {
+                                        tmp+=w ( i ) *S ( i );
+                                }
+                                return tmp;
+                        }
+                        mat covariance() const
+                        {
+                                const vec &w = eSmp._w();
+                                const Array<vec> &S = eSmp._samples();
+
+                                vec mea = mean();
+
+                                cout << sum ( w ) << "," << w*w <<endl;
+
+                                mat Tmp=zeros ( dim, dim );
+                                for ( int i=0; i<Ns; i++ )
+                                {
+                                        Tmp+=w ( i ) *outer_product ( S ( i ), S ( i ) );
+                                }
+                                return Tmp-outer_product ( mea,mea );
+                        }
+                        vec variance() const
+                        {
+                                const vec &w = eSmp._w();
+                                const Array<vec> &S = eSmp._samples();
+
+                                vec tmp=zeros ( dim );
+                                for ( int i=0; i<Ns; i++ )
+                                {
+                                        tmp+=w ( i ) *pow ( S ( i ),2 );
+                                }
+                                return tmp-pow ( mean(),2 );
+                        }
 //! for future use
-        virtual ~merger() {
-                for ( int i=0; i<n; i++ ) {
-                        delete dls ( i );
-                        delete zdls ( i );
-                }
+                        virtual ~merger()
+                        {
+                                for ( int i=0; i<n; i++ )
+                                {
+                                        delete dls ( i );
+                                        delete zdls ( i );
+                                }
+                                if ( DBG ) delete dbg;
+                        };
+
+//! Access function
+                        MixEF& _Mix() {return Mix;}
+//! Access function
+                        eEmp& _Smp() {return eSmp;}
         };
 
-//! Access function
-        MixEF& _Mix() {return Mix;}
-//! Access function
-        eEmp& _Smp() {return eSmp;}
-};
-
 }
 

bdm/stat/libEF.h

@@ -139 +139 @@
                         vec mean() const {return mu;}
                         vec variance() const {return diag ( R.to_mat() );}
-//      mlnorm<sq_T>* condition ( const RV &rvn ) const ;
+//      mlnorm<sq_T>* condition ( const RV &rvn ) const ; <=========== fails to cmpile. Why?
                         mpdf* condition ( const RV &rvn ) const ;
-//      enorm<sq_T>* marginal ( const RV &rv ) const;
-                        epdf* marginal ( const RV &rv ) const;
+        enorm<sq_T>* marginal ( const RV &rv ) const;
+//                      epdf* marginal ( const RV &rv ) const;
                         //!@}
 
@@ -1082 +1082 @@
 
         template<class sq_T>
-        epdf* enorm<sq_T>::marginal ( const RV &rvn ) const
+        enorm<sq_T>* enorm<sq_T>::marginal ( const RV &rvn ) const
         {
                 it_assert_debug ( isnamed(), "rv description is not assigned" );

mpdm/CMakeLists.txt

@@ -5 +5 @@
 EXEC(merg_pred)
 EXEC(merg_giw)
-EXEC(merger_iter_cond)
-EXEC(merg_2a)
+EXEC(TR2244/merger_iter_cond)
+EXEC(SYSID09/merg_2a)

mpdm/TR2244/merger_iter_cond.cpp

@@ -33 +33 @@
 
         merger M ( A );
-        enorm<fsqmat> g0; g0.set_rv ( all );
-        g0.set_parameters ( vec ( "1 -1 1" ),3*eye ( 3 ));// +1*ones ( 3,3 ) );
+        M.debug_file("iter_cond_debug.it");
+        enorm<ldmat> g0; g0.set_rv ( all );
+        mat Cov=0.3*eye ( 3 );
+        Cov(1,2)=0.29;
+        Cov(2,1)=0.29;
+        g0.set_parameters ( vec ( "1 1 1" ),Cov);// +1*ones ( 3,3 ) );
 
+        enorm<ldmat>* teste=g0.marginal(concat(u1,u2));
+        mlnorm<ldmat>* testm=(mlnorm<ldmat>*)teste->condition(u2);
+        
         M.set_parameters ( 1.2,1000,1 );
+        
+        Array<vec> YUU(3); 
+        YUU(0)=linspace(-2.9,3.1,20);
+        YUU(1)=linspace(-5,5,20);
+        YUU(2)=linspace(-3,3,20);
 
-        int Ntrials=100;
+        M.set_grid(YUU);
+        
+        int Ntrials=1;
         vec A1s ( Ntrials );
         vec A2s ( Ntrials );
@@ -51 +65 @@
                 MixEF &MM = M._Mix();
                 epdf* MP = MM._Coms ( 0 )->epredictor ( );
+                MP->set_rv(all);
 
                 RV yu1 = y; yu1.add ( u1 );
@@ -66 +81 @@
                 C2s(it) = P2c->_mu_const()(0);
 
+                cout << "mean: " << MM._Coms(0)->_e()->mean() <<endl;
         }
+        
+        
+        
+        cout << "A1s:" <<A1s<<endl;
+        cout << "C2s:" <<C2s<<endl;
         double A1mean = sum(A1s)/Ntrials;
         double A2mean = sum(A2s)/Ntrials;
@@ -73 +94 @@
         double R1mean = sum(R1s)/Ntrials;
         double R2mean = sum(R2s)/Ntrials;
-        cout << "A1: " << A1mean << " +- " << 2*(sum_sqr(A1s)/Ntrials-A1mean*A1mean) <<endl;
-        cout << "A2: " << A2mean << " +- " << 2*(sum_sqr(A2s)/Ntrials-A2mean*A2mean) <<endl;
-        cout << "C1: " << C1mean << " +- " << 2*(sum_sqr(C1s)/Ntrials-C1mean*C1mean) <<endl;
-        cout << "C2: " << C2mean << " +- " << 2*(sum_sqr(C2s)/Ntrials-C2mean*C2mean) <<endl;
-        cout << "R1: " << R1mean << " +- " << 2*(sum_sqr(R1s)/Ntrials-R1mean*R1mean) <<endl;
-        cout << "R2: " << R2mean << " +- " << 2*(sum_sqr(R2s)/Ntrials-R2mean*R2mean) <<endl;
+        cout << "A1: " << A1mean << " +- " << 2*sqrt(sum_sqr(A1s)/Ntrials-A1mean*A1mean) <<endl;
+        cout << "A2: " << A2mean << " +- " << 2*sqrt(sum_sqr(A2s)/Ntrials-A2mean*A2mean) <<endl;
+        cout << "C1: " << C1mean << " +- " << 2*sqrt(sum_sqr(C1s)/Ntrials-C1mean*C1mean) <<endl;
+        cout << "C2: " << C2mean << " +- " << 2*sqrt(sum_sqr(C2s)/Ntrials-C2mean*C2mean) <<endl;
+        cout << "R1: " << R1mean << " +- " << 2*sqrt(sum_sqr(R1s)/Ntrials-R1mean*R1mean) <<endl;
+        cout << "R2: " << R2mean << " +- " << 2*sqrt(sum_sqr(R2s)/Ntrials-R2mean*R2mean) <<endl;
 }