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LatCore compatibility

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Antonin Portelli 2015-02-23 18:11:37 +00:00
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0
ChangeLog
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370
INSTALL
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@ -1,370 +0,0 @@
Installation Instructions
*************************
Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
Inc.
Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
notice and this notice are preserved. This file is offered as-is,
without warranty of any kind.
Basic Installation
==================
Briefly, the shell commands `./configure; make; make install' should
configure, build, and install this package. The following
more-detailed instructions are generic; see the `README' file for
instructions specific to this package. Some packages provide this
`INSTALL' file but do not implement all of the features documented
below. The lack of an optional feature in a given package is not
necessarily a bug. More recommendations for GNU packages can be found
in *note Makefile Conventions: (standards)Makefile Conventions.
The `configure' shell script attempts to guess correct values for
various system-dependent variables used during compilation. It uses
those values to create a `Makefile' in each directory of the package.
It may also create one or more `.h' files containing system-dependent
definitions. Finally, it creates a shell script `config.status' that
you can run in the future to recreate the current configuration, and a
file `config.log' containing compiler output (useful mainly for
debugging `configure').
It can also use an optional file (typically called `config.cache'
and enabled with `--cache-file=config.cache' or simply `-C') that saves
the results of its tests to speed up reconfiguring. Caching is
disabled by default to prevent problems with accidental use of stale
cache files.
If you need to do unusual things to compile the package, please try
to figure out how `configure' could check whether to do them, and mail
diffs or instructions to the address given in the `README' so they can
be considered for the next release. If you are using the cache, and at
some point `config.cache' contains results you don't want to keep, you
may remove or edit it.
The file `configure.ac' (or `configure.in') is used to create
`configure' by a program called `autoconf'. You need `configure.ac' if
you want to change it or regenerate `configure' using a newer version
of `autoconf'.
The simplest way to compile this package is:
1. `cd' to the directory containing the package's source code and type
`./configure' to configure the package for your system.
Running `configure' might take a while. While running, it prints
some messages telling which features it is checking for.
2. Type `make' to compile the package.
3. Optionally, type `make check' to run any self-tests that come with
the package, generally using the just-built uninstalled binaries.
4. Type `make install' to install the programs and any data files and
documentation. When installing into a prefix owned by root, it is
recommended that the package be configured and built as a regular
user, and only the `make install' phase executed with root
privileges.
5. Optionally, type `make installcheck' to repeat any self-tests, but
this time using the binaries in their final installed location.
This target does not install anything. Running this target as a
regular user, particularly if the prior `make install' required
root privileges, verifies that the installation completed
correctly.
6. You can remove the program binaries and object files from the
source code directory by typing `make clean'. To also remove the
files that `configure' created (so you can compile the package for
a different kind of computer), type `make distclean'. There is
also a `make maintainer-clean' target, but that is intended mainly
for the package's developers. If you use it, you may have to get
all sorts of other programs in order to regenerate files that came
with the distribution.
7. Often, you can also type `make uninstall' to remove the installed
files again. In practice, not all packages have tested that
uninstallation works correctly, even though it is required by the
GNU Coding Standards.
8. Some packages, particularly those that use Automake, provide `make
distcheck', which can by used by developers to test that all other
targets like `make install' and `make uninstall' work correctly.
This target is generally not run by end users.
Compilers and Options
=====================
Some systems require unusual options for compilation or linking that
the `configure' script does not know about. Run `./configure --help'
for details on some of the pertinent environment variables.
You can give `configure' initial values for configuration parameters
by setting variables in the command line or in the environment. Here
is an example:
./configure CC=c99 CFLAGS=-g LIBS=-lposix
*Note Defining Variables::, for more details.
Compiling For Multiple Architectures
====================================
You can compile the package for more than one kind of computer at the
same time, by placing the object files for each architecture in their
own directory. To do this, you can use GNU `make'. `cd' to the
directory where you want the object files and executables to go and run
the `configure' script. `configure' automatically checks for the
source code in the directory that `configure' is in and in `..'. This
is known as a "VPATH" build.
With a non-GNU `make', it is safer to compile the package for one
architecture at a time in the source code directory. After you have
installed the package for one architecture, use `make distclean' before
reconfiguring for another architecture.
On MacOS X 10.5 and later systems, you can create libraries and
executables that work on multiple system types--known as "fat" or
"universal" binaries--by specifying multiple `-arch' options to the
compiler but only a single `-arch' option to the preprocessor. Like
this:
./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
CPP="gcc -E" CXXCPP="g++ -E"
This is not guaranteed to produce working output in all cases, you
may have to build one architecture at a time and combine the results
using the `lipo' tool if you have problems.
Installation Names
==================
By default, `make install' installs the package's commands under
`/usr/local/bin', include files under `/usr/local/include', etc. You
can specify an installation prefix other than `/usr/local' by giving
`configure' the option `--prefix=PREFIX', where PREFIX must be an
absolute file name.
You can specify separate installation prefixes for
architecture-specific files and architecture-independent files. If you
pass the option `--exec-prefix=PREFIX' to `configure', the package uses
PREFIX as the prefix for installing programs and libraries.
Documentation and other data files still use the regular prefix.
In addition, if you use an unusual directory layout you can give
options like `--bindir=DIR' to specify different values for particular
kinds of files. Run `configure --help' for a list of the directories
you can set and what kinds of files go in them. In general, the
default for these options is expressed in terms of `${prefix}', so that
specifying just `--prefix' will affect all of the other directory
specifications that were not explicitly provided.
The most portable way to affect installation locations is to pass the
correct locations to `configure'; however, many packages provide one or
both of the following shortcuts of passing variable assignments to the
`make install' command line to change installation locations without
having to reconfigure or recompile.
The first method involves providing an override variable for each
affected directory. For example, `make install
prefix=/alternate/directory' will choose an alternate location for all
directory configuration variables that were expressed in terms of
`${prefix}'. Any directories that were specified during `configure',
but not in terms of `${prefix}', must each be overridden at install
time for the entire installation to be relocated. The approach of
makefile variable overrides for each directory variable is required by
the GNU Coding Standards, and ideally causes no recompilation.
However, some platforms have known limitations with the semantics of
shared libraries that end up requiring recompilation when using this
method, particularly noticeable in packages that use GNU Libtool.
The second method involves providing the `DESTDIR' variable. For
example, `make install DESTDIR=/alternate/directory' will prepend
`/alternate/directory' before all installation names. The approach of
`DESTDIR' overrides is not required by the GNU Coding Standards, and
does not work on platforms that have drive letters. On the other hand,
it does better at avoiding recompilation issues, and works well even
when some directory options were not specified in terms of `${prefix}'
at `configure' time.
Optional Features
=================
If the package supports it, you can cause programs to be installed
with an extra prefix or suffix on their names by giving `configure' the
option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
Some packages pay attention to `--enable-FEATURE' options to
`configure', where FEATURE indicates an optional part of the package.
They may also pay attention to `--with-PACKAGE' options, where PACKAGE
is something like `gnu-as' or `x' (for the X Window System). The
`README' should mention any `--enable-' and `--with-' options that the
package recognizes.
For packages that use the X Window System, `configure' can usually
find the X include and library files automatically, but if it doesn't,
you can use the `configure' options `--x-includes=DIR' and
`--x-libraries=DIR' to specify their locations.
Some packages offer the ability to configure how verbose the
execution of `make' will be. For these packages, running `./configure
--enable-silent-rules' sets the default to minimal output, which can be
overridden with `make V=1'; while running `./configure
--disable-silent-rules' sets the default to verbose, which can be
overridden with `make V=0'.
Particular systems
==================
On HP-UX, the default C compiler is not ANSI C compatible. If GNU
CC is not installed, it is recommended to use the following options in
order to use an ANSI C compiler:
./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
and if that doesn't work, install pre-built binaries of GCC for HP-UX.
HP-UX `make' updates targets which have the same time stamps as
their prerequisites, which makes it generally unusable when shipped
generated files such as `configure' are involved. Use GNU `make'
instead.
On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
parse its `<wchar.h>' header file. The option `-nodtk' can be used as
a workaround. If GNU CC is not installed, it is therefore recommended
to try
./configure CC="cc"
and if that doesn't work, try
./configure CC="cc -nodtk"
On Solaris, don't put `/usr/ucb' early in your `PATH'. This
directory contains several dysfunctional programs; working variants of
these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
in your `PATH', put it _after_ `/usr/bin'.
On Haiku, software installed for all users goes in `/boot/common',
not `/usr/local'. It is recommended to use the following options:
./configure --prefix=/boot/common
Specifying the System Type
==========================
There may be some features `configure' cannot figure out
automatically, but needs to determine by the type of machine the package
will run on. Usually, assuming the package is built to be run on the
_same_ architectures, `configure' can figure that out, but if it prints
a message saying it cannot guess the machine type, give it the
`--build=TYPE' option. TYPE can either be a short name for the system
type, such as `sun4', or a canonical name which has the form:
CPU-COMPANY-SYSTEM
where SYSTEM can have one of these forms:
OS
KERNEL-OS
See the file `config.sub' for the possible values of each field. If
`config.sub' isn't included in this package, then this package doesn't
need to know the machine type.
If you are _building_ compiler tools for cross-compiling, you should
use the option `--target=TYPE' to select the type of system they will
produce code for.
If you want to _use_ a cross compiler, that generates code for a
platform different from the build platform, you should specify the
"host" platform (i.e., that on which the generated programs will
eventually be run) with `--host=TYPE'.
Sharing Defaults
================
If you want to set default values for `configure' scripts to share,
you can create a site shell script called `config.site' that gives
default values for variables like `CC', `cache_file', and `prefix'.
`configure' looks for `PREFIX/share/config.site' if it exists, then
`PREFIX/etc/config.site' if it exists. Or, you can set the
`CONFIG_SITE' environment variable to the location of the site script.
A warning: not all `configure' scripts look for a site script.
Defining Variables
==================
Variables not defined in a site shell script can be set in the
environment passed to `configure'. However, some packages may run
configure again during the build, and the customized values of these
variables may be lost. In order to avoid this problem, you should set
them in the `configure' command line, using `VAR=value'. For example:
./configure CC=/usr/local2/bin/gcc
causes the specified `gcc' to be used as the C compiler (unless it is
overridden in the site shell script).
Unfortunately, this technique does not work for `CONFIG_SHELL' due to
an Autoconf limitation. Until the limitation is lifted, you can use
this workaround:
CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
`configure' Invocation
======================
`configure' recognizes the following options to control how it
operates.
`--help'
`-h'
Print a summary of all of the options to `configure', and exit.
`--help=short'
`--help=recursive'
Print a summary of the options unique to this package's
`configure', and exit. The `short' variant lists options used
only in the top level, while the `recursive' variant lists options
also present in any nested packages.
`--version'
`-V'
Print the version of Autoconf used to generate the `configure'
script, and exit.
`--cache-file=FILE'
Enable the cache: use and save the results of the tests in FILE,
traditionally `config.cache'. FILE defaults to `/dev/null' to
disable caching.
`--config-cache'
`-C'
Alias for `--cache-file=config.cache'.
`--quiet'
`--silent'
`-q'
Do not print messages saying which checks are being made. To
suppress all normal output, redirect it to `/dev/null' (any error
messages will still be shown).
`--srcdir=DIR'
Look for the package's source code in directory DIR. Usually
`configure' can determine that directory automatically.
`--prefix=DIR'
Use DIR as the installation prefix. *note Installation Names::
for more details, including other options available for fine-tuning
the installation locations.
`--no-create'
`-n'
Run the configure checks, but stop before creating any output
files.
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.

0
NEWS
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0
README
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2
bootstrap.sh
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@ -1,7 +1,5 @@
#!/usr/bin/env bash
echo "extracting Eigen headers..."
./update_eigen.sh eigen-eigen-*.tar.bz2
rm -rf .buildutils
mkdir -p .buildutils/m4
autoreconf -fvi

11
configure.ac
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@ -8,7 +8,7 @@ AC_CONFIG_SRCDIR([lib/Global.cpp])
AC_CONFIG_SRCDIR([utils/sample_read.cpp])
AC_CONFIG_SRCDIR([examples/exMathInterpreter.cpp])
AC_CONFIG_MACRO_DIR([.buildutils/m4])
AM_INIT_AUTOMAKE([-Wall -Werror subdir-objects])
AM_INIT_AUTOMAKE([-Wall -Werror foreign])
AM_SILENT_RULES([yes])
AC_CONFIG_HEADERS([config.h])
@ -51,6 +51,13 @@ AC_ARG_WITH([Minuit2],
[AM_LDFLAGS="$AM_LDFLAGS -L$with_Minuit2/lib"],
[]
)
AC_ARG_WITH([LatCore],
[AS_HELP_STRING([--with-LatCore=prefix],
[use this option for a non-standard install prefix of the LatCore library])],
[AM_CXXFLAGS="$AM_CXXFLAGS -I$with_LatCore/include"]
[AM_LDFLAGS="$AM_LDFLAGS -L$with_LatCore/lib"],
[]
)
CFLAGS="$AM_CFLAGS $CFLAGS"
CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
@ -79,6 +86,8 @@ AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"],
# Checks for libraries.
AC_CHECK_LIB([m],[cos],[],[AC_MSG_ERROR([libm library not found])])
AC_CHECK_LIB([gsl],[gsl_blas_dgemm],[LIBS="$LIBS -lgsl -lgslcblas"],[AC_MSG_ERROR([GSL library not found])])
AC_CHECK_LIB([LatCore],[_ZN7LatCore12testFunctionEv],[],
[AC_MSG_ERROR([LatCore library not found])])
SAVED_LDFLAGS=$LDFLAGS
LDFLAGS="$LDFLAGS -lMinuit2"
AC_MSG_CHECKING([for ROOT::Minuit2::BasicMinimumError in -lMinuit2]);

BIN
eigen-eigen-ffa86ffb5570.tar.bz2
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2
lib/Chi2Function.cpp
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@ -146,7 +146,7 @@ void Chi2Function::resizeBuffer(void) const
// compute variance matrix inverse /////////////////////////////////////////////
void Chi2Function::setVarianceBlock(const Index l1, const Index l2,
ConstBlock<DMatBase> m) const
ConstBlock<MatBase<double>> m) const
{
const Index nPoint = data_.getNFitPoint();

2
lib/Chi2Function.hpp
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@ -67,7 +67,7 @@ private:
// compute variance matrix inverse
void setVarianceBlock(const Index l1, const Index l2,
ConstBlock<DMatBase> m) const;
ConstBlock<MatBase<double>> m) const;
void initBuffer(void) const;
private:
const XYStatData &data_;

19
lib/Global.cpp
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@ -31,22 +31,3 @@ const string Env::msgPrefix = "[" + strFrom(PACKAGE_NAME) + " v"
void Env::function(void)
{}
ostream & Latan::operator<<(ostream &out, const ProgressBar &&bar)
{
const Index nTick = bar.nCol_*bar.current_/bar.total_;
out << "[";
for (Index i = 0; i < nTick; ++i)
{
out << "=";
}
for (Index i = nTick; i < bar.nCol_; ++i)
{
out << " ";
}
out << "] " << bar.current_ << "/" << bar.total_;
out.flush();
return out;
}

238
lib/Global.hpp
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@ -20,10 +20,7 @@
#ifndef Latan_Global_hpp_
#define Latan_Global_hpp_
// supress warning for the osbolete use of 'register' keyword in Eigen
#pragma GCC diagnostic ignored "-Wdeprecated-register"
#include <LatAnalyze/Eigen/Dense>
#include <LatCore/LatCore.hpp>
#include <complex>
#include <fstream>
#include <iostream>
@ -34,117 +31,18 @@
#include <vector>
#include <cstdlib>
#define BEGIN_LATAN_NAMESPACE namespace Latan {
#define BEGIN_LATAN_NAMESPACE \
namespace Latan {\
using namespace LatCore;
#define END_LATAN_NAMESPACE }
// macro utilities
#define unique_arg(...) __VA_ARGS__
#define DEBUG_VAR(x) std::cout << #x << "= " << x << std::endl
#define DEBUG_MAT(m) std::cout << #m << "=\n" << m << std::endl
// attribute to switch off unused warnings with gcc
#ifndef __GNUC__
#define __unused
#endif
// max length for paths
#define MAX_PATH_LENGTH 512u
// copy/assignement from Eigen expression
#define EIGEN_EXPR_CTOR(ctorName, Class, Base, ExprType) \
template <typename Derived>\
ctorName(const ExprType<Derived> &m): Base(m) {}\
template<typename Derived>\
Class & operator=(const ExprType<Derived> &m)\
{\
this->Base::operator=(m);\
return *this;\
}
BEGIN_LATAN_NAMESPACE
// Eigen type aliases //////////////////////////////////////////////////////////
const int dynamic = -1;
// array types
template <typename Derived>
using ArrayExpr = Eigen::ArrayBase<Derived>;
template <typename T, int nRow = dynamic, int nCol = dynamic>
using Array = Eigen::Array<T, nRow, nCol>;
// matrix types
template <typename Derived>
using MatExpr = Eigen::MatrixBase<Derived>;
template <typename T, int nRow = dynamic, int nCol = dynamic>
using MatBase = Eigen::Matrix<T, nRow, nCol>;
typedef MatBase<double> DMatBase;
// vector types
template <typename T>
using Vec = MatBase<T, dynamic, 1>;
typedef Vec<int> IVec;
typedef Vec<long int> LVec;
typedef Vec<double> DVec;
typedef Vec<std::complex<double>> CVec;
#define FOR_VEC(vec, i) for (Latan::Index i = 0; i < (vec).size(); ++i)
#define FOR_ARRAY(ar, i) FOR_VEC(ar, i)
// block types
template <typename Derived>
using Block = Eigen::Block<Derived>;
template <typename Derived>
using ConstBlock = const Eigen::Block<const Derived>;
template <typename Derived>
using Row = typename Derived::RowXpr;
template <typename Derived>
using ConstRow = typename Derived::ConstRowXpr;
template <typename Derived>
using Col = typename Derived::ColXpr;
template <typename Derived>
using ConstCol = typename Derived::ConstColXpr;
// map type
template <typename Derived>
using Map = Eigen::Map<Derived>;
template <typename Derived>
using ConstMap = Eigen::Map<const Derived>;
// Index type //////////////////////////////////////////////////////////////////
typedef MatBase<double>::Index Index;
// Placeholder type ////////////////////////////////////////////////////////////
struct PlaceHolder {};
extern PlaceHolder _;
// Type utilities //////////////////////////////////////////////////////////////
// pointer type test
template <typename Derived, typename Base>
inline bool isDerivedFrom(const Base *pt)
{
return (dynamic_cast<const Derived *>(pt) != nullptr);
}
// static logical or
template <bool... b>
struct static_or;
template <bool... tail>
struct static_or<true, tail...> : static_or<tail...> {};
template <bool... tail>
struct static_or<false, tail...> : std::false_type {};
template <>
struct static_or<> : std::true_type {};
// Environment /////////////////////////////////////////////////////////////////
namespace Env
{
@ -156,134 +54,6 @@ namespace Env
void function(void);
}
// String conversions //////////////////////////////////////////////////////////
template <typename T>
inline T strTo(const std::string &str)
{
T buf;
std::istringstream stream(str);
stream >> buf;
return buf;
}
// optimized specializations
template <>
inline float strTo<float>(const std::string &str)
{
return strtof(str.c_str(), (char **)NULL);
}
template <>
inline double strTo<double>(const std::string &str)
{
return strtod(str.c_str(), (char **)NULL);
}
template <>
inline int strTo<int>(const std::string &str)
{
return (int)(strtol(str.c_str(), (char **)NULL, 10));
}
template <>
inline long strTo<long>(const std::string &str)
{
return strtol(str.c_str(), (char **)NULL, 10);
}
template <>
inline std::string strTo<std::string>(const std::string &str)
{
return str;
}
template <typename T>
inline std::string strFrom(const T x)
{
std::ostringstream stream;
stream << x;
return stream.str();
}
// specialization for vectors
template<>
inline DVec strTo<DVec>(const std::string &str)
{
DVec res;
std::vector<double> vbuf;
double buf;
std::istringstream stream(str);
while (!stream.eof())
{
stream >> buf;
vbuf.push_back(buf);
}
res = Map<DVec>(vbuf.data(), static_cast<Index>(vbuf.size()));
return res;
}
template<>
inline IVec strTo<IVec>(const std::string &str)
{
IVec res;
std::vector<int> vbuf;
int buf;
std::istringstream stream(str);
while (!stream.eof())
{
stream >> buf;
vbuf.push_back(buf);
}
res = Map<IVec>(vbuf.data(), static_cast<Index>(vbuf.size()));
return res;
}
// Manifest file reader ////////////////////////////////////////////////////////
inline std::vector<std::string> readManifest(const std::string manFileName)
{
std::vector<std::string> list;
std::ifstream manFile;
char buf[MAX_PATH_LENGTH];
manFile.open(manFileName);
while (!manFile.eof())
{
manFile.getline(buf, MAX_PATH_LENGTH);
if (!std::string(buf).empty())
{
list.push_back(buf);
}
}
manFile.close();
return list;
}
// Progress bar class //////////////////////////////////////////////////////////
class ProgressBar
{
public:
// constructor
template <typename A, typename B>
ProgressBar(const A current, const B total, const Index nCol = 60);
// IO
friend std::ostream & operator<<(std::ostream &out,
const ProgressBar &&bar);
private:
Index current_, total_, nCol_;
};
template <typename A, typename B>
ProgressBar::ProgressBar(const A current, const B total, const Index nCol)
: current_(static_cast<Index>(current))
, total_(static_cast<Index>(total))
, nCol_(nCol)
{}
END_LATAN_NAMESPACE
#include <LatAnalyze/Exceptions.hpp>

29
lib/Makefile.am
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@ -1,29 +1,19 @@
if CC_GNU
COM_CFLAGS = -Wall -W -pedantic
else
if CC_INTEL
COM_CFLAGS = -Wall
endif
endif
COM_CXXFLAGS = -Wall -Wconversion
if CXX_GNU
COM_CXXFLAGS = -Wall -W -pedantic
COM_CXXFLAGS += -W -pedantic
else
if CXX_INTEL
COM_CXXFLAGS = -Wall
COM_CXXFLAGS +=
endif
endif
AM_LFLAGS = -olex.yy.c
AM_YFLAGS = -d
include eigen_files.mk
nobase_dist_pkginclude_HEADERS = $(eigen_files) XML/tinyxml2.hpp
BUILT_SOURCES = AsciiParser.hpp MathParser.hpp
lib_LTLIBRARIES = libLatAnalyze.la
lib_LTLIBRARIES = libLatAnalyze.la
libLatAnalyze_la_SOURCES = \
AsciiFile.cpp \
AsciiParser.ypp \
@ -53,10 +43,8 @@ libLatAnalyze_la_SOURCES = \
RootFinder.cpp \
Solver.cpp \
TabFunction.cpp \
XmlReader.cpp \
XYSampleData.cpp \
XYStatData.cpp \
XML/tinyxml2.cpp \
../config.h
libLatAnalyze_ladir = $(pkgincludedir)
libLatAnalyze_la_HEADERS = \
@ -88,15 +76,12 @@ libLatAnalyze_la_HEADERS = \
TabFunction.hpp \
Solver.hpp \
StatArray.hpp \
XmlReader.hpp \
XYSampleData.hpp \
XYStatData.hpp
if HAVE_MINUIT
libLatAnalyze_la_SOURCES += MinuitMinimizer.cpp
libLatAnalyze_la_HEADERS += MinuitMinimizer.hpp
libLatAnalyze_la_SOURCES += MinuitMinimizer.cpp
libLatAnalyze_la_HEADERS += MinuitMinimizer.hpp
endif
libLatAnalyze_la_CFLAGS = $(COM_CFLAGS)
libLatAnalyze_la_CXXFLAGS = $(COM_CXXFLAGS)
ACLOCAL_AMFLAGS = -I .buildutils/m4

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62
lib/XYStatData.cpp
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@ -89,36 +89,40 @@ void XYStatData::reinitChi2(const bool doReinit)
reinitChi2_ = doReinit;
}
Block<DMatBase> XYStatData::x(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused)
Block<MatBase<double>> XYStatData::x(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused)
{
return x_.block(0, 0, getNData(), getXDim());
}
ConstBlock<DMatBase> XYStatData::x(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused) const
ConstBlock<MatBase<double>> XYStatData::x(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused)
const
{
return x_.block(0, 0, getNData(), getXDim());
}
Block<DMatBase> XYStatData::x(const Index i, const PlaceHolder ph2 __unused)
Block<MatBase<double>> XYStatData::x(const Index i,
const PlaceHolder ph2 __unused)
{
return x_.block(0, i, getNData(), 1);
}
ConstBlock<DMatBase> XYStatData::x(const Index i,
const PlaceHolder ph2 __unused) const
ConstBlock<MatBase<double>> XYStatData::x(const Index i,
const PlaceHolder ph2 __unused)
const
{
return x_.block(0, i, getNData(), 1);
}
Block<DMatBase> XYStatData::x(const PlaceHolder ph1 __unused, const Index k)
Block<MatBase<double>> XYStatData::x(const PlaceHolder ph1 __unused,
const Index k)
{
return x_.block(k, 0, 1, getXDim());
}
ConstBlock<DMatBase> XYStatData::x(const PlaceHolder ph1 __unused,
const Index k) const
ConstBlock<MatBase<double>> XYStatData::x(const PlaceHolder ph1 __unused,
const Index k) const
{
return x_.block(k, 0, 1, getXDim());
}
@ -133,36 +137,39 @@ const double & XYStatData::x(const Index i, const Index k) const
return x_(k, i);
}
Block<DMatBase> XYStatData::y(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused)
Block<MatBase<double>> XYStatData::y(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused)
{
return y_.block(0, 0, getNData(), getYDim());
}
ConstBlock<DMatBase> XYStatData::y(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused) const
ConstBlock<MatBase<double>> XYStatData::y(const PlaceHolder ph1 __unused,
const PlaceHolder ph2 __unused)
const
{
return y_.block(0, 0, getNData(), getYDim());
}
Block<DMatBase> XYStatData::y(const Index j, const PlaceHolder ph2 __unused)
Block<MatBase<double>> XYStatData::y(const Index j,
const PlaceHolder ph2 __unused)
{
return y_.block(0, j, getNData(), 1);
}
ConstBlock<DMatBase> XYStatData::y(const Index j,
const PlaceHolder ph2 __unused) const
ConstBlock<MatBase<double>> XYStatData::y(const Index j,
const PlaceHolder ph2 __unused)
const
{
return y_.block(0, j, getNData(), 1);
}
Block<DMatBase> XYStatData::y(const PlaceHolder ph1 __unused, const Index k)
Block<MatBase<double>> XYStatData::y(const PlaceHolder ph1 __unused, const Index k)
{
return y_.block(k, 0, 1, getYDim());
}
ConstBlock<DMatBase> XYStatData::y(const PlaceHolder ph1 __unused,
const Index k) const
ConstBlock<MatBase<double>> XYStatData::y(const PlaceHolder ph1 __unused,
const Index k) const
{
return y_.block(k, 0, 1, getYDim());
}
@ -179,32 +186,35 @@ const double & XYStatData::y(const Index j, const Index k) const
#define FULL_BLOCK(m) (m).block(0, 0, (m).rows(), (m).cols())
Block<DMatBase> XYStatData::xxVar(const Index i1, const Index i2)
Block<MatBase<double>> XYStatData::xxVar(const Index i1, const Index i2)
{
return FULL_BLOCK(var_[xx](i1, i2));
}
ConstBlock<DMatBase> XYStatData::xxVar(const Index i1, const Index i2) const
ConstBlock<MatBase<double>> XYStatData::xxVar(const Index i1,
const Index i2) const
{
return FULL_BLOCK(var_[xx](i1, i2));
}
Block<DMatBase> XYStatData::yyVar(const Index j1, const Index j2)
Block<MatBase<double>> XYStatData::yyVar(const Index j1, const Index j2)
{
return FULL_BLOCK(var_[yy](j1, j2));
}
ConstBlock<DMatBase> XYStatData::yyVar(const Index j1, const Index j2) const
ConstBlock<MatBase<double>> XYStatData::yyVar(const Index j1,
const Index j2) const
{
return FULL_BLOCK(var_[yy](j1, j2));
}
Block<DMatBase> XYStatData::yxVar(const Index j, const Index i)
Block<MatBase<double>> XYStatData::yxVar(const Index j, const Index i)
{
return FULL_BLOCK(var_[yx](j, i));
}
ConstBlock<DMatBase> XYStatData::yxVar(const Index j, const Index i) const
ConstBlock<MatBase<double>> XYStatData::yxVar(const Index j,
const Index i) const
{
return FULL_BLOCK(var_[yx](j, i));
}

56
lib/XYStatData.hpp
View File

@ -76,32 +76,36 @@ public:
void resize(const Index nData, const Index xDim,
const Index yDim);
void reinitChi2(const bool doReinit = true);
Block<DMatBase> x(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _);
ConstBlock<DMatBase> x(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _) const;
Block<DMatBase> x(const Index i, const PlaceHolder ph2 = _);
ConstBlock<DMatBase> x(const Index i, const PlaceHolder ph2 = _) const;
Block<DMatBase> x(const PlaceHolder ph1, const Index k);
ConstBlock<DMatBase> x(const PlaceHolder ph1, const Index k) const;
double & x(const Index i, const Index k);
const double & x(const Index i, const Index k) const;
Block<DMatBase> y(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _);
ConstBlock<DMatBase> y(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _) const;
Block<DMatBase> y(const Index i, const PlaceHolder ph2 = _);
ConstBlock<DMatBase> y(const Index i, const PlaceHolder ph2 = _) const;
Block<DMatBase> y(const PlaceHolder ph1, const Index k);
ConstBlock<DMatBase> y(const PlaceHolder ph1, const Index k) const;
double & y(const Index i, const Index k);
const double & y(const Index i, const Index k) const;
Block<DMatBase> xxVar(const Index i1, const Index i2);
ConstBlock<DMatBase> xxVar(const Index i1, const Index i2) const;
Block<DMatBase> yyVar(const Index j1, const Index j2);
ConstBlock<DMatBase> yyVar(const Index j1, const Index j2) const;
Block<DMatBase> yxVar(const Index j, const Index i);
ConstBlock<DMatBase> yxVar(const Index j, const Index i) const;
Block<MatBase<double>> x(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _);
ConstBlock<MatBase<double>> x(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _) const;
Block<MatBase<double>> x(const Index i, const PlaceHolder ph2 = _);
ConstBlock<MatBase<double>> x(const Index i,
const PlaceHolder ph2 = _) const;
Block<MatBase<double>> x(const PlaceHolder ph1, const Index k);
ConstBlock<MatBase<double>> x(const PlaceHolder ph1,
const Index k) const;
double & x(const Index i, const Index k);
const double & x(const Index i, const Index k) const;
Block<MatBase<double>> y(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _);
ConstBlock<MatBase<double>> y(const PlaceHolder ph1 = _,
const PlaceHolder ph2 = _) const;
Block<MatBase<double>> y(const Index i, const PlaceHolder ph2 = _);
ConstBlock<MatBase<double>> y(const Index i,
const PlaceHolder ph2 = _) const;
Block<MatBase<double>> y(const PlaceHolder ph1, const Index k);
ConstBlock<MatBase<double>> y(const PlaceHolder ph1,
const Index k) const;
double & y(const Index i, const Index k);
const double & y(const Index i, const Index k) const;
Block<MatBase<double>> xxVar(const Index i1, const Index i2);
ConstBlock<MatBase<double>> xxVar(const Index i1, const Index i2) const;
Block<MatBase<double>> yyVar(const Index j1, const Index j2);
ConstBlock<MatBase<double>> yyVar(const Index j1, const Index j2) const;
Block<MatBase<double>> yxVar(const Index j, const Index i);
ConstBlock<MatBase<double>> yxVar(const Index j, const Index i) const;
// fit
FitResult fit(Minimizer &minimizer, const DVec &init,
const std::vector<const DoubleModel *> &modelVector);

69
lib/XmlReader.cpp
View File

@ -1,69 +0,0 @@
/*
* XmlReader.cpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2014 Antonin Portelli
*
* LatAnalyze 3 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* LatAnalyze 3 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/XmlReader.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;
using namespace Latan;
/******************************************************************************
* XmlReader implementation *
******************************************************************************/
// constructor /////////////////////////////////////////////////////////////////
XmlReader::XmlReader(const string &fileName)
{
open(fileName);
}
// IO //////////////////////////////////////////////////////////////////////////
void XmlReader::open(const std::string &fileName)
{
name_ = fileName;
doc_.LoadFile(name_.c_str());
if (doc_.Error())
{
string errMsg1, errMsg2;
if (doc_.GetErrorStr1())
{
errMsg1 = doc_.GetErrorStr1();
}
if (doc_.GetErrorStr2())
{
errMsg2 = doc_.GetErrorStr2();
}
LATAN_ERROR(Io, "tinyxml2 code " + strFrom(doc_.ErrorID()) + ": " +
errMsg1 + " - " + errMsg2);
}
root_ = doc_.RootElement();
}
// XML structure access ////////////////////////////////////////////////////////
const XmlNode * XmlReader::getNextNode(const XmlNode *node)
{
if (node)
{
return node->NextSiblingElement();
}
else
{
return nullptr;
}
}

181
lib/XmlReader.hpp
View File

@ -1,181 +0,0 @@
/*
* XmlReader.hpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2014 Antonin Portelli
*
* LatAnalyze 3 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* LatAnalyze 3 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef Latan_XmlReader_hpp_
#define Latan_XmlReader_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/XML/tinyxml2.hpp>
#include <iostream>
#include <vector>
BEGIN_LATAN_NAMESPACE
/******************************************************************************
* XML parameter file reader *
******************************************************************************/
typedef tinyxml2::XMLElement XmlNode;
class XmlReader
{
public:
// constructor
XmlReader(void) = default;
explicit XmlReader(const std::string &fileName);
// destructor
virtual ~XmlReader(void) = default;
// IO
void open(const std::string &fileName);
// XML structure access
template <typename... Strs>
static const XmlNode * getFirstNode(const XmlNode *startNode,
const std::string &nodeName,
Strs... nodeNames);
template <typename... Strs>
const XmlNode * getFirstNode(const std::string &nodeName,
Strs... nodeNames) const;
static const XmlNode * getNextNode(const XmlNode *node);
template <typename T>
static T getValue(const XmlNode *node);
template <typename T, typename... Strs>
static T getFirstValue(const XmlNode *startNode,
const std::string &nodeName, Strs... nodeNames);
template <typename T, typename... Strs>
T getFirstValue(const std::string &nodeName, Strs... nodeNames) const;
template <typename T, typename... Strs>
static std::vector<T> getAllValues(const XmlNode *startNode,
const std::string &nodeName,
Strs... nodeNames);
template <typename T, typename... Strs>
std::vector<T> getAllValues(const std::string &nodeName,
Strs... nodeNames) const;
private:
private:
std::string name_;
tinyxml2::XMLDocument doc_;
XmlNode *root_{nullptr};
};
/******************************************************************************
* XmlReader template implementation *
******************************************************************************/
// XML structure access ////////////////////////////////////////////////////////
template <typename... Strs>
const XmlNode * XmlReader::getFirstNode(const XmlNode *startNode,
const std::string &nodeName,
Strs... nodeNames)
{
static_assert(static_or<std::is_assignable<std::string, Strs>::value...>::value,
"getFirstValue arguments are not compatible with std::string");
const unsigned int nName = sizeof...(nodeNames) + 1;
const std::string name[] = {nodeName, nodeNames...};
const XmlNode *node = startNode;
if (!node)
{
LATAN_ERROR(Io, "root node is null, no XML file opened");
}
for (unsigned int i = 0; i < nName; ++i)
{
node = node->FirstChildElement(name[i].c_str());
if (!node)
{
LATAN_ERROR(Parsing, "XML node " + name[i] + " not found");
}
}
return node;
}
template <typename... Strs>
const XmlNode * XmlReader::getFirstNode(const std::string &nodeName,
Strs... nodeNames) const
{
if (!root_)
{
LATAN_ERROR(Io, "root node is null, no XML file opened");
}
return getFirstNode(root_, nodeName, nodeNames...);
}
template <typename T>
T XmlReader::getValue(const XmlNode *node)
{
if (node)
{
if (node->GetText())
{
return strTo<T>(node->GetText());
}
else
{
return T();
}
}
else
{
return T();
}
}
template <typename T, typename... Strs>
T XmlReader::getFirstValue(const XmlNode *startNode,
const std::string &nodeName, Strs... nodeNames)
{
const XmlNode *node = getFirstNode(startNode, nodeName, nodeNames...);
return getValue<T>(node);
}
template <typename T, typename... Strs>
T XmlReader::getFirstValue(const std::string &nodeName, Strs... nodeNames) const
{
return getFirstValue<T>(root_, nodeName, nodeNames...);
}
template <typename T, typename... Strs>
std::vector<T> XmlReader::getAllValues(const XmlNode *startNode,
const std::string &nodeName,
Strs... nodeNames)
{
const XmlNode *node = getFirstNode(startNode, nodeName, nodeNames...);
std::vector<T> value;
while (node)
{
value.push_back(getValue<T>(node));
node = getNextNode(node);
}
return value;
}
template <typename T, typename... Strs>
std::vector<T> XmlReader::getAllValues(const std::string &nodeName,
Strs... nodeNames) const
{
return getAllValues<T>(root_, nodeName, nodeNames...);
}
END_LATAN_NAMESPACE
#endif // Latan_XmlReader_hpp_

18
update_eigen.sh
View File

@ -1,18 +0,0 @@
#!/usr/bin/env bash
if (( $# != 1 )); then
echo "usage: `basename $0` <archive>" 1>&2
fi
ARC=$1
INITDIR=`pwd`
rm -rf latan/Eigen
ARCDIR=`tar -tf ${ARC} | head -n1 | sed -e 's@/.*@@'`
tar -xf ${ARC}
cd ${ARCDIR}
tar -cf - Eigen --exclude='*.txt' | tar -xf - -C ../latan/
cd ../latan
echo 'eigen_files =\' > eigen_files.mk
find Eigen -type f -print | sed 's/^/ /;$q;s/$/ \\/' >> eigen_files.mk
cd ${INITDIR}
rm -rf ${ARCDIR}