From 919470dcf4e08bb2ea926ad61dd816479c2c26c6 Mon Sep 17 00:00:00 2001
From: Simon Spannagel <simon.spannagel@cern.ch>
Date: Wed, 6 Nov 2019 11:41:50 +0100
Subject: [PATCH] Add GBL
---
3rdparty/GeneralBrokenLines/CMakeLists.txt | 66 +
3rdparty/GeneralBrokenLines/COPYING.LIB | 481 +++++
3rdparty/GeneralBrokenLines/README | 35 +
3rdparty/GeneralBrokenLines/doc/Doxyfile.in | 1784 +++++++++++++++++
.../include/BorderedBandMatrix.h | 104 +
3rdparty/GeneralBrokenLines/include/GblData.h | 267 +++
.../GeneralBrokenLines/include/GblPoint.h | 434 ++++
.../include/GblTrajectory.h | 331 +++
.../GeneralBrokenLines/include/MilleBinary.h | 102 +
3rdparty/GeneralBrokenLines/include/VMatrix.h | 129 ++
.../src/BorderedBandMatrix.cpp | 384 ++++
3rdparty/GeneralBrokenLines/src/GblData.cpp | 264 +++
3rdparty/GeneralBrokenLines/src/GblPoint.cpp | 522 +++++
.../GeneralBrokenLines/src/GblTrajectory.cpp | 1428 +++++++++++++
.../GeneralBrokenLines/src/MilleBinary.cpp | 129 ++
3rdparty/GeneralBrokenLines/src/VMatrix.cpp | 427 ++++
16 files changed, 6887 insertions(+)
create mode 100644 3rdparty/GeneralBrokenLines/CMakeLists.txt
create mode 100644 3rdparty/GeneralBrokenLines/COPYING.LIB
create mode 100644 3rdparty/GeneralBrokenLines/README
create mode 100644 3rdparty/GeneralBrokenLines/doc/Doxyfile.in
create mode 100644 3rdparty/GeneralBrokenLines/include/BorderedBandMatrix.h
create mode 100644 3rdparty/GeneralBrokenLines/include/GblData.h
create mode 100644 3rdparty/GeneralBrokenLines/include/GblPoint.h
create mode 100644 3rdparty/GeneralBrokenLines/include/GblTrajectory.h
create mode 100644 3rdparty/GeneralBrokenLines/include/MilleBinary.h
create mode 100644 3rdparty/GeneralBrokenLines/include/VMatrix.h
create mode 100644 3rdparty/GeneralBrokenLines/src/BorderedBandMatrix.cpp
create mode 100644 3rdparty/GeneralBrokenLines/src/GblData.cpp
create mode 100644 3rdparty/GeneralBrokenLines/src/GblPoint.cpp
create mode 100644 3rdparty/GeneralBrokenLines/src/GblTrajectory.cpp
create mode 100644 3rdparty/GeneralBrokenLines/src/MilleBinary.cpp
create mode 100644 3rdparty/GeneralBrokenLines/src/VMatrix.cpp
diff --git a/3rdparty/GeneralBrokenLines/CMakeLists.txt b/3rdparty/GeneralBrokenLines/CMakeLists.txt
new file mode 100644
index 000000000..6e0ee2f9f
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/CMakeLists.txt
@@ -0,0 +1,66 @@
+# #require a certain version
+CMAKE_MINIMUM_REQUIRED( VERSION 3.1 )
+
+# declare the project name
+PROJECT(GBL)
+
+# project version
+SET( ${PROJECT_NAME}_VERSION_MAJOR 2 )
+SET( ${PROJECT_NAME}_VERSION_MINOR 1 )
+SET( ${PROJECT_NAME}_VERSION_PATCH 6 )
+
+# make life easier and simply use the ilcsoft default settings
+# load default ilcsoft settings (install prefix, build type, rpath, etc.)
+LIST( APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake )
+
+# enable ROOT support
+OPTION( SUPPORT_ROOT "Support ROOT for user I/O" True )
+IF( SUPPORT_ROOT )
+ FIND_PACKAGE(ROOT REQUIRED)
+ ADD_DEFINITIONS(-DGBL_EIGEN_SUPPORT_ROOT)
+ENDIF()
+FIND_PACKAGE(Eigen3 REQUIRED)
+
+# require proper c++
+#ADD_DEFINITIONS( "-Wall -g -ansi -pedantic -Wno-long-long" )
+
+# include directories
+IF( SUPPORT_ROOT )
+ INCLUDE_DIRECTORIES(SYSTEM BEFORE ./include ${ROOT_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIR} )
+ELSE()
+ INCLUDE_DIRECTORIES(SYSTEM BEFORE ./include ${EIGEN3_INCLUDE_DIR} )
+ENDIF()
+INSTALL( DIRECTORY ./include DESTINATION . PATTERN ".svn" EXCLUDE )
+
+# declare the stupid ROOT library path
+LINK_DIRECTORIES(${ROOT_LIBRARY_DIR})
+
+# add library
+AUX_SOURCE_DIRECTORY( ./src library_sources )
+ADD_LIBRARY(${PROJECT_NAME} SHARED ${library_sources})
+INSTALL( TARGETS ${PROJECT_NAME} DESTINATION lib )
+
+TARGET_LINK_LIBRARIES(${PROJECT_NAME} ${ROOT_LIBS})
+
+# the examples, build with "make examples"
+ADD_SUBDIRECTORY( examples/ )
+
+# add a target to generate API documentation with Doxygen
+FIND_PACKAGE(Doxygen)
+
+if(DOXYGEN_FOUND)
+
+ INCLUDE(GlobalSVNRevision)
+
+ CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile @ONLY)
+
+ ADD_CUSTOM_TARGET(doc
+ ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+ COMMENT "Generating API documentation with Doxygen" VERBATIM
+ )
+
+ELSE()
+ MESSAGE( STATUS "Doxygen not installed or found -- API documentation can't be generatred!" )
+
+ENDIF(DOXYGEN_FOUND)
diff --git a/3rdparty/GeneralBrokenLines/COPYING.LIB b/3rdparty/GeneralBrokenLines/COPYING.LIB
new file mode 100644
index 000000000..5bc8fb2c8
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/COPYING.LIB
@@ -0,0 +1,481 @@
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+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
+
+ <signature of Ty Coon>, 1 April 1990
+ Ty Coon, President of Vice
+
+That's all there is to it!
diff --git a/3rdparty/GeneralBrokenLines/README b/3rdparty/GeneralBrokenLines/README
new file mode 100644
index 000000000..5088ed035
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/README
@@ -0,0 +1,35 @@
+README: GeneralBrokenLines cmake compilation/installation
+Version 10.April 2017
+
+Requirements:
+To build the code, you need to have CMake and Eigen3 (and optionally root) installed on your system.
+
+The support of root for user input and output is selected in CMakeLists.txt (default: True).
+
+Build procedure:
+If you've already worked with CMake, the following steps should be known.
+The build philosophy is to encourage out-of-source builds, but this is not enforced.
+
+Execute the following steps:
+ 1) create a compilation directory, e.g. 'build' and change into it
+ mkdir build; cd build
+ 2) create the Makefile by invoking cmake on the configuration file (similar to the usual ./configure step of autotools)
+ cmake ..
+ 3) start the build process
+ make
+As a result of successful compilation, the shared library will be created in the lib/ sub directory, and the executable example can be found in bin/.
+
+Installation:
+If you want to use the General Broken Lines as a project in another CMake managed project, or want (slightly) simpler path also invoke:
+ make install
+This will create some configuration files for inclusion and also create the lib/ and bin/ directory in the directory of the source code.
+(You can also install the library in /usr/lib if wanted, this needs a slight modification of the CMakeLists.txt file.)
+
+Documentation:
+To build the documentation, you need doxygen (version > 1.7.0 recommended ) on your system.
+Invoke, also in the build directory:
+ make doc
+
+All steps in one:
+The shortest way to build everything, if you have the required packages installed (CMake, root and doxygen) is to execute from the current (project root) directory (e.g. copy and execute the following line):
+ mkdir build; cd build; cmake ..; make; make doc; make install
diff --git a/3rdparty/GeneralBrokenLines/doc/Doxyfile.in b/3rdparty/GeneralBrokenLines/doc/Doxyfile.in
new file mode 100644
index 000000000..f83628184
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/doc/Doxyfile.in
@@ -0,0 +1,1784 @@
+# Doxyfile 1.7.6.1
+
+# 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 sequence of words) that should
+# identify the project. Note that if you do not use Doxywizard you need
+# to put quotes around the project name if it contains spaces.
+
+PROJECT_NAME = GeneralBrokenLines
+
+# 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 = Rev: @GLOBAL_SVN_REVISION@
+
+# Using the PROJECT_BRIEF tag one can provide an optional one line description
+# for a project that appears at the top of each page and should give viewer
+# a quick idea about the purpose of the project. Keep the description short.
+
+PROJECT_BRIEF =
+
+# With the PROJECT_LOGO tag one can specify an logo or icon that is
+# included in the documentation. The maximum height of the logo should not
+# exceed 55 pixels and the maximum width should not exceed 200 pixels.
+# Doxygen will copy the logo to the output directory.
+
+PROJECT_LOGO = @CMAKE_CURRENT_SOURCE_DIR@/doc/gbl-logo.png
+
+# 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 =
+
+# 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, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+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 =
+
+# 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 = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip.
+
+STRIP_FROM_PATH =
+
+# 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 if your file system
+# 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
+
+# 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 =
+
+# This tag can be used to specify a number of word-keyword mappings (TCL only).
+# A mapping has the form "name=value". For example adding
+# "class=itcl::class" will allow you to use the command class in the
+# itcl::class meaning.
+
+TCL_SUBST =
+
+# 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, CSharp, 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. Note that for custom extensions
+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+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 makes 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 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 the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
+# unions are shown inside the group in which they are included (e.g. using
+# @ingroup) instead of on a separate page (for HTML and Man pages) or
+# section (for LaTeX and RTF).
+
+INLINE_GROUPED_CLASSES = NO
+
+# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
+# unions with only public data fields will be shown inline in the documentation
+# of the scope in which they are defined (i.e. file, namespace, or group
+# documentation), provided this scope is documented. If set to NO (the default),
+# structs, classes, and unions are shown on a separate page (for HTML and Man
+# pages) or section (for LaTeX and RTF).
+
+INLINE_SIMPLE_STRUCTS = NO
+
+# 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 penalty.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+SYMBOL_CACHE_SIZE = 0
+
+# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
+# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
+# their name and scope. Since this can be an expensive process and often the
+# same symbol appear multiple times in the code, doxygen keeps a cache of
+# pre-resolved symbols. If the cache is too small doxygen will become slower.
+# If the cache is too large, memory is wasted. The cache size is given by this
+# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols.
+
+LOOKUP_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = YES
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = YES
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = 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 namespaces are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = 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 FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# 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_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = 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
+
+# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
+# do proper type resolution of all parameters of a function it will reject a
+# match between the prototype and the implementation of a member function even
+# if there is only one candidate or it is obvious which candidate to choose
+# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
+# will still accept a match between prototype and implementation in such cases.
+
+STRICT_PROTO_MATCHING = 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 macro 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 macros in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. The create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE =
+
+# The CITE_BIB_FILES tag can be used to specify one or more bib files
+# containing the references data. This must be a list of .bib files. The
+# .bib extension is automatically appended if omitted. Using this command
+# requires the bibtex tool to be installed. See also
+# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
+# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
+# feature you need bibtex and perl available in the search path.
+
+CITE_BIB_FILES =
+
+#---------------------------------------------------------------------------
+# 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
+
+# The WARN_NO_PARAMDOC option can be enabled 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 = @CMAKE_CURRENT_SOURCE_DIR@/src
+INPUT += @CMAKE_CURRENT_SOURCE_DIR@/include
+
+
+# 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++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.for *.vhd *.vhdl
+
+FILE_PATTERNS =
+
+# 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 = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should be
+# 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.
+# Note that relative paths are relative to the directory from which doxygen is
+# run.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
+# directories that are symbolic links (a Unix file system 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 =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty or if
+# non of the patterns match the file name, INPUT_FILTER is applied.
+
+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
+
+# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
+# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
+# and it is also possible to disable source filtering for a specific pattern
+# using *.ext= (so without naming a filter). This option only has effect when
+# FILTER_SOURCE_FILES is enabled.
+
+FILTER_SOURCE_PATTERNS =
+
+#---------------------------------------------------------------------------
+# 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 = YES
+
+# 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. Note that when using a custom header you are responsible
+# for the proper inclusion of any scripts and style sheets that doxygen
+# needs, which is dependent on the configuration options used.
+# It is advised to generate a default header using "doxygen -w html
+# header.html footer.html stylesheet.css YourConfigFile" and then modify
+# that header. Note that the header is subject to change so you typically
+# have to redo this when upgrading to a newer version of doxygen or when
+# changing the value of configuration settings such as GENERATE_TREEVIEW!
+
+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
+# style sheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET =
+
+# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
+# other source files which should be copied to the HTML output directory. Note
+# that these files will be copied to the base HTML output directory. Use the
+# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# files. In the HTML_STYLESHEET file, use the file name only. Also note that
+# the files will be copied as-is; there are no commands or markers available.
+
+HTML_EXTRA_FILES =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the style sheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP = YES
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# 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 =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+# will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
+# at top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it. Since the tabs have the same information as the
+# navigation tree you can set this option to NO if you already set
+# GENERATE_TREEVIEW to YES.
+
+DISABLE_INDEX = NO
+
+# 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 YES, 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 (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+# Since the tree basically has the same information as the tab index you
+# could consider to set DISABLE_INDEX to NO when enabling this option.
+
+GENERATE_TREEVIEW = NO
+
+# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
+# (range [0,1..20]) that doxygen will group on one line in the generated HTML
+# documentation. Note that a value of 0 will completely suppress the enum
+# values from appearing in the overview section.
+
+ENUM_VALUES_PER_LINE = 4
+
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+USE_INLINE_TREES = NO
+
+# 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
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the
+# mathjax.org site, so you can quickly see the result without installing
+# MathJax, but it is strongly recommended to install a local copy of MathJax
+# before deployment.
+
+MATHJAX_RELPATH = http://www.mathjax.org/mathjax
+
+# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
+# names that should be enabled during MathJax rendering.
+
+MATHJAX_EXTENSIONS =
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE = YES
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a PHP enabled web server instead of at the web client
+# using Javascript. Doxygen will generate the search PHP script and index
+# file to put on the web server. The advantage of the server
+# based approach is that it scales better to large projects and allows
+# full text search. The disadvantages are that it is more difficult to setup
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH = NO
+
+#---------------------------------------------------------------------------
+# 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 = YES
+
+# 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.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
+
+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, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4
+
+# 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 =
+
+# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
+# the generated latex document. The footer should contain everything after
+# the last chapter. If it is left blank doxygen will generate a
+# standard footer. Notice: only use this tag if you know what you are doing!
+
+LATEX_FOOTER =
+
+# 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
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE = NO
+
+# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
+# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
+# http://en.wikipedia.org/wiki/BibTeX for more info.
+
+LATEX_BIB_STYLE = plain
+
+#---------------------------------------------------------------------------
+# 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 style sheet 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
+# pointed to by INCLUDE_PATH will be searched when a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition that
+# overrules the definition found in the source code.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all references to function-like macros
+# that are alone on a line, have an all uppercase name, and do not end with a
+# semicolon, because these will confuse the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# this location is as follows:
+#
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+#
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths or
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = NO
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS = 0
+
+# By default doxygen will use the Helvetica font for all dot files that
+# doxygen generates. When you want a differently looking font you can specify
+# the font name using DOT_FONTNAME. You need to make sure dot is able to find
+# the font, which can be done by putting it in a standard location or by setting
+# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
+# directory containing the font.
+
+DOT_FONTNAME = Helvetica
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the Helvetica font.
+# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
+# set the path where dot can find it.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will generate a graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are svg, png, jpg, or gif.
+# If left blank png will be used. If you choose svg you need to set
+# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible in IE 9+ (other browsers do not have this requirement).
+
+DOT_IMAGE_FORMAT = png
+
+# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+# enable generation of interactive SVG images that allow zooming and panning.
+# Note that this requires a modern browser other than Internet Explorer.
+# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
+# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+# visible. Older versions of IE do not have SVG support.
+
+INTERACTIVE_SVG = NO
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
diff --git a/3rdparty/GeneralBrokenLines/include/BorderedBandMatrix.h b/3rdparty/GeneralBrokenLines/include/BorderedBandMatrix.h
new file mode 100644
index 000000000..dacb11202
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/include/BorderedBandMatrix.h
@@ -0,0 +1,104 @@
+/*
+ * BorderedBandMatrix.h
+ *
+ * Created on: Aug 14, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * BorderedBandMatrix definition.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2017 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#ifndef BORDEREDBANDMATRIX_H_
+#define BORDEREDBANDMATRIX_H_
+
+#include <cstdlib>
+#include <iostream>
+#include <math.h>
+#include <vector>
+#include "Eigen/Core"
+#include "VMatrix.h"
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// (Symmetric) Bordered Band Matrix.
+ /**
+ * Separate storage of border, mixed and band parts (as vector<double>).
+ *
+ *\verbatim
+ * Example for matrix size=8 with border size and band width of two
+ *
+ * +- -+
+ * | B11 B12 M13 M14 M15 M16 M17 M18 |
+ * | B12 B22 M23 M24 M25 M26 M27 M28 |
+ * | M13 M23 C33 C34 C35 0. 0. 0. |
+ * | M14 M24 C34 C44 C45 C46 0. 0. |
+ * | M15 M25 C35 C45 C55 C56 C57 0. |
+ * | M16 M26 0. C46 C56 C66 C67 C68 |
+ * | M17 M27 0. 0. C57 C67 C77 C78 |
+ * | M18 M28 0. 0. 0. C68 C78 C88 |
+ * +- -+
+ *
+ * Is stored as::
+ *
+ * +- -+ +- -+
+ * | B11 B12 | | M13 M14 M15 M16 M17 M18 |
+ * | B12 B22 | | M23 M24 M25 M26 M27 M28 |
+ * +- -+ +- -+
+ *
+ * +- -+
+ * | C33 C44 C55 C66 C77 C88 |
+ * | C34 C45 C56 C67 C78 0. |
+ * | C35 C46 C57 C68 0. 0. |
+ * +- -+
+ *\endverbatim
+ */
+
+ class BorderedBandMatrix {
+ public:
+ BorderedBandMatrix();
+ virtual ~BorderedBandMatrix();
+ void resize(unsigned int nSize, unsigned int nBorder = 1, unsigned int nBand = 5);
+ void solveAndInvertBorderedBand(const VVector& aRightHandSide, VVector& aSolution);
+ void addBlockMatrix(double aWeight, const std::vector<unsigned int>* anIndex, const std::vector<double>* aVector);
+ void addBlockMatrix(double aWeight, unsigned int nSimple, unsigned int* anIndex, double* aVector);
+ Eigen::MatrixXd getBlockMatrix(const std::vector<unsigned int> anIndex) const;
+ Eigen::MatrixXd getBlockMatrix(unsigned int aSize, unsigned int* anIndex) const;
+ void printMatrix() const;
+
+ private:
+ unsigned int numSize; ///< Matrix size
+ unsigned int numBorder; ///< Border size
+ unsigned int numBand; ///< Band width
+ unsigned int numCol; ///< Band matrix size
+ VSymMatrix theBorder; ///< Border part
+ VMatrix theMixed; ///< Mixed part
+ VMatrix theBand; ///< Band part
+
+ void decomposeBand();
+ VVector solveBand(const VVector& aRightHandSide) const;
+ VMatrix solveBand(const VMatrix& aRightHandSide) const;
+ VMatrix invertBand();
+ VMatrix bandOfAVAT(const VMatrix& anArray, const VSymMatrix& aSymArray) const;
+ };
+}
+#endif /* BORDEREDBANDMATRIX_H_ */
diff --git a/3rdparty/GeneralBrokenLines/include/GblData.h b/3rdparty/GeneralBrokenLines/include/GblData.h
new file mode 100644
index 000000000..8f7842880
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/include/GblData.h
@@ -0,0 +1,267 @@
+/*
+ * GblData.h
+ *
+ * Created on: Aug 18, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * GblData definition.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ * \author Gregor Mittag, DESY, 2017 (templates and other optimizations)
+ *
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2016 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#ifndef GBLDATA_H_
+#define GBLDATA_H_
+
+#include <array>
+#include <iostream>
+#include <math.h>
+#include <vector>
+#include "VMatrix.h"
+
+#include "Eigen/Core"
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ typedef Eigen::Matrix<double, 5, 5> Matrix5d;
+ typedef Eigen::Matrix<double, 2, 7> Matrix27d;
+
+ enum dataBlockType { None, InternalMeasurement, InternalKink, ExternalSeed, ExternalMeasurement };
+
+ /// Data (block) for independent scalar measurement
+ /**
+ * Data (block) containing value, precision and derivatives for measurements, kinks and seeds.
+ * Created from attributes of GblPoints, used to construct linear equation system for track fit.
+ */
+ class GblData {
+ public:
+ GblData(unsigned int aLabel,
+ dataBlockType aType,
+ double aMeas,
+ double aPrec,
+ unsigned int aTraj = 0,
+ unsigned int aPoint = 0);
+ GblData(const GblData&) = default;
+ GblData& operator=(const GblData&) = default;
+ GblData(GblData&&) = default;
+ GblData& operator=(GblData&&) = default;
+ virtual ~GblData();
+
+ /// Add derivatives from measurement.
+ /**
+ * Add (non-zero) derivatives to data block. Fill list of labels of used fit parameters.
+ * \tparam LocalDerivative Local derivatives matrix
+ * \tparam ExtDerivative External derivatives matrix
+ * \param [in] iRow Row index (0-4) in up to 5D measurement
+ * \param [in] labDer Labels for derivatives
+ * \param [in] matDer Derivatives (matrix) 'measurement vs track fit parameters'
+ * \param [in] iOff Offset for row index for additional parameters
+ * \param [in] derLocal Derivatives (matrix) for additional local parameters
+ * \param [in] extOff Offset for external parameters
+ * \param [in] extDer Derivatives for external Parameters
+ */
+ template <typename LocalDerivative, typename ExtDerivative>
+ void addDerivatives(unsigned int iRow,
+ const std::array<unsigned int, 5>& labDer,
+ const Matrix5d& matDer,
+ unsigned int iOff,
+ const Eigen::MatrixBase<LocalDerivative>& derLocal,
+ unsigned int extOff,
+ const Eigen::MatrixBase<ExtDerivative>& extDer);
+
+ /// Add derivatives from kink.
+ /**
+ * Add (non-zero) derivatives to data block. Fill list of labels of used fit parameters.
+ * \tparam ExtDerivative External derivatives matrix
+ * \param [in] iRow Row index (0-1) in 2D kink
+ * \param [in] labDer Labels for derivatives
+ * \param [in] matDer Derivatives (matrix) 'kink vs track fit parameters'
+ * \param [in] extOff Offset for external parameters
+ * \param [in] extDer Derivatives for external Parameters
+ */
+ template <typename ExtDerivative>
+ void addDerivatives(unsigned int iRow,
+ const std::array<unsigned int, 7>& labDer,
+ const Matrix27d& matDer,
+ unsigned int extOff,
+ const Eigen::MatrixBase<ExtDerivative>& extDer);
+
+ void addDerivatives(const std::vector<unsigned int>& index, const std::vector<double>& derivatives);
+
+ void setPrediction(const VVector& aVector);
+ double setDownWeighting(unsigned int aMethod);
+ double getChi2() const;
+ void printData() const;
+ unsigned int getLabel() const;
+ dataBlockType getType() const;
+ unsigned int getNumSimple() const;
+ void
+ getLocalData(double& aValue, double& aWeight, unsigned int& numLocal, unsigned int*& indLocal, double*& derLocal);
+ void getAllData(double& aValue,
+ double& aErr,
+ unsigned int& numLocal,
+ unsigned int*& indLocal,
+ double*& derLocal,
+ unsigned int& aTraj,
+ unsigned int& aPoint,
+ unsigned int& aRow);
+ void getResidual(double& aResidual,
+ double& aVariance,
+ double& aDownWeight,
+ unsigned int& numLocal,
+ unsigned int*& indLocal,
+ double*& derLocal);
+
+ private:
+ unsigned int theLabel; ///< Label (of corresponding point)
+ unsigned int theRow; ///< Row number (of measurement)
+ dataBlockType theType; ///< Type (None, InternalMeasurement, InternalKink, ExternalSeed, ExternalMeasurement)
+ double theValue; ///< Value (residual)
+ double thePrecision; ///< Precision (1/sigma**2)
+ unsigned int theTrajectory; ///< Trajectory number
+ unsigned int thePoint; ///< Point number (on trajectory)
+ unsigned int theDWMethod; ///< Down-weighting method (0: None, 1: Tukey, 2: Huber, 3: Cauchy)
+ double theDownWeight; ///< Down-weighting factor (0-1)
+ double thePrediction; ///< Prediction from fit
+ // standard local parameters (curvature, offsets), fixed size
+ unsigned int theNumLocal; ///< Number of (non zero) local derivatives (max 7 for kinks)
+ unsigned int theParameters[7]; ///< List of parameters (with non zero derivatives)
+ double theDerivatives[7]; ///< List of derivatives for fit
+ // more local parameters, dynamic size
+ std::vector<unsigned int> moreParameters; ///< List of fit parameters (with non zero derivatives)
+ std::vector<double> moreDerivatives; ///< List of derivatives for fit
+ };
+
+ template <typename LocalDerivative, typename ExtDerivative>
+ void GblData::addDerivatives(unsigned int iRow,
+ const std::array<unsigned int, 5>& labDer,
+ const Matrix5d& matDer,
+ unsigned int iOff,
+ const Eigen::MatrixBase<LocalDerivative>& derLocal,
+ unsigned int extOff,
+ const Eigen::MatrixBase<ExtDerivative>& extDer) {
+
+ unsigned int nParMax = 5 + derLocal.cols() + extDer.cols();
+ theRow = iRow - iOff;
+ if(nParMax > 7) {
+ // dynamic data block size
+ moreParameters.reserve(nParMax); // have to be sorted
+ moreDerivatives.reserve(nParMax);
+
+ for(int i = 0; i < derLocal.cols(); ++i) // local derivatives
+ {
+ if(derLocal(iRow - iOff, i)) {
+ moreParameters.push_back(i + 1);
+ moreDerivatives.push_back(derLocal(iRow - iOff, i));
+ }
+ }
+
+ for(int i = 0; i < extDer.cols(); ++i) // external derivatives
+ {
+ if(extDer(iRow - iOff, i)) {
+ moreParameters.push_back(extOff + i + 1);
+ moreDerivatives.push_back(extDer(iRow - iOff, i));
+ }
+ }
+
+ for(size_t i = 0; i < labDer.size(); ++i) // curvature, offset derivatives
+ {
+ if(labDer[i] and matDer(iRow, i)) {
+ moreParameters.push_back(labDer[i]);
+ moreDerivatives.push_back(matDer(iRow, i));
+ }
+ }
+ } else {
+ // simple (static) data block
+ for(int i = 0; i < derLocal.cols(); ++i) // local derivatives
+ {
+ if(derLocal(iRow - iOff, i)) {
+ theParameters[theNumLocal] = i + 1;
+ theDerivatives[theNumLocal] = derLocal(iRow - iOff, i);
+ theNumLocal++;
+ }
+ }
+
+ for(int i = 0; i < extDer.cols(); ++i) // external derivatives
+ {
+ if(extDer(iRow - iOff, i)) {
+ theParameters[theNumLocal] = extOff + i + 1;
+ theDerivatives[theNumLocal] = extDer(iRow - iOff, i);
+ theNumLocal++;
+ }
+ }
+ for(size_t i = 0; i < labDer.size(); ++i) // curvature, offset derivatives
+ {
+ if(labDer[i] and matDer(iRow, i)) {
+ theParameters[theNumLocal] = labDer[i];
+ theDerivatives[theNumLocal] = matDer(iRow, i);
+ theNumLocal++;
+ }
+ }
+ }
+ }
+
+ template <typename ExtDerivative>
+ void GblData::addDerivatives(unsigned int iRow,
+ const std::array<unsigned int, 7>& labDer,
+ const Matrix27d& matDer,
+ unsigned int extOff,
+ const Eigen::MatrixBase<ExtDerivative>& extDer) {
+
+ unsigned int nParMax = 7 + extDer.cols();
+ theRow = iRow;
+ if(nParMax > 7) {
+ // dynamic data block size
+ moreParameters.reserve(nParMax); // have to be sorted
+ moreDerivatives.reserve(nParMax);
+
+ for(int i = 0; i < extDer.cols(); ++i) // external derivatives
+ {
+ if(extDer(iRow, i)) {
+ moreParameters.push_back(extOff + i + 1);
+ moreDerivatives.push_back(extDer(iRow, i));
+ }
+ }
+
+ for(size_t i = 0; i < labDer.size(); ++i) // curvature, offset derivatives
+ {
+ if(labDer[i] and matDer(iRow, i)) {
+ moreParameters.push_back(labDer[i]);
+ moreDerivatives.push_back(matDer(iRow, i));
+ }
+ }
+ } else {
+ // simple (static) data block
+ for(size_t i = 0; i < labDer.size(); ++i) // curvature, offset derivatives
+ {
+ if(labDer[i] and matDer(iRow, i)) {
+ theParameters[theNumLocal] = labDer[i];
+ theDerivatives[theNumLocal] = matDer(iRow, i);
+ theNumLocal++;
+ }
+ }
+ }
+ }
+}
+
+#endif /* GBLDATA_H_ */
diff --git a/3rdparty/GeneralBrokenLines/include/GblPoint.h b/3rdparty/GeneralBrokenLines/include/GblPoint.h
new file mode 100644
index 000000000..5bbbc17d9
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/include/GblPoint.h
@@ -0,0 +1,434 @@
+/*
+ * GblPoint.h
+ *
+ * Created on: Aug 18, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * GblPoint definition.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ * \author Gregor Mittag, DESY, 2017 (templates and other optimizations)
+ *
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2017 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#ifndef GBLPOINT_H_
+#define GBLPOINT_H_
+
+#include <iostream>
+#include <math.h>
+#include <stdexcept>
+#include <vector>
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+#include "TMatrixD.h"
+#include "TMatrixDSym.h"
+#include "TMatrixDSymEigen.h"
+#include "TVectorD.h"
+#endif
+
+#include "Eigen/Dense"
+
+namespace gbl {
+
+ typedef Eigen::Matrix<double, 5, 1> Vector5d;
+ typedef Eigen::Matrix<double, 2, 3> Matrix23d;
+ typedef Eigen::Matrix<double, 2, 5> Matrix25d;
+ typedef Eigen::Matrix<double, 2, 7> Matrix27d;
+ typedef Eigen::Matrix<double, 3, 2> Matrix32d;
+ typedef Eigen::Matrix<double, 5, 5> Matrix5d;
+
+ /// Point on trajectory
+ /**
+ * User supplied point on (initial) trajectory.
+ *
+ * Must have jacobian for propagation from previous point. May have:
+ *
+ * -# Measurement (1D - 5D)
+ * -# Scatterer (thin, 2D kinks)
+ * -# Additional local parameters (with derivatives). Fitted together with track parameters.
+ * -# Additional global parameters (with labels and derivatives). Not fitted, only passed
+ * on to (binary) file for fitting with Millepede-II.
+ */
+ class GblPoint {
+ public:
+ GblPoint(const Matrix5d& aJacobian);
+ GblPoint(const GblPoint&) = default;
+ GblPoint& operator=(const GblPoint&) = default;
+ GblPoint(GblPoint&&) = default;
+ GblPoint& operator=(GblPoint&&) = default;
+ virtual ~GblPoint();
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ // input via ROOT
+ GblPoint(const TMatrixD& aJacobian);
+ void addMeasurement(const TMatrixD& aProjection,
+ const TVectorD& aResiduals,
+ const TVectorD& aPrecision,
+ double minPrecision = 0.);
+ void addMeasurement(const TMatrixD& aProjection,
+ const TVectorD& aResiduals,
+ const TMatrixDSym& aPrecision,
+ double minPrecision = 0.);
+ void addMeasurement(const TVectorD& aResiduals, const TVectorD& aPrecision, double minPrecision = 0.);
+ void addMeasurement(const TVectorD& aResiduals, const TMatrixDSym& aPrecision, double minPrecision = 0.);
+ void addScatterer(const TVectorD& aResiduals, const TVectorD& aPrecision);
+ void addScatterer(const TVectorD& aResiduals, const TMatrixDSym& aPrecision);
+ void addLocals(const TMatrixD& aDerivatives);
+ void addGlobals(const std::vector<int>& aLabels, const TMatrixD& aDerivatives);
+#endif
+ // input via Eigen
+
+ /// Add a measurement to a point.
+ /**
+ * Add measurement (in measurement system) with arbitrary precision (inverse covariance) matrix.
+ * Will be diagonalized.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \tparam Projection Projection matrix
+ * \tparam Residuals Residuals vector
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aProjection Projection from local to measurement system (derivative of measurement vs local
+ * parameters)
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (matrix)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ template <typename Projection,
+ typename Residuals,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime != 1)>::type* = nullptr>
+ void addMeasurement(const Eigen::MatrixBase<Projection>& aProjection,
+ const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision = 0.);
+
+ /// Add a measurement to a point.
+ /**
+ * Add measurement (in measurement system) with diagonal precision (inverse covariance) matrix.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \tparam Projection Projection matrix
+ * \tparam Residuals Residuals vector
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aProjection Projection from local to measurement system (derivative of measurement vs local
+ * parameters)
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (vector with diagonal)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ template <typename Projection,
+ typename Residuals,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type* = nullptr>
+ void addMeasurement(const Eigen::MatrixBase<Projection>& aProjection,
+ const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision = 0.);
+
+ /// Add a measurement to a point.
+ /**
+ * Add measurement in local system with arbitrary precision (inverse covariance) matrix.
+ * Will be diagonalized.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \tparam Residuals Residuals vector
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (matrix)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ template <typename Residuals,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime != 1)>::type* = nullptr>
+ void addMeasurement(const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision = 0.);
+
+ /// Add a measurement to a point.
+ /**
+ * Add measurement in local system with diagonal precision (inverse covariance) matrix.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \tparam Residuals Residuals vector
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (vector with diagonal)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ template <typename Residuals,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type* = nullptr>
+ void addMeasurement(const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision = 0.);
+
+ /// Add a (thin) scatterer to a point.
+ /**
+ * Add scatterer with arbitrary precision (inverse covariance) matrix.
+ * Will be diagonalized. Changes local track direction.
+ *
+ * The precision matrix for the local slopes is defined by the
+ * angular scattering error theta_0 and the scalar products c_1, c_2 of the
+ * offset directions in the local frame with the track direction:
+ *
+ * (1 - c_1*c_1 - c_2*c_2) | 1 - c_1*c_1 - c_1*c_2 |
+ * P = ----------------------- * | |
+ * theta_0*theta_0 | - c_1*c_2 1 - c_2*c_2 |
+ *
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aResiduals Scatterer residuals
+ * \param [in] aPrecision Scatterer precision (full matrix)
+ */
+ template <typename Precision, typename std::enable_if<(Precision::ColsAtCompileTime == 2)>::type* = nullptr>
+ void addScatterer(const Eigen::Vector2d& aResiduals, const Eigen::MatrixBase<Precision>& aPrecision);
+
+ /// Add a (thin) scatterer to a point.
+ /**
+ * Add scatterer with diagonal precision (inverse covariance) matrix.
+ * Changes local track direction.
+ *
+ * The precision matrix for the local slopes is defined by the
+ * angular scattering error theta_0 and the scalar products c_1, c_2 of the
+ * offset directions in the local frame with the track direction:
+ *
+ * (1 - c_1*c_1 - c_2*c_2) | 1 - c_1*c_1 - c_1*c_2 |
+ * P = ----------------------- * | |
+ * theta_0*theta_0 | - c_1*c_2 1 - c_2*c_2 |
+ *
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aResiduals Scatterer residuals
+ * \param [in] aPrecision Scatterer precision (vector with diagonal)
+ */
+ template <typename Precision, typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type* = nullptr>
+ void addScatterer(const Eigen::Vector2d& aResiduals, const Eigen::MatrixBase<Precision>& aPrecision);
+
+ /// Add local derivatives to a point.
+ /**
+ * Point needs to have a measurement.
+ * \tparam Derivative Derivatives matrix
+ * \param [in] aDerivatives Local derivatives (matrix)
+ */
+ template <typename Derivative> void addLocals(const Eigen::MatrixBase<Derivative>& aDerivatives);
+ template <typename Derivative>
+
+ /// Add global derivatives to a point.
+ /**
+ * Point needs to have a measurement.
+ * \tparam Derivative Derivatives matrix
+ * \param [in] aLabels Global derivatives labels
+ * \param [in] aDerivatives Global derivatives (matrix)
+ */
+ void addGlobals(const std::vector<int>& aLabels, const Eigen::MatrixBase<Derivative>& aDerivatives);
+ //
+ unsigned int hasMeasurement() const;
+ double getMeasPrecMin() const;
+ void getMeasurement(Matrix5d& aProjection, Vector5d& aResiduals, Vector5d& aPrecision) const;
+ void getMeasTransformation(Eigen::MatrixXd& aTransformation) const;
+ bool hasScatterer() const;
+ void getScatterer(Eigen::Matrix2d& aTransformation, Eigen::Vector2d& aResiduals, Eigen::Vector2d& aPrecision) const;
+ void getScatTransformation(Eigen::Matrix2d& aTransformation) const;
+ unsigned int getNumLocals() const;
+ const Eigen::MatrixXd& getLocalDerivatives() const;
+ unsigned int getNumGlobals() const;
+ void getGlobalLabels(std::vector<int>& aLabels) const;
+ void getGlobalDerivatives(Eigen::MatrixXd& aDerivatives) const;
+ void
+ getGlobalLabelsAndDerivatives(unsigned int aRow, std::vector<int>& aLabels, std::vector<double>& aDerivatives) const;
+ unsigned int getLabel() const;
+ int getOffset() const;
+ const Matrix5d& getP2pJacobian() const;
+ void getDerivatives(int aDirection, Eigen::Matrix2d& matW, Eigen::Matrix2d& matWJ, Eigen::Vector2d& vecWd) const;
+ void printPoint(unsigned int level = 0) const;
+
+ private:
+ friend class GblTrajectory; // to have the following setters private
+ void setLabel(unsigned int aLabel);
+ void setOffset(int anOffset);
+ void addPrevJacobian(const Matrix5d& aJac);
+ void addNextJacobian(const Matrix5d& aJac);
+
+ unsigned int theLabel; ///< Label identifying point
+ int theOffset; ///< Offset number at point if not negative (else interpolation needed)
+ Matrix5d p2pJacobian; ///< Point-to-point jacobian from previous point
+ Matrix5d prevJacobian; ///< Jacobian to previous scatterer (or first measurement)
+ Matrix5d nextJacobian; ///< Jacobian to next scatterer (or last measurement)
+ unsigned int measDim; ///< Dimension of measurement (1-5), 0 indicates absence of measurement
+ double measPrecMin; ///< Minimal measurement precision (for usage)
+ Matrix5d measProjection; ///< Projection from measurement to local system
+
+ Vector5d measResiduals; ///< Measurement residuals
+ Vector5d measPrecision; ///< Measurement precision (diagonal of inverse covariance matrix)
+ bool transFlag; ///< Transformation exists?
+ Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::ColMajor /* default */, 5, 5>
+ measTransformation; ///< Transformation of diagonalization (of meas. precision matrix)
+ bool scatFlag; ///< Scatterer present?
+ Eigen::Matrix2d scatTransformation; ///< Transformation of diagonalization (of scat. precision matrix)
+ Eigen::Vector2d scatResiduals; ///< Scattering residuals (initial kinks if iterating)
+ Eigen::Vector2d scatPrecision; ///< Scattering precision (diagonal of inverse covariance matrix)
+ Eigen::MatrixXd localDerivatives; ///< Derivatives of measurement vs additional local (fit) parameters
+ std::vector<int> globalLabels; ///< Labels of global (MP-II) derivatives
+ Eigen::MatrixXd globalDerivatives; ///< Derivatives of measurement vs additional global (MP-II) parameters
+ };
+
+ template <typename Projection,
+ typename Residuals,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime != 1)>::type*>
+ void GblPoint::addMeasurement(const Eigen::MatrixBase<Projection>& aProjection,
+ const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision) {
+ static_assert(static_cast<int>(Residuals::ColsAtCompileTime) == 1,
+ "addMeasurement: cols(Residuals) must be 1 (vector)");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) <= 5 or
+ static_cast<int>(Residuals::RowsAtCompileTime) == Eigen::Dynamic,
+ "addMeasurement: rows(Residuals) must be 1-5 or dynamic");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) == static_cast<int>(Precision::RowsAtCompileTime),
+ "addMeasurement: rows(Residuals) and rows(Precision) must be equal");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) == static_cast<int>(Projection::RowsAtCompileTime),
+ "addMeasurement: rows(Residuals) and rows(Projection) must be equal");
+ static_assert(static_cast<int>(Precision::RowsAtCompileTime) == static_cast<int>(Precision::ColsAtCompileTime),
+ "addMeasurement: rows(Precision) and cols(Precision) must be equal");
+ static_assert(static_cast<int>(Projection::RowsAtCompileTime) == static_cast<int>(Projection::ColsAtCompileTime),
+ "addMeasurement: rows(Projection) and cols(Projection) must be equal");
+ measDim = aResiduals.rows();
+ measPrecMin = minPrecision;
+ // arbitrary precision matrix
+ Eigen::SelfAdjointEigenSolver<typename Precision::PlainObject> measEigen{aPrecision};
+ measTransformation = measEigen.eigenvectors().transpose();
+ transFlag = true;
+ measResiduals.tail(measDim) = measTransformation * aResiduals;
+ measPrecision.tail(measDim) = measEigen.eigenvalues();
+ measProjection.bottomRightCorner(measDim, measDim) = measTransformation * aProjection;
+ }
+
+ template <typename Projection,
+ typename Residuals,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type*>
+ void GblPoint::addMeasurement(const Eigen::MatrixBase<Projection>& aProjection,
+ const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision) {
+ static_assert(static_cast<int>(Residuals::ColsAtCompileTime) == 1,
+ "addMeasurement: cols(Residuals) must be 1 (vector)");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) <= 5 or
+ static_cast<int>(Residuals::RowsAtCompileTime) == Eigen::Dynamic,
+ "addMeasurement: rows(Residuals) must be 1-5 or dynamic");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) == static_cast<int>(Precision::RowsAtCompileTime),
+ "addMeasurement: rows(Residuals) and rows(Precision) must be equal");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) == static_cast<int>(Projection::RowsAtCompileTime),
+ "addMeasurement: rows(Residuals) and rows(Projection) must be equal");
+ static_assert(static_cast<int>(Projection::RowsAtCompileTime) == static_cast<int>(Projection::ColsAtCompileTime),
+ "addMeasurement: rows(Projection) and cols(Projection) must be equal");
+ measDim = aResiduals.rows();
+ measPrecMin = minPrecision;
+ // diagonal precision matrix
+ measResiduals.tail(measDim) = aResiduals;
+ measPrecision.tail(measDim) = aPrecision;
+ measProjection.bottomRightCorner(measDim, measDim) = aProjection;
+ }
+
+ template <typename Residuals, typename Precision, typename std::enable_if<(Precision::ColsAtCompileTime != 1)>::type*>
+ void GblPoint::addMeasurement(const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision) {
+ static_assert(static_cast<int>(Residuals::ColsAtCompileTime) == 1,
+ "addMeasurement: cols(Residuals) must be 1 (vector)");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) <= 5 or
+ static_cast<int>(Residuals::RowsAtCompileTime) == Eigen::Dynamic,
+ "addMeasurement: rows(Residuals) must be 1-5 or dynamic");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) == static_cast<int>(Precision::RowsAtCompileTime),
+ "addMeasurement: rows(Residuals) and rows(Precision) must be equal");
+ measDim = aResiduals.rows();
+ measPrecMin = minPrecision;
+ // arbitrary precision matrix
+ Eigen::SelfAdjointEigenSolver<typename Precision::PlainObject> measEigen{aPrecision};
+ measTransformation = measEigen.eigenvectors().transpose();
+ transFlag = true;
+ measResiduals.tail(measDim) = measTransformation * aResiduals;
+ measPrecision.tail(measDim) = measEigen.eigenvalues();
+ measProjection.bottomRightCorner(measDim, measDim) = measTransformation;
+ }
+
+ template <typename Residuals, typename Precision, typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type*>
+ void GblPoint::addMeasurement(const Eigen::MatrixBase<Residuals>& aResiduals,
+ const Eigen::MatrixBase<Precision>& aPrecision,
+ double minPrecision) {
+ static_assert(static_cast<int>(Residuals::ColsAtCompileTime) == 1,
+ "addMeasurement: cols(Residuals) must be 1 (vector)");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) <= 5 or
+ static_cast<int>(Residuals::RowsAtCompileTime) == Eigen::Dynamic,
+ "addMeasurement: rows(Residuals) must be 1-5 or dynamic");
+ static_assert(static_cast<int>(Residuals::RowsAtCompileTime) == static_cast<int>(Precision::RowsAtCompileTime),
+ "addMeasurement: rows(Residuals) and rows(Precision) must be equal");
+ measDim = aResiduals.rows();
+ measPrecMin = minPrecision;
+ // diagonal precision matrix
+ measResiduals.tail(measDim) = aResiduals;
+ measPrecision.tail(measDim) = aPrecision;
+ measProjection.setIdentity();
+ }
+
+ template <typename Precision, typename std::enable_if<(Precision::ColsAtCompileTime == 2)>::type*>
+ void GblPoint::addScatterer(const Eigen::Vector2d& aResiduals, const Eigen::MatrixBase<Precision>& aPrecision) {
+ static_assert(static_cast<int>(Precision::RowsAtCompileTime) == 2 or
+ static_cast<int>(Precision::RowsAtCompileTime) == Eigen::Dynamic,
+ "addScatterer: rows(Precision) must be 2 or dynamic");
+ scatFlag = true;
+ // arbitrary precision matrix
+ Eigen::SelfAdjointEigenSolver<typename Precision::PlainObject> scatEigen{aPrecision};
+ scatTransformation = scatEigen.eigenvectors();
+ scatTransformation.transposeInPlace();
+ scatResiduals = scatTransformation * aResiduals;
+ scatPrecision = scatEigen.eigenvalues();
+ }
+
+ template <typename Precision, typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type*>
+ void GblPoint::addScatterer(const Eigen::Vector2d& aResiduals, const Eigen::MatrixBase<Precision>& aPrecision) {
+ static_assert(static_cast<int>(Precision::RowsAtCompileTime) == 2 or
+ static_cast<int>(Precision::RowsAtCompileTime) == Eigen::Dynamic,
+ "addScatterer: rows(Precision) must be 2 or dynamic");
+ scatFlag = true;
+ scatResiduals = aResiduals;
+ scatPrecision = aPrecision;
+ scatTransformation.setIdentity();
+ }
+
+ template <typename Derivative> void GblPoint::addLocals(const Eigen::MatrixBase<Derivative>& aDerivatives) {
+ if(measDim) {
+ localDerivatives.resize(aDerivatives.rows(), aDerivatives.cols());
+ if(transFlag) {
+ localDerivatives = measTransformation * aDerivatives;
+ } else {
+ localDerivatives = aDerivatives;
+ }
+ }
+ }
+
+ template <typename Derivative>
+ void GblPoint::addGlobals(const std::vector<int>& aLabels, const Eigen::MatrixBase<Derivative>& aDerivatives) {
+ if(measDim) {
+ globalLabels = aLabels;
+ globalDerivatives.resize(aDerivatives.rows(), aDerivatives.cols());
+ if(transFlag) {
+ globalDerivatives = measTransformation * aDerivatives;
+ } else {
+ globalDerivatives = aDerivatives;
+ }
+ }
+ }
+}
+#endif /* GBLPOINT_H_ */
diff --git a/3rdparty/GeneralBrokenLines/include/GblTrajectory.h b/3rdparty/GeneralBrokenLines/include/GblTrajectory.h
new file mode 100644
index 000000000..5a68ff3ec
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/include/GblTrajectory.h
@@ -0,0 +1,331 @@
+/*
+ * GblTrajectory.h
+ *
+ * Created on: Aug 18, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * GblTrajectory definition.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ * \author Gregor Mittag, DESY, 2017 (templates and other optimizations)
+ *
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2018 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#ifndef GBLTRAJECTORY_H_
+#define GBLTRAJECTORY_H_
+
+#include <array>
+#include "BorderedBandMatrix.h"
+#include "GblData.h"
+#include "GblPoint.h"
+#include "MilleBinary.h"
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// GBL trajectory.
+ /**
+ * List of GblPoints ordered by arc length.
+ * Can be fitted and optionally written to MP-II binary file.
+ */
+ class GblTrajectory {
+ public:
+ GblTrajectory(const std::vector<GblPoint>& aPointList,
+ bool flagCurv = true,
+ bool flagU1dir = true,
+ bool flagU2dir = true);
+ GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, Eigen::MatrixXd>>& aPointsAndTransList);
+
+ /// Create new (simple) trajectory from list of points with external seed.
+ /**
+ * Curved trajectory in space (default) or without curvature (q/p) or in one
+ * plane (u-direction) only.
+ * \tparam Seed Seed precision matrix
+ * \param [in] aPointList List of points
+ * \param [in] aLabel (Signed) label of point for external seed
+ * (<0: in front, >0: after point, slope changes at scatterer!)
+ * \param [in] aSeed Precision matrix of external seed
+ * \param [in] flagCurv Use q/p
+ * \param [in] flagU1dir Use in u1 direction
+ * \param [in] flagU2dir Use in u2 direction
+ */
+ template <typename Seed>
+ GblTrajectory(const std::vector<GblPoint>& aPointList,
+ unsigned int aLabel,
+ const Eigen::MatrixBase<Seed>& aSeed,
+ bool flagCurv = true,
+ bool flagU1dir = true,
+ bool flagU2dir = true);
+
+ /// Create new composed trajectory from list of points and transformations with arbitrary external measurements.
+ /**
+ * Composed of curved trajectories in space. The precision matrix for the external measurements is specified as
+ * matrix.
+ *
+ * \tparam Derivatives External derivatives
+ * \tparam Measurements Residuals vector
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aPointsAndTransList List containing pairs with list of points and transformation (at inner (first)
+ * point)
+ * \param [in] extDerivatives Derivatives of external measurements vs external parameters
+ * \param [in] extMeasurements External measurements (residuals)
+ * \param [in] extPrecisions Precision of external measurements (matrix)
+ */
+ template <typename Derivatives,
+ typename Measurements,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime != 1)>::type* = nullptr>
+ GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, Eigen::MatrixXd>>& aPointsAndTransList,
+ const Eigen::MatrixBase<Derivatives>& extDerivatives,
+ const Eigen::MatrixBase<Measurements>& extMeasurements,
+ const Eigen::MatrixBase<Precision>& extPrecisions);
+
+ /// Create new composed trajectory from list of points and transformations with independent external measurements.
+ /**
+ * Composed of curved trajectories in space. The (diagonal) precision matrix for the external measurements is
+ * specified as vector
+ * (containing the diagonal).
+ *
+ * \tparam Derivatives External derivatives
+ * \tparam Measurements Residuals vector
+ * \tparam Precision Precision matrix or vector (with diagonal)
+ * \param [in] aPointsAndTransList List containing pairs with list of points and transformation (at inner (first)
+ * point)
+ * \param [in] extDerivatives Derivatives of external measurements vs external parameters
+ * \param [in] extMeasurements External measurements (residuals)
+ * \param [in] extPrecisions Precision of external measurements (vector with diagonal)
+ */
+ template <typename Derivatives,
+ typename Measurements,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type* = nullptr>
+ GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, Eigen::MatrixXd>>& aPointsAndTransList,
+ const Eigen::MatrixBase<Derivatives>& extDerivatives,
+ const Eigen::MatrixBase<Measurements>& extMeasurements,
+ const Eigen::MatrixBase<Precision>& extPrecisions);
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ // input from ROOT
+ GblTrajectory(const std::vector<GblPoint>& aPointList,
+ unsigned int aLabel,
+ const TMatrixDSym& aSeed,
+ bool flagCurv = true,
+ bool flagU1dir = true,
+ bool flagU2dir = true);
+ GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, TMatrixD>>& aPointsAndTransList);
+ GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, TMatrixD>>& aPointsAndTransList,
+ const TMatrixD& extDerivatives,
+ const TVectorD& extMeasurements,
+ const TVectorD& extPrecisions);
+ GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, TMatrixD>>& aPointsAndTransList,
+ const TMatrixD& extDerivatives,
+ const TVectorD& extMeasurements,
+ const TMatrixDSym& extPrecisions);
+#endif
+ virtual ~GblTrajectory();
+ bool isValid() const;
+ unsigned int getNumPoints() const;
+ unsigned int getResults(int aSignedLabel, Eigen::VectorXd& localPar, Eigen::MatrixXd& localCov) const;
+ unsigned int getMeasResults(unsigned int aLabel,
+ unsigned int& numData,
+ Eigen::VectorXd& aResiduals,
+ Eigen::VectorXd& aMeasErrors,
+ Eigen::VectorXd& aResErrors,
+ Eigen::VectorXd& aDownWeights);
+ unsigned int getScatResults(unsigned int aLabel,
+ unsigned int& numData,
+ Eigen::VectorXd& aResiduals,
+ Eigen::VectorXd& aMeasErrors,
+ Eigen::VectorXd& aResErrors,
+ Eigen::VectorXd& aDownWeights);
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ // input from ROOT
+ unsigned int getResults(int aSignedLabel, TVectorD& localPar, TMatrixDSym& localCov) const;
+ unsigned int getMeasResults(unsigned int aLabel,
+ unsigned int& numData,
+ TVectorD& aResiduals,
+ TVectorD& aMeasErrors,
+ TVectorD& aResErrors,
+ TVectorD& aDownWeights);
+ unsigned int getScatResults(unsigned int aLabel,
+ unsigned int& numData,
+ TVectorD& aResiduals,
+ TVectorD& aMeasErrors,
+ TVectorD& aResErrors,
+ TVectorD& aDownWeights);
+#endif
+ unsigned int getLabels(std::vector<unsigned int>& aLabelList) const;
+ unsigned int getLabels(std::vector<std::vector<unsigned int>>& aLabelList) const;
+ unsigned int
+ fit(double& Chi2, int& Ndf, double& lostWeight, const std::string& optionList = "", unsigned int aLabel = 0);
+ void milleOut(MilleBinary& aMille);
+ void printTrajectory(unsigned int level = 0) const;
+ void printPoints(unsigned int level = 0) const;
+ void printData() const;
+
+ private:
+ unsigned int numAllPoints; ///< Number of all points on trajectory
+ std::vector<unsigned int> numPoints; ///< Number of points on (sub)trajectory
+ unsigned int numTrajectories; ///< Number of trajectories (in composed trajectory)
+ unsigned int numOffsets; ///< Number of (points with) offsets on trajectory
+ unsigned int numInnerTrans; ///< Number of inner transformations to external parameters
+ unsigned int numCurvature; ///< Number of curvature parameters (0 or 1) or external parameters
+ unsigned int numParameters; ///< Number of fit parameters
+ unsigned int numLocals; ///< Total number of (additional) local parameters
+ unsigned int numMeasurements; ///< Total number of measurements
+ unsigned int externalPoint; ///< Label of external point (or 0)
+ unsigned int skippedMeasLabel; ///< Label of point with measurements skipped in fit (for unbiased residuals) (or 0)
+ unsigned int maxNumGlobals; ///< Max. number of global labels/derivatives per point
+ bool constructOK; ///< Trajectory has been successfully constructed (ready for fit/output)
+ bool fitOK; ///< Trajectory has been successfully fitted (results are valid)
+ std::vector<unsigned int> theDimension; ///< List of active dimensions (0=u1, 1=u2) in fit
+ std::vector<std::vector<GblPoint>> thePoints; ///< (list of) List of points on trajectory
+ std::vector<GblData> theData; ///< List of data blocks
+ std::vector<unsigned int> measDataIndex; ///< mapping points to data blocks from measurements
+ std::vector<unsigned int> scatDataIndex; ///< mapping points to data blocks from scatterers
+ Eigen::MatrixXd externalSeed; ///< Precision (inverse covariance matrix) of external seed
+ std::vector<Eigen::MatrixXd> innerTransformations; ///< Transformations at innermost points of
+ // composed trajectory (from common external parameters)
+ Eigen::MatrixXd externalDerivatives; // Derivatives for external measurements of composed trajectory
+ Eigen::VectorXd externalMeasurements; // Residuals for external measurements of composed trajectory
+ Eigen::VectorXd externalPrecisions; // Precisions for external measurements of composed trajectory
+ // linear equation system
+ VVector theVector; ///< Vector of linear equation system
+ BorderedBandMatrix theMatrix; ///< (Bordered band) matrix of linear equation system
+
+ std::pair<std::vector<unsigned int>, Eigen::MatrixXd> getJacobian(int aSignedLabel) const;
+ void getFitToLocalJacobian(std::array<unsigned int, 5>& anIndex,
+ Matrix5d& aJacobian,
+ const GblPoint& aPoint,
+ unsigned int measDim,
+ unsigned int nJacobian = 1) const;
+ void getFitToKinkJacobian(std::array<unsigned int, 7>& anIndex, Matrix27d& aJacobian, const GblPoint& aPoint) const;
+ void construct();
+ void defineOffsets();
+ void calcJacobians();
+ void prepare();
+ void buildLinearEquationSystem();
+ void predict();
+ double downWeight(unsigned int aMethod);
+ void getResAndErr(
+ unsigned int aData, bool used, double& aResidual, double& aMeadsError, double& aResError, double& aDownWeight);
+ };
+
+ template <typename Seed>
+ GblTrajectory::GblTrajectory(const std::vector<GblPoint>& aPointList,
+ unsigned int aLabel,
+ const Eigen::MatrixBase<Seed>& aSeed,
+ bool flagCurv,
+ bool flagU1dir,
+ bool flagU2dir)
+ : numAllPoints(aPointList.size()), numPoints(), numOffsets(0), numInnerTrans(0), numCurvature(flagCurv ? 1 : 0),
+ numParameters(0), numLocals(0), numMeasurements(0), externalPoint(aLabel), skippedMeasLabel(0), maxNumGlobals(0),
+ theDimension(0), thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(aSeed),
+ innerTransformations(), externalDerivatives(), externalMeasurements(), externalPrecisions() {
+
+ if(flagU1dir)
+ theDimension.push_back(0);
+ if(flagU2dir)
+ theDimension.push_back(1);
+ // simple (single) trajectory
+ thePoints.push_back(aPointList);
+ numPoints.push_back(numAllPoints);
+ construct(); // construct trajectory
+ }
+
+ template <typename Derivatives,
+ typename Measurements,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime != 1)>::type*>
+ GblTrajectory::GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, Eigen::MatrixXd>>& aPointsAndTransList,
+ const Eigen::MatrixBase<Derivatives>& extDerivatives,
+ const Eigen::MatrixBase<Measurements>& extMeasurements,
+ const Eigen::MatrixBase<Precision>& extPrecisions)
+ : numAllPoints(), numPoints(), numOffsets(0), numInnerTrans(aPointsAndTransList.size()), numParameters(0),
+ numLocals(0), numMeasurements(0), externalPoint(0), skippedMeasLabel(0), maxNumGlobals(0), theDimension(0),
+ thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations() {
+
+ static_assert(static_cast<int>(Measurements::ColsAtCompileTime) == 1,
+ "GblTrajectory: cols(Measurements) must be 1 (vector)");
+ static_assert(static_cast<int>(Measurements::RowsAtCompileTime) == static_cast<int>(Derivatives::RowsAtCompileTime),
+ "GblTrajectory: rows(Measurements) and rows(Derivatives) must be equal");
+ static_assert(static_cast<int>(Measurements::RowsAtCompileTime) == static_cast<int>(Precision::RowsAtCompileTime),
+ "GblTrajectory: rows(Measurements) and rows(Precision) must be equal");
+ static_assert(static_cast<int>(Precision::RowsAtCompileTime) == static_cast<int>(Precision::ColsAtCompileTime),
+ "GblTrajectory: rows(Precision) and cols(Precision) must be equal");
+ // diagonalize external measurement
+ Eigen::SelfAdjointEigenSolver<typename Precision::PlainObject> extEigen{extPrecisions};
+ // @TODO if (extEigen.info() != Success) abort();
+ auto extTransformation = extEigen.eigenvectors().transpose();
+ externalDerivatives.resize(extDerivatives.rows(), extDerivatives.cols());
+ externalDerivatives = extTransformation * extDerivatives;
+ externalMeasurements.resize(extMeasurements.size());
+ externalMeasurements = extTransformation * extMeasurements;
+ externalPrecisions.resize(extMeasurements.size());
+ externalPrecisions = extEigen.eigenvalues();
+
+ for(unsigned int iTraj = 0; iTraj < aPointsAndTransList.size(); ++iTraj) {
+ thePoints.push_back(aPointsAndTransList[iTraj].first);
+ numPoints.push_back(thePoints.back().size());
+ numAllPoints += numPoints.back();
+ innerTransformations.push_back(aPointsAndTransList[iTraj].second);
+ }
+ theDimension.push_back(0);
+ theDimension.push_back(1);
+ numCurvature = innerTransformations[0].cols();
+ construct(); // construct (composed) trajectory
+ }
+
+ template <typename Derivatives,
+ typename Measurements,
+ typename Precision,
+ typename std::enable_if<(Precision::ColsAtCompileTime == 1)>::type*>
+ GblTrajectory::GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, Eigen::MatrixXd>>& aPointsAndTransList,
+ const Eigen::MatrixBase<Derivatives>& extDerivatives,
+ const Eigen::MatrixBase<Measurements>& extMeasurements,
+ const Eigen::MatrixBase<Precision>& extPrecisions)
+ : numAllPoints(), numPoints(), numOffsets(0), numInnerTrans(aPointsAndTransList.size()), numParameters(0),
+ numLocals(0), numMeasurements(0), externalPoint(0), skippedMeasLabel(0), maxNumGlobals(0), theDimension(0),
+ thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations() {
+ static_assert(static_cast<int>(Measurements::ColsAtCompileTime) == 1,
+ "GblTrajectory: cols(Measurements) must be 1 (vector)");
+ static_assert(static_cast<int>(Measurements::RowsAtCompileTime) == static_cast<int>(Derivatives::RowsAtCompileTime),
+ "GblTrajectory: rows(Measurements) and rows(Derivatives) must be equal");
+ static_assert(static_cast<int>(Measurements::RowsAtCompileTime) == static_cast<int>(Precision::RowsAtCompileTime),
+ "GblTrajectory: rows(Measurements) and rows(Precision) must be equal");
+
+ externalDerivatives = extDerivatives;
+ externalMeasurements = extMeasurements;
+ externalPrecisions = extPrecisions;
+
+ for(unsigned int iTraj = 0; iTraj < aPointsAndTransList.size(); ++iTraj) {
+ thePoints.push_back(aPointsAndTransList[iTraj].first);
+ numPoints.push_back(thePoints.back().size());
+ numAllPoints += numPoints.back();
+ innerTransformations.push_back(aPointsAndTransList[iTraj].second);
+ }
+ theDimension.push_back(0);
+ theDimension.push_back(1);
+ numCurvature = innerTransformations[0].cols();
+ construct(); // construct (composed) trajectory
+ }
+}
+#endif /* GBLTRAJECTORY_H_ */
diff --git a/3rdparty/GeneralBrokenLines/include/MilleBinary.h b/3rdparty/GeneralBrokenLines/include/MilleBinary.h
new file mode 100644
index 000000000..aa350acfd
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/include/MilleBinary.h
@@ -0,0 +1,102 @@
+/*
+ * MilleBinary.h
+ *
+ * Created on: Aug 31, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * MilleBinary definition.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2018 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#ifndef MILLEBINARY_H_
+#define MILLEBINARY_H_
+
+#include <fstream>
+#include <vector>
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// Millepede-II (binary) record.
+ /**
+ * Containing information for local (track) and global fit.
+ *
+ * The data blocks are collected in two arrays, a real array
+ * (containing float or double values) and integer array, of same length.
+ * A positive record length indicate _float_ and a negative one _double_ values.
+ * The content of the record is:
+ *\verbatim
+ * real array integer array
+ * 0 0.0 error count (this record)
+ * 1 RMEAS, measured value 0 -+
+ * 2 local derivative index of local derivative |
+ * 3 local derivative index of local derivative |
+ * 4 ... | block
+ * SIGMA, error (>0) 0 |
+ * global derivative label of global derivative |
+ * global derivative label of global derivative |
+ * ... -+
+ * RMEAS, measured value 0
+ * local derivative index of local derivative
+ * local derivative index of local derivative
+ * ...
+ * SIGMA, error 0
+ * global derivative label of global derivative
+ * global derivative label of global derivative
+ * ...
+ * global derivative label of global derivative
+ *\endverbatim
+ *
+ * Special data block (other/debug information).
+ * Contains no local derivatives and (error) SIGMA is negative (-Number of SPecial data words).
+ *
+ *\verbatim
+ * real array integer array
+ * 0.0 0 -+
+ * -float(NSP) 0 |
+ * special data special data | special block (2+NSP words)
+ * special data special data |
+ * ... -+
+ *\endverbatim
+ */
+ class MilleBinary {
+ public:
+ MilleBinary(const std::string& fileName = "milleBinaryISN.dat", bool doublePrec = false, unsigned int aSize = 2000);
+ virtual ~MilleBinary();
+ void addData(double aMeas,
+ double aErr,
+ unsigned int numLocal,
+ unsigned int* indLocal,
+ double* derLocal,
+ const std::vector<int>& labGlobal,
+ const std::vector<double>& derGlobal);
+ void writeRecord();
+
+ private:
+ std::ofstream binaryFile; ///< Binary File
+ std::vector<int> intBuffer; ///< Integer buffer
+ std::vector<float> floatBuffer; ///< Float buffer
+ std::vector<double> doubleBuffer; ///< Double buffer
+ bool doublePrecision; ///< Flag for storage in as *double* values
+ };
+}
+#endif /* MILLEBINARY_H_ */
diff --git a/3rdparty/GeneralBrokenLines/include/VMatrix.h b/3rdparty/GeneralBrokenLines/include/VMatrix.h
new file mode 100644
index 000000000..d7fe72954
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/include/VMatrix.h
@@ -0,0 +1,129 @@
+/*
+ * VMatrix.h
+ *
+ * Created on: Feb 15, 2012
+ * Author: kleinwrt
+ */
+
+/** \file
+ * VMatrix definition.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2016 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#ifndef VMATRIX_H_
+#define VMATRIX_H_
+
+#include <cstring>
+#include <iomanip>
+#include <iostream>
+#include <math.h>
+#include <vector>
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// Simple Vector based on std::vector<double>
+ class VVector {
+ public:
+ VVector(const unsigned int nRows = 0);
+ VVector(const VVector& aVector);
+ virtual ~VVector();
+ void resize(const unsigned int nRows);
+ VVector getVec(unsigned int len, unsigned int start = 0) const;
+ void putVec(const VVector& aVector, unsigned int start = 0);
+ inline double& operator()(unsigned int i);
+ inline double operator()(unsigned int i) const;
+ unsigned int getNumRows() const;
+ void print() const;
+ VVector operator-(const VVector& aVector) const;
+ VVector& operator=(const VVector& aVector);
+
+ private:
+ unsigned int numRows; ///< Number of rows
+ std::vector<double> theVec; ///< Data
+ };
+
+ /// Simple Matrix based on std::vector<double>
+ class VMatrix {
+ public:
+ VMatrix(const unsigned int nRows = 0, const unsigned int nCols = 0);
+ VMatrix(const VMatrix& aMatrix);
+ virtual ~VMatrix();
+ void resize(const unsigned int nRows, const unsigned int nCols);
+ VMatrix transpose() const;
+ inline double& operator()(unsigned int i, unsigned int j);
+ inline double operator()(unsigned int i, unsigned int j) const;
+ unsigned int getNumRows() const;
+ unsigned int getNumCols() const;
+ void print() const;
+ VVector operator*(const VVector& aVector) const;
+ VMatrix operator*(const VMatrix& aMatrix) const;
+ VMatrix operator+(const VMatrix& aMatrix) const;
+ VMatrix& operator=(const VMatrix& aMatrix);
+
+ private:
+ unsigned int numRows; ///< Number of rows
+ unsigned int numCols; ///< Number of columns
+ std::vector<double> theVec; ///< Data
+ };
+
+ /// Simple symmetric Matrix based on std::vector<double>
+ class VSymMatrix {
+ public:
+ VSymMatrix(const unsigned int nRows = 0);
+ virtual ~VSymMatrix();
+ void resize(const unsigned int nRows);
+ unsigned int invert();
+ inline double& operator()(unsigned int i, unsigned int j);
+ inline double operator()(unsigned int i, unsigned int j) const;
+ unsigned int getNumRows() const;
+ void print() const;
+ VSymMatrix operator-(const VMatrix& aMatrix) const;
+ VVector operator*(const VVector& aVector) const;
+ VMatrix operator*(const VMatrix& aMatrix) const;
+
+ private:
+ unsigned int numRows; ///< Number of rows
+ std::vector<double> theVec; ///< Data (symmetric storage)
+ };
+
+ /// access element (i,j)
+ inline double& VMatrix::operator()(unsigned int iRow, unsigned int iCol) { return theVec[numCols * iRow + iCol]; }
+
+ /// access element (i,j)
+ inline double VMatrix::operator()(unsigned int iRow, unsigned int iCol) const { return theVec[numCols * iRow + iCol]; }
+
+ /// access element (i)
+ inline double& VVector::operator()(unsigned int iRow) { return theVec[iRow]; }
+
+ /// access element (i)
+ inline double VVector::operator()(unsigned int iRow) const { return theVec[iRow]; }
+
+ /// access element (i,j) assuming i>=j
+ inline double& VSymMatrix::operator()(unsigned int iRow, unsigned int iCol) {
+ return theVec[(iRow * iRow + iRow) / 2 + iCol]; // assuming iCol <= iRow
+ }
+
+ /// access element (i,j) assuming i>=j
+ inline double VSymMatrix::operator()(unsigned int iRow, unsigned int iCol) const {
+ return theVec[(iRow * iRow + iRow) / 2 + iCol]; // assuming iCol <= iRow
+ }
+}
+#endif /* VMATRIX_H_ */
diff --git a/3rdparty/GeneralBrokenLines/src/BorderedBandMatrix.cpp b/3rdparty/GeneralBrokenLines/src/BorderedBandMatrix.cpp
new file mode 100644
index 000000000..724cbdec1
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/src/BorderedBandMatrix.cpp
@@ -0,0 +1,384 @@
+/*
+ * BorderedBandMatrix.cpp
+ *
+ * Created on: Aug 14, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * BorderedBandMatrix methods.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2017 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#include "BorderedBandMatrix.h"
+using namespace Eigen;
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// Create bordered band matrix.
+ BorderedBandMatrix::BorderedBandMatrix() : numSize(0), numBorder(0), numBand(0), numCol(0) {}
+
+ BorderedBandMatrix::~BorderedBandMatrix() {}
+
+ /// Resize bordered band matrix.
+ /**
+ * \param nSize [in] Size of matrix
+ * \param nBorder [in] Size of border (=1 for q/p + additional local parameters)
+ * \param nBand [in] Band width (usually = 5, for simplified jacobians = 4)
+ */
+ void BorderedBandMatrix::resize(unsigned int nSize, unsigned int nBorder, unsigned int nBand) {
+ numSize = nSize;
+ numBorder = nBorder;
+ numCol = nSize - nBorder;
+ numBand = 0;
+ theBorder.resize(numBorder);
+ theMixed.resize(numBorder, numCol);
+ theBand.resize((nBand + 1), numCol);
+ }
+
+ /// Add symmetric block matrix.
+ /**
+ * Add (extended) block matrix defined by 'aVector * aWeight * aVector.T'
+ * to bordered band matrix:
+ * BBmatrix(anIndex(i),anIndex(j)) += aVector(i) * aWeight * aVector(j).
+ * \param aWeight [in] Weight
+ * \param anIndex [in] List of rows/colums to be used
+ * \param aVector [in] Vector
+ */
+ void BorderedBandMatrix::addBlockMatrix(double aWeight,
+ const std::vector<unsigned int>* anIndex,
+ const std::vector<double>* aVector) {
+ int nBorder = numBorder;
+ for(unsigned int i = 0; i < anIndex->size(); ++i) {
+ int iIndex = (*anIndex)[i] - 1; // anIndex has to be sorted
+ for(unsigned int j = 0; j <= i; ++j) {
+ int jIndex = (*anIndex)[j] - 1;
+ if(iIndex < nBorder) {
+ theBorder(iIndex, jIndex) += (*aVector)[i] * aWeight * (*aVector)[j];
+ } else if(jIndex < nBorder) {
+ theMixed(jIndex, iIndex - nBorder) += (*aVector)[i] * aWeight * (*aVector)[j];
+ } else {
+ unsigned int nBand = iIndex - jIndex;
+ theBand(nBand, jIndex - nBorder) += (*aVector)[i] * aWeight * (*aVector)[j];
+ numBand = std::max(numBand, nBand); // update band width
+ }
+ }
+ }
+ }
+
+ /// Add symmetric block matrix.
+ /**
+ * Add (extended) block matrix defined by 'aVector * aWeight * aVector.T'
+ * to bordered band matrix:
+ * BBmatrix(anIndex(i),anIndex(j)) += aVector(i) * aWeight * aVector(j).
+ * \param aWeight [in] Weight
+ * \param aSize [in] Size of block matrix
+ * \param anIndex [in] List of rows/colums to be used
+ * \param aVector [in] Vector
+ */
+ void BorderedBandMatrix::addBlockMatrix(double aWeight, unsigned int aSize, unsigned int* anIndex, double* aVector) {
+ int nBorder = numBorder;
+ for(unsigned int i = 0; i < aSize; ++i) {
+ int iIndex = anIndex[i] - 1; // anIndex has to be sorted
+ for(unsigned int j = 0; j <= i; ++j) {
+ int jIndex = anIndex[j] - 1;
+ if(iIndex < nBorder) {
+ theBorder(iIndex, jIndex) += aVector[i] * aWeight * aVector[j];
+ } else if(jIndex < nBorder) {
+ theMixed(jIndex, iIndex - nBorder) += aVector[i] * aWeight * aVector[j];
+ } else {
+ unsigned int nBand = iIndex - jIndex;
+ theBand(nBand, jIndex - nBorder) += aVector[i] * aWeight * aVector[j];
+ numBand = std::max(numBand, nBand); // update band width
+ }
+ }
+ }
+ }
+
+ /// Retrieve symmetric block matrix.
+ /**
+ * Get (compressed) block from bordered band matrix: aMatrix(i,j) = BBmatrix(anIndex(i),anIndex(j)).
+ * \param anIndex [in] List of rows/colums to be used
+ */
+ MatrixXd BorderedBandMatrix::getBlockMatrix(const std::vector<unsigned int> anIndex) const {
+
+ MatrixXd aMatrix(anIndex.size(), anIndex.size());
+ int nBorder = numBorder;
+ for(unsigned int i = 0; i < anIndex.size(); ++i) {
+ int iIndex = anIndex[i] - 1; // anIndex has to be sorted
+ for(unsigned int j = 0; j <= i; ++j) {
+ int jIndex = anIndex[j] - 1;
+ if(iIndex < nBorder) {
+ aMatrix(i, j) = theBorder(iIndex, jIndex); // border part of inverse
+ } else if(jIndex < nBorder) {
+ aMatrix(i, j) = -theMixed(jIndex, iIndex - nBorder); // mixed part of inverse
+ } else {
+ unsigned int nBand = iIndex - jIndex;
+ aMatrix(i, j) = theBand(nBand, jIndex - nBorder); // band part of inverse
+ }
+ aMatrix(j, i) = aMatrix(i, j);
+ }
+ }
+ return aMatrix;
+ }
+
+ /// Retrieve symmetric block matrix.
+ /**
+ * Get (compressed) block from bordered band matrix: aMatrix(i,j) = BBmatrix(anIndex(i),anIndex(j)).
+ * \param aSize [in] Matrix size
+ * \param anIndex [in] Array of rows/colums to be used
+ */
+ MatrixXd BorderedBandMatrix::getBlockMatrix(unsigned int aSize, unsigned int* anIndex) const {
+
+ MatrixXd aMatrix(aSize, aSize);
+ int nBorder = numBorder;
+ for(unsigned int i = 0; i < aSize; ++i) {
+ int iIndex = anIndex[i] - 1; // anIndex has to be sorted
+ for(unsigned int j = 0; j <= i; ++j) {
+ int jIndex = anIndex[j] - 1;
+ if(iIndex < nBorder) {
+ aMatrix(i, j) = theBorder(iIndex, jIndex); // border part of inverse
+ } else if(jIndex < nBorder) {
+ aMatrix(i, j) = -theMixed(jIndex, iIndex - nBorder); // mixed part of inverse
+ } else {
+ unsigned int nBand = iIndex - jIndex;
+ aMatrix(i, j) = theBand(nBand, jIndex - nBorder); // band part of inverse
+ }
+ aMatrix(j, i) = aMatrix(i, j);
+ }
+ }
+ return aMatrix;
+ }
+
+ /// Solve linear equation system, partially calculate inverse.
+ /**
+ * Solve linear equation A*x=b system with bordered band matrix A,
+ * calculate bordered band part of inverse of A. Use decomposition
+ * in border and band part for block matrix algebra:
+ *
+ * | A Ct | | x1 | | b1 | , A is the border part
+ * | | * | | = | | , Ct is the mixed part
+ * | C D | | x2 | | b2 | , D is the band part
+ *
+ * Explicit inversion of D is avoided by using solution X of D*X=C (X=D^-1*C,
+ * obtained from Cholesky decomposition and forward/backward substitution)
+ *
+ * | x1 | | E*b1 - E*Xt*b2 | , E^-1 = A-Ct*D^-1*C = A-Ct*X
+ * | | = | |
+ * | x2 | | x - X*x1 | , x is solution of D*x=b2 (x=D^-1*b2)
+ *
+ * Inverse matrix is:
+ *
+ * | E -E*Xt |
+ * | | , only band part of (D^-1 + X*E*Xt)
+ * | -X*E D^-1 + X*E*Xt | is calculated
+ *
+ *
+ * \param [in] aRightHandSide Right hand side (vector) 'b' of A*x=b
+ * \param [out] aSolution Solution (vector) x of A*x=b
+ */
+ void BorderedBandMatrix::solveAndInvertBorderedBand(const VVector& aRightHandSide, VVector& aSolution) {
+
+ // decompose band
+ decomposeBand();
+ // invert band
+ VMatrix inverseBand = invertBand();
+ if(numBorder > 0) { // need to use block matrix decomposition to solve
+ // solve for mixed part
+ const VMatrix auxMat = solveBand(theMixed); // = Xt
+ const VMatrix auxMatT = auxMat.transpose(); // = X
+ // solve for border part
+ const VVector auxVec =
+ aRightHandSide.getVec(numBorder) - auxMat * aRightHandSide.getVec(numCol, numBorder); // = b1 - Xt*b2
+ VSymMatrix inverseBorder = theBorder - theMixed * auxMatT;
+ inverseBorder.invert(); // = E
+ const VVector borderSolution = inverseBorder * auxVec; // = x1
+ // solve for band part
+ const VVector bandSolution = solveBand(aRightHandSide.getVec(numCol, numBorder)); // = x
+ aSolution.putVec(borderSolution);
+ aSolution.putVec(bandSolution - auxMatT * borderSolution, numBorder); // = x2
+ // parts of inverse
+ theBorder = inverseBorder; // E
+ theMixed = inverseBorder * auxMat; // E*Xt (-mixed part of inverse) !!!
+ theBand = inverseBand + bandOfAVAT(auxMatT, inverseBorder); // band(D^-1 + X*E*Xt)
+ } else {
+ aSolution.putVec(solveBand(aRightHandSide));
+ theBand = inverseBand;
+ }
+ }
+
+ /// Print bordered band matrix.
+ void BorderedBandMatrix::printMatrix() const {
+ std::cout << "Border part " << std::endl;
+ theBorder.print();
+ std::cout << "Mixed part " << std::endl;
+ theMixed.print();
+ std::cout << "Band part " << std::endl;
+ theBand.print();
+ }
+
+ /*============================================================================
+ from Dbandmatrix.F (MillePede-II by V. Blobel, Univ. Hamburg)
+ ============================================================================*/
+ /// (root free) Cholesky decomposition of band part: C=LDL^T
+ /**
+ * Decompose band matrix into diagonal matrix D and lower triangular band matrix
+ * L (diagonal=1). Overwrite band matrix with D and off-diagonal part of L.
+ * \exception 2 : matrix is singular.
+ * \exception 3 : matrix is not positive definite.
+ */
+ void BorderedBandMatrix::decomposeBand() {
+
+ int nRow = numBand + 1;
+ int nCol = numCol;
+ VVector auxVec(nCol);
+ for(int i = 0; i < nCol; ++i) {
+ auxVec(i) = theBand(0, i) * 16.0; // save diagonal elements
+ }
+ for(int i = 0; i < nCol; ++i) {
+ if((theBand(0, i) + auxVec(i)) != theBand(0, i)) {
+ theBand(0, i) = 1.0 / theBand(0, i);
+ if(theBand(0, i) < 0.) {
+ throw 3; // not positive definite
+ }
+ } else {
+ theBand(0, i) = 0.0;
+ throw 2; // singular
+ }
+ for(int j = 1; j < std::min(nRow, nCol - i); ++j) {
+ double rxw = theBand(j, i) * theBand(0, i);
+ for(int k = 0; k < std::min(nRow, nCol - i) - j; ++k) {
+ theBand(k, i + j) -= theBand(k + j, i) * rxw;
+ }
+ theBand(j, i) = rxw;
+ }
+ }
+ }
+
+ /// Solve for band part.
+ /**
+ * Solve C*x=b for band part using decomposition C=LDL^T
+ * and forward (L*z=b) and backward substitution (L^T*x=D^-1*z).
+ * \param [in] aRightHandSide Right hand side (vector) 'b' of C*x=b
+ * \return Solution (vector) 'x' of C*x=b
+ */
+ VVector BorderedBandMatrix::solveBand(const VVector& aRightHandSide) const {
+
+ int nRow = theBand.getNumRows();
+ int nCol = theBand.getNumCols();
+ VVector aSolution(aRightHandSide);
+ for(int i = 0; i < nCol; ++i) // forward substitution
+ {
+ for(int j = 1; j < std::min(nRow, nCol - i); ++j) {
+ aSolution(j + i) -= theBand(j, i) * aSolution(i);
+ }
+ }
+ for(int i = nCol - 1; i >= 0; i--) // backward substitution
+ {
+ double rxw = theBand(0, i) * aSolution(i);
+ for(int j = 1; j < std::min(nRow, nCol - i); ++j) {
+ rxw -= theBand(j, i) * aSolution(j + i);
+ }
+ aSolution(i) = rxw;
+ }
+ return aSolution;
+ }
+
+ /// solve band part for mixed part (border rows).
+ /**
+ * Solve C*X=B for mixed part using decomposition C=LDL^T
+ * and forward and backward substitution.
+ * \param [in] aRightHandSide Right hand side (matrix) 'B' of C*X=B
+ * \return Solution (matrix) 'X' of C*X=B
+ */
+ VMatrix BorderedBandMatrix::solveBand(const VMatrix& aRightHandSide) const {
+
+ int nRow = theBand.getNumRows();
+ int nCol = theBand.getNumCols();
+ VMatrix aSolution(aRightHandSide);
+ for(unsigned int iBorder = 0; iBorder < numBorder; iBorder++) {
+ for(int i = 0; i < nCol; ++i) // forward substitution
+ {
+ for(int j = 1; j < std::min(nRow, nCol - i); ++j) {
+ aSolution(iBorder, j + i) -= theBand(j, i) * aSolution(iBorder, i);
+ }
+ }
+ for(int i = nCol - 1; i >= 0; i--) // backward substitution
+ {
+ double rxw = theBand(0, i) * aSolution(iBorder, i);
+ for(int j = 1; j < std::min(nRow, nCol - i); ++j) {
+ rxw -= theBand(j, i) * aSolution(iBorder, j + i);
+ }
+ aSolution(iBorder, i) = rxw;
+ }
+ }
+ return aSolution;
+ }
+
+ /// Invert band part.
+ /**
+ * \return Inverted band
+ */
+ VMatrix BorderedBandMatrix::invertBand() {
+
+ int nRow = numBand + 1;
+ int nCol = numCol;
+ VMatrix inverseBand(nRow, nCol);
+
+ for(int i = nCol - 1; i >= 0; i--) {
+ double rxw = theBand(0, i);
+ for(int j = i; j >= std::max(0, i - nRow + 1); j--) {
+ for(int k = j + 1; k < std::min(nCol, j + nRow); ++k) {
+ rxw -= inverseBand(abs(i - k), std::min(i, k)) * theBand(k - j, j);
+ }
+ inverseBand(i - j, j) = rxw;
+ rxw = 0.;
+ }
+ }
+ return inverseBand;
+ }
+
+ /// Calculate band part of: 'anArray * aSymArray * anArray.T'.
+ /**
+ * \return Band part of product
+ */
+ VMatrix BorderedBandMatrix::bandOfAVAT(const VMatrix& anArray, const VSymMatrix& aSymArray) const {
+ int nBand = numBand;
+ int nCol = numCol;
+ int nBorder = numBorder;
+ double sum;
+ VMatrix aBand((nBand + 1), nCol);
+ for(int i = 0; i < nCol; ++i) {
+ for(int j = std::max(0, i - nBand); j <= i; ++j) {
+ sum = 0.;
+ for(int l = 0; l < nBorder; ++l) { // diagonal
+ sum += anArray(i, l) * aSymArray(l, l) * anArray(j, l);
+ for(int k = 0; k < l; ++k) { // off diagonal
+ sum += anArray(i, l) * aSymArray(l, k) * anArray(j, k) +
+ anArray(i, k) * aSymArray(l, k) * anArray(j, l);
+ }
+ }
+ aBand(i - j, j) = sum;
+ }
+ }
+ return aBand;
+ }
+}
diff --git a/3rdparty/GeneralBrokenLines/src/GblData.cpp b/3rdparty/GeneralBrokenLines/src/GblData.cpp
new file mode 100644
index 000000000..6fee61350
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/src/GblData.cpp
@@ -0,0 +1,264 @@
+/*
+ * GblData.cpp
+ *
+ * Created on: Aug 18, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * GblData methods.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2016 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#include "GblData.h"
+using namespace Eigen;
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// Create data block.
+ /**
+ * \param [in] aLabel Label of corresponding point
+ * \param [in] aType Type of (scalar) measurement
+ * \param [in] aValue Value of (scalar) measurement
+ * \param [in] aPrec Precision of (scalar) measurement
+ * \param [in] aTraj Trajectory number
+ * \param [in] aPoint Point number
+ */
+ GblData::GblData(
+ unsigned int aLabel, dataBlockType aType, double aValue, double aPrec, unsigned int aTraj, unsigned int aPoint)
+ : theLabel(aLabel), theRow(0), theType(aType), theValue(aValue), thePrecision(aPrec), theTrajectory(aTraj),
+ thePoint(aPoint), theDWMethod(0), theDownWeight(1.), thePrediction(0.), theNumLocal(0), moreParameters(),
+ moreDerivatives() {}
+
+ GblData::~GblData() {}
+
+ /// Add derivatives from external seed.
+ /**
+ * Add (non-zero) derivatives to data block. Fill list of labels of used fit parameters.
+ * \param [in] index Labels for derivatives
+ * \param [in] derivatives Derivatives (vector)
+ */
+ void GblData::addDerivatives(const std::vector<unsigned int>& index, const std::vector<double>& derivatives) {
+ for(unsigned int i = 0; i < derivatives.size(); ++i) // any derivatives
+ {
+ if(derivatives[i]) {
+ moreParameters.push_back(index[i]);
+ moreDerivatives.push_back(derivatives[i]);
+ }
+ }
+ }
+
+ /// Calculate prediction for data from fit (by GblTrajectory::fit).
+ void GblData::setPrediction(const VVector& aVector) {
+
+ thePrediction = 0.;
+ if(theNumLocal > 0) {
+ for(unsigned int i = 0; i < theNumLocal; ++i) {
+ thePrediction += theDerivatives[i] * aVector(theParameters[i] - 1);
+ }
+ } else {
+ for(unsigned int i = 0; i < moreDerivatives.size(); ++i) {
+ thePrediction += moreDerivatives[i] * aVector(moreParameters[i] - 1);
+ }
+ }
+ }
+
+ /// Outlier down weighting with M-estimators (by GblTrajectory::fit).
+ /**
+ * \param [in] aMethod M-estimator (1: Tukey, 2:Huber, 3:Cauchy)
+ */
+ double GblData::setDownWeighting(unsigned int aMethod) {
+
+ theDWMethod = aMethod;
+ double aWeight = 1.;
+ double scaledResidual = fabs(theValue - thePrediction) * sqrt(thePrecision);
+ if(aMethod == 1) // Tukey
+ {
+ if(scaledResidual < 4.6851) {
+ aWeight = (1.0 - 0.045558 * scaledResidual * scaledResidual);
+ aWeight *= aWeight;
+ } else {
+ aWeight = 0.;
+ }
+ } else if(aMethod == 2) // Huber
+ {
+ if(scaledResidual >= 1.345) {
+ aWeight = 1.345 / scaledResidual;
+ }
+ } else if(aMethod == 3) // Cauchy
+ {
+ aWeight = 1.0 / (1.0 + (scaledResidual * scaledResidual / 5.6877));
+ }
+ theDownWeight = aWeight;
+ return aWeight;
+ }
+
+ /// Calculate Chi2 contribution.
+ /**
+ * For down-weighting with M-estimators the corresponding objective function is used.
+ *
+ * \return (down-weighted) Chi2
+ */
+ double GblData::getChi2() const {
+ double scaledResidual = fabs(theValue - thePrediction) * sqrt(thePrecision);
+ double chi2 = scaledResidual * scaledResidual;
+ if(theDWMethod == 1) // Tukey
+ {
+ if(scaledResidual < 4.6851) {
+ chi2 = (1.0 - pow(1.0 - 0.045558 * scaledResidual * scaledResidual, 3)) / (3. * 0.045558);
+ } else {
+ chi2 = 1.0 / (3. * 0.045558);
+ }
+ } else if(theDWMethod == 2) // Huber
+ {
+ if(scaledResidual >= 1.345) {
+ chi2 = 1.345 * (2. * scaledResidual - 1.345);
+ }
+ } else if(theDWMethod == 3) // Cauchy
+ {
+ chi2 = log(1.0 + (scaledResidual * scaledResidual / 5.6877)) * 5.6877;
+ }
+ return chi2;
+ }
+
+ /// Print data block.
+ void GblData::printData() const {
+
+ std::cout << " measurement at label " << theLabel << " of type " << theType << " from row " << theRow << ": "
+ << theValue << ", " << thePrecision << std::endl;
+ std::cout << " param " << moreParameters.size() + theNumLocal << ":";
+ for(unsigned int i = 0; i < moreParameters.size(); ++i) {
+ std::cout << " " << moreParameters[i];
+ }
+ for(unsigned int i = 0; i < theNumLocal; ++i) {
+ std::cout << " " << theParameters[i];
+ }
+ std::cout << std::endl;
+ std::cout << " deriv " << moreDerivatives.size() + theNumLocal << ":";
+ for(unsigned int i = 0; i < moreDerivatives.size(); ++i) {
+ std::cout << " " << moreDerivatives[i];
+ }
+ for(unsigned int i = 0; i < theNumLocal; ++i) {
+ std::cout << " " << theDerivatives[i];
+ }
+ std::cout << std::endl;
+ }
+
+ /// Get label.
+ /**
+ * \return label of corresponding point
+ */
+ unsigned int GblData::getLabel() const { return theLabel; }
+
+ /// Get type.
+ /**
+ * \return type
+ */
+ dataBlockType GblData::getType() const { return theType; }
+
+ /// Get Data for local fit.
+ /**
+ * \param [out] aValue Value
+ * \param [out] aWeight Weight
+ * \param [out] numLocal Number of local labels/derivatives
+ * \param [out] indLocal Array of labels of used (local) fit parameters
+ * \param [out] derLocal Array of derivatives for used (local) fit parameters
+ */
+ void GblData::getLocalData(
+ double& aValue, double& aWeight, unsigned int& numLocal, unsigned int*& indLocal, double*& derLocal) {
+
+ aValue = theValue;
+ aWeight = thePrecision * theDownWeight;
+ if(theNumLocal > 0) {
+ numLocal = theNumLocal;
+ indLocal = theParameters;
+ derLocal = theDerivatives;
+ } else {
+ numLocal = moreParameters.size();
+ indLocal = &moreParameters[0];
+ derLocal = &moreDerivatives[0];
+ }
+ }
+
+ /// Get all Data for MP-II binary record.
+ /**
+ * \param [out] aValue Value
+ * \param [out] aErr Error
+ * \param [out] numLocal Number of local labels/derivatives
+ * \param [out] indLocal Array of labels of used (local) fit parameters
+ * \param [out] derLocal Array of derivatives for used (local) fit parameters
+ * \param [out] aTraj Trajectory number
+ * \param [out] aPoint Point number
+ * \param [out] aRow Row number
+ */
+ void GblData::getAllData(double& aValue,
+ double& aErr,
+ unsigned int& numLocal,
+ unsigned int*& indLocal,
+ double*& derLocal,
+ unsigned int& aTraj,
+ unsigned int& aPoint,
+ unsigned int& aRow) {
+ aValue = theValue;
+ aErr = 1.0 / sqrt(thePrecision);
+ if(theNumLocal > 0) {
+ numLocal = theNumLocal;
+ indLocal = theParameters;
+ derLocal = theDerivatives;
+ } else {
+ numLocal = moreParameters.size();
+ indLocal = &moreParameters[0];
+ derLocal = &moreDerivatives[0];
+ }
+ aTraj = theTrajectory;
+ aPoint = thePoint;
+ aRow = theRow;
+ }
+
+ /// Get data for residual (and errors).
+ /**
+ * \param [out] aResidual Measurement-Prediction
+ * \param [out] aVariance Variance (of measurement)
+ * \param [out] aDownWeight Down-weighting factor
+ * \param [out] numLocal Number of local labels/derivatives
+ * \param [out] indLocal Array of labels of used (local) fit parameters
+ * \param [out] derLocal Array of derivatives for used (local) fit parameters
+ */
+ void GblData::getResidual(double& aResidual,
+ double& aVariance,
+ double& aDownWeight,
+ unsigned int& numLocal,
+ unsigned int*& indLocal,
+ double*& derLocal) {
+ aResidual = theValue - thePrediction;
+ aVariance = 1.0 / thePrecision;
+ aDownWeight = theDownWeight;
+ if(theNumLocal > 0) {
+ numLocal = theNumLocal;
+ indLocal = theParameters;
+ derLocal = theDerivatives;
+ } else {
+ numLocal = moreParameters.size();
+ indLocal = &moreParameters[0];
+ derLocal = &moreDerivatives[0];
+ }
+ }
+}
diff --git a/3rdparty/GeneralBrokenLines/src/GblPoint.cpp b/3rdparty/GeneralBrokenLines/src/GblPoint.cpp
new file mode 100644
index 000000000..fd137fac2
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/src/GblPoint.cpp
@@ -0,0 +1,522 @@
+/*
+ * GblPoint.cpp
+ *
+ * Created on: Aug 18, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * GblPoint methods.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2017 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#include "GblPoint.h"
+using namespace Eigen;
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// Create a point.
+ /**
+ * Create point on (initial) trajectory. Needs transformation jacobian from previous point.
+ * \param [in] aJacobian Transformation jacobian from previous point
+ */
+ GblPoint::GblPoint(const Matrix5d& aJacobian)
+ : theLabel(0), theOffset(0), p2pJacobian(aJacobian), measDim(0), measPrecMin(0.), transFlag(false),
+ measTransformation(), scatFlag(false), localDerivatives(), globalLabels(), globalDerivatives() {}
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ /// Create a point.
+ /**
+ * Create point on (initial) trajectory. Needs transformation jacobian from previous point.
+ * \param [in] aJacobian Transformation jacobian from previous point
+ */
+ GblPoint::GblPoint(const TMatrixD& aJacobian)
+ : theLabel(0), theOffset(0), measDim(0), measPrecMin(0.), transFlag(false), measTransformation(), scatFlag(false),
+ localDerivatives(), globalLabels(), globalDerivatives() {
+
+ for(unsigned int i = 0; i < 5; ++i) {
+ for(unsigned int j = 0; j < 5; ++j) {
+ p2pJacobian(i, j) = aJacobian(i, j);
+ }
+ }
+ }
+#endif
+
+ GblPoint::~GblPoint() {}
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ /// Add a measurement to a point.
+ /**
+ * Add measurement (in meas. system) with diagonal precision (inverse covariance) matrix.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \param [in] aProjection Projection from local to measurement system
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (diagonal)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ void GblPoint::addMeasurement(const TMatrixD& aProjection,
+ const TVectorD& aResiduals,
+ const TVectorD& aPrecision,
+ double minPrecision) {
+ measDim = aResiduals.GetNrows();
+ measPrecMin = minPrecision;
+ unsigned int iOff = 5 - measDim;
+ for(unsigned int i = 0; i < measDim; ++i) {
+ measResiduals(iOff + i) = aResiduals[i];
+ measPrecision(iOff + i) = aPrecision[i];
+ for(unsigned int j = 0; j < measDim; ++j) {
+ measProjection(iOff + i, iOff + j) = aProjection(i, j);
+ }
+ }
+ }
+
+ /// Add a measurement to a point.
+ /**
+ * Add measurement (in meas. system) with arbitrary precision (inverse covariance) matrix.
+ * Will be diagonalized.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \param [in] aProjection Projection from local to measurement system
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (matrix)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ void GblPoint::addMeasurement(const TMatrixD& aProjection,
+ const TVectorD& aResiduals,
+ const TMatrixDSym& aPrecision,
+ double minPrecision) {
+ measDim = aResiduals.GetNrows();
+ measPrecMin = minPrecision;
+ TMatrixDSymEigen measEigen(aPrecision);
+ TMatrixD tmpTransformation(measDim, measDim);
+ tmpTransformation = measEigen.GetEigenVectors();
+ tmpTransformation.T();
+ transFlag = true;
+ TVectorD transResiduals = tmpTransformation * aResiduals;
+ TVectorD transPrecision = measEigen.GetEigenValues();
+ TMatrixD transProjection = tmpTransformation * aProjection;
+ measTransformation.resize(measDim, measDim);
+ unsigned int iOff = 5 - measDim;
+ for(unsigned int i = 0; i < measDim; ++i) {
+ measResiduals(iOff + i) = transResiduals[i];
+ measPrecision(iOff + i) = transPrecision[i];
+ for(unsigned int j = 0; j < measDim; ++j) {
+ measTransformation(i, j) = tmpTransformation(i, j);
+ measProjection(iOff + i, iOff + j) = transProjection(i, j);
+ }
+ }
+ }
+
+ /// Add a measurement to a point.
+ /**
+ * Add measurement in local system with diagonal precision (inverse covariance) matrix.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (diagonal)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ void GblPoint::addMeasurement(const TVectorD& aResiduals, const TVectorD& aPrecision, double minPrecision) {
+ measDim = aResiduals.GetNrows();
+ measPrecMin = minPrecision;
+ unsigned int iOff = 5 - measDim;
+ for(unsigned int i = 0; i < measDim; ++i) {
+ measResiduals(iOff + i) = aResiduals[i];
+ measPrecision(iOff + i) = aPrecision[i];
+ }
+ measProjection.setIdentity();
+ }
+
+ /// Add a measurement to a point.
+ /**
+ * Add measurement in local system with arbitrary precision (inverse covariance) matrix.
+ * Will be diagonalized.
+ * ((up to) 2D: position, 4D: slope+position, 5D: curvature+slope+position)
+ * \param [in] aResiduals Measurement residuals
+ * \param [in] aPrecision Measurement precision (matrix)
+ * \param [in] minPrecision Minimal precision to accept measurement
+ */
+ void GblPoint::addMeasurement(const TVectorD& aResiduals, const TMatrixDSym& aPrecision, double minPrecision) {
+ measDim = aResiduals.GetNrows();
+ measPrecMin = minPrecision;
+ TMatrixDSymEigen measEigen(aPrecision);
+ TMatrixD tmpTransformation(measDim, measDim);
+ tmpTransformation = measEigen.GetEigenVectors();
+ tmpTransformation.T();
+ transFlag = true;
+ TVectorD transResiduals = tmpTransformation * aResiduals;
+ TVectorD transPrecision = measEigen.GetEigenValues();
+ measTransformation.resize(measDim, measDim);
+ unsigned int iOff = 5 - measDim;
+ for(unsigned int i = 0; i < measDim; ++i) {
+ measResiduals(iOff + i) = transResiduals[i];
+ measPrecision(iOff + i) = transPrecision[i];
+ for(unsigned int j = 0; j < measDim; ++j) {
+ measTransformation(i, j) = tmpTransformation(i, j);
+ measProjection(iOff + i, iOff + j) = measTransformation(i, j);
+ }
+ }
+ }
+#endif
+
+ /// Check for measurement at a point.
+ /**
+ * Get dimension of measurement (0 = none).
+ * \return measurement dimension
+ */
+ unsigned int GblPoint::hasMeasurement() const { return measDim; }
+
+ /// get precision cutoff.
+ /**
+ * \return minimal measurement precision (for usage)
+ */
+ double GblPoint::getMeasPrecMin() const { return measPrecMin; }
+
+ /// Retrieve measurement of a point.
+ /**
+ * \param [out] aProjection Projection from (diagonalized) measurement to local system
+ * \param [out] aResiduals Measurement residuals
+ * \param [out] aPrecision Measurement precision (diagonal)
+ */
+ void GblPoint::getMeasurement(Matrix5d& aProjection, Vector5d& aResiduals, Vector5d& aPrecision) const {
+ aProjection.bottomRightCorner(measDim, measDim) = measProjection.bottomRightCorner(measDim, measDim);
+ aResiduals.tail(measDim) = measResiduals.tail(measDim);
+ aPrecision.tail(measDim) = measPrecision.tail(measDim);
+ }
+
+ /// Get measurement transformation (from diagonalization).
+ /**
+ * \param [out] aTransformation Transformation matrix
+ */
+ void GblPoint::getMeasTransformation(MatrixXd& aTransformation) const {
+ aTransformation.resize(measDim, measDim);
+ if(transFlag) {
+ aTransformation = measTransformation;
+ } else {
+ aTransformation.setIdentity();
+ }
+ }
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ /// Add a (thin) scatterer to a point.
+ /**
+ * Add scatterer with diagonal precision (inverse covariance) matrix.
+ * Changes local track direction.
+ *
+ * \param [in] aResiduals Scatterer residuals
+ * \param [in] aPrecision Scatterer precision (diagonal of inverse covariance matrix)
+ */
+ void GblPoint::addScatterer(const TVectorD& aResiduals, const TVectorD& aPrecision) {
+ scatFlag = true;
+ scatResiduals(0) = aResiduals[0];
+ scatResiduals(1) = aResiduals[1];
+ scatPrecision(0) = aPrecision[0];
+ scatPrecision(1) = aPrecision[1];
+ scatTransformation.setIdentity();
+ }
+
+ /// Add a (thin) scatterer to a point.
+ /**
+ * Add scatterer with arbitrary precision (inverse covariance) matrix.
+ * Will be diagonalized. Changes local track direction.
+ *
+ * The precision matrix for the local slopes is defined by the
+ * angular scattering error theta_0 and the scalar products c_1, c_2 of the
+ * offset directions in the local frame with the track direction:
+ *
+ * (1 - c_1*c_1 - c_2*c_2) | 1 - c_1*c_1 - c_1*c_2 |
+ * P = ----------------------- * | |
+ * theta_0*theta_0 | - c_1*c_2 1 - c_2*c_2 |
+ *
+ * \param [in] aResiduals Scatterer residuals
+ * \param [in] aPrecision Scatterer precision (matrix)
+ */
+ void GblPoint::addScatterer(const TVectorD& aResiduals, const TMatrixDSym& aPrecision) {
+ scatFlag = true;
+ TMatrixDSymEigen scatEigen(aPrecision);
+ TMatrixD aTransformation = scatEigen.GetEigenVectors();
+ aTransformation.T();
+ TVectorD transResiduals = aTransformation * aResiduals;
+ TVectorD transPrecision = scatEigen.GetEigenValues();
+ scatTransformation.resize(2, 2);
+ for(unsigned int i = 0; i < 2; ++i) {
+ scatResiduals(i) = transResiduals[i];
+ scatPrecision(i) = transPrecision[i];
+ for(unsigned int j = 0; j < 2; ++j) {
+ scatTransformation(i, j) = aTransformation(i, j);
+ }
+ }
+ }
+#endif
+
+ /// Check for scatterer at a point.
+ bool GblPoint::hasScatterer() const { return scatFlag; }
+
+ /// Retrieve scatterer of a point.
+ /**
+ * \param [out] aTransformation Scatterer transformation from diagonalization
+ * \param [out] aResiduals Scatterer residuals
+ * \param [out] aPrecision Scatterer precision (diagonal)
+ */
+ void GblPoint::getScatterer(Matrix2d& aTransformation, Vector2d& aResiduals, Vector2d& aPrecision) const {
+ aTransformation = scatTransformation;
+ aResiduals = scatResiduals;
+ aPrecision = scatPrecision;
+ }
+
+ /// Get scatterer transformation (from diagonalization).
+ /**
+ * \param [out] aTransformation Transformation matrix
+ */
+ void GblPoint::getScatTransformation(Matrix2d& aTransformation) const {
+ if(scatFlag) {
+ aTransformation = scatTransformation;
+ } else {
+ aTransformation.setIdentity();
+ }
+ }
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ /// Add local derivatives to a point.
+ /**
+ * Point needs to have a measurement.
+ * \param [in] aDerivatives Local derivatives (matrix)
+ */
+ void GblPoint::addLocals(const TMatrixD& aDerivatives) {
+ if(measDim) {
+ unsigned int numDer = aDerivatives.GetNcols();
+ localDerivatives.resize(measDim, numDer);
+ // convert from ROOT
+ MatrixXd tmpDerivatives(measDim, numDer);
+ for(unsigned int i = 0; i < measDim; ++i) {
+ for(unsigned int j = 0; j < numDer; ++j)
+ tmpDerivatives(i, j) = aDerivatives(i, j);
+ }
+ if(transFlag) {
+ localDerivatives = measTransformation * tmpDerivatives;
+ } else {
+ localDerivatives = tmpDerivatives;
+ }
+ }
+ }
+#endif
+
+ /// Retrieve number of local derivatives from a point.
+ unsigned int GblPoint::getNumLocals() const { return localDerivatives.cols(); }
+
+ /// Retrieve local derivatives from a point.
+ const MatrixXd& GblPoint::getLocalDerivatives() const { return localDerivatives; }
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ /// Add global derivatives to a point.
+ /**
+ * Point needs to have a measurement.
+ * \param [in] aLabels Global derivatives labels
+ * \param [in] aDerivatives Global derivatives (matrix)
+ */
+ void GblPoint::addGlobals(const std::vector<int>& aLabels, const TMatrixD& aDerivatives) {
+ if(measDim) {
+ globalLabels = aLabels;
+ unsigned int numDer = aDerivatives.GetNcols();
+ globalDerivatives.resize(measDim, numDer);
+ // convert from ROOT
+ MatrixXd tmpDerivatives(measDim, numDer);
+ for(unsigned int i = 0; i < measDim; ++i) {
+ for(unsigned int j = 0; j < numDer; ++j)
+ tmpDerivatives(i, j) = aDerivatives(i, j);
+ }
+ if(transFlag) {
+ globalDerivatives = measTransformation * tmpDerivatives;
+ } else {
+ globalDerivatives = tmpDerivatives;
+ }
+ }
+ }
+#endif
+
+ /// Retrieve number of global derivatives from a point.
+ unsigned int GblPoint::getNumGlobals() const { return globalDerivatives.cols(); }
+
+ /// Retrieve global derivatives labels from a point.
+ /**
+ * \param [out] aLabels Global labels
+ */
+ void GblPoint::getGlobalLabels(std::vector<int>& aLabels) const { aLabels = globalLabels; }
+
+ /// Retrieve global derivatives from a point.
+ /**
+ * \param [out] aDerivatives Global derivatives
+ */
+ void GblPoint::getGlobalDerivatives(MatrixXd& aDerivatives) const { aDerivatives = globalDerivatives; }
+
+ /// Retrieve global derivatives from a point for a single row.
+ /**
+ * \param [in] aRow Row number
+ * \param [out] aLabels Global labels
+ * \param [out] aDerivatives Global derivatives
+ */
+ void GblPoint::getGlobalLabelsAndDerivatives(unsigned int aRow,
+ std::vector<int>& aLabels,
+ std::vector<double>& aDerivatives) const {
+ aLabels.resize(globalDerivatives.cols());
+ aDerivatives.resize(globalDerivatives.cols());
+ for(unsigned int i = 0; i < globalDerivatives.cols(); ++i) {
+ aLabels[i] = globalLabels[i];
+ aDerivatives[i] = globalDerivatives(aRow, i);
+ }
+ }
+
+ /// Define label of point (by GBLTrajectory constructor)
+ /**
+ * \param [in] aLabel Label identifying point
+ */
+ void GblPoint::setLabel(unsigned int aLabel) { theLabel = aLabel; }
+
+ /// Retrieve label of point
+ unsigned int GblPoint::getLabel() const { return theLabel; }
+
+ /// Define offset for point (by GBLTrajectory constructor)
+ /**
+ * \param [in] anOffset Offset number
+ */
+ void GblPoint::setOffset(int anOffset) { theOffset = anOffset; }
+
+ /// Retrieve offset for point
+ int GblPoint::getOffset() const { return theOffset; }
+
+ /// Retrieve point-to-(previous)point jacobian
+ const Matrix5d& GblPoint::getP2pJacobian() const { return p2pJacobian; }
+
+ /// Define jacobian to previous scatterer (by GBLTrajectory constructor)
+ /**
+ * \param [in] aJac Jacobian
+ */
+ void GblPoint::addPrevJacobian(const Matrix5d& aJac) {
+ // to optimize: need only two last rows of inverse
+ // prevJacobian = aJac.inverse();
+ // block matrix algebra
+ Matrix23d CA = aJac.block<2, 3>(3, 0) * aJac.block<3, 3>(0, 0).inverse(); // C*A^-1
+ Matrix2d DCAB = aJac.block<2, 2>(3, 3) - CA * aJac.block<3, 2>(0, 3); // D - C*A^-1 *B
+ Matrix2d DCABInv = DCAB.inverse();
+ prevJacobian.block<2, 2>(3, 3) = DCABInv;
+ prevJacobian.block<2, 3>(3, 0) = -DCABInv * CA;
+ }
+
+ /// Define jacobian to next scatterer (by GBLTrajectory constructor)
+ /**
+ * \param [in] aJac Jacobian
+ */
+ void GblPoint::addNextJacobian(const Matrix5d& aJac) { nextJacobian = aJac; }
+
+ /// Retrieve derivatives of local track model
+ /**
+ * Linearized track model: F_u(q/p,u',u) = J*u + S*u' + d*q/p,
+ * W is inverse of S, negated for backward propagation.
+ * \param [in] aDirection Propagation direction (>0 forward, else backward)
+ * \param [out] matW W
+ * \param [out] matWJ W*J
+ * \param [out] vecWd W*d
+ * \exception std::overflow_error : matrix S is singular.
+ */
+ void GblPoint::getDerivatives(int aDirection, Matrix2d& matW, Matrix2d& matWJ, Vector2d& vecWd) const {
+
+ Matrix2d matJ;
+ Vector2d vecd;
+ if(aDirection < 1) {
+ matJ = prevJacobian.block<2, 2>(3, 3);
+ matW = -prevJacobian.block<2, 2>(3, 1);
+ vecd = prevJacobian.block<2, 1>(3, 0);
+ } else {
+ matJ = nextJacobian.block<2, 2>(3, 3);
+ matW = nextJacobian.block<2, 2>(3, 1);
+ vecd = nextJacobian.block<2, 1>(3, 0);
+ }
+
+ if(!matW.determinant()) {
+ std::cout << " GblPoint::getDerivatives failed to invert matrix " << std::endl;
+ std::cout << " Possible reason for singular matrix: multiple GblPoints at same arc-length" << std::endl;
+ throw std::overflow_error("Singular matrix inversion exception");
+ }
+ matW = matW.inverse().eval();
+ matWJ = matW * matJ;
+ vecWd = matW * vecd;
+ }
+
+ /// Print GblPoint
+ /**
+ * \param [in] level print level (0: minimum, >0: more)
+ */
+ void GblPoint::printPoint(unsigned int level) const {
+ std::cout << " GblPoint";
+ if(theLabel) {
+ std::cout << ", label " << theLabel;
+ if(theOffset >= 0) {
+ std::cout << ", offset " << theOffset;
+ }
+ }
+ if(measDim) {
+ std::cout << ", " << measDim << " measurements";
+ }
+ if(scatFlag) {
+ std::cout << ", scatterer";
+ }
+ if(transFlag) {
+ std::cout << ", diagonalized";
+ }
+ if(localDerivatives.cols()) {
+ std::cout << ", " << localDerivatives.cols() << " local derivatives";
+ }
+ if(globalDerivatives.cols()) {
+ std::cout << ", " << globalDerivatives.cols() << " global derivatives";
+ }
+ std::cout << std::endl;
+ if(level > 0) {
+ IOFormat CleanFmt(4, 0, ", ", "\n", "[", "]");
+ if(measDim) {
+ std::cout << " Measurement" << std::endl;
+ std::cout << " Projection: " << std::endl << measProjection.format(CleanFmt) << std::endl;
+ std::cout << " Residuals: " << measResiduals.transpose().format(CleanFmt) << std::endl;
+ std::cout << " Precision (min.: " << measPrecMin << "): " << measPrecision.transpose().format(CleanFmt)
+ << std::endl;
+ }
+ if(scatFlag) {
+ std::cout << " Scatterer" << std::endl;
+ std::cout << " Residuals: " << scatResiduals.transpose().format(CleanFmt) << std::endl;
+ std::cout << " Precision: " << scatPrecision.transpose().format(CleanFmt) << std::endl;
+ }
+ if(localDerivatives.cols()) {
+ std::cout << " Local Derivatives:" << std::endl << localDerivatives.format(CleanFmt) << std::endl;
+ }
+ if(globalDerivatives.cols()) {
+ std::cout << " Global Labels:";
+ for(unsigned int i = 0; i < globalLabels.size(); ++i) {
+ std::cout << " " << globalLabels[i];
+ }
+ std::cout << std::endl;
+ std::cout << " Global Derivatives:" << globalDerivatives.format(CleanFmt) << std::endl;
+ }
+ std::cout << " Jacobian " << std::endl;
+ std::cout << " Point-to-point " << std::endl << p2pJacobian.format(CleanFmt) << std::endl;
+ if(theLabel) {
+ std::cout << " To previous offset " << std::endl << prevJacobian.format(CleanFmt) << std::endl;
+ std::cout << " To next offset " << std::endl << nextJacobian.format(CleanFmt) << std::endl;
+ }
+ }
+ }
+}
diff --git a/3rdparty/GeneralBrokenLines/src/GblTrajectory.cpp b/3rdparty/GeneralBrokenLines/src/GblTrajectory.cpp
new file mode 100644
index 000000000..509daec36
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/src/GblTrajectory.cpp
@@ -0,0 +1,1428 @@
+/*
+ * GblTrajectory.cpp
+ *
+ * Created on: Aug 18, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * GblTrajectory methods.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2018 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+/** \mainpage General information
+ *
+ * \section intro_sec Introduction
+ *
+ * For a track with an initial trajectory from a prefit of the
+ * measurements (internal seed) or an external prediction
+ * (external seed) the description of multiple scattering is
+ * added by offsets in a local system. Along the initial
+ * trajectory points are defined with can describe a measurement
+ * or a (thin) scatterer or both. Measurements are arbitrary
+ * functions of the local track parameters at a point (e.g. 2D:
+ * position, 4D: direction+position). The refit provides corrections
+ * to the local track parameters (in the local system) and the
+ * corresponding covariance matrix at any of those points.
+ * Non-diagonal covariance matrices of
+ * measurements will be diagonalized internally.
+ * Outliers can be down-weighted by use of M-estimators.
+ * At one point the measurements can be omitted from the refit
+ * to calculate unbiased residuals.
+ *
+ * A position measurement is in a plane defined by two directions.
+ * Along one direction the measurement precision may be zero,
+ * defining a 1D measurement in the other direction.
+ *
+ * The broken lines trajectory is defined by (2D) offsets at the
+ * first and last point and all points with a scatterer. The
+ * prediction for a measurement is obtained by interpolation of
+ * the enclosing offsets and for triplets of adjacent offsets
+ * kink angles are determined. This requires for all points the
+ * jacobians for propagation to the previous and next offset.
+ * These are calculated from the point-to-point jacobians along
+ * the initial trajectory. The sequence of points has to be
+ * strictly monotonic in arc-length.
+ *
+ * Additional local or global parameters can be added and the
+ * trajectories can be written to special binary files for
+ * calibration and alignment with Millepede-II.
+ * (V. Blobel, NIM A, 566 (2006), pp. 5-13).
+ *
+ * Besides simple trajectories describing the path of a single
+ * particle composed trajectories are supported. These are
+ * constructed from the trajectories of multiple particles and
+ * some external parameters (like those describing a decay)
+ * and transformations at the first points from the external
+ * to the local track parameters.
+ *
+ * The conventions for the coordinate systems follow:
+ * Derivation of Jacobians for the propagation of covariance
+ * matrices of track parameters in homogeneous magnetic fields
+ * A. Strandlie, W. Wittek, NIM A, 566 (2006) 687-698.
+ *
+ * The source code is available at the DESY SVN server, see:
+ * https://www.wiki.terascale.de/index.php/GeneralBrokenLines
+ *
+ * \section call_sec Calling sequence
+ *
+ * -# Create list of points on initial trajectory:\n
+ * <tt>std::vector<GblPoint> list</tt>
+ * -# For all points on initial trajectory:
+ * - Create points and add appropriate attributes:\n
+ * - <tt>point = gbl::GblPoint(..)</tt>
+ * - <tt>point.addMeasurement(..)</tt>
+ * - Add additional local or global parameters to measurement:\n
+ * - <tt>point.addLocals(..)</tt>
+ * - <tt>point.addGlobals(..)</tt>
+ * - <tt>point.addScatterer(..)</tt>
+ * - Add point (ordered by arc length) to list:\n
+ * <tt>list.push_back(point)</tt>
+ * -# Create (simple) trajectory from list of points:\n
+ * <tt>traj = gbl::GblTrajectory (list)</tt>
+ * -# Optionally with external seed:\n
+ * <tt>traj = gbl::GblTrajectory (list,seed)</tt>
+ * -# Optionally check validity of trajectory:\n
+ * <tt>if (!traj.isValid()) .. //abort</tt>
+ * -# Fit trajectory (potentially several times with different options), return error code,
+ * get Chi2, Ndf (and weight lost by M-estimators):\n
+ * <tt>ierr = traj.fit(..)</tt>
+ * -# For any point on initial trajectory:
+ * - Get corrections and covariance matrix for track parameters:\n
+ * <tt>[..] = traj.getResults(label)</tt>
+ * - Optionally get residuals with errors for measurements:\n
+ * <tt>[..] = traj.getMeasResults(label) </tt>
+ * - Optionally get residuals with errors for scatterers:\n
+ * <tt>[..] = traj.getScatResults(label) </tt>
+ * -# Optionally write trajectory to MP binary file (doesn't needs to be fitted):\n
+ * <tt>traj.milleOut(..)</tt>
+ *
+ * \section loc_sec Local system and local parameters
+ * At each point on the trajectory a local coordinate system with local track
+ * parameters has to be defined. The first of the five parameters describes
+ * the bending, the next two the direction and the last two the position (offsets).
+ * The curvilinear system (T,U,V) with parameters (q/p, lambda, phi, x_t, y_t)
+ * is well suited.
+ *
+ * \section impl_sec Implementation
+ *
+ * Matrices are implemented with the EIGEN template library (eigen.tuxfamily.org). User input or output is in the
+ * form of MatrixXd. With the preprocessor directive <tt>GBL_EIGEN_SUPPORT_ROOT</tt> user input and output with
+ * ROOT (root.cern.ch) matrices is supported too.
+ * Internally Matrix<n>d are used for fixed sized and simple matrices
+ * based on std::vector<> for variable sized matrices.
+ * Several GBL methods are implemented as templates to allow more EIGEN compile time optimization.
+ *
+ * \section example_sec Examples
+ * Technical examples are given in example1.cpp, example2.cpp and example3.cpp.
+ * An example silicon tracker is described in exampleSit.cpp
+ * and an example sector of forward drift chambers in exampleDc.cpp.
+ *
+ * \section ref_sec References
+ * - V. Blobel, C. Kleinwort, F. Meier,
+ * Fast alignment of a complex tracking detector using advanced track models,
+ * Computer Phys. Communications (2011), doi:10.1016/j.cpc.2011.03.017
+ * - C. Kleinwort, General Broken Lines as advanced track fitting method,
+ * NIM A, 673 (2012), 107-110, doi:10.1016/j.nima.2012.01.024
+ */
+
+#include "GblTrajectory.h"
+using namespace Eigen;
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// Create new (simple) trajectory from list of points.
+ /**
+ * Curved trajectory in space (default) or without curvature (q/p) or in one
+ * plane (u-direction) only.
+ * \param [in] aPointList List of points
+ * \param [in] flagCurv Use q/p
+ * \param [in] flagU1dir Use in u1 direction
+ * \param [in] flagU2dir Use in u2 direction
+ */
+ GblTrajectory::GblTrajectory(const std::vector<GblPoint>& aPointList, bool flagCurv, bool flagU1dir, bool flagU2dir)
+ : numAllPoints(aPointList.size()), numPoints(), numOffsets(0), numInnerTrans(0), numCurvature(flagCurv ? 1 : 0),
+ numParameters(0), numLocals(0), numMeasurements(0), externalPoint(0), skippedMeasLabel(0), maxNumGlobals(0),
+ theDimension(0), thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations(),
+ externalDerivatives(), externalMeasurements(), externalPrecisions() {
+
+ if(flagU1dir)
+ theDimension.push_back(0);
+ if(flagU2dir)
+ theDimension.push_back(1);
+ // simple (single) trajectory
+ thePoints.emplace_back(std::move(aPointList));
+ numPoints.push_back(numAllPoints);
+ construct(); // construct trajectory
+ }
+
+ /// Create new composed trajectory from list of points and transformations.
+ /**
+ * Composed of curved trajectories in space.
+ * \param [in] aPointsAndTransList List containing pairs with list of points and transformation (at inner (first) point)
+ */
+ GblTrajectory::GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, Eigen::MatrixXd>>& aPointsAndTransList)
+ : numAllPoints(), numPoints(), numOffsets(0), numInnerTrans(aPointsAndTransList.size()), numParameters(0),
+ numLocals(0), numMeasurements(0), externalPoint(0), skippedMeasLabel(0), maxNumGlobals(0), theDimension(0),
+ thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations(),
+ externalDerivatives(), externalMeasurements(), externalPrecisions() {
+
+ for(unsigned int iTraj = 0; iTraj < aPointsAndTransList.size(); ++iTraj) {
+ thePoints.push_back(aPointsAndTransList[iTraj].first);
+ numPoints.push_back(thePoints.back().size());
+ numAllPoints += numPoints.back();
+ innerTransformations.push_back(aPointsAndTransList[iTraj].second);
+ }
+ theDimension.push_back(0);
+ theDimension.push_back(1);
+ numCurvature = innerTransformations[0].cols();
+ construct(); // construct (composed) trajectory
+ }
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ /// Create new (simple) trajectory from list of points with external seed.
+ /**
+ * Curved trajectory in space (default) or without curvature (q/p) or in one
+ * plane (u-direction) only.
+ * \param [in] aPointList List of points
+ * \param [in] aLabel (Signed) label of point for external seed
+ * (<0: in front, >0: after point, slope changes at scatterer!)
+ * \param [in] aSeed Precision matrix of external seed
+ * \param [in] flagCurv Use q/p
+ * \param [in] flagU1dir Use in u1 direction
+ * \param [in] flagU2dir Use in u2 direction
+ */
+ GblTrajectory::GblTrajectory(const std::vector<GblPoint>& aPointList,
+ unsigned int aLabel,
+ const TMatrixDSym& aSeed,
+ bool flagCurv,
+ bool flagU1dir,
+ bool flagU2dir)
+ : numAllPoints(aPointList.size()), numPoints(), numOffsets(0), numInnerTrans(0), numCurvature(flagCurv ? 1 : 0),
+ numParameters(0), numLocals(0), numMeasurements(0), externalPoint(aLabel), skippedMeasLabel(0), maxNumGlobals(0),
+ theDimension(0), thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations(),
+ externalDerivatives(), externalMeasurements(), externalPrecisions() {
+
+ if(flagU1dir)
+ theDimension.push_back(0);
+ if(flagU2dir)
+ theDimension.push_back(1);
+ // convert from ROOT
+ unsigned int nParSeed = aSeed.GetNrows();
+ externalSeed.resize(nParSeed, nParSeed);
+ for(unsigned int i = 0; i < nParSeed; ++i) {
+ for(unsigned int j = 0; j < nParSeed; ++j) {
+ externalSeed(i, j) = aSeed(i, j);
+ }
+ }
+ // simple (single) trajectory
+ thePoints.emplace_back(std::move(aPointList));
+ numPoints.push_back(numAllPoints);
+ construct(); // construct trajectory
+ }
+
+ /// Create new composed trajectory from list of points and transformations.
+ /**
+ * Composed of curved trajectories in space.
+ * \param [in] aPointsAndTransList List containing pairs with list of points and transformation (at inner (first) point)
+ */
+ GblTrajectory::GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, TMatrixD>>& aPointsAndTransList)
+ : numAllPoints(), numPoints(), numOffsets(0), numInnerTrans(aPointsAndTransList.size()), numParameters(0),
+ numLocals(0), numMeasurements(0), externalPoint(0), skippedMeasLabel(0), maxNumGlobals(0), theDimension(0),
+ thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations(),
+ externalDerivatives(), externalMeasurements(), externalPrecisions() {
+
+ for(unsigned int iTraj = 0; iTraj < aPointsAndTransList.size(); ++iTraj) {
+ thePoints.emplace_back(std::move(aPointsAndTransList[iTraj].first));
+ numPoints.push_back(thePoints.back().size());
+ numAllPoints += numPoints.back();
+ // convert from ROOT
+ unsigned int nRowTrans = aPointsAndTransList[iTraj].second.GetNrows();
+ unsigned int nColTrans = aPointsAndTransList[iTraj].second.GetNcols();
+ MatrixXd aTrans(nRowTrans, nColTrans);
+ for(unsigned int i = 0; i < nRowTrans; ++i) {
+ for(unsigned int j = 0; j < nColTrans; ++j) {
+ aTrans(i, j) = aPointsAndTransList[iTraj].second(i, j);
+ }
+ }
+ innerTransformations.emplace_back(std::move(aTrans));
+ }
+ theDimension.push_back(0);
+ theDimension.push_back(1);
+ numCurvature = innerTransformations[0].cols();
+ construct(); // construct (composed) trajectory
+ }
+
+ /// Create new composed trajectory from list of points and transformations with (independent) external measurements.
+ /**
+ * Composed of curved trajectories in space.
+ * \param [in] aPointsAndTransList List containing pairs with list of points and transformation (at inner (first) point)
+ * \param [in] extDerivatives Derivatives of external measurements vs external parameters
+ * \param [in] extMeasurements External measurements (residuals)
+ * \param [in] extPrecisions Precision of external measurements
+ */
+ GblTrajectory::GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, TMatrixD>>& aPointsAndTransList,
+ const TMatrixD& extDerivatives,
+ const TVectorD& extMeasurements,
+ const TVectorD& extPrecisions)
+ : numAllPoints(), numPoints(), numOffsets(0), numInnerTrans(aPointsAndTransList.size()), numParameters(0),
+ numLocals(0), numMeasurements(0), externalPoint(0), skippedMeasLabel(0), maxNumGlobals(0), theDimension(0),
+ thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations(),
+ externalDerivatives(), externalMeasurements(), externalPrecisions() {
+
+ // convert from ROOT
+ unsigned int nExtMeas = extDerivatives.GetNrows();
+ unsigned int nExtPar = extDerivatives.GetNcols();
+ externalDerivatives.resize(nExtMeas, nExtPar);
+ externalMeasurements.resize(nExtMeas);
+ externalPrecisions.resize(nExtMeas);
+ for(unsigned int i = 0; i < nExtMeas; ++i) {
+ externalMeasurements(i) = extMeasurements[i];
+ externalPrecisions(i) = extPrecisions[i];
+ for(unsigned int j = 0; j < nExtPar; ++j) {
+ externalDerivatives(i, j) = extDerivatives(i, j);
+ }
+ }
+ for(unsigned int iTraj = 0; iTraj < aPointsAndTransList.size(); ++iTraj) {
+ thePoints.emplace_back(std::move(aPointsAndTransList[iTraj].first));
+ numPoints.push_back(thePoints.back().size());
+ numAllPoints += numPoints.back();
+ // convert from ROOT
+ unsigned int nRowTrans = aPointsAndTransList[iTraj].second.GetNrows();
+ unsigned int nColTrans = aPointsAndTransList[iTraj].second.GetNcols();
+ MatrixXd aTrans(nRowTrans, nColTrans);
+ for(unsigned int i = 0; i < nRowTrans; ++i) {
+ for(unsigned int j = 0; j < nColTrans; ++j) {
+ aTrans(i, j) = aPointsAndTransList[iTraj].second(i, j);
+ }
+ }
+ innerTransformations.emplace_back(std::move(aTrans));
+ }
+ theDimension.push_back(0);
+ theDimension.push_back(1);
+ numCurvature = innerTransformations[0].cols();
+ construct(); // construct (composed) trajectory
+ }
+
+ /// Create new composed trajectory from list of points and transformations with (correlated) external measurements.
+ /**
+ * Composed of curved trajectories in space.
+ * \param [in] aPointsAndTransList List containing pairs with list of points and transformation (at inner (first) point)
+ * \param [in] extDerivatives Derivatives of external measurements vs external parameters
+ * \param [in] extMeasurements External measurements (residuals)
+ * \param [in] extPrecisions Precision of external measurements
+ */
+ GblTrajectory::GblTrajectory(const std::vector<std::pair<std::vector<GblPoint>, TMatrixD>>& aPointsAndTransList,
+ const TMatrixD& extDerivatives,
+ const TVectorD& extMeasurements,
+ const TMatrixDSym& extPrecisions)
+ : numAllPoints(), numPoints(), numOffsets(0), numInnerTrans(aPointsAndTransList.size()), numParameters(0),
+ numLocals(0), numMeasurements(0), externalPoint(0), skippedMeasLabel(0), maxNumGlobals(0), theDimension(0),
+ thePoints(), theData(), measDataIndex(), scatDataIndex(), externalSeed(), innerTransformations() {
+
+ // diagonalize external measurement
+ TMatrixDSymEigen extEigen(extPrecisions);
+ TMatrixD extTransformation = extEigen.GetEigenVectors();
+ extTransformation.T();
+ TMatrixD aDerivatives = extTransformation * extDerivatives;
+ TVectorD aMeasurements = extTransformation * extMeasurements;
+ TVectorD aPrecisions = extEigen.GetEigenValues();
+ // convert from ROOT
+ unsigned int nExtMeas = aDerivatives.GetNrows();
+ unsigned int nExtPar = aDerivatives.GetNcols();
+ externalDerivatives.resize(nExtMeas, nExtPar);
+ externalMeasurements.resize(nExtMeas);
+ externalPrecisions.resize(nExtMeas);
+ for(unsigned int i = 0; i < nExtMeas; ++i) {
+ externalMeasurements(i) = aMeasurements[i];
+ externalPrecisions(i) = aPrecisions[i];
+ for(unsigned int j = 0; j < nExtPar; ++j) {
+ externalDerivatives(i, j) = aDerivatives(i, j);
+ }
+ }
+ for(unsigned int iTraj = 0; iTraj < aPointsAndTransList.size(); ++iTraj) {
+ thePoints.emplace_back(std::move(aPointsAndTransList[iTraj].first));
+ numPoints.push_back(thePoints.back().size());
+ numAllPoints += numPoints.back();
+ // convert from ROOT
+ unsigned int nRowTrans = aPointsAndTransList[iTraj].second.GetNrows();
+ unsigned int nColTrans = aPointsAndTransList[iTraj].second.GetNcols();
+ MatrixXd aTrans(nRowTrans, nColTrans);
+ for(unsigned int i = 0; i < nRowTrans; ++i) {
+ for(unsigned int j = 0; j < nColTrans; ++j) {
+ aTrans(i, j) = aPointsAndTransList[iTraj].second(i, j);
+ }
+ }
+ innerTransformations.emplace_back(std::move(aTrans));
+ }
+ theDimension.push_back(0);
+ theDimension.push_back(1);
+ numCurvature = innerTransformations[0].cols();
+ construct(); // construct (composed) trajectory
+ }
+#endif
+
+ GblTrajectory::~GblTrajectory() {}
+
+ /// Retrieve validity of trajectory
+ bool GblTrajectory::isValid() const { return constructOK; }
+
+ /// Retrieve number of point from trajectory
+ unsigned int GblTrajectory::getNumPoints() const { return numAllPoints; }
+
+ /// Construct trajectory from list of points.
+ /**
+ * Trajectory is prepared for fit or output to binary file, may consists of sub-trajectories.
+ */
+ void GblTrajectory::construct() {
+
+ constructOK = false;
+ fitOK = false;
+ unsigned int aLabel = 0;
+ if(numAllPoints < 2) {
+ std::cout << " GblTrajectory construction failed: too few GblPoints " << std::endl;
+ return;
+ }
+ // loop over trajectories
+ numTrajectories = thePoints.size();
+ // std::cout << " numTrajectories: " << numTrajectories << ", " << innerTransformations.size() << std::endl;
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ std::vector<GblPoint>::iterator itPoint;
+ for(itPoint = thePoints[iTraj].begin(); itPoint < thePoints[iTraj].end(); ++itPoint) {
+ numLocals = std::max(numLocals, itPoint->getNumLocals());
+ numMeasurements += itPoint->hasMeasurement();
+ itPoint->setLabel(++aLabel);
+ }
+ }
+ defineOffsets();
+ calcJacobians();
+ try {
+ prepare();
+ } catch(std::overflow_error& e) {
+ std::cout << " GblTrajectory construction failed: " << e.what() << std::endl;
+ return;
+ }
+
+ constructOK = true;
+ // number of fit parameters
+ numParameters = (numOffsets - 2 * numInnerTrans) * theDimension.size() + numCurvature + numLocals;
+ }
+
+ /// Define offsets from list of points.
+ /**
+ * Define offsets at points with scatterers and first and last point.
+ * All other points need interpolation from adjacent points with offsets.
+ */
+ void GblTrajectory::defineOffsets() {
+
+ // loop over trajectories
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ // first point is offset
+ thePoints[iTraj].front().setOffset(numOffsets++);
+ // intermediate scatterers are offsets
+ std::vector<GblPoint>::iterator itPoint;
+ for(itPoint = thePoints[iTraj].begin() + 1; itPoint < thePoints[iTraj].end() - 1; ++itPoint) {
+ if(itPoint->hasScatterer()) {
+ itPoint->setOffset(numOffsets++);
+ } else {
+ itPoint->setOffset(-numOffsets);
+ }
+ }
+ // last point is offset
+ thePoints[iTraj].back().setOffset(numOffsets++);
+ }
+ }
+
+ /// Calculate Jacobians to previous/next scatterer from point to point ones.
+ void GblTrajectory::calcJacobians() {
+
+ Matrix5d scatJacobian;
+ // loop over trajectories
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ // forward propagation (all)
+ GblPoint* previousPoint = &thePoints[iTraj].front();
+ unsigned int numStep = 0;
+ std::vector<GblPoint>::iterator itPoint;
+ for(itPoint = thePoints[iTraj].begin() + 1; itPoint < thePoints[iTraj].end(); ++itPoint) {
+ if(numStep == 0) {
+ scatJacobian = itPoint->getP2pJacobian();
+ } else {
+ scatJacobian = itPoint->getP2pJacobian() * scatJacobian;
+ }
+ numStep++;
+ itPoint->addPrevJacobian(scatJacobian); // iPoint -> previous scatterer
+ if(itPoint->getOffset() >= 0) {
+ previousPoint->addNextJacobian(scatJacobian); // lastPoint -> next scatterer
+ numStep = 0;
+ previousPoint = &(*itPoint);
+ }
+ }
+ // backward propagation (without scatterers)
+ for(itPoint = thePoints[iTraj].end() - 1; itPoint > thePoints[iTraj].begin(); --itPoint) {
+ if(itPoint->getOffset() >= 0) {
+ scatJacobian = itPoint->getP2pJacobian();
+ continue; // skip offsets
+ }
+ itPoint->addNextJacobian(scatJacobian); // iPoint -> next scatterer
+ scatJacobian = scatJacobian * itPoint->getP2pJacobian();
+ }
+ }
+ }
+
+ /// Get jacobian for transformation from fit to track parameters at point.
+ /**
+ * Jacobian broken lines (q/p,..,u_i,u_i+1..) to track (q/p,u',u) parameters
+ * including additional local parameters.
+ * \param [in] aSignedLabel (Signed) label of point for external seed
+ * (<0: in front, >0: after point, slope changes at scatterer!)
+ * \return List of fit parameters with non zero derivatives and
+ * corresponding transformation matrix
+ */
+ std::pair<std::vector<unsigned int>, MatrixXd> GblTrajectory::getJacobian(int aSignedLabel) const {
+
+ unsigned int nDim = theDimension.size();
+ unsigned int nCurv = numCurvature;
+ unsigned int nLocals = numLocals;
+ unsigned int nBorder = nCurv + nLocals;
+ unsigned int nParBRL = nBorder + 2 * nDim;
+ unsigned int nParLoc = nLocals + 5;
+ std::vector<unsigned int> anIndex;
+ anIndex.reserve(nParBRL);
+ MatrixXd aJacobian(nParLoc, nParBRL);
+ aJacobian.setZero();
+
+ unsigned int aLabel = abs(aSignedLabel);
+ unsigned int firstLabel = 1;
+ unsigned int lastLabel = 0;
+ unsigned int aTrajectory = 0;
+ // loop over trajectories
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ aTrajectory = iTraj;
+ lastLabel += numPoints[iTraj];
+ if(aLabel <= lastLabel)
+ break;
+ if(iTraj < numTrajectories - 1)
+ firstLabel += numPoints[iTraj];
+ }
+ int nJacobian; // 0: prev, 1: next
+ // check consistency of (index, direction)
+ if(aSignedLabel > 0) {
+ nJacobian = 1;
+ if(aLabel >= lastLabel) {
+ aLabel = lastLabel;
+ nJacobian = 0;
+ }
+ } else {
+ nJacobian = 0;
+ if(aLabel <= firstLabel) {
+ aLabel = firstLabel;
+ nJacobian = 1;
+ }
+ }
+ const GblPoint aPoint = thePoints[aTrajectory][aLabel - firstLabel];
+ std::array<unsigned int, 5> labDer;
+ Matrix5d matDer;
+ getFitToLocalJacobian(labDer, matDer, aPoint, 5, nJacobian);
+
+ // from local parameters
+ for(unsigned int i = 0; i < nLocals; ++i) {
+ aJacobian(i + 5, i) = 1.0;
+ anIndex.push_back(i + 1);
+ }
+ // from trajectory parameters
+ unsigned int iCol = nLocals;
+ for(unsigned int i = 0; i < 5; ++i) {
+ if(labDer[i] > 0) {
+ anIndex.push_back(labDer[i]);
+ for(unsigned int j = 0; j < 5; ++j) {
+ aJacobian(j, iCol) = matDer(j, i);
+ }
+ ++iCol;
+ }
+ }
+ return std::make_pair(anIndex, aJacobian);
+ }
+
+ /// Get (part of) jacobian for transformation from (trajectory) fit to track parameters at point.
+ /**
+ * Jacobian broken lines (q/p,..,u_i,u_i+1..) to local (q/p,u',u) parameters.
+ * \param [out] anIndex List of fit parameters (zero for zero derivatives)
+ * \param [out] aJacobian Corresponding transformation matrix
+ * \param [in] aPoint Point to use
+ * \param [in] measDim Dimension of 'measurement'
+ * (<=2: calculate only offset part, >2: complete matrix)
+ * \param [in] nJacobian Direction (0: to previous offset, 1: to next offset)
+ */
+ void GblTrajectory::getFitToLocalJacobian(std::array<unsigned int, 5>& anIndex,
+ Matrix5d& aJacobian,
+ const GblPoint& aPoint,
+ unsigned int measDim,
+ unsigned int nJacobian) const {
+
+ unsigned int nDim = theDimension.size();
+ unsigned int nCurv = numCurvature;
+ unsigned int nLocals = numLocals;
+
+ int nOffset = aPoint.getOffset();
+
+ anIndex = {}; // reset to 0
+ aJacobian.setZero();
+ if(nOffset < 0) // need interpolation
+ {
+ Matrix2d prevW, prevWJ, nextW, nextWJ, matN;
+ Vector2d prevWd, nextWd;
+ aPoint.getDerivatives(0, prevW, prevWJ, prevWd); // W-, W- * J-, W- * d-
+ aPoint.getDerivatives(1, nextW, nextWJ, nextWd); // W+, W+ * J+, W+ * d+
+ const Matrix2d sumWJ(prevWJ + nextWJ);
+ matN = sumWJ.inverse(); // N = (W- * J- + W+ * J+)^-1
+ // derivatives for u_int
+ const Matrix2d prevNW(matN * prevW); // N * W-
+ const Matrix2d nextNW(matN * nextW); // N * W+
+ const Vector2d prevNd(matN * prevWd); // N * W- * d-
+ const Vector2d nextNd(matN * nextWd); // N * W+ * d+
+
+ unsigned int iOff = nDim * (-nOffset - 1) + nLocals + nCurv + 1; // first offset ('i' in u_i)
+
+ // local offset
+ if(nCurv > 0) {
+ aJacobian.block<2, 1>(3, 0) = -prevNd - nextNd; // from curvature
+ anIndex[0] = nLocals + 1;
+ }
+ aJacobian.block<2, 2>(3, 1) = prevNW; // from 1st Offset
+ aJacobian.block<2, 2>(3, 3) = nextNW; // from 2nd Offset
+ for(unsigned int i = 0; i < nDim; ++i) {
+ anIndex[1 + theDimension[i]] = iOff + i;
+ anIndex[3 + theDimension[i]] = iOff + nDim + i;
+ }
+
+ // local slope and curvature
+ if(measDim > 2) {
+ // derivatives for u'_int
+ const Matrix2d prevWPN(nextWJ * prevNW); // W+ * J+ * N * W-
+ const Matrix2d nextWPN(prevWJ * nextNW); // W- * J- * N * W+
+ const Vector2d prevWNd(nextWJ * prevNd); // W+ * J+ * N * W- * d-
+ const Vector2d nextWNd(prevWJ * nextNd); // W- * J- * N * W+ * d+
+ if(nCurv > 0) {
+ aJacobian(0, 0) = 1.0;
+ aJacobian.block<2, 1>(1, 0) = prevWNd - nextWNd; // from curvature
+ }
+ aJacobian.block<2, 2>(1, 1) = -prevWPN; // from 1st Offset
+ aJacobian.block<2, 2>(1, 3) = nextWPN; // from 2nd Offset
+ }
+ } else { // at point
+ // anIndex must be sorted
+ // forward : iOff2 = iOff1 + nDim, index1 = 1, index2 = 3
+ // backward: iOff2 = iOff1 - nDim, index1 = 3, index2 = 1
+ unsigned int iOff1 = nDim * nOffset + nCurv + nLocals + 1; // first offset ('i' in u_i)
+ unsigned int index1 = 3 - 2 * nJacobian; // index of first offset
+ unsigned int iOff2 = iOff1 + nDim * (nJacobian * 2 - 1); // second offset ('i' in u_i)
+ unsigned int index2 = 1 + 2 * nJacobian; // index of second offset
+ // local offset
+ aJacobian(3, index1) = 1.0; // from 1st Offset
+ aJacobian(4, index1 + 1) = 1.0;
+ for(unsigned int i = 0; i < nDim; ++i) {
+ anIndex[index1 + theDimension[i]] = iOff1 + i;
+ }
+
+ // local slope and curvature
+ if(measDim > 2) {
+ Matrix2d matW, matWJ;
+ Vector2d vecWd;
+ aPoint.getDerivatives(nJacobian, matW, matWJ, vecWd); // W, W * J, W * d
+ double sign = (nJacobian > 0) ? 1. : -1.;
+ if(nCurv > 0) {
+ aJacobian(0, 0) = 1.0;
+ aJacobian.block<2, 1>(1, 0) = -sign * vecWd; // from curvature
+ anIndex[0] = nLocals + 1;
+ }
+ aJacobian.block<2, 2>(1, index1) = -sign * matWJ; // from 1st Offset
+ aJacobian.block<2, 2>(1, index2) = sign * matW; // from 2nd Offset
+ for(unsigned int i = 0; i < nDim; ++i) {
+ anIndex[index2 + theDimension[i]] = iOff2 + i;
+ }
+ }
+ }
+ }
+
+ /// Get jacobian for transformation from (trajectory) fit to kink parameters at point.
+ /**
+ * Jacobian broken lines (q/p,..,u_i-1,u_i,u_i+1..) to kink (du') parameters.
+ * \param [out] anIndex List of fit parameters (zero for zero derivatives)
+ * \param [out] aJacobian Corresponding transformation matrix
+ * \param [in] aPoint Point to use
+ */
+ void GblTrajectory::getFitToKinkJacobian(std::array<unsigned int, 7>& anIndex,
+ Matrix27d& aJacobian,
+ const GblPoint& aPoint) const {
+
+ unsigned int nDim = theDimension.size();
+ unsigned int nCurv = numCurvature;
+ unsigned int nLocals = numLocals;
+
+ int nOffset = aPoint.getOffset();
+
+ anIndex = {}; // reset to 0
+ aJacobian.setZero();
+
+ Matrix2d prevW, prevWJ, nextW, nextWJ;
+ Vector2d prevWd, nextWd;
+ aPoint.getDerivatives(0, prevW, prevWJ, prevWd); // W-, W- * J-, W- * d-
+ aPoint.getDerivatives(1, nextW, nextWJ, nextWd); // W-, W- * J-, W- * d-
+ const Matrix2d sumWJ(prevWJ + nextWJ); // W- * J- + W+ * J+
+ const Vector2d sumWd(prevWd + nextWd); // W+ * d+ + W- * d-
+
+ unsigned int iOff = (nOffset - 1) * nDim + nCurv + nLocals + 1; // first offset ('i' in u_i)
+
+ // local offset
+ if(nCurv > 0) {
+ aJacobian.block<2, 1>(0, 0) = -sumWd; // from curvature
+ anIndex[0] = nLocals + 1;
+ }
+ aJacobian.block<2, 2>(0, 1) = prevW; // from 1st Offset
+ aJacobian.block<2, 2>(0, 3) = -sumWJ; // from 2nd Offset
+ aJacobian.block<2, 2>(0, 5) = nextW; // from 1st Offset
+ for(unsigned int i = 0; i < nDim; ++i) {
+ anIndex[1 + theDimension[i]] = iOff + i;
+ anIndex[3 + theDimension[i]] = iOff + nDim + i;
+ anIndex[5 + theDimension[i]] = iOff + nDim * 2 + i;
+ }
+ }
+
+ /// Get fit results at point.
+ /**
+ * Get corrections and covariance matrix for local track and additional parameters
+ * in forward or backward direction.
+ *
+ * The point is identified by its label (1..number(points)), the sign distinguishes the
+ * backward (facing previous point) and forward 'side' (facing next point).
+ * For scatterers the track direction may change in between.
+ *
+ * \param [in] aSignedLabel (Signed) label of point on trajectory
+ * (<0: in front, >0: after point, slope changes at scatterer!)
+ * \param [out] localPar Corrections for local parameters
+ * \param [out] localCov Covariance for local parameters
+ * \return error code (non-zero if trajectory not fitted successfully)
+ */
+ unsigned int GblTrajectory::getResults(int aSignedLabel, Eigen::VectorXd& localPar, Eigen::MatrixXd& localCov) const {
+ if(not fitOK)
+ return 1;
+ std::pair<std::vector<unsigned int>, MatrixXd> indexAndJacobian = getJacobian(aSignedLabel);
+ unsigned int nParBrl = indexAndJacobian.first.size();
+ VectorXd aVec(nParBrl); // compressed vector
+ for(unsigned int i = 0; i < nParBrl; ++i) {
+ aVec[i] = theVector(indexAndJacobian.first[i] - 1);
+ }
+ MatrixXd aMat = theMatrix.getBlockMatrix(indexAndJacobian.first); // compressed matrix
+ localPar = indexAndJacobian.second * aVec;
+ localCov = indexAndJacobian.second * aMat * indexAndJacobian.second.adjoint();
+ return 0;
+ }
+
+ /// Get residuals from fit at point for measurement.
+ /**
+ * Get (diagonalized) residual, error of measurement and residual and down-weighting
+ * factor for measurement at point
+ *
+ * \param [in] aLabel Label of point on trajectory
+ * \param [out] numData Number of data blocks from measurement at point
+ * \param [out] aResiduals Measurements-Predictions
+ * \param [out] aMeasErrors Errors of Measurements
+ * \param [out] aResErrors Errors of Residuals (including correlations from track fit)
+ * \param [out] aDownWeights Down-Weighting factors
+ * \return error code (non-zero if trajectory not fitted successfully)
+ */
+ unsigned int GblTrajectory::getMeasResults(unsigned int aLabel,
+ unsigned int& numData,
+ Eigen::VectorXd& aResiduals,
+ Eigen::VectorXd& aMeasErrors,
+ Eigen::VectorXd& aResErrors,
+ Eigen::VectorXd& aDownWeights) {
+ numData = 0;
+ if(not fitOK)
+ return 1;
+
+ unsigned int firstData = measDataIndex[aLabel - 1]; // first data block with measurement
+ numData = measDataIndex[aLabel] - firstData; // number of data blocks
+ for(unsigned int i = 0; i < numData; ++i) {
+ getResAndErr(
+ firstData + i, (aLabel != skippedMeasLabel), aResiduals(i), aMeasErrors(i), aResErrors(i), aDownWeights(i));
+ }
+ return 0;
+ }
+
+ /// Get (kink) residuals from fit at point for scatterer.
+ /**
+ * Get (diagonalized) residual, error of measurement and residual and down-weighting
+ * factor for scatterering kinks at point
+ *
+ * \param [in] aLabel Label of point on trajectory
+ * \param [out] numData Number of data blocks from scatterer at point
+ * \param [out] aResiduals (kink)Measurements-(kink)Predictions
+ * \param [out] aMeasErrors Errors of (kink)Measurements
+ * \param [out] aResErrors Errors of Residuals (including correlations from track fit)
+ * \param [out] aDownWeights Down-Weighting factors
+ * \return error code (non-zero if trajectory not fitted successfully)
+ */
+ unsigned int GblTrajectory::getScatResults(unsigned int aLabel,
+ unsigned int& numData,
+ Eigen::VectorXd& aResiduals,
+ Eigen::VectorXd& aMeasErrors,
+ Eigen::VectorXd& aResErrors,
+ Eigen::VectorXd& aDownWeights) {
+ numData = 0;
+ if(not fitOK)
+ return 1;
+
+ unsigned int firstData = scatDataIndex[aLabel - 1]; // first data block with scatterer
+ numData = scatDataIndex[aLabel] - firstData; // number of data blocks
+ for(unsigned int i = 0; i < numData; ++i) {
+ getResAndErr(firstData + i, true, aResiduals(i), aMeasErrors(i), aResErrors(i), aDownWeights(i));
+ }
+ return 0;
+ }
+
+#ifdef GBL_EIGEN_SUPPORT_ROOT
+ /// Get fit results at point.
+ /**
+ * Get corrections and covariance matrix for local track and additional parameters
+ * in forward or backward direction.
+ *
+ * The point is identified by its label (1..number(points)), the sign distinguishes the
+ * backward (facing previous point) and forward 'side' (facing next point).
+ * For scatterers the track direction may change in between.
+ *
+ * \param [in] aSignedLabel (Signed) label of point on trajectory
+ * (<0: in front, >0: after point, slope changes at scatterer!)
+ * \param [out] localPar Corrections for local parameters
+ * \param [out] localCov Covariance for local parameters
+ * \return error code (non-zero if trajectory not fitted successfully)
+ */
+ unsigned int GblTrajectory::getResults(int aSignedLabel, TVectorD& localPar, TMatrixDSym& localCov) const {
+ if(not fitOK)
+ return 1;
+ std::pair<std::vector<unsigned int>, MatrixXd> indexAndJacobian = getJacobian(aSignedLabel);
+ unsigned int nParBrl = indexAndJacobian.first.size();
+ VectorXd aVec(nParBrl); // compressed vector
+ for(unsigned int i = 0; i < nParBrl; ++i) {
+ aVec[i] = theVector(indexAndJacobian.first[i] - 1);
+ }
+ MatrixXd aMat = theMatrix.getBlockMatrix(indexAndJacobian.first); // compressed matrix
+ VectorXd aLocalPar = indexAndJacobian.second * aVec;
+ MatrixXd aLocalCov = indexAndJacobian.second * aMat * indexAndJacobian.second.adjoint();
+ // convert to ROOT
+ unsigned int nParOut = localPar.GetNrows();
+ for(unsigned int i = 0; i < nParOut; ++i) {
+ localPar[i] = aLocalPar(i);
+ for(unsigned int j = 0; j < nParOut; ++j) {
+ localCov(i, j) = aLocalCov(i, j);
+ }
+ }
+ return 0;
+ }
+
+ /// Get residuals from fit at point for measurement.
+ /**
+ * Get (diagonalized) residual, error of measurement and residual and down-weighting
+ * factor for measurement at point
+ *
+ * \param [in] aLabel Label of point on trajectory
+ * \param [out] numData Number of data blocks from measurement at point
+ * \param [out] aResiduals Measurements-Predictions
+ * \param [out] aMeasErrors Errors of Measurements
+ * \param [out] aResErrors Errors of Residuals (including correlations from track fit)
+ * \param [out] aDownWeights Down-Weighting factors
+ * \return error code (non-zero if trajectory not fitted successfully)
+ */
+ unsigned int GblTrajectory::getMeasResults(unsigned int aLabel,
+ unsigned int& numData,
+ TVectorD& aResiduals,
+ TVectorD& aMeasErrors,
+ TVectorD& aResErrors,
+ TVectorD& aDownWeights) {
+ numData = 0;
+ if(not fitOK)
+ return 1;
+
+ unsigned int firstData = measDataIndex[aLabel - 1]; // first data block with measurement
+ numData = measDataIndex[aLabel] - firstData; // number of data blocks
+ for(unsigned int i = 0; i < numData; ++i) {
+ getResAndErr(
+ firstData + i, (aLabel != skippedMeasLabel), aResiduals[i], aMeasErrors[i], aResErrors[i], aDownWeights[i]);
+ }
+ return 0;
+ }
+
+ /// Get (kink) residuals from fit at point for scatterer.
+ /**
+ * Get (diagonalized) residual, error of measurement and residual and down-weighting
+ * factor for scatterering kinks at point
+ *
+ * \param [in] aLabel Label of point on trajectory
+ * \param [out] numData Number of data blocks from scatterer at point
+ * \param [out] aResiduals (kink)Measurements-(kink)Predictions
+ * \param [out] aMeasErrors Errors of (kink)Measurements
+ * \param [out] aResErrors Errors of Residuals (including correlations from track fit)
+ * \param [out] aDownWeights Down-Weighting factors
+ * \return error code (non-zero if trajectory not fitted successfully)
+ */
+ unsigned int GblTrajectory::getScatResults(unsigned int aLabel,
+ unsigned int& numData,
+ TVectorD& aResiduals,
+ TVectorD& aMeasErrors,
+ TVectorD& aResErrors,
+ TVectorD& aDownWeights) {
+ numData = 0;
+ if(not fitOK)
+ return 1;
+
+ unsigned int firstData = scatDataIndex[aLabel - 1]; // first data block with scatterer
+ numData = scatDataIndex[aLabel] - firstData; // number of data blocks
+ for(unsigned int i = 0; i < numData; ++i) {
+ getResAndErr(firstData + i, true, aResiduals[i], aMeasErrors[i], aResErrors[i], aDownWeights[i]);
+ }
+ return 0;
+ }
+
+#endif
+
+ /// Get (list of) labels of points on (simple) valid trajectory
+ /**
+ * \param [out] aLabelList List of labels (aLabelList[i] = i+1)
+ * \return error code (non-zero if trajectory not valid (constructed successfully))
+ */
+ unsigned int GblTrajectory::getLabels(std::vector<unsigned int>& aLabelList) const {
+ if(not constructOK)
+ return 1;
+
+ unsigned int aLabel = 0;
+ unsigned int nPoint = thePoints[0].size();
+ aLabelList.resize(nPoint);
+ for(unsigned i = 0; i < nPoint; ++i) {
+ aLabelList[i] = ++aLabel;
+ }
+ return 0;
+ }
+
+ /// Get (list of lists of) labels of points on (composed) valid trajectory
+ /**
+ * \param [out] aLabelList List of of lists of labels
+ * \return error code (non-zero if trajectory not valid (constructed successfully))
+ */
+ unsigned int GblTrajectory::getLabels(std::vector<std::vector<unsigned int>>& aLabelList) const {
+ if(not constructOK)
+ return 1;
+
+ unsigned int aLabel = 0;
+ aLabelList.resize(numTrajectories);
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ unsigned int nPoint = thePoints[iTraj].size();
+ aLabelList[iTraj].resize(nPoint);
+ for(unsigned i = 0; i < nPoint; ++i) {
+ aLabelList[iTraj][i] = ++aLabel;
+ }
+ }
+ return 0;
+ }
+
+ /// Get residual and errors from data block.
+ /**
+ * Get residual, error of measurement and residual and down-weighting
+ * factor for (single) data block
+ * \param [in] aData Label of data block
+ * \param [in] used Flag for usage of data block in fit
+ * \param [out] aResidual Measurement-Prediction
+ * \param [out] aMeasError Error of Measurement
+ * \param [out] aResError Error of Residual (including correlations from track fit)
+ * \param [out] aDownWeight Down-Weighting factor
+ */
+ void GblTrajectory::getResAndErr(
+ unsigned int aData, bool used, double& aResidual, double& aMeasError, double& aResError, double& aDownWeight) {
+
+ double aMeasVar;
+ unsigned int numLocal;
+ unsigned int* indLocal;
+ double* derLocal;
+ theData[aData].getResidual(aResidual, aMeasVar, aDownWeight, numLocal, indLocal, derLocal);
+ VectorXd aVec(numLocal); // compressed vector of derivatives
+ for(unsigned int j = 0; j < numLocal; ++j) {
+ aVec[j] = derLocal[j];
+ }
+ MatrixXd aMat = theMatrix.getBlockMatrix(numLocal, indLocal); // compressed (covariance) matrix
+ double aFitVar = aVec.transpose() * aMat * aVec; // variance from track fit
+ aFitVar *= aDownWeight; // account for down-weighting (of measurement in fit)
+ aMeasError = sqrt(aMeasVar); // error of measurement
+ if(used)
+ aResError = (aFitVar < aMeasVar ? sqrt(aMeasVar - aFitVar) : 0.); // error of (biased) residual
+ else
+ aResError = sqrt(aMeasVar + aFitVar); // error of (unbiased) residual
+ }
+
+ /// Build linear equation system from data (blocks).
+ void GblTrajectory::buildLinearEquationSystem() {
+ unsigned int nBorder = numCurvature + numLocals;
+ theVector.resize(numParameters);
+ theMatrix.resize(numParameters, nBorder);
+ double aValue, aWeight;
+ unsigned int* indLocal;
+ double* derLocal;
+ unsigned int numLocal;
+
+ std::vector<GblData>::iterator itData;
+ for(itData = theData.begin(); itData < theData.end(); ++itData) {
+ // skipped (internal) measurement ?
+ if(itData->getLabel() == skippedMeasLabel && itData->getType() == InternalMeasurement)
+ continue;
+ itData->getLocalData(aValue, aWeight, numLocal, indLocal, derLocal);
+ for(unsigned int j = 0; j < numLocal; ++j) {
+ theVector(indLocal[j] - 1) += derLocal[j] * aWeight * aValue;
+ }
+ theMatrix.addBlockMatrix(aWeight, numLocal, indLocal, derLocal);
+ }
+ }
+
+ /// Prepare fit for simple or composed trajectory
+ /**
+ * Generate data (blocks) from measurements, kinks, external seed and measurements.
+ */
+ void GblTrajectory::prepare() {
+ unsigned int nDim = theDimension.size();
+ // upper limit
+ unsigned int maxData = numMeasurements + nDim * (numOffsets - 2) + externalSeed.rows();
+ theData.reserve(maxData);
+ measDataIndex.resize(numAllPoints + 3); // include external seed and measurements
+ scatDataIndex.resize(numAllPoints + 1);
+ unsigned int nData = 0;
+ std::vector<MatrixXd> innerTransDer;
+ std::vector<std::array<unsigned int, 5>> innerTransLab;
+ // composed trajectory ?
+ if(numInnerTrans > 0) {
+ // std::cout << "composed trajectory" << std::endl;
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ // innermost point
+ GblPoint* innerPoint = &thePoints[iTraj].front();
+ // transformation fit to local track parameters
+ std::array<unsigned int, 5> firstLabels;
+ Matrix5d matFitToLocal, matLocalToFit;
+ getFitToLocalJacobian(firstLabels, matFitToLocal, *innerPoint, 5);
+ // transformation local track to fit parameters
+ matLocalToFit = matFitToLocal.inverse();
+ // transformation external to fit parameters at inner (first) point
+ innerTransDer.emplace_back(matLocalToFit * innerTransformations[iTraj]);
+ innerTransLab.push_back(firstLabels);
+ }
+ }
+
+ Matrix5d matP; // measurements
+ std::vector<GblPoint>::iterator itPoint;
+ // limit the scope of proDer:
+ {
+ // transform for external parameters
+ Eigen::Matrix<double, Eigen::Dynamic, 5, Eigen::ColMajor /* default */, 5, 5> proDer;
+ // loop over trajectories
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ for(itPoint = thePoints[iTraj].begin(); itPoint < thePoints[iTraj].end(); ++itPoint) {
+ Vector5d aMeas, aPrec;
+ unsigned int nLabel = itPoint->getLabel();
+ unsigned int measDim = itPoint->hasMeasurement();
+ if(measDim) {
+ const MatrixXd localDer = itPoint->getLocalDerivatives();
+ maxNumGlobals = std::max(maxNumGlobals, itPoint->getNumGlobals());
+ MatrixXd transDer;
+ itPoint->getMeasurement(matP, aMeas, aPrec);
+ double minPrecision = itPoint->getMeasPrecMin();
+ unsigned int iOff = 5 - measDim; // first active component
+ std::array<unsigned int, 5> labDer;
+ Matrix5d matDer, matPDer;
+ unsigned int nJacobian =
+ (itPoint < thePoints[iTraj].end() - 1) ? 1 : 0; // last point needs backward propagation
+ getFitToLocalJacobian(labDer, matDer, *itPoint, measDim, nJacobian);
+ if(measDim > 2) {
+ matPDer = matP * matDer;
+ } else { // 'shortcut' for position measurements
+ matPDer.setZero();
+ matPDer.block<2, 5>(3, 0) = matP.block<2, 2>(3, 3) * matDer.block<2, 5>(3, 0);
+ }
+
+ if(numInnerTrans > 0) {
+ // transform for external parameters
+ proDer.resize(measDim, Eigen::NoChange);
+ proDer.setZero();
+ // match parameters
+ unsigned int ifirst = 0;
+ unsigned int ilabel = 0;
+ unsigned int numRelated = 0;
+ while(ilabel < 5) {
+ if(labDer[ilabel] > 0) {
+ while(innerTransLab[iTraj][ifirst] != labDer[ilabel] and ifirst < 5) {
+ ++ifirst;
+ }
+ if(ifirst >= 5) {
+ labDer[ilabel] -= 2 * nDim * (iTraj + 1); // adjust label
+ } else {
+ // match
+ labDer[ilabel] = 0; // mark as related to external parameters
+ numRelated++;
+ for(unsigned int k = iOff; k < 5; ++k) {
+ proDer(k - iOff, ifirst) = matPDer(k, ilabel);
+ }
+ }
+ }
+ ++ilabel;
+ }
+ if(numRelated > 0) {
+ transDer.resize(measDim, numCurvature);
+ transDer = proDer * innerTransDer[iTraj];
+ }
+ }
+ for(unsigned int i = iOff; i < 5; ++i) {
+ if(aPrec(i) > minPrecision) {
+ GblData aData(nLabel,
+ InternalMeasurement,
+ aMeas(i),
+ aPrec(i),
+ iTraj,
+ itPoint - thePoints[iTraj].begin());
+ aData.addDerivatives(i, labDer, matPDer, iOff, localDer, numLocals, transDer);
+ theData.emplace_back(std::move(aData));
+ nData++;
+ }
+ }
+ }
+ measDataIndex[nLabel] = nData;
+ }
+ }
+ } // end of scope for proDer
+
+ Matrix2d matT; // kinks
+ // limit the scope of proDer:
+ {
+ // transform for external parameters
+ Eigen::Matrix<double, Eigen::Dynamic, 5, Eigen::ColMajor /* default */, 5, 5> proDer;
+ scatDataIndex[0] = nData;
+ scatDataIndex[1] = nData;
+ // loop over trajectories
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ for(itPoint = thePoints[iTraj].begin() + 1; itPoint < thePoints[iTraj].end() - 1; ++itPoint) {
+ Vector2d aMeas, aPrec;
+ unsigned int nLabel = itPoint->getLabel();
+ if(itPoint->hasScatterer()) {
+ itPoint->getScatterer(matT, aMeas, aPrec);
+ MatrixXd transDer;
+ std::array<unsigned int, 7> labDer;
+ Matrix27d matDer, matTDer;
+ getFitToKinkJacobian(labDer, matDer, *itPoint);
+ matTDer = matT * matDer;
+ if(numInnerTrans > 0) {
+ // transform for external parameters
+ proDer.resize(nDim, Eigen::NoChange);
+ proDer.setZero();
+ // match parameters
+ unsigned int ifirst = 0;
+ unsigned int ilabel = 0;
+ unsigned int numRelated = 0;
+ while(ilabel < 7) {
+ if(labDer[ilabel] > 0) {
+ while(innerTransLab[iTraj][ifirst] != labDer[ilabel] and ifirst < 5) {
+ ++ifirst;
+ }
+ if(ifirst >= 5) {
+ labDer[ilabel] -= 2 * nDim * (iTraj + 1); // adjust label
+ } else {
+ // match
+ labDer[ilabel] = 0; // mark as related to external parameters
+ numRelated++;
+ for(unsigned int k = 0; k < nDim; ++k) {
+ proDer(k, ifirst) = matTDer(k, ilabel);
+ }
+ }
+ }
+ ++ilabel;
+ }
+ if(numRelated > 0) {
+ transDer.resize(nDim, numCurvature);
+ transDer = proDer * innerTransDer[iTraj];
+ }
+ }
+ for(unsigned int i = 0; i < nDim; ++i) {
+ unsigned int iDim = theDimension[i];
+ if(aPrec(iDim) > 0.) {
+ GblData aData(nLabel,
+ InternalKink,
+ aMeas(iDim),
+ aPrec(iDim),
+ iTraj,
+ itPoint - thePoints[iTraj].begin());
+ aData.addDerivatives(iDim, labDer, matTDer, numLocals, transDer);
+ theData.emplace_back(std::move(aData));
+ nData++;
+ }
+ }
+ }
+ scatDataIndex[nLabel] = nData;
+ }
+ scatDataIndex[thePoints[iTraj].back().getLabel()] = nData;
+ }
+ }
+
+ // external seed
+ if(externalPoint > 0) {
+ std::pair<std::vector<unsigned int>, MatrixXd> indexAndJacobian = getJacobian(externalPoint);
+ std::vector<unsigned int> externalSeedIndex = indexAndJacobian.first;
+ std::vector<double> externalSeedDerivatives(externalSeedIndex.size());
+ SelfAdjointEigenSolver<MatrixXd> externalSeedEigen(externalSeed);
+ VectorXd valEigen = externalSeedEigen.eigenvalues();
+ MatrixXd vecEigen = externalSeedEigen.eigenvectors();
+ vecEigen = vecEigen.transpose() * indexAndJacobian.second;
+ for(int i = 0; i < externalSeed.rows(); ++i) {
+ if(valEigen(i) > 0.) {
+ for(int j = 0; j < externalSeed.cols(); ++j) {
+ externalSeedDerivatives[j] = vecEigen(i, j);
+ }
+ GblData aData(externalPoint, ExternalSeed, 0., valEigen(i));
+ aData.addDerivatives(externalSeedIndex, externalSeedDerivatives);
+ theData.emplace_back(std::move(aData));
+ nData++;
+ }
+ }
+ }
+ measDataIndex[numAllPoints + 1] = nData;
+ // external measurements
+ unsigned int nExt = externalMeasurements.rows();
+ if(nExt > 0) {
+ std::vector<unsigned int> index(numCurvature);
+ std::vector<double> derivatives(numCurvature);
+ for(unsigned int iExt = 0; iExt < nExt; ++iExt) {
+ for(unsigned int iCol = 0; iCol < numCurvature; ++iCol) {
+ index[iCol] = numLocals + iCol + 1;
+ derivatives[iCol] = externalDerivatives(iExt, iCol);
+ }
+ GblData aData(1U, ExternalMeasurement, externalMeasurements(iExt), externalPrecisions(iExt));
+ aData.addDerivatives(index, derivatives);
+ theData.emplace_back(std::move(aData));
+ nData++;
+ }
+ }
+ measDataIndex[numAllPoints + 2] = nData;
+ }
+
+ /// Calculate predictions for all points.
+ void GblTrajectory::predict() {
+ std::vector<GblData>::iterator itData;
+ for(itData = theData.begin(); itData < theData.end(); ++itData) {
+ itData->setPrediction(theVector);
+ }
+ }
+
+ /// Down-weight all points.
+ /**
+ * \param [in] aMethod M-estimator (1: Tukey, 2:Huber, 3:Cauchy)
+ */
+ double GblTrajectory::downWeight(unsigned int aMethod) {
+ double aLoss = 0.;
+ std::vector<GblData>::iterator itData;
+ for(itData = theData.begin(); itData < theData.end(); ++itData) {
+ aLoss += (1. - itData->setDownWeighting(aMethod));
+ }
+ return aLoss;
+ }
+
+ /// Perform fit of (valid) trajectory.
+ /**
+ * Optionally iterate for outlier down-weighting.
+ * Fit may fail due to singular or not positive definite matrices (internal exceptions 1-3).
+ *
+ * \param [out] Chi2 Chi2 sum (corrected for down-weighting)
+ * \param [out] Ndf Number of degrees of freedom
+ * \param [out] lostWeight Sum of weights lost due to down-weighting
+ * \param [in] optionList Iterations for down-weighting
+ * (One character per iteration: t,h,c (or T,H,C) for Tukey, Huber or Cauchy function)
+ * \param [in] aLabel Label of point where to skip measurements (for unbiased residuals)
+ * \return Error code (non zero value indicates failure of fit)
+ */
+ unsigned int
+ GblTrajectory::fit(double& Chi2, int& Ndf, double& lostWeight, const std::string& optionList, unsigned int aLabel) {
+ const double normChi2[4] = {1.0, 0.8737, 0.9326, 0.8228};
+ const std::string methodList = "TtHhCc";
+
+ Chi2 = 0.;
+ Ndf = -1;
+ lostWeight = 0.;
+ if(not constructOK)
+ return 10;
+
+ unsigned int aMethod = 0;
+ skippedMeasLabel = aLabel;
+
+ buildLinearEquationSystem();
+ lostWeight = 0.;
+ unsigned int ierr = 0;
+ try {
+
+ theMatrix.solveAndInvertBorderedBand(theVector, theVector);
+ predict();
+
+ for(unsigned int i = 0; i < optionList.size(); ++i) // down weighting iterations
+ {
+ size_t aPosition = methodList.find(optionList[i]);
+ if(aPosition != std::string::npos) {
+ aMethod = aPosition / 2 + 1;
+ lostWeight = downWeight(aMethod);
+ buildLinearEquationSystem();
+ theMatrix.solveAndInvertBorderedBand(theVector, theVector);
+ predict();
+ }
+ }
+ Ndf = -numParameters;
+ Chi2 = 0.;
+ for(unsigned int i = 0; i < theData.size(); ++i) {
+ // skipped (internal) measurement ?
+ if(theData[i].getLabel() == skippedMeasLabel && theData[i].getType() == InternalMeasurement)
+ continue;
+ Chi2 += theData[i].getChi2();
+ Ndf++;
+ }
+ Chi2 /= normChi2[aMethod];
+ fitOK = true;
+
+ } catch(int e) {
+ std::cout << " GblTrajectory::fit exception " << e << std::endl;
+ ierr = e;
+ }
+ return ierr;
+ }
+
+ /// Write valid trajectory to Millepede-II binary file.
+ /**
+ * Trajectory state after construction (independent of fitting) is used.
+ */
+ void GblTrajectory::milleOut(MilleBinary& aMille) {
+ double aValue;
+ double aErr;
+ unsigned int aTraj;
+ unsigned int aPoint;
+ unsigned int aRow;
+ unsigned int numLocal;
+ unsigned int* labLocal;
+ double* derLocal;
+ std::vector<int> labGlobal;
+ std::vector<double> derGlobal;
+
+ if(not constructOK)
+ return;
+
+ // data: measurements, kinks and external seed
+ labGlobal.reserve(maxNumGlobals);
+ derGlobal.reserve(maxNumGlobals);
+ std::vector<GblData>::iterator itData;
+ for(itData = theData.begin(); itData != theData.end(); ++itData) {
+ itData->getAllData(aValue, aErr, numLocal, labLocal, derLocal, aTraj, aPoint, aRow);
+ if(itData->getType() == InternalMeasurement)
+ thePoints[aTraj][aPoint].getGlobalLabelsAndDerivatives(aRow, labGlobal, derGlobal);
+ else
+ labGlobal.resize(0);
+ aMille.addData(aValue, aErr, numLocal, labLocal, derLocal, labGlobal, derGlobal);
+ }
+ aMille.writeRecord();
+ }
+
+ /// Print GblTrajectory
+ /**
+ * \param [in] level print level (0: minimum, >0: more)
+ */
+ void GblTrajectory::printTrajectory(unsigned int level) const {
+ if(numInnerTrans) {
+ std::cout << "Composed GblTrajectory, " << numInnerTrans << " subtrajectories" << std::endl;
+ } else {
+ std::cout << "Simple GblTrajectory" << std::endl;
+ }
+ if(theDimension.size() < 2) {
+ std::cout << " 2D-trajectory" << std::endl;
+ }
+ std::cout << " Number of GblPoints : " << numAllPoints << std::endl;
+ std::cout << " Number of points with offsets: " << numOffsets << std::endl;
+ std::cout << " Number of fit parameters : " << numParameters << std::endl;
+ std::cout << " Number of measurements : " << numMeasurements << std::endl;
+ if(externalMeasurements.rows()) {
+ std::cout << " Number of ext. measurements : " << externalMeasurements.rows() << std::endl;
+ }
+ if(externalPoint) {
+ std::cout << " Label of point with ext. seed: " << externalPoint << std::endl;
+ }
+ if(constructOK) {
+ std::cout << " Constructed OK " << std::endl;
+ }
+ if(fitOK) {
+ std::cout << " Fitted OK " << std::endl;
+ }
+ if(level > 0) {
+ IOFormat CleanFmt(4, 0, ", ", "\n", "[", "]");
+ if(numInnerTrans) {
+ std::cout << " Inner transformations" << std::endl;
+ for(unsigned int i = 0; i < numInnerTrans; ++i) {
+ std::cout << innerTransformations[i].format(CleanFmt) << std::endl;
+ }
+ }
+ if(externalMeasurements.rows()) {
+ std::cout << " External measurements" << std::endl;
+ std::cout << " Measurements:" << std::endl;
+ std::cout << externalMeasurements.format(CleanFmt) << std::endl;
+ std::cout << " Precisions:" << std::endl;
+ std::cout << externalPrecisions.format(CleanFmt) << std::endl;
+ std::cout << " Derivatives:" << std::endl;
+ std::cout << externalDerivatives.format(CleanFmt) << std::endl;
+ }
+ if(externalPoint) {
+ std::cout << " External seed:" << std::endl;
+ std::cout << externalSeed.format(CleanFmt) << std::endl;
+ }
+ if(fitOK) {
+ std::cout << " Fit results" << std::endl;
+ std::cout << " Parameters:" << std::endl;
+ theVector.print();
+ std::cout << " Covariance matrix (bordered band part):" << std::endl;
+ theMatrix.printMatrix();
+ }
+ }
+ }
+
+ /// Print \link GblPoint GblPoints \endlink on trajectory
+ /**
+ * \param [in] level print level (0: minimum, >0: more)
+ */
+ void GblTrajectory::printPoints(unsigned int level) const {
+ std::cout << "GblPoints " << std::endl;
+ for(unsigned int iTraj = 0; iTraj < numTrajectories; ++iTraj) {
+ std::vector<GblPoint>::const_iterator itPoint;
+ for(itPoint = thePoints[iTraj].begin(); itPoint < thePoints[iTraj].end(); ++itPoint) {
+ itPoint->printPoint(level);
+ }
+ }
+ }
+
+ /// Print GblData blocks for trajectory
+ void GblTrajectory::printData() const {
+ std::cout << "GblData blocks " << std::endl;
+ std::vector<GblData>::const_iterator itData;
+ for(itData = theData.begin(); itData < theData.end(); ++itData) {
+ itData->printData();
+ }
+ }
+}
diff --git a/3rdparty/GeneralBrokenLines/src/MilleBinary.cpp b/3rdparty/GeneralBrokenLines/src/MilleBinary.cpp
new file mode 100644
index 000000000..39d6a94dc
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/src/MilleBinary.cpp
@@ -0,0 +1,129 @@
+/*
+ * MilleBinary.cpp
+ *
+ * Created on: Aug 31, 2011
+ * Author: kleinwrt
+ */
+
+/** \file
+ * MilleBinary methods.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2017 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#include "MilleBinary.h"
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /// Create binary file.
+ /**
+ * \param [in] fileName File name
+ * \param [in] doublePrec Flag for storage as double values
+ * \param [in] aSize Buffer size
+ */
+ MilleBinary::MilleBinary(const std::string& fileName, bool doublePrec, unsigned int aSize)
+ : binaryFile(fileName.c_str(), std::ios::binary | std::ios::out), intBuffer(), floatBuffer(), doubleBuffer(),
+ doublePrecision(doublePrec) {
+
+ intBuffer.reserve(aSize);
+ intBuffer.push_back(0); // first word is error counter
+ if(doublePrecision) {
+ doubleBuffer.reserve(aSize);
+ doubleBuffer.push_back(0.);
+
+ } else {
+ floatBuffer.reserve(aSize);
+ floatBuffer.push_back(0.);
+ }
+ }
+
+ MilleBinary::~MilleBinary() { binaryFile.close(); }
+
+ /// Add data block to (end of) record.
+ /**
+ * \param [in] aMeas Value
+ * \param [in] aErr Error
+ * \param [in] numLocal Number of local labels/derivatives
+ * \param [in] indLocal Array of labels of local parameters
+ * \param [in] derLocal Array of derivatives for local parameters
+ * \param [in] labGlobal List of labels of global parameters
+ * \param [in] derGlobal List of derivatives for global parameters
+ */
+ void MilleBinary::addData(double aMeas,
+ double aErr,
+ unsigned int numLocal,
+ unsigned int* indLocal,
+ double* derLocal,
+ const std::vector<int>& labGlobal,
+ const std::vector<double>& derGlobal) {
+
+ if(doublePrecision) {
+ // double values
+ intBuffer.push_back(0);
+ doubleBuffer.push_back(aMeas);
+ for(unsigned int i = 0; i < numLocal; ++i) {
+ intBuffer.push_back(indLocal[i]);
+ doubleBuffer.push_back(derLocal[i]);
+ }
+ intBuffer.push_back(0);
+ doubleBuffer.push_back(aErr);
+ for(unsigned int i = 0; i < labGlobal.size(); ++i) {
+ if(derGlobal[i]) {
+ intBuffer.push_back(labGlobal[i]);
+ doubleBuffer.push_back(derGlobal[i]);
+ }
+ }
+ } else {
+ // float values
+ intBuffer.push_back(0);
+ floatBuffer.push_back(aMeas);
+ for(unsigned int i = 0; i < numLocal; ++i) {
+ intBuffer.push_back(indLocal[i]);
+ floatBuffer.push_back(derLocal[i]);
+ }
+ intBuffer.push_back(0);
+ floatBuffer.push_back(aErr);
+ for(unsigned int i = 0; i < labGlobal.size(); ++i) {
+ if(derGlobal[i]) {
+ intBuffer.push_back(labGlobal[i]);
+ floatBuffer.push_back(derGlobal[i]);
+ }
+ }
+ }
+ }
+
+ /// Write record to file.
+ void MilleBinary::writeRecord() {
+
+ const int recordLength = (doublePrecision) ? -intBuffer.size() * 2 : intBuffer.size() * 2;
+ binaryFile.write(reinterpret_cast<const char*>(&recordLength), sizeof(recordLength));
+ if(doublePrecision)
+ binaryFile.write(reinterpret_cast<char*>(&doubleBuffer[0]), doubleBuffer.size() * sizeof(doubleBuffer[0]));
+ else
+ binaryFile.write(reinterpret_cast<char*>(&floatBuffer[0]), floatBuffer.size() * sizeof(floatBuffer[0]));
+ binaryFile.write(reinterpret_cast<char*>(&intBuffer[0]), intBuffer.size() * sizeof(intBuffer[0]));
+ // start with new record
+ intBuffer.resize(1);
+ if(doublePrecision)
+ doubleBuffer.resize(1);
+ else
+ floatBuffer.resize(1);
+ }
+}
diff --git a/3rdparty/GeneralBrokenLines/src/VMatrix.cpp b/3rdparty/GeneralBrokenLines/src/VMatrix.cpp
new file mode 100644
index 000000000..7b2ec569d
--- /dev/null
+++ b/3rdparty/GeneralBrokenLines/src/VMatrix.cpp
@@ -0,0 +1,427 @@
+/*
+ * VMatrix.cpp
+ *
+ * Created on: Feb 15, 2012
+ * Author: kleinwrt
+ */
+
+/** \file
+ * VMatrix methods.
+ *
+ * \author Claus Kleinwort, DESY, 2011 (Claus.Kleinwort@desy.de)
+ *
+ * \copyright
+ * Copyright (c) 2011 - 2017 Deutsches Elektronen-Synchroton,
+ * Member of the Helmholtz Association, (DESY), HAMBURG, GERMANY \n\n
+ * This library is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Library General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version. \n\n
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Library General Public License for more details. \n\n
+ * You should have received a copy of the GNU Library General Public
+ * License along with this program (see the file COPYING.LIB for more
+ * details); if not, write to the Free Software Foundation, Inc.,
+ * 675 Mass Ave, Cambridge, MA 02139, USA.
+ */
+
+#include "VMatrix.h"
+
+//! Namespace for the general broken lines package
+namespace gbl {
+
+ /*********** simple Matrix based on std::vector<double> **********/
+
+ VMatrix::VMatrix(const unsigned int nRows, const unsigned int nCols)
+ : numRows(nRows), numCols(nCols), theVec(nRows * nCols) {}
+
+ VMatrix::VMatrix(const VMatrix& aMatrix) : numRows(aMatrix.numRows), numCols(aMatrix.numCols), theVec(aMatrix.theVec) {}
+
+ VMatrix::~VMatrix() {}
+
+ /// Resize Matrix.
+ /**
+ * \param [in] nRows Number of rows.
+ * \param [in] nCols Number of columns.
+ */
+ void VMatrix::resize(const unsigned int nRows, const unsigned int nCols) {
+ numRows = nRows;
+ numCols = nCols;
+ theVec.resize(nRows * nCols);
+ }
+
+ /// Get transposed matrix.
+ /**
+ * \return Transposed matrix.
+ */
+ VMatrix VMatrix::transpose() const {
+ VMatrix aResult(numCols, numRows);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ for(unsigned int j = 0; j < numCols; ++j) {
+ aResult(j, i) = theVec[numCols * i + j];
+ }
+ }
+ return aResult;
+ }
+
+ /// Get number of rows.
+ /**
+ * \return Number of rows.
+ */
+ unsigned int VMatrix::getNumRows() const { return numRows; }
+
+ /// Get number of columns.
+ /**
+ * \return Number of columns.
+ */
+ unsigned int VMatrix::getNumCols() const { return numCols; }
+
+ /// Print matrix.
+ void VMatrix::print() const {
+ std::cout << " VMatrix: " << numRows << "*" << numCols << std::endl;
+ for(unsigned int i = 0; i < numRows; ++i) {
+ for(unsigned int j = 0; j < numCols; ++j) {
+ if(j % 5 == 0) {
+ std::cout << std::endl
+ << std::setw(4) << i << "," << std::setw(4) << j << "-" << std::setw(4)
+ << std::min(j + 4, numCols) << ":";
+ }
+ std::cout << std::setw(13) << theVec[numCols * i + j];
+ }
+ }
+ std::cout << std::endl << std::endl;
+ }
+
+ /// Multiplication Matrix*Vector.
+ VVector VMatrix::operator*(const VVector& aVector) const {
+ VVector aResult(numRows);
+ for(unsigned int i = 0; i < this->numRows; ++i) {
+ double sum = 0.0;
+ for(unsigned int j = 0; j < this->numCols; ++j) {
+ sum += theVec[numCols * i + j] * aVector(j);
+ }
+ aResult(i) = sum;
+ }
+ return aResult;
+ }
+
+ /// Multiplication Matrix*Matrix.
+ VMatrix VMatrix::operator*(const VMatrix& aMatrix) const {
+
+ VMatrix aResult(numRows, aMatrix.numCols);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ for(unsigned int j = 0; j < aMatrix.numCols; ++j) {
+ double sum = 0.0;
+ for(unsigned int k = 0; k < numCols; ++k) {
+ sum += theVec[numCols * i + k] * aMatrix(k, j);
+ }
+ aResult(i, j) = sum;
+ }
+ }
+ return aResult;
+ }
+
+ /// Addition Matrix+Matrix.
+ VMatrix VMatrix::operator+(const VMatrix& aMatrix) const {
+ VMatrix aResult(numRows, numCols);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ for(unsigned int j = 0; j < numCols; ++j) {
+ aResult(i, j) = theVec[numCols * i + j] + aMatrix(i, j);
+ }
+ }
+ return aResult;
+ }
+
+ /// Assignment Matrix=Matrix.
+ VMatrix& VMatrix::operator=(const VMatrix& aMatrix) {
+ if(this != &aMatrix) { // Gracefully handle self assignment
+ numRows = aMatrix.getNumRows();
+ numCols = aMatrix.getNumCols();
+ theVec.resize(numRows * numCols);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ for(unsigned int j = 0; j < numCols; ++j) {
+ theVec[numCols * i + j] = aMatrix(i, j);
+ }
+ }
+ }
+ return *this;
+ }
+
+ /*********** simple symmetric Matrix based on std::vector<double> **********/
+
+ VSymMatrix::VSymMatrix(const unsigned int nRows) : numRows(nRows), theVec((nRows * nRows + nRows) / 2) {}
+
+ VSymMatrix::~VSymMatrix() {}
+
+ /// Resize symmetric matrix.
+ /**
+ * \param [in] nRows Number of rows.
+ */
+ void VSymMatrix::resize(const unsigned int nRows) {
+ numRows = nRows;
+ theVec.resize((nRows * nRows + nRows) / 2);
+ }
+
+ /// Get number of rows (= number of colums).
+ /**
+ * \return Number of rows.
+ */
+ unsigned int VSymMatrix::getNumRows() const { return numRows; }
+
+ /// Print matrix.
+ void VSymMatrix::print() const {
+ std::cout << " VSymMatrix: " << numRows << "*" << numRows << std::endl;
+ for(unsigned int i = 0; i < numRows; ++i) {
+ for(unsigned int j = 0; j <= i; ++j) {
+ if(j % 5 == 0) {
+ std::cout << std::endl
+ << std::setw(4) << i << "," << std::setw(4) << j << "-" << std::setw(4) << std::min(j + 4, i)
+ << ":";
+ }
+ std::cout << std::setw(13) << theVec[(i * i + i) / 2 + j];
+ }
+ }
+ std::cout << std::endl << std::endl;
+ }
+
+ /// Subtraction SymMatrix-(sym)Matrix.
+ VSymMatrix VSymMatrix::operator-(const VMatrix& aMatrix) const {
+ VSymMatrix aResult(numRows);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ for(unsigned int j = 0; j <= i; ++j) {
+ aResult(i, j) = theVec[(i * i + i) / 2 + j] - aMatrix(i, j);
+ }
+ }
+ return aResult;
+ }
+
+ /// Multiplication SymMatrix*Vector.
+ VVector VSymMatrix::operator*(const VVector& aVector) const {
+ VVector aResult(numRows);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ aResult(i) = theVec[(i * i + i) / 2 + i] * aVector(i);
+ for(unsigned int j = 0; j < i; ++j) {
+ aResult(j) += theVec[(i * i + i) / 2 + j] * aVector(i);
+ aResult(i) += theVec[(i * i + i) / 2 + j] * aVector(j);
+ }
+ }
+ return aResult;
+ }
+
+ /// Multiplication SymMatrix*Matrix.
+ VMatrix VSymMatrix::operator*(const VMatrix& aMatrix) const {
+ unsigned int nCol = aMatrix.getNumCols();
+ VMatrix aResult(numRows, nCol);
+ for(unsigned int l = 0; l < nCol; ++l) {
+ for(unsigned int i = 0; i < numRows; ++i) {
+ aResult(i, l) = theVec[(i * i + i) / 2 + i] * aMatrix(i, l);
+ for(unsigned int j = 0; j < i; ++j) {
+ aResult(j, l) += theVec[(i * i + i) / 2 + j] * aMatrix(i, l);
+ aResult(i, l) += theVec[(i * i + i) / 2 + j] * aMatrix(j, l);
+ }
+ }
+ }
+ return aResult;
+ }
+
+ /*********** simple Vector based on std::vector<double> **********/
+
+ VVector::VVector(const unsigned int nRows) : numRows(nRows), theVec(nRows) {}
+
+ VVector::VVector(const VVector& aVector) : numRows(aVector.numRows), theVec(aVector.theVec) {}
+
+ VVector::~VVector() {}
+
+ /// Resize vector.
+ /**
+ * \param [in] nRows Number of rows.
+ */
+ void VVector::resize(const unsigned int nRows) {
+ numRows = nRows;
+ theVec.resize(nRows);
+ }
+
+ /// Get part of vector.
+ /**
+ * \param [in] len Length of part.
+ * \param [in] start Offset of part.
+ * \return Part of vector.
+ */
+ VVector VVector::getVec(unsigned int len, unsigned int start) const {
+ VVector aResult(len);
+ std::memcpy(&aResult.theVec[0], &theVec[start], sizeof(double) * len);
+ return aResult;
+ }
+
+ /// Put part of vector.
+ /**
+ * \param [in] aVector Vector with part.
+ * \param [in] start Offset of part.
+ */
+ void VVector::putVec(const VVector& aVector, unsigned int start) {
+ std::memcpy(&theVec[start], &aVector.theVec[0], sizeof(double) * aVector.numRows);
+ }
+
+ /// Get number of rows.
+ /**
+ * \return Number of rows.
+ */
+ unsigned int VVector::getNumRows() const { return numRows; }
+
+ /// Print vector.
+ void VVector::print() const {
+ std::cout << " VVector: " << numRows << std::endl;
+ for(unsigned int i = 0; i < numRows; ++i) {
+
+ if(i % 5 == 0) {
+ std::cout << std::endl << std::setw(4) << i << "-" << std::setw(4) << std::min(i + 4, numRows) << ":";
+ }
+ std::cout << std::setw(13) << theVec[i];
+ }
+ std::cout << std::endl << std::endl;
+ }
+
+ /// Subtraction Vector-Vector.
+ VVector VVector::operator-(const VVector& aVector) const {
+ VVector aResult(numRows);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ aResult(i) = theVec[i] - aVector(i);
+ }
+ return aResult;
+ }
+
+ /// Assignment Vector=Vector.
+ VVector& VVector::operator=(const VVector& aVector) {
+ if(this != &aVector) { // Gracefully handle self assignment
+ numRows = aVector.getNumRows();
+ theVec.resize(numRows);
+ for(unsigned int i = 0; i < numRows; ++i) {
+ theVec[i] = aVector(i);
+ }
+ }
+ return *this;
+ }
+
+ /*============================================================================
+ from mpnum.F (MillePede-II by V. Blobel, Univ. Hamburg)
+ ============================================================================*/
+ /// Matrix inversion.
+ /**
+ * Invert symmetric N-by-N matrix V in symmetric storage mode
+ * V(1) = V11, V(2) = V12, V(3) = V22, V(4) = V13, . . .
+ * replaced by inverse matrix
+ *
+ * Method of solution is by elimination selecting the pivot on the
+ * diagonal each stage. The rank of the matrix is returned in NRANK.
+ * For NRANK ne N, all remaining rows and cols of the resulting
+ * matrix V are set to zero.
+ * \exception 1 : matrix is singular.
+ * \return Rank of matrix.
+ */
+ unsigned int VSymMatrix::invert() {
+
+ const double eps = 1.0E-10;
+ unsigned int aSize = numRows;
+ std::vector<int> next(aSize);
+ std::vector<double> diag(aSize);
+ int nSize = aSize;
+
+ int first = 1;
+ for(int i = 1; i <= nSize; ++i) {
+ next[i - 1] = i + 1; // set "next" pointer
+ diag[i - 1] = fabs(theVec[(i * i + i) / 2 - 1]); // save abs of diagonal elements
+ }
+ next[aSize - 1] = -1; // end flag
+
+ unsigned int nrank = 0;
+ for(int i = 1; i <= nSize; ++i) { // start of loop
+ int kp = 0;
+ double vkk = 0.0;
+
+ int jp = first;
+ int previous = 0;
+ int last = previous;
+ // look for pivot
+ while(jp > 0) {
+ int jj = (jp * jp + jp) / 2 - 1;
+ if(fabs(theVec[jj]) > std::max(fabs(vkk), eps * diag[jp - 1])) {
+ vkk = theVec[jj];
+ kp = jp;
+ last = previous;
+ }
+ previous = jp;
+ jp = next[jp - 1];
+ }
+ // pivot found
+ if(kp > 0) {
+ int kk = (kp * kp + kp) / 2 - 1;
+ if(last <= 0) {
+ first = next[kp - 1];
+ } else {
+ next[last - 1] = next[kp - 1];
+ }
+ next[kp - 1] = 0; // index is used, reset
+ nrank++; // increase rank and ...
+
+ vkk = 1.0 / vkk;
+ theVec[kk] = -vkk;
+ int jk = kk - kp;
+ int jl = -1;
+ for(int j = 1; j <= nSize; ++j) { // elimination
+ if(j == kp) {
+ jk = kk;
+ jl += j;
+ } else {
+ if(j < kp) {
+ ++jk;
+ } else {
+ jk += j - 1;
+ }
+
+ double vjk = theVec[jk];
+ theVec[jk] = vkk * vjk;
+ int lk = kk - kp;
+ if(j >= kp) {
+ for(int l = 1; l <= kp - 1; ++l) {
+ ++jl;
+ ++lk;
+ theVec[jl] -= theVec[lk] * vjk;
+ }
+ ++jl;
+ lk = kk;
+ for(int l = kp + 1; l <= j; ++l) {
+ ++jl;
+ lk += l - 1;
+ theVec[jl] -= theVec[lk] * vjk;
+ }
+ } else {
+ for(int l = 1; l <= j; ++l) {
+ ++jl;
+ ++lk;
+ theVec[jl] -= theVec[lk] * vjk;
+ }
+ }
+ }
+ }
+ } else {
+ for(int k = 1; k <= nSize; ++k) {
+ if(next[k - 1] >= 0) {
+ int kk = (k * k - k) / 2 - 1;
+ for(int j = 1; j <= nSize; ++j) {
+ if(next[j - 1] >= 0) {
+ theVec[kk + j] = 0.0; // clear matrix row/col
+ }
+ }
+ }
+ }
+ throw 1; // singular
+ }
+ }
+ for(int ij = 0; ij < (nSize * nSize + nSize) / 2; ++ij) {
+ theVec[ij] = -theVec[ij]; // finally reverse sign of all matrix elements
+ }
+ return nrank;
+ }
+}
--
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