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Merge branch 'release/3.5'

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This commit is contained in:
Antonin Portelli
2019-12-12 18:23:50 +00:00
parent 9f101686fa dfaea5f156
commit 80d50e3e45
124 changed files with 8020 additions and 476 deletions
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5
.gitignore vendored
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@@ -31,11 +31,6 @@ lib/eigen_files.mk
# CI builds
ci-scripts/local/*
# CLion stuff
.idea/*
CMakeLists.txt
cmake-build-debug/*
# VS Code Studio stuff
.vscode
*.code-workspace

7
.travis.yml
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@@ -21,7 +21,6 @@ matrix:
- ubuntu-toolchain-r-test
packages:
- g++-7
- libgsl0-dev
- flex
- bison
env: VERSION=-7
@@ -32,7 +31,6 @@ matrix:
- ubuntu-toolchain-r-test
packages:
- g++-7
- libgsl0-dev
- flex
- bison
env: CLANG_LINK=http://releases.llvm.org/7.0.1/clang+llvm-7.0.1-x86_64-linux-gnu-ubuntu-14.04.tar.xz
@@ -44,8 +42,7 @@ before_install:
- if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="${LATDIR}/ci-scripts/clang/bin:${PATH}"; fi
- if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export LD_LIBRARY_PATH="${LATDIR}/ci-scripts/clang/lib:${LD_LIBRARY_PATH}"; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex cmake; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi
- if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc@${VERSION#-}; fi
install:
@@ -63,4 +60,4 @@ install:
script:
- cd ci-scripts
- ./install-latan.sh `pwd`/local $TRAVIS_OS_NAME
- ./install-latan.sh `pwd`/local

44
Readme.md
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@@ -1,5 +1,4 @@
# LatAnalyze
Contributors: Antonin Portelli, Matt Spraggs
License: GNU General Public License v3
@@ -41,20 +40,55 @@ The main features are the following:
The head of the `master` branch always points to the latest stable release. The `develop` branch is the main unstable branch of LatAnalyze.
LatAnalyze is written in C++11 and requires a rather recent C++ compiler to be built. It has been successfully built on various Linux and OS X platforms using clang (from 3.7), GCC (from 4.9) and the Intel C++ compiler (2016).
The strict dependencies are the [GSL](http://www.gnu.org/software/gsl/) and [LatCore](https://github.com/aportelli/LatCore).
The only strict dependencies is the [GSL](http://www.gnu.org/software/gsl/).
Additionally, autoconf, automake (from 1.11), libtool, bison (from 3.0) and flex are necessary to build the library. Unless you use a very exotic system, these tools are standard on any Unix platform and should be already present or easy to install through a package manager.
Optional dependencies are [HDF5](https://www.hdfgroup.org/HDF5/) (built with C++ support), [Minuit](http://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/) and [NLopt](http://ab-initio.mit.edu/wiki/index.php/NLopt).
Below are instructions for a quick installation. For a more customised installation, one first needs to generate the build system by running `./bootstrap.sh` in the root directory. Then the library can be built and installed through the usual GNU mantra `./configure <options> && make && make install`. Use `./configure --help` to obtain a list of possible options for `./configure`. Because Eigen expressions rely a lot on inlining and compiler optimisations it is strongly recommended to set the `CXXFLAGS` variable to `-O3 -march=native -mtune=native`.
### General quick installation
For a quick installation with all possible extensions execute:
```
./install-latan.sh <prefix> {osx|linux}
./install-latan.sh <prefix>
```
in the `ci-scripts` directory where `<prefix>` is where you want LatAnalyze (and its dependencies) to be installed and `{osx|linux}` should be the name of your OS. This script will automatically download, build and install LatCore, HDF5, Minuit and NLopt. It is assumed that the GSL can be found in a standard location (_e.g._ it has been installed through a package manager for Linux and is present in `/usr/local` for OS X).
in the `ci-scripts` directory where `<prefix>` is where you want LatAnalyze (and its dependencies) to be installed. This script will automatically download, build and install GSL, HDF5, Minuit, and NLopt.
For a more customised installation, one first needs to generate the build system by running `./bootstrap.sh` in the root directory. Then the library can be built and installed through the usual GNU mantra `./configure <options> && make && make install`. Use `./configure --help` to obtain a list of possible options for `./configure`. Because Eigen expressions rely a lot on inlining and compiler optimisations it is strongly recommended to set the `CXXFLAGS` variable to `-O3 -march=native -mtune=native`.
### Quick installation on macOS with dependencies through Homebrew
All the dependencies of LatAnalyze can be installed through the [Homebrew](https://brew.sh) package manager.
```
brew install automake autoconf libtool bison flex gsl minuit2 nlopt hdf5
```
Then generate the build system in LatAnalyze main directory by running the `./bootstrap.sh` script. Finally, build the library
```
mkdir build
cd build
../configure --prefix=<prefix> --with-minuit=/usr/local --with-nlopt=/usr/local \
--with-hdf5=/usr/local --with-gsl=/usr/local \
CXXFLAGS='-g -O3 -march=native -mtune=native'
make -j <n>
make install
```
where `<prefix>` should be replaced by the desired prefix for LatAnalyze installation, and `<n>` is the number of parallel build processes (typically twice your number of cores).
## History
#### v3.5
Additions:
* 'Impulse' & line type plots
* Plot line width & dash modifiers
* Plot palettes (`category10` by default)
* Multivariate Gaussian RNG
* 2-pt fitter 'scan' mode over all possible fit ranges
* Command line utility for plotting data
Changes:
* Complete overhaul of the header structure
* Integration of LatCore in LatAnalyze
* p-value is now a 2-sided chi^2 test, 1-sided value kept as 'chi^2 CCDF'
Fixes:
* Matrix plot data now saving correctly
* Many compatibility fixes
#### v3.4
Additions:
* `latan-config` utility to easily compile LatAnalyze-based programs

1
bootstrap.sh
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@@ -2,4 +2,5 @@
rm -rf .buildutils
mkdir -p .buildutils/m4
./update_eigen.sh eigen-3.3.7.tar.bz2
autoreconf -fvi

5
ci-scripts/install-deps.sh
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@@ -1,16 +1,15 @@
#!/usr/bin/env bash
if (( $# != 1 )); then
echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
echo "usage: `basename $0` <prefix>" 1>&2
exit 1
fi
PREFIX=$1
set -ex
mkdir -p local/build
for d in nlopt minuit hdf5; do
for d in gsl nlopt minuit hdf5; do
if [ ! -e local/.built.${d} ]; then
./install-${d}.sh ${PREFIX}
fi
done
./install-latcore.sh ${PREFIX}

23
ci-scripts/install-gsl.sh Executable file
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@@ -0,0 +1,23 @@
#!/usr/bin/env bash
NAME='gsl-2.6'
if (( $# != 1 )); then
echo "usage: `basename $0` <prefix>" 1>&2
exit 1
fi
PREFIX=$1
set -ex
INITDIR=`pwd`
cd local/build
wget http://ftpmirror.gnu.org/gsl/${NAME}.tar.gz
tar -xzvf ${NAME}.tar.gz
mkdir -p ${NAME}/build
cd ${NAME}/build
../configure --prefix=${PREFIX}
make -j4
make install
cd ${INITDIR}/local
touch .built.gsl
cd ${INITDIR}

4
ci-scripts/install-hdf5.sh
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@@ -1,9 +1,9 @@
#!/usr/bin/env bash
NAME='hdf5-1.10.1'
NAME='hdf5-1.10.5'
if (( $# != 1 )); then
echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
echo "usage: `basename $0` <prefix>" 1>&2
exit 1
fi
PREFIX=$1

7
ci-scripts/install-latan.sh
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@@ -1,7 +1,7 @@
#!/usr/bin/env bash
if (( $# != 2 )); then
echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
if (( $# != 1 )); then
echo "usage: `basename $0` <prefix>" 1>&2
exit 1
fi
PREFIX=$1
@@ -13,7 +13,6 @@ cd ..
./bootstrap.sh
mkdir -p build
cd build
if [[ "$OS" == "osx" ]]; then EXTRA_FLAGS='--with-gsl=/usr/local'; fi
../configure --prefix=$PREFIX --with-minuit=$PREFIX --with-nlopt=$PREFIX --with-latcore=$PREFIX --with-hdf5=$PREFIX $EXTRA_FLAGS CXXFLAGS="${CXXFLAGS} -O3 -march=native -mtune=native"
../configure --prefix=$PREFIX --with-minuit=$PREFIX --with-nlopt=$PREFIX --with-latcore=$PREFIX --with-hdf5=$PREFIX --with-gsl=$PREFIX CXXFLAGS="${CXXFLAGS} -O3 -march=native -mtune=native"
make -j4
make install

25
ci-scripts/install-latcore.sh
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@@ -1,25 +0,0 @@
#!/usr/bin/env bash
if (( $# != 1 )); then
echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
exit 1
fi
PREFIX=$1
set -ex
INITDIR=`pwd`
cd local/build
if [ -d LatCore ]; then
cd LatCore
git pull origin master
else
git clone https://github.com/aportelli/LatCore.git
mkdir LatCore/build
cd LatCore
./bootstrap.sh
fi
cd build
../configure --prefix=${PREFIX}
make -j4
make install
cd ${INITDIR}

2
ci-scripts/install-minuit.sh
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@@ -3,7 +3,7 @@
NAME='Minuit2-5.34.14'
if (( $# != 1 )); then
echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
echo "usage: `basename $0` <prefix>" 1>&2
exit 1
fi
PREFIX=$1

11
ci-scripts/install-nlopt.sh
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@@ -1,9 +1,9 @@
#!/usr/bin/env bash
NAME='nlopt-2.4.2'
NAME='2.6.1'
if (( $# != 1 )); then
echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
echo "usage: `basename $0` <prefix>" 1>&2
exit 1
fi
PREFIX=$1
@@ -11,11 +11,12 @@ PREFIX=$1
set -ex
INITDIR=`pwd`
cd local/build
wget http://ab-initio.mit.edu/nlopt/${NAME}.tar.gz
tar -xzvf ${NAME}.tar.gz
wget https://github.com/stevengj/nlopt/archive/v${NAME}.tar.gz
tar -xzvf v${NAME}.tar.gz
NAME=nlopt-${NAME}
mkdir -p ${NAME}/build
cd ${NAME}/build
../configure --prefix=${PREFIX} --with-cxx --without-guile --without-python --without-octave --without-matlab --with-pic
cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
make -j4
make install
cd ${INITDIR}/local

26
configure.ac
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@@ -2,13 +2,13 @@
# Initialization
AC_PREREQ([2.63])
AC_INIT([LatAnalyze],[3.4],[antonin.portelli@me.com],[LatAnalyze])
AC_INIT([LatAnalyze],[3.5],[antonin.portelli@me.com],[LatAnalyze])
AC_CONFIG_AUX_DIR([.buildutils])
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([1.11 -Wall -Werror foreign])
AM_INIT_AUTOMAKE([1.11 -Wall -Werror foreign subdir-objects])
AM_SILENT_RULES([yes])
AC_CONFIG_HEADERS([config.h])
AM_CONDITIONAL([HAVE_AM_MINOR_LE_11],
@@ -48,11 +48,6 @@ AC_ARG_WITH([hdf5],
[try this for a non-standard install prefix of the HDF5 library])],
[AM_CXXFLAGS="$AM_CXXFLAGS -I$with_hdf5/include"]
[AM_LDFLAGS="$AM_LDFLAGS -L$with_hdf5/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"])
# Get compilers informations
AX_COMPILER_VENDOR
@@ -83,12 +78,12 @@ AC_CHECK_LIB([m],[cos],[],[AC_MSG_ERROR([libm library not found])])
AC_CHECK_LIB([gslcblas],[cblas_dgemm],[],
[AC_MSG_ERROR([GSL CBLAS library not found])])
AC_CHECK_LIB([gsl],[gsl_blas_dgemm],[],[AC_MSG_ERROR([GSL library not found])])
AC_CHECK_LIB([nlopt_cxx],[nlopt_create],
AC_CHECK_LIB([nlopt],[nlopt_create],
[AC_DEFINE([HAVE_NLOPT],
[1],
[Define to 1 if you have the `NLopt' library (-lnlopt_cxx).])]
[Define to 1 if you have the `NLopt' library (-lnlopt).])]
[have_nlopt=true]
[LIBS="$LIBS -lnlopt_cxx"],[])
[LIBS="$LIBS -lnlopt"],[])
AM_CONDITIONAL([HAVE_NLOPT], [test x$have_nlopt = xtrue])
AC_CHECK_LIB([hdf5_cpp],[H5Fopen],
[LIBS="$LIBS -lhdf5_cpp -lhdf5"],
@@ -109,17 +104,6 @@ AC_LINK_IFELSE(
[AC_MSG_RESULT([no])])
AM_CONDITIONAL([HAVE_MINUIT], [test x$have_minuit = xtrue])
LDFLAGS=$SAVED_LDFLAGS
SAVED_LDFLAGS=$LDFLAGS
LDFLAGS="$LDFLAGS -lLatCore"
AC_MSG_CHECKING([for LatCore::XmlReader in -lLatCore]);
AC_LINK_IFELSE(
[AC_LANG_PROGRAM([#include <LatCore/XmlReader.hpp>],
[LatCore::XmlReader dummy()])],
[LIBS="$LIBS -lLatCore"]
[AC_MSG_RESULT([yes])],
[AC_MSG_RESULT([no])]
[AC_MSG_ERROR([LatCore library not found])])
LDFLAGS=$SAVED_LDFLAGS
CXXFLAGS=$CXXFLAGS_CPY
LDFLAGS=$LDFLAGS_CPY

BIN
eigen-3.3.7.tar.bz2 Normal file
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5
examples/Makefile.am
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@@ -17,6 +17,7 @@ noinst_PROGRAMS = \
exMathInterpreter \
exMin \
exPlot \
exPValue \
exRand \
exRootFinder
@@ -60,6 +61,10 @@ exPlot_SOURCES = exPlot.cpp
exPlot_CXXFLAGS = $(COM_CXXFLAGS)
exPlot_LDFLAGS = -L../lib/.libs -lLatAnalyze
exPValue_SOURCES = exPValue.cpp
exPValue_CXXFLAGS = $(COM_CXXFLAGS)
exPValue_LDFLAGS = -L../lib/.libs -lLatAnalyze
exRand_SOURCES = exRand.cpp
exRand_CXXFLAGS = $(COM_CXXFLAGS)
exRand_LDFLAGS = -L../lib/.libs -lLatAnalyze

2
examples/exCompiledDoubleFunction.cpp
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@@ -1,4 +1,4 @@
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/Functional/CompiledFunction.hpp>
using namespace std;
using namespace Latan;

6
examples/exDerivative.cpp
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@@ -1,6 +1,6 @@
#include <LatAnalyze/Derivative.hpp>
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Numerical/Derivative.hpp>
#include <LatAnalyze/Functional/CompiledFunction.hpp>
#include <LatAnalyze/Core/Math.hpp>
using namespace std;
using namespace Latan;

10
examples/exFit.cpp
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@@ -1,10 +1,10 @@
#include <iostream>
#include <cmath>
#include <LatAnalyze/CompiledModel.hpp>
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/GslMinimizer.hpp>
#include <LatAnalyze/Plot.hpp>
#include <LatAnalyze/XYStatData.hpp>
#include <LatAnalyze/Functional/CompiledModel.hpp>
#include <LatAnalyze/Io/Io.hpp>
#include <LatAnalyze/Numerical/GslMinimizer.hpp>
#include <LatAnalyze/Core/Plot.hpp>
#include <LatAnalyze/Statistics/XYStatData.hpp>
using namespace std;
using namespace Latan;

8
examples/exFitSample.cpp
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@@ -1,7 +1,7 @@
#include <LatAnalyze/CompiledModel.hpp>
#include <LatAnalyze/GslMinimizer.hpp>
#include <LatAnalyze/Plot.hpp>
#include <LatAnalyze/XYSampleData.hpp>
#include <LatAnalyze/Functional/CompiledModel.hpp>
#include <LatAnalyze/Numerical/GslMinimizer.hpp>
#include <LatAnalyze/Core/Plot.hpp>
#include <LatAnalyze/Statistics/XYSampleData.hpp>
using namespace std;
using namespace Latan;

4
examples/exIntegrator.cpp
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@@ -1,5 +1,5 @@
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/GslQagsIntegrator.hpp>
#include <LatAnalyze/Functional/CompiledFunction.hpp>
#include <LatAnalyze/Numerical/GslQagsIntegrator.hpp>
using namespace std;
using namespace Latan;

2
examples/exInterp.cpp
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@@ -1,4 +1,4 @@
#include <LatAnalyze/TabFunction.hpp>
#include <LatAnalyze/Functional/TabFunction.hpp>
int main(void)
{

6
examples/exMat.cpp
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@@ -1,6 +1,6 @@
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Io/Io.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Core/Math.hpp>
using namespace std;
using namespace Latan;

4
examples/exMathInterpreter.cpp
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@@ -1,5 +1,5 @@
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/MathInterpreter.hpp>
#include <LatAnalyze/Core/Math.hpp>
#include <LatAnalyze/Core/MathInterpreter.hpp>
using namespace std;
using namespace Latan;

4
examples/exMin.cpp
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@@ -1,5 +1,5 @@
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/GslMinimizer.hpp>
#include <LatAnalyze/Functional/CompiledFunction.hpp>
#include <LatAnalyze/Numerical/GslMinimizer.hpp>
using namespace std;
using namespace Latan;

23
examples/exPValue.cpp Normal file
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@@ -0,0 +1,23 @@
#include <LatAnalyze/Core/Math.hpp>
using namespace std;
using namespace Latan;
int main(int argc, char* argv[])
{
double chi2, ndof;
if (argc != 3)
{
cerr << "usage: " << argv[0] << " <chi^2> <ndof>" << endl;
return EXIT_FAILURE;
}
chi2 = strTo<double>(argv[1]);
ndof = strTo<double>(argv[2]);
cout << "Two-sided p-value: " << Math::chi2PValue(chi2, ndof) << endl;
cout << "chi^2 CCDF : " << Math::chi2Ccdf(chi2, ndof) << endl;
return EXIT_SUCCESS;
}

8
examples/exPlot.cpp
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@@ -1,7 +1,7 @@
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Plot.hpp>
#include <LatAnalyze/TabFunction.hpp>
#include <LatAnalyze/Functional/CompiledFunction.hpp>
#include <LatAnalyze/Core/Math.hpp>
#include <LatAnalyze/Core/Plot.hpp>
#include <LatAnalyze/Functional/TabFunction.hpp>
using namespace std;
using namespace Latan;

29
examples/exRand.cpp
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@@ -1,11 +1,15 @@
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/Plot.hpp>
#include <LatAnalyze/Io/Io.hpp>
#include <LatAnalyze/Functional/CompiledFunction.hpp>
#include <LatAnalyze/Core/Plot.hpp>
#include <LatAnalyze/Statistics/Random.hpp>
#include <LatAnalyze/Statistics/MatSample.hpp>
using namespace std;
using namespace Latan;
constexpr Index size = 8;
constexpr Index nDraw = 20000;
constexpr Index nSample = 2000;
const string stateFileName = "exRand.seed";
int main(void)
@@ -36,5 +40,24 @@ int main(void)
p << PlotFunction(compile("return exp(-x_0^2/2)/sqrt(2*pi);", 1), -5., 5.);
p.display();
DMat var(size, size);
DVec mean(size);
DMatSample sample(nSample, size, 1);
cout << "-- generating " << nSample << " Gaussian random vectors..." << endl;
var = DMat::Random(size, size);
var *= var.adjoint();
mean = DVec::Random(size);
RandomNormal mgauss(mean, var, rd());
sample[central] = mgauss();
FOR_STAT_ARRAY(sample, s)
{
sample[s] = mgauss();
}
cout << "* original variance matrix:\n" << var << endl;
cout << "* measured variance matrix:\n" << sample.varianceMatrix() << endl;
cout << "* original mean:\n" << mean << endl;
cout << "* measured mean:\n" << sample.mean() << endl;
return EXIT_SUCCESS;
}

4
examples/exRootFinder.cpp
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@@ -1,5 +1,5 @@
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/GslHybridRootFinder.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Numerical/GslHybridRootFinder.hpp>
using namespace std;
using namespace Latan;

123
lib/Core/Eigen.hpp Normal file
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@@ -0,0 +1,123 @@
/*
* Eigen.hpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2016 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/>.
*/
// Eigen inclusion
#define EIGEN_DONT_PARALLELIZE
#define EIGEN_MATRIXBASE_PLUGIN <LatAnalyze/Core/EigenPlugin.hpp>
#include <LatAnalyze/Eigen/Dense>
// 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;\
}
#define FOR_MAT(mat, i, j) \
for (Latan::Index j = 0; j < mat.cols(); ++j)\
for (Latan::Index i = 0; i < mat.rows(); ++i)
BEGIN_LATAN_NAMESPACE
const int dynamic = Eigen::Dynamic;
// 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>;
template <int nRow, int nCol>
using SFMat = Eigen::Matrix<float, nRow, nCol>;
template <int nRow, int nCol>
using SDMat = Eigen::Matrix<double, nRow, nCol>;
template <int nRow, int nCol>
using SCMat = Eigen::Matrix<std::complex<double>, nRow, nCol>;
// vector types
template <typename T, int size = dynamic>
using Vec = MatBase<T, size, 1>;
template <int size>
using SIVec = Vec<int, size>;
template <int size>
using SUVec = Vec<unsigned int, size>;
template <int size>
using SFVec = Vec<float, size>;
template <int size>
using SDVec = Vec<double, size>;
template <int size>
using SCVec = Vec<std::complex<double>, size>;
typedef SIVec<dynamic> IVec;
typedef SUVec<dynamic> UVec;
typedef SDVec<dynamic> DVec;
typedef SCVec<dynamic> CVec;
// 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 <int stride>
using InnerStride = Eigen::InnerStride<stride>;
template <int rowStride, int colStride>
using Stride = Eigen::Stride<rowStride, colStride>;
template <typename Derived, typename StrideType = Stride<0, 0>>
using Map = Eigen::Map<Derived, Eigen::Unaligned, StrideType>;
template <typename Derived, typename StrideType = Stride<0, 0>>
using ConstMap = Eigen::Map<const Derived, Eigen::Unaligned, StrideType>;
// Index type //////////////////////////////////////////////////////////////////
typedef MatBase<int>::Index Index;
#define FOR_VEC(vec, i) for (Latan::Index i = 0; i < (vec).size(); ++i)
#define FOR_ARRAY(ar, i) FOR_VEC(ar, i)
END_LATAN_NAMESPACE

60
lib/Core/EigenPlugin.hpp Normal file
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@@ -0,0 +1,60 @@
/*
* EigenPlugin.hpp, part of LatAnalyze
*
* Copyright (C) 2015 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
Derived pInverse(const double tolerance = 1.0e-10)
{
auto svd = jacobiSvd(Eigen::ComputeThinU|Eigen::ComputeThinV);
const auto u = svd.matrixU();
const auto v = svd.matrixV();
auto s = svd.singularValues();
double maxsv = 0.;
unsigned int elim = 0;
for (Index i = 0; i < s.rows(); ++i)
{
if (fabs(s(i)) > maxsv) maxsv = fabs(s(i));
}
for (Index i = 0; i < s.rows(); ++i)
{
if (fabs(s(i)) > maxsv*tolerance)
{
s(i) = 1./s(i);
}
else
{
elim++;
s(i) = 0.;
}
}
if (elim)
{
std::cerr << "warning: pseudoinverse: " << elim << "/";
std::cerr << s.rows() << " singular value(s) eliminated (tolerance= ";
std::cerr << tolerance << ")" << std::endl;
}
return v*s.asDiagonal()*u.transpose();
}
Derived singularValues(void)
{
auto svd = jacobiSvd();
return svd.singularValues();
}

2
lib/Exceptions.cpp → lib/Core/Exceptions.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Exceptions.hpp>
#include <LatAnalyze/Core/Exceptions.hpp>
#include <LatAnalyze/includes.hpp>
#ifndef ERR_SUFF

0
lib/Exceptions.hpp → lib/Core/Exceptions.hpp
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2
lib/Mat.cpp → lib/Core/Mat.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

6
lib/Mat.hpp → lib/Core/Mat.hpp
View File

@@ -21,11 +21,7 @@
#define Latan_Mat_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/IoObject.hpp>
#define FOR_MAT(mat, i, j) \
for (Latan::Index j = 0; j < mat.cols(); ++j)\
for (Latan::Index i = 0; i < mat.rows(); ++i)
#include <LatAnalyze/Io/IoObject.hpp>
BEGIN_LATAN_NAMESPACE

8
lib/Math.cpp → lib/Core/Math.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Core/Math.hpp>
#include <LatAnalyze/includes.hpp>
#include <gsl/gsl_cdf.h>
@@ -107,8 +107,14 @@ DEF_STD_FUNC_1ARG(fabs)
// p-value
auto chi2PValueVecFunc = [](const double arg[2])
{
return 2.*min(gsl_cdf_chisq_P(arg[0], arg[1]), gsl_cdf_chisq_Q(arg[0], arg[1]));
};
auto chi2CcdfVecFunc = [](const double arg[2])
{
return gsl_cdf_chisq_Q(arg[0], arg[1]);
};
DoubleFunction MATH_NAMESPACE::chi2PValue(chi2PValueVecFunc, 2);
DoubleFunction MATH_NAMESPACE::chi2Ccdf(chi2CcdfVecFunc, 2);

6
lib/Math.hpp → lib/Core/Math.hpp
View File

@@ -21,8 +21,8 @@
#define Latan_Math_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/MathInterpreter.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Core/MathInterpreter.hpp>
BEGIN_LATAN_NAMESPACE
@@ -75,6 +75,7 @@ namespace MATH_NAMESPACE
constexpr double pi = 3.1415926535897932384626433832795028841970;
constexpr double e = 2.7182818284590452353602874713526624977572;
constexpr double inf = std::numeric_limits<double>::infinity();
constexpr double nan = std::numeric_limits<double>::quiet_NaN();
}
@@ -152,6 +153,7 @@ DECL_STD_FUNC(fabs)
namespace MATH_NAMESPACE
{
extern DoubleFunction chi2PValue;
extern DoubleFunction chi2Ccdf;
}
END_LATAN_NAMESPACE

4
lib/MathInterpreter.cpp → lib/Core/MathInterpreter.cpp
View File

@@ -17,9 +17,9 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/MathInterpreter.hpp>
#include <LatAnalyze/Core/MathInterpreter.hpp>
#include <LatAnalyze/includes.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Core/Math.hpp>
using namespace std;
using namespace Latan;

4
lib/MathInterpreter.hpp → lib/Core/MathInterpreter.hpp
View File

@@ -20,9 +20,9 @@
#ifndef Latan_MathInterpreter_hpp_
#define Latan_MathInterpreter_hpp_
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/ParserState.hpp>
#include <LatAnalyze/Core/ParserState.hpp>
#define MAXIDLENGTH 256

2
lib/MathLexer.lpp → lib/Core/MathLexer.lpp
View File

@@ -25,7 +25,7 @@
%option yylineno
%{
#include <LatAnalyze/MathInterpreter.hpp>
#include <LatAnalyze/Core/MathInterpreter.hpp>
#include "MathParser.hpp"
using namespace std;

2
lib/MathParser.ypp → lib/Core/MathParser.ypp
View File

@@ -19,7 +19,7 @@
%{
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/MathInterpreter.hpp>
#include <LatAnalyze/Core/MathInterpreter.hpp>
using namespace std;
using namespace Latan;

299
lib/Core/OptParser.cpp Normal file
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@@ -0,0 +1,299 @@
/*
* OptParser.cpp, part of LatAnalyze
*
* Copyright (C) 2016 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Core/OptParser.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;
using namespace Latan;
static char optRegex[] = "(-([a-zA-Z])(.+)?)|(--([a-zA-Z_-]+)=?(.+)?)";
/******************************************************************************
* OptParser implementation *
******************************************************************************/
// regular expressions /////////////////////////////////////////////////////////
const regex OptParser::optRegex_(optRegex);
// access //////////////////////////////////////////////////////////////////////
void OptParser::addOption(const std::string shortName,
const std::string longName,
const OptType type, const bool optional,
const std::string helpMessage,
const std::string defaultVal)
{
OptPar par;
par.shortName = shortName;
par.longName = longName;
par.defaultVal = defaultVal;
par.helpMessage = helpMessage;
par.type = type;
par.optional = optional;
auto it = std::find_if(opt_.begin(), opt_.end(), [&par](const OptPar & p)
{
bool match = false;
match |= (par.shortName == p.shortName) and !par.shortName.empty();
match |= (par.longName == p.longName) and !par.longName.empty();
return match;
});
if (it != opt_.end())
{
string opt;
if (!it->shortName.empty())
{
opt += "-" + it->shortName;
}
if (!opt.empty())
{
opt += "/";
}
if (!it->longName.empty())
{
opt += "--" + it->longName;
}
throw(logic_error("duplicate option " + opt + " (in the code, not in the command line)"));
}
opt_.push_back(par);
}
bool OptParser::gotOption(const std::string name) const
{
int i = optIndex(name);
if (result_.size() != opt_.size())
{
throw(runtime_error("options not parsed"));
}
if (i >= 0)
{
return result_[i].present;
}
else
{
throw(out_of_range("no option with name '" + name + "'"));
}
}
const vector<string> & OptParser::getArgs(void) const
{
return arg_;
}
// parse ///////////////////////////////////////////////////////////////////////
bool OptParser::parse(int argc, char *argv[])
{
smatch sm;
queue<string> arg;
int expectVal = -1;
bool isCorrect = true;
for (int i = 1; i < argc; ++i)
{
arg.push(argv[i]);
}
result_.clear();
result_.resize(opt_.size());
arg_.clear();
for (unsigned int i = 0; i < opt_.size(); ++i)
{
result_[i].value = opt_[i].defaultVal;
}
while (!arg.empty())
{
// option
if (regex_match(arg.front(), sm, optRegex_))
{
// should it be a value?
if (expectVal >= 0)
{
cerr << "warning: expected value for option ";
cerr << optName(opt_[expectVal]);
cerr << ", got option '" << arg.front() << "' instead" << endl;
expectVal = -1;
isCorrect = false;
}
// short option
if (sm[1].matched)
{
string optName = sm[2].str();
// find option
auto it = find_if(opt_.begin(), opt_.end(),
[&optName](const OptPar &p)
{
return (p.shortName == optName);
});
// parse if found
if (it != opt_.end())
{
unsigned int i = it - opt_.begin();
result_[i].present = true;
if (opt_[i].type == OptType::value)
{
if (sm[3].matched)
{
result_[i].value = sm[3].str();
}
else
{
expectVal = i;
}
}
}
// warning if not found
else
{
cerr << "warning: unknown option '" << arg.front() << "'";
cerr << endl;
}
}
// long option
else if (sm[4].matched)
{
string optName = sm[5].str();
// find option
auto it = find_if(opt_.begin(), opt_.end(),
[&optName](const OptPar &p)
{
return (p.longName == optName);
});
// parse if found
if (it != opt_.end())
{
unsigned int i = it - opt_.begin();
result_[i].present = true;
if (opt_[i].type == OptType::value)
{
if (sm[6].matched)
{
result_[i].value = sm[6].str();
}
else
{
expectVal = i;
}
}
}
// warning if not found
else
{
cerr << "warning: unknown option '" << arg.front() << "'";
cerr << endl;
}
}
}
else if (expectVal >= 0)
{
result_[expectVal].value = arg.front();
expectVal = -1;
}
else
{
arg_.push_back(arg.front());
}
arg.pop();
}
if (expectVal >= 0)
{
cerr << "warning: expected value for option ";
cerr << optName(opt_[expectVal]) << endl;
expectVal = -1;
isCorrect = false;
}
for (unsigned int i = 0; i < opt_.size(); ++i)
{
if (!opt_[i].optional and !result_[i].present)
{
cerr << "warning: mandatory option " << optName(opt_[i]);
cerr << " is missing" << endl;
isCorrect = false;
}
}
return isCorrect;
}
// find option index ///////////////////////////////////////////////////////////
int OptParser::optIndex(const string name) const
{
auto it = find_if(opt_.begin(), opt_.end(), [&name](const OptPar &p)
{
return (p.shortName == name) or (p.longName == name);
});
if (it != opt_.end())
{
return static_cast<int>(it - opt_.begin());
}
else
{
return -1;
}
}
// option name for messages ////////////////////////////////////////////////////
std::string OptParser::optName(const OptPar &opt)
{
std::string res = "";
if (!opt.shortName.empty())
{
res += "-" + opt.shortName;
if (!opt.longName.empty())
{
res += "/";
}
}
if (!opt.longName.empty())
{
res += "--" + opt.longName;
if (opt.type == OptParser::OptType::value)
{
res += "=";
}
}
return res;
}
// print option list ///////////////////////////////////////////////////////////
std::ostream & Latan::operator<<(std::ostream &out, const OptParser &parser)
{
for (auto &o: parser.opt_)
{
out << setw(20) << OptParser::optName(o);
out << ": " << o.helpMessage;
if (!o.defaultVal.empty())
{
out << " (default: " << o.defaultVal << ")";
}
out << endl;
}
return out;
}

103
lib/Core/OptParser.hpp Normal file
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@@ -0,0 +1,103 @@
/*
* OptParser.hpp, part of LatAnalyze
*
* Copyright (C) 2016 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef LatAnalyze_OptParser_hpp_
#define LatAnalyze_OptParser_hpp_
#include <LatAnalyze/Global.hpp>
BEGIN_LATAN_NAMESPACE
/******************************************************************************
* command-line option parser *
******************************************************************************/
class OptParser
{
public:
enum class OptType {value, trigger};
private:
struct OptPar
{
std::string shortName, longName, defaultVal, helpMessage;
OptType type;
bool optional;
};
struct OptRes
{
std::string value;
bool present;
};
public:
// constructor
OptParser(void) = default;
// destructor
virtual ~OptParser(void) = default;
// access
void addOption(const std::string shortName, const std::string longName,
const OptType type, const bool optional = false,
const std::string helpMessage = "",
const std::string defaultVal = "");
bool gotOption(const std::string name) const;
template <typename T = std::string>
T optionValue(const std::string name) const;
const std::vector<std::string> & getArgs(void) const;
// parse
bool parse(int argc, char *argv[]);
// print option list
friend std::ostream & operator<<(std::ostream &out,
const OptParser &parser);
private:
// find option index
int optIndex(const std::string name) const;
// option name for messages
static std::string optName(const OptPar &opt);
private:
std::vector<OptPar> opt_;
std::vector<OptRes> result_;
std::vector<std::string> arg_;
static const std::regex optRegex_;
};
std::ostream & operator<<(std::ostream &out, const OptParser &parser);
/******************************************************************************
* OptParser template implementation *
******************************************************************************/
template <typename T>
T OptParser::optionValue(const std::string name) const
{
int i = optIndex(name);
if (result_.size() != opt_.size())
{
throw(std::runtime_error("options not parsed"));
}
if (i >= 0)
{
return strTo<T>(result_[i].value);
}
else
{
throw(std::out_of_range("no option with name '" + name + "'"));
}
}
END_LATAN_NAMESPACE
#endif // LatAnalyze_OptParser_hpp_

0
lib/ParserState.hpp → lib/Core/ParserState.hpp
View File

159
lib/Plot.cpp → lib/Core/Plot.cpp
View File

@@ -17,9 +17,9 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Plot.hpp>
#include <LatAnalyze/Core/Plot.hpp>
#include <LatAnalyze/includes.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/Core/Mat.hpp>
using namespace std;
using namespace Latan;
@@ -116,7 +116,7 @@ PlotData::PlotData(const DMatSample &x, const DMatSample &y)
{
if (x[central].rows() != y[central].rows())
{
LATAN_ERROR(Size, "x and y vector does not have the same size");
LATAN_ERROR(Size, "x and y vectors do not have the same size");
}
DMat d(x[central].rows(), 4);
@@ -153,7 +153,7 @@ PlotData::PlotData(const DMatSample &x, const DVec &y)
{
if (x[central].rows() != y.rows())
{
LATAN_ERROR(Size, "x and y vector does not have the same size");
LATAN_ERROR(Size, "x and y vectors do not have the same size");
}
DMat d(x[central].rows(), 3), xerr, yerr;
@@ -177,6 +177,24 @@ PlotData::PlotData(const XYStatData &data, const Index i, const Index j)
setCommand("'" + tmpFileName + "' " + usingCmd);
}
// PlotLine constructor ////////////////////////////////////////////////////////
PlotLine::PlotLine(const DVec &x, const DVec &y)
{
if (x.size() != y.size())
{
LATAN_ERROR(Size, "x and y vectors do not have the same size");
}
DMat d(x.size(), 2);
string usingCmd, tmpFileName;
d.col(0) = x;
d.col(1) = y;
tmpFileName = dumpToTmpFile(d);
pushTmpFile(tmpFileName);
setCommand("'" + tmpFileName + "' u 1:2 w lines");
}
// PlotHLine constructor ///////////////////////////////////////////////////////
PlotHLine::PlotHLine(const double y)
{
@@ -216,6 +234,41 @@ PlotFunction::PlotFunction(const DoubleFunction &function, const double xMin,
}
// PlotPredBand constructor ////////////////////////////////////////////////////
void PlotPredBand::makePredBand(const DMat &low, const DMat &high, const double opacity)
{
string lowFileName, highFileName;
lowFileName = dumpToTmpFile(low);
highFileName = dumpToTmpFile(high);
pushTmpFile(lowFileName);
pushTmpFile(highFileName);
setCommand("'< (cat " + lowFileName + "; tac " + highFileName +
"; head -n1 " + lowFileName + ")' u 1:2 w filledcurves closed" +
" fs solid " + strFrom(opacity) + " noborder");
}
PlotPredBand::PlotPredBand(const DVec &x, const DVec &y, const DVec &yerr,
const double opacity)
{
if (x.size() != y.size())
{
LATAN_ERROR(Size, "x and y vectors do not have the same size");
}
if (y.size() != yerr.size())
{
LATAN_ERROR(Size, "y and y error vectors do not have the same size");
}
Index nPoint = x.size();
DMat dLow(nPoint, 2), dHigh(nPoint, 2);
dLow.col(0) = x;
dLow.col(1) = y - yerr;
dHigh.col(0) = x;
dHigh.col(1) = y + yerr;
makePredBand(dLow, dHigh, opacity);
}
PlotPredBand::PlotPredBand(const DoubleFunctionSample &function,
const double xMin, const double xMax,
const unsigned int nPoint, const double opacity)
@@ -236,15 +289,10 @@ PlotPredBand::PlotPredBand(const DoubleFunctionSample &function,
dHigh(i, 0) = x;
dHigh(i, 1) = pred[central] + err;
}
lowFileName = dumpToTmpFile(dLow);
highFileName = dumpToTmpFile(dHigh);
pushTmpFile(lowFileName);
pushTmpFile(highFileName);
setCommand("'< (cat " + lowFileName + "; tac " + highFileName +
"; head -n1 " + lowFileName + ")' u 1:2 w filledcurves closed" +
" fs solid " + strFrom(opacity) + " noborder");
makePredBand(dLow, dHigh, opacity);
}
// PlotHistogram constructor ///////////////////////////////////////////////////
PlotHistogram::PlotHistogram(const Histogram &h)
{
@@ -261,11 +309,33 @@ PlotHistogram::PlotHistogram(const Histogram &h)
setCommand("'" + tmpFileName + "' u 1:2 w steps");
}
// PlotImpulses constructor ////////////////////////////////////////////////////
PlotImpulses::PlotImpulses(const DVec &x, const DVec &y)
{
if (x.rows() != y.rows())
{
LATAN_ERROR(Size, "x and y vector does not have the same size");
}
DMat d(x.rows(), 2);
string tmpFileName;
for (Index i = 0; i < x.rows(); ++i)
{
d(i, 0) = x(i);
d(i, 1) = y(i);
}
tmpFileName = dumpToTmpFile(d);
pushTmpFile(tmpFileName);
setCommand("'" + tmpFileName + "' u 1:2 w impulses");
}
// PlotMatrixNoRange constructor ///////////////////////////////////////////////
PlotMatrixNoRange::PlotMatrixNoRange(const DMat &m)
{
string tmpFileName = dumpToTmpFile(m);
pushTmpFile(tmpFileName);
setCommand("'" + tmpFileName + "' matrix w image");
}
@@ -306,6 +376,28 @@ void Color::operator()(PlotOptions &option) const
option.lineColor = color_;
}
// LineWidth constructor ///////////////////////////////////////////////////////
LineWidth::LineWidth(const unsigned int width)
: width_(width)
{}
// LineWidth modifier //////////////////////////////////////////////////////////
void LineWidth::operator()(PlotOptions &option) const
{
option.lineWidth = static_cast<int>(width_);
}
// Dash constructor ///////////////////////////////////////////////////////////
Dash::Dash(const string &dash)
: dash_(dash)
{}
// Dash modifier //////////////////////////////////////////////////////////////
void Dash::operator()(PlotOptions &option) const
{
option.dashType = dash_;
}
// LogScale constructor ////////////////////////////////////////////////////////
LogScale::LogScale(const Axis axis)
: axis_(axis)
@@ -371,6 +463,31 @@ void Title::operator()(PlotOptions &option) const
option.title = title_;
}
// Palette constructor /////////////////////////////////////////////////////////
Palette::Palette(const std::vector<std::string> &palette)
: palette_(palette)
{}
// Palette modifier ////////////////////////////////////////////////////////////
void Palette::operator()(PlotOptions &option) const
{
option.palette = palette_;
}
// category10 palette //////////////////////////////////////////////////////////
const std::vector<std::string> Palette::category10 =
{
"rgb '#1f77b4'",
"rgb '#ff7f0e'",
"rgb '#2ca02c'",
"rgb '#d62728'",
"rgb '#9467bd'",
"rgb '#8c564b'",
"rgb '#e377c2'",
"rgb '#7f7f7f'",
"rgb '#bcbd22'"
};
/******************************************************************************
* Plot implementation *
******************************************************************************/
@@ -394,6 +511,9 @@ void Plot::initOptions(void)
options_.label[0] = "";
options_.label[1] = "";
options_.lineColor = "";
options_.lineWidth = -1;
options_.dashType = "";
options_.palette = Palette::category10;
}
// plot reset //////////////////////////////////////////////////////////////////
@@ -423,6 +543,16 @@ Plot & Plot::operator<<(PlotObject &&command)
commandStr += " lc " + options_.lineColor;
options_.lineColor = "";
}
if (options_.lineWidth > 0)
{
commandStr += " lw " + strFrom(options_.lineWidth);
options_.lineWidth = -1;
}
if (!options_.dashType.empty())
{
commandStr += " dt " + options_.dashType;
options_.dashType = "";
}
if (options_.title.empty())
{
commandStr += " notitle";
@@ -528,7 +658,7 @@ void Plot::display(void)
LATAN_ERROR(System, "cannot find DISPLAY variable: is it set ?");
}
getProgramPath();
command = gnuplotPath_ + "/" + gnuplotBin_;
command = gnuplotPath_ + "/" + gnuplotBin_ + " 2>/dev/null";
gnuplotPipe = popen(command.c_str(), "w");
if (!gnuplotPipe)
{
@@ -674,6 +804,11 @@ ostream & Latan::operator<<(ostream &out, const Plot &plot)
{
out << "set ylabel '" << plot.options_.label[y] << "'" << endl;
}
for (unsigned int i = 0; i < plot.options_.palette.size(); ++i)
{
out << "set linetype " << i + 1 << " lc "
<< plot.options_.palette[i] << endl;
}
for (unsigned int i = 0; i < plot.headCommand_.size(); ++i)
{
out << plot.headCommand_[i] << endl;

92
lib/Plot.hpp → lib/Core/Plot.hpp
View File

@@ -21,11 +21,11 @@
#define Latan_Plot_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/Histogram.hpp>
#include <LatAnalyze/XYStatData.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Statistics/MatSample.hpp>
#include <LatAnalyze/Statistics/Histogram.hpp>
#include <LatAnalyze/Statistics/XYStatData.hpp>
// gnuplot default parameters
#ifndef GNUPLOT_BIN
@@ -106,6 +106,15 @@ public:
virtual ~PlotHLine(void) = default;
};
class PlotLine: public PlotObject
{
public:
// constructor
PlotLine(const DVec &x, const DVec &y);
// destructor
virtual ~PlotLine(void) = default;
};
class PlotBand: public PlotObject
{
public:
@@ -130,11 +139,15 @@ class PlotPredBand: public PlotObject
{
public:
// constructor
PlotPredBand(const DVec &x, const DVec &y, const DVec &yerr,
const double opacity = 0.15);
PlotPredBand(const DoubleFunctionSample &function, const double xMin,
const double xMax, const unsigned int nPoint = 1000,
const double opacity = 0.15);
// destructor
virtual ~PlotPredBand(void) = default;
private:
void makePredBand(const DMat &low, const DMat &high, const double opacity);
};
class PlotHistogram: public PlotObject
@@ -146,6 +159,15 @@ public:
virtual ~PlotHistogram(void) = default;
};
class PlotImpulses: public PlotObject
{
public:
// constructor
PlotImpulses(const DVec &x, const DVec &y);
// destructor
virtual ~PlotImpulses(void) = default;
};
class PlotMatrixNoRange: public PlotObject
{
public:
@@ -172,14 +194,17 @@ struct Range
struct PlotOptions
{
std::string terminal;
std::string output;
std::string caption;
std::string title;
unsigned int scaleMode[2];
Range scale[2];
std::string label[2];
std::string lineColor;
std::string terminal;
std::string output;
std::string caption;
std::string title;
unsigned int scaleMode[2];
Range scale[2];
std::string label[2];
std::string lineColor;
int lineWidth;
std::string dashType;
std::vector<std::string> palette;
};
class PlotModifier
@@ -231,6 +256,32 @@ private:
const std::string color_;
};
class LineWidth: public PlotModifier
{
public:
// constructor
explicit LineWidth(const unsigned int width);
// destructor
virtual ~LineWidth(void) = default;
// modifier
virtual void operator()(PlotOptions &option) const;
private:
const unsigned width_;
};
class Dash: public PlotModifier
{
public:
// constructor
explicit Dash(const std::string &dash);
// destructor
virtual ~Dash(void) = default;
// modifier
virtual void operator()(PlotOptions &option) const;
private:
const std::string dash_;
};
class LogScale: public PlotModifier
{
public:
@@ -286,6 +337,21 @@ private:
const std::string title_;
};
class Palette: public PlotModifier
{
public:
static const std::vector<std::string> category10;
public:
// constructor
explicit Palette(const std::vector<std::string> &palette);
// destructor
virtual ~Palette(void) = default;
// modifier
virtual void operator()(PlotOptions &option) const;
private:
const std::vector<std::string> palette_;
};
/******************************************************************************
* Plot class *
******************************************************************************/

137
lib/Core/Utilities.cpp Normal file
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@@ -0,0 +1,137 @@
/*
* Utilities.cpp, part of LatAnalyze
*
* Copyright (C) 2013 - 2015 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Core/Utilities.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;
using namespace Latan;
void Latan::testFunction(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;
}
int Latan::mkdir(const std::string dirName)
{
if (access(dirName.c_str(), R_OK|W_OK|X_OK))
{
mode_t mode755;
char tmp[MAX_PATH_LENGTH];
char *p = NULL;
size_t len;
mode755 = S_IRWXU|S_IRGRP|S_IXGRP|S_IROTH|S_IXOTH;
snprintf(tmp, sizeof(tmp), "%s", dirName.c_str());
len = strlen(tmp);
if(tmp[len - 1] == '/')
{
tmp[len - 1] = 0;
}
for(p = tmp + 1; *p; p++)
{
if(*p == '/')
{
*p = 0;
::mkdir(tmp, mode755);
*p = '/';
}
}
return ::mkdir(tmp, mode755);
}
else
{
return 0;
}
}
string Latan::basename(const string &s)
{
constexpr char sep = '/';
size_t i = s.rfind(sep, s.length());
if (i != string::npos)
{
return s.substr(i+1, s.length() - i);
}
else
{
return s;
}
}
std::string Latan::dirname(const std::string &s)
{
constexpr char sep = '/';
size_t i = s.rfind(sep, s.length());
if (i != std::string::npos)
{
return s.substr(0, i);
}
else
{
return "";
}
}
VarName::VarName(const string defName)
: defName_(defName)
{}
string VarName::getName(const Index i) const
{
if (hasName(i))
{
return name_.at(i);
}
else
{
return defName_ + "_" + strFrom(i);
}
}
void VarName::setName(const Index i, const string name)
{
name_[i] = name;
}
bool VarName::hasName(const Index i) const
{
return (name_.find(i) != name_.end());
}

250
lib/Core/Utilities.hpp Normal file
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@@ -0,0 +1,250 @@
/*
* Utilities.hpp, part of LatAnalyze
*
* Copyright (C) 2013 - 2015 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef LatAnalyze_Utilities_hpp_
#define LatAnalyze_Utilities_hpp_
#ifndef LATAN_GLOBAL_HPP_
#include <LatAnalyze/Global.hpp>
#endif
BEGIN_LATAN_NAMESPACE
// Random seed type ////////////////////////////////////////////////////////////
typedef std::random_device::result_type SeedType;
// 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 /////////////////////////////////////////////////////////////////
void testFunction(void);
// String utilities ////////////////////////////////////////////////////////////
inline std::string extension(const std::string fileName)
{
return fileName.substr(fileName.find_last_of(".") + 1);
}
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;
}
template<>
inline UVec strTo<UVec>(const std::string &str)
{
UVec res;
std::vector<unsigned int> vbuf;
unsigned int buf;
std::istringstream stream(str);
while (!stream.eof())
{
stream >> buf;
vbuf.push_back(buf);
}
res = Map<UVec>(vbuf.data(), static_cast<Index>(vbuf.size()));
return res;
}
template <typename T>
void tokenReplace(std::string &str, const std::string token,
const T &x, const std::string mark = "@")
{
std::string fullToken = mark + token + mark;
auto pos = str.find(fullToken);
if (pos != std::string::npos)
{
str.replace(pos, fullToken.size(), strFrom(x));
}
}
// 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;
}
// Recursive directory creation ////////////////////////////////////////////////
int mkdir(const std::string dirName);
// C++ version of basename/dirname /////////////////////////////////////////////
std::string basename(const std::string& s);
std::string dirname(const std::string& s);
// 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)
{}
std::ostream & operator<<(std::ostream &out, const ProgressBar &&bar);
// named variable interface ////////////////////////////////////////////////////
// FIXME: check redundant names and variable number limit
class VarName
{
public:
// constructor
VarName(const std::string defName);
// destructor
virtual ~VarName(void) = default;
// access
std::string getName(const Index i) const;
void setName(const Index i, const std::string name);
// test
bool hasName(const Index i) const;
private:
std::string defName_;
std::unordered_map<Index, std::string> name_;
};
END_LATAN_NAMESPACE
#endif // LatAnalyze_Utilities_hpp_

56
lib/Core/stdincludes.hpp Normal file
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@@ -0,0 +1,56 @@
/*
* stdincludes.hpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2016 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_stdincludes_hpp_
#define Latan_stdincludes_hpp_
#include <algorithm>
#include <array>
#include <chrono>
#include <complex>
#include <fstream>
#include <functional>
#include <iostream>
#include <iomanip>
#include <iterator>
#include <limits>
#include <list>
#include <map>
#include <memory>
#include <queue>
#include <random>
#include <regex>
#include <set>
#include <stack>
#include <string>
#include <sstream>
#include <type_traits>
#include <unordered_map>
#include <utility>
#include <vector>
#include <cfloat>
#include <climits>
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <sys/stat.h>
#include <unistd.h>
#endif // Latan_stdincludes_hpp_

4
lib/CompiledFunction.cpp → lib/Functional/CompiledFunction.cpp
View File

@@ -17,8 +17,8 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Functional/CompiledFunction.hpp>
#include <LatAnalyze/Core/Math.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

4
lib/CompiledFunction.hpp → lib/Functional/CompiledFunction.hpp
View File

@@ -21,8 +21,8 @@
#define Latan_CompiledFunction_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/MathInterpreter.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Core/MathInterpreter.hpp>
BEGIN_LATAN_NAMESPACE

4
lib/CompiledModel.cpp → lib/Functional/CompiledModel.cpp
View File

@@ -17,8 +17,8 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/CompiledModel.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Functional/CompiledModel.hpp>
#include <LatAnalyze/Core/Math.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

4
lib/CompiledModel.hpp → lib/Functional/CompiledModel.hpp
View File

@@ -21,8 +21,8 @@
#define Latan_CompiledModel_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Model.hpp>
#include <LatAnalyze/MathInterpreter.hpp>
#include <LatAnalyze/Functional/Model.hpp>
#include <LatAnalyze/Core/MathInterpreter.hpp>
BEGIN_LATAN_NAMESPACE

36
lib/Function.cpp → lib/Functional/Function.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;
@@ -111,6 +111,20 @@ double DoubleFunction::operator()(void) const
return (*this)(nullptr);
}
std::map<double, double> DoubleFunction::operator()(const std::map<double, double> &m) const
{
checkSize(1);
std::map<double, double> res;
for (auto &val: m)
{
res[val.first] = (*this)(val.second);
}
return res;
}
// bind ////////////////////////////////////////////////////////////////////////
DoubleFunction DoubleFunction::bind(const Index argIndex,
const double val) const
@@ -165,6 +179,26 @@ DoubleFunction DoubleFunction::bind(const Index argIndex,
return bindFunc;
}
// sample //////////////////////////////////////////////////////////////////////
DVec DoubleFunction::sample(const DMat &x) const
{
if (x.cols() != getNArg())
{
LATAN_ERROR(Size, "sampling point matrix and number of arguments "
"mismatch (matrix has " + strFrom(x.cols())
+ ", number of arguments is " + strFrom(getNArg()) + ")");
}
DVec res(x.rows());
for (Index i = 0; i < res.size(); ++i)
{
res(i) = (*this)(x.row(i));
}
return res;
}
// arithmetic operators ////////////////////////////////////////////////////////
DoubleFunction DoubleFunction::operator-(void) const
{

7
lib/Function.hpp → lib/Functional/Function.hpp
View File

@@ -21,8 +21,8 @@
#define Latan_Function_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Statistics/MatSample.hpp>
BEGIN_LATAN_NAMESPACE
@@ -52,9 +52,12 @@ public:
double operator()(void) const;
template <typename... Ts>
double operator()(const double arg0, const Ts... args) const;
std::map<double, double> operator()(const std::map<double, double> &m) const;
// bind
DoubleFunction bind(const Index argIndex, const double val) const;
DoubleFunction bind(const Index argIndex, const DVec &x) const;
// sample
DVec sample(const DMat &x) const;
// arithmetic operators
DoubleFunction operator-(void) const;
DoubleFunction & operator+=(const DoubleFunction &f);

2
lib/Model.cpp → lib/Functional/Model.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Model.hpp>
#include <LatAnalyze/Functional/Model.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

4
lib/Model.hpp → lib/Functional/Model.hpp
View File

@@ -21,8 +21,8 @@
#define Latan_Model_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Core/Mat.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/TabFunction.cpp → lib/Functional/TabFunction.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/TabFunction.hpp>
#include <LatAnalyze/Functional/TabFunction.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

6
lib/TabFunction.hpp → lib/Functional/TabFunction.hpp
View File

@@ -21,9 +21,9 @@
#define Latan_TabFunction_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/XYStatData.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Core/Math.hpp>
#include <LatAnalyze/Statistics/XYStatData.hpp>
BEGIN_LATAN_NAMESPACE

24
lib/Global.hpp
View File

@@ -20,13 +20,27 @@
#ifndef Latan_Global_hpp_
#define Latan_Global_hpp_
#include <LatCore/LatCore.hpp>
#include <LatAnalyze/Core/stdincludes.hpp>
#define BEGIN_LATAN_NAMESPACE \
namespace Latan {\
using namespace LatCore;
namespace Latan {
#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
#ifdef __GNUC__
#define __dumb __attribute__((unused))
#else
#define __dumb
#endif
// max length for paths
#define MAX_PATH_LENGTH 512u
BEGIN_LATAN_NAMESPACE
// Placeholder type ////////////////////////////////////////////////////////////
@@ -47,6 +61,8 @@ namespace Env
END_LATAN_NAMESPACE
#include <LatAnalyze/Exceptions.hpp>
#include <LatAnalyze/Core/Eigen.hpp>
#include <LatAnalyze/Core/Exceptions.hpp>
#include <LatAnalyze/Core/Utilities.hpp>
#endif // Latan_Global_hpp_

2
lib/AsciiFile.cpp → lib/Io/AsciiFile.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Io/AsciiFile.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

8
lib/AsciiFile.hpp → lib/Io/AsciiFile.hpp
View File

@@ -21,10 +21,10 @@
#define Latan_AsciiFile_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/File.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/ParserState.hpp>
#include <LatAnalyze/Io/File.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Statistics/MatSample.hpp>
#include <LatAnalyze/Core/ParserState.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/AsciiLexer.lpp → lib/Io/AsciiLexer.lpp
View File

@@ -25,7 +25,7 @@
%option yylineno
%{
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Io/AsciiFile.hpp>
#include "AsciiParser.hpp"
using namespace std;

6
lib/AsciiParser.ypp → lib/Io/AsciiParser.ypp
View File

@@ -19,9 +19,9 @@
%{
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/Io/AsciiFile.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Statistics/MatSample.hpp>
using namespace std;
using namespace Latan;

81
lib/Io/BinReader.cpp Normal file
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@@ -0,0 +1,81 @@
/*
* BinReader.cpp, part of LatAnalyze
*
* Copyright (C) 2015 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Io/BinReader.hpp>
#include <LatAnalyze/includes.hpp>
#if (defined __GNUC__)||(defined __clang__)
#pragma GCC diagnostic ignored "-Wunreachable-code"
#endif
using namespace std;
using namespace Latan;
BinIO::BinIO(string msg, string loc)
: runtime_error("Binary reader error: " + msg + " (" + loc + ")")
{}
/******************************************************************************
* BinReader implementation *
******************************************************************************/
// constructor /////////////////////////////////////////////////////////////////
BinReader::BinReader(const string fileName, const uint32_t endianness,
const bool isColMaj)
{
open(fileName, endianness, isColMaj);
}
// I/O /////////////////////////////////////////////////////////////////////////
void BinReader::open(const string fileName, const uint32_t endianness,
const bool isColMaj)
{
fileName_ = fileName;
endianness_ = endianness;
isColMaj_ = isColMaj;
file_.reset(new ifstream(fileName_, ios::in|ios::binary|ios::ate));
if (!file_->is_open())
{
LATAN_ERROR(Io, "impossible to open file '" + fileName_ + "'");
}
size_ = static_cast<size_t>(file_->tellg());
file_->seekg(0, ios::beg);
}
void BinReader::close(void)
{
file_.reset(nullptr);
}
template <>
std::string BinReader::read(void)
{
std::string s;
char c = 'a';
while (c != '\n')
{
c = read<char>();
if (c != '\n')
{
s.push_back(c);
}
}
return s;
}

196
lib/Io/BinReader.hpp Normal file
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@@ -0,0 +1,196 @@
/*
* BinReader.hpp, part of LatAnalyze
*
* Copyright (C) 2015 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef LatAnalyze_BinReader_hpp_
#define LatAnalyze_BinReader_hpp_
#include <LatAnalyze/Global.hpp>
BEGIN_LATAN_NAMESPACE
// I/O exception
class BinIO: public std::runtime_error
{
public:
BinIO(std::string msg, std::string loc);
};
/******************************************************************************
* Byte manipulation utilities *
******************************************************************************/
class Endianness
{
public:
enum: uint32_t
{
little = 0x00000001,
big = 0x01000000,
unknown = 0xffffffff
};
};
class ByteManip
{
public:
static constexpr uint32_t getHostEndianness(void)
{
return ((0xffffffff & 1) == Endianness::little) ? Endianness::little
: (((0xffffffff & 1) == Endianness::big) ? Endianness::big
: Endianness::unknown);
}
template <typename T>
static T swapBytes(const T);
};
/******************************************************************************
* template implementation *
******************************************************************************/
template <typename T>
T ByteManip::swapBytes(const T u)
{
static_assert (CHAR_BIT == 8, "CHAR_BIT != 8");
union
{
T u;
unsigned char u8[sizeof(T)];
} source, dest;
source.u = u;
for (size_t k = 0; k < sizeof(T); ++k)
{
dest.u8[k] = source.u8[sizeof(T) - k - 1];
}
return dest.u;
}
/******************************************************************************
* Utility to read binary files *
******************************************************************************/
class BinReader
{
public:
// constructor
BinReader(void) = default;
BinReader(const std::string fileName,
const uint32_t endianness = ByteManip::getHostEndianness(),
const bool isColMaj = false);
// destructor
virtual ~BinReader(void) = default;
// I/O
void open(const std::string fileName,
const uint32_t endianness = ByteManip::getHostEndianness(),
const bool isColMaj = false);
void close(void);
template <typename T>
void read(T *pt, Index size);
template <typename T>
T read(void);
template <typename T>
MatBase<T> read(const Index nRow, const Index nCol);
private:
std::unique_ptr<std::ifstream> file_{nullptr};
std::string fileName_;
size_t size_;
uint32_t endianness_;
bool isColMaj_;
};
/******************************************************************************
* template implementation *
******************************************************************************/
template <typename T>
void BinReader::read(T *pt, Index n)
{
if (file_ != nullptr)
{
file_->read(reinterpret_cast<char *>(pt),
static_cast<long>(sizeof(T))*n);
if (endianness_ != ByteManip::getHostEndianness())
{
for (Index i = 0; i < n; ++i)
{
pt[i] = ByteManip::swapBytes(pt[i]);
}
}
}
else
{
LATAN_ERROR(Io, "file is not opened");
}
}
template <typename T>
T BinReader::read(void)
{
T x;
if (file_ != nullptr)
{
read(&x, 1);
}
else
{
LATAN_ERROR(Io, "file is not opened");
}
return x;
}
template <>
std::string BinReader::read(void);
template <typename T>
MatBase<T> BinReader::read(const Index nRow, const Index nCol)
{
MatBase<T> m;
// Eigen matrices use column-major ordering
if (isColMaj_)
{
m.resize(nRow, nCol);
}
else
{
m.resize(nCol, nRow);
}
if (file_ != nullptr)
{
read(m.data(), nRow*nCol);
}
else
{
LATAN_ERROR(Io, "file is not opened");
}
if (isColMaj_)
{
return m;
}
else
{
return m.transpose();
}
}
END_LATAN_NAMESPACE
#endif // LatAnalyze_BinReader_hpp_

2
lib/File.cpp → lib/Io/File.cpp
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@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/File.hpp>
#include <LatAnalyze/Io/File.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

6
lib/File.hpp → lib/Io/File.hpp
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@@ -21,9 +21,9 @@
#define Latan_File_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/IoObject.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/Io/IoObject.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Statistics/MatSample.hpp>
BEGIN_LATAN_NAMESPACE

4
lib/Hdf5File.cpp → lib/Io/Hdf5File.cpp
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@@ -17,8 +17,8 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Hdf5File.hpp>
#include <LatAnalyze/IoObject.hpp>
#include <LatAnalyze/Io/Hdf5File.hpp>
#include <LatAnalyze/Io/IoObject.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

6
lib/Hdf5File.hpp → lib/Io/Hdf5File.hpp
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@@ -21,9 +21,9 @@
#define Latan_Hdf5File_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/File.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/Io/File.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Statistics/MatSample.hpp>
#include <H5Cpp.h>
BEGIN_LATAN_NAMESPACE

6
lib/Io.cpp → lib/Io/Io.cpp
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@@ -17,10 +17,10 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/Io/Io.hpp>
#include <LatAnalyze/includes.hpp>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Hdf5File.hpp>
#include <LatAnalyze/Io/AsciiFile.hpp>
#include <LatAnalyze/Io/Hdf5File.hpp>
using namespace std;
using namespace Latan;

2
lib/Io.hpp → lib/Io/Io.hpp
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@@ -21,7 +21,7 @@
#define Latan_Io_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/File.hpp>
#include <LatAnalyze/Io/File.hpp>
BEGIN_LATAN_NAMESPACE

0
lib/IoObject.hpp → lib/Io/IoObject.hpp
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2791
lib/Io/Xml/tinyxml2.cpp Normal file
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lib/Io/Xml/tinyxml2.hpp Normal file
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84
lib/Io/XmlReader.cpp Normal file
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@@ -0,0 +1,84 @@
/*
* XmlReader.cpp, part of LatAnalyze
*
* Copyright (C) 2013 - 2014 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Io/XmlReader.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;
using namespace Latan;
XmlParsing::XmlParsing(string msg, string loc)
: runtime_error("XML reader error: " + msg + " (" + loc + ")")
{}
/******************************************************************************
* XmlReader implementation *
******************************************************************************/
// constructor /////////////////////////////////////////////////////////////////
XmlReader::XmlReader(const string &fileName)
{
open(fileName);
}
// IO //////////////////////////////////////////////////////////////////////////
void XmlReader::open(const string &fileName)
{
name_ = fileName;
doc_.LoadFile(name_.c_str());
if (doc_.Error())
{
string errMsg;
if (doc_.ErrorStr())
{
errMsg = doc_.ErrorStr();
}
LATAN_ERROR(Io, "cannot open file " + fileName + " [tinyxml2 code "
+ strFrom(doc_.ErrorID()) + ": " + errMsg + "]");
}
root_ = doc_.RootElement();
}
// XML structure access ////////////////////////////////////////////////////////
const XmlNode * XmlReader::getNextNode(const XmlNode *node,
const string &nodeName)
{
const char *pt = (nodeName.empty()) ? nullptr : nodeName.c_str();
if (node)
{
return node->NextSiblingElement(pt);
}
else
{
return nullptr;
}
}
const XmlNode * XmlReader::getNextSameNode(const XmlNode *node)
{
if (node)
{
return getNextNode(node, node->Name());
}
else
{
return nullptr;
}
}

235
lib/Io/XmlReader.hpp Normal file
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@@ -0,0 +1,235 @@
/*
* XmlReader.hpp, part of LatAnalyze
*
* Copyright (C) 2013 - 2015 Antonin Portelli
*
* LatAnalyze 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 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. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef LatAnalyze_XmlReader_hpp_
#define LatAnalyze_XmlReader_hpp_
#include <LatAnalyze/Global.hpp>
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wsign-conversion"
#include <LatAnalyze/Io/Xml/tinyxml2.hpp>
#pragma GCC diagnostic pop
BEGIN_LATAN_NAMESPACE
// parsing exception
class XmlParsing: public std::runtime_error
{
public:
XmlParsing(std::string msg, std::string loc);
};
/******************************************************************************
* 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,
const std::string &nodeName = "");
static const XmlNode * getNextSameNode(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;
// XML structure test
template <typename... Strs>
static bool hasNode(const XmlNode *startNode, const std::string &nodeName,
Strs... nodeNames);
template <typename... Strs>
bool hasNode(const std::string &nodeName, Strs... nodeNames) const;
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,
"getFirstNode 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(Io, "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 Latan::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 = getNextSameNode(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...);
}
// XML structure test //////////////////////////////////////////////////////////
template <typename... Strs>
bool XmlReader::hasNode(const XmlNode *startNode, const std::string &nodeName,
Strs... nodeNames)
{
static_assert(static_or<std::is_assignable<std::string, Strs>::value...>::value,
"hasNode 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)
{
return false;
}
}
return true;
}
template <typename... Strs>
bool XmlReader::hasNode(const std::string &nodeName, Strs... nodeNames) const
{
if (!root_)
{
LATAN_ERROR(Io, "root node is null, no XML file opened");
}
return hasNode(root_, nodeName, nodeNames...);
}
END_LATAN_NAMESPACE
#endif // LatAnalyze_XmlReader_hpp_

188
lib/Makefile.am
View File

@@ -7,115 +7,133 @@ if CXX_INTEL
endif
endif
include eigen_files.mk
AM_LFLAGS = -olex.yy.c
AM_YFLAGS = -d
AM_YFLAGS = -y -d -Wno-yacc -Wno-deprecated
lib_LTLIBRARIES = libLatAnalyze.la
noinst_LTLIBRARIES = libLexers.la
libLexers_la_SOURCES = AsciiLexer.lpp MathLexer.lpp
libLexers_la_SOURCES = Io/AsciiLexer.lpp Core/MathLexer.lpp
if CXX_GNU
libLexers_la_CXXFLAGS = $(COM_CXXFLAGS) -Wno-unused-parameter -Wno-unused-function -Wno-deprecated-register
else
libLexers_la_CXXFLAGS = $(COM_CXXFLAGS)
endif
libLatAnalyze_la_SOURCES = \
AsciiFile.cpp \
AsciiParser.ypp \
CompiledFunction.cpp \
CompiledModel.cpp \
Derivative.cpp \
Exceptions.cpp \
File.cpp \
FitInterface.cpp \
Function.cpp \
Global.cpp \
GslFFT.cpp \
GslHybridRootFinder.cpp\
GslMinimizer.cpp \
GslQagsIntegrator.cpp \
Hdf5File.cpp \
Histogram.cpp \
includes.hpp \
Io.cpp \
Mat.cpp \
Math.cpp \
MathInterpreter.cpp \
MathParser.ypp \
Minimizer.cpp \
Model.cpp \
Plot.cpp \
RootFinder.cpp \
Solver.cpp \
StatArray.cpp \
TabFunction.cpp \
XYSampleData.cpp \
XYStatData.cpp \
libLatAnalyze_la_SOURCES = \
includes.hpp \
Global.cpp \
Core/Exceptions.cpp \
Core/Mat.cpp \
Core/Math.cpp \
Core/MathInterpreter.cpp \
Core/MathParser.ypp \
Core/OptParser.cpp \
Core/Plot.cpp \
Core/Utilities.cpp \
Functional/CompiledFunction.cpp \
Functional/CompiledModel.cpp \
Functional/Function.cpp \
Functional/Model.cpp \
Functional/TabFunction.cpp \
Io/AsciiFile.cpp \
Io/AsciiParser.ypp \
Io/BinReader.cpp \
Io/File.cpp \
Io/Hdf5File.cpp \
Io/Io.cpp \
Io/XmlReader.cpp \
Io/Xml/tinyxml2.cpp \
Numerical/Derivative.cpp \
Numerical/GslFFT.cpp \
Numerical/GslHybridRootFinder.cpp\
Numerical/GslMinimizer.cpp \
Numerical/GslQagsIntegrator.cpp \
Numerical/Minimizer.cpp \
Numerical/RootFinder.cpp \
Numerical/Solver.cpp \
Statistics/FitInterface.cpp \
Statistics/Histogram.cpp \
Statistics/Random.cpp \
Statistics/StatArray.cpp \
Statistics/XYSampleData.cpp \
Statistics/XYStatData.cpp \
../config.h
libLatAnalyze_ladir = $(pkgincludedir)
libLatAnalyze_la_HEADERS = \
AsciiFile.hpp \
CompiledFunction.hpp \
CompiledModel.hpp \
Dataset.hpp \
Derivative.hpp \
Exceptions.hpp \
FFT.hpp \
Function.hpp \
File.hpp \
FitInterface.hpp \
Global.hpp \
GslFFT.hpp \
GslHybridRootFinder.hpp\
GslMinimizer.hpp \
GslQagsIntegrator.hpp \
Hdf5File.hpp \
Histogram.hpp \
Integrator.hpp \
Io.hpp \
IoObject.hpp \
Mat.hpp \
Math.hpp \
MathInterpreter.hpp \
MatSample.hpp \
Minimizer.hpp \
Model.hpp \
ParserState.hpp \
Plot.hpp \
RootFinder.hpp \
TabFunction.hpp \
Solver.hpp \
StatArray.hpp \
XYSampleData.hpp \
XYStatData.hpp
HPPFILES = \
Global.hpp \
Core/Eigen.hpp \
Core/EigenPlugin.hpp \
Core/Exceptions.hpp \
Core/Mat.hpp \
Core/Math.hpp \
Core/MathInterpreter.hpp \
Core/OptParser.hpp \
Core/ParserState.hpp \
Core/Plot.hpp \
Core/stdincludes.hpp \
Core/Utilities.hpp \
Functional/CompiledFunction.hpp \
Functional/CompiledModel.hpp \
Functional/Function.hpp \
Functional/Model.hpp \
Functional/TabFunction.hpp \
Io/AsciiFile.hpp \
Io/BinReader.hpp \
Io/File.hpp \
Io/Hdf5File.hpp \
Io/Io.hpp \
Io/IoObject.hpp \
Io/XmlReader.hpp \
Numerical/Derivative.hpp \
Numerical/FFT.hpp \
Numerical/GslFFT.hpp \
Numerical/GslHybridRootFinder.hpp\
Numerical/GslMinimizer.hpp \
Numerical/GslQagsIntegrator.hpp \
Numerical/Integrator.hpp \
Numerical/Minimizer.hpp \
Numerical/RootFinder.hpp \
Numerical/Solver.hpp \
Statistics/Dataset.hpp \
Statistics/FitInterface.hpp \
Statistics/Histogram.hpp \
Statistics/MatSample.hpp \
Statistics/Random.hpp \
Statistics/StatArray.hpp \
Statistics/XYSampleData.hpp \
Statistics/XYStatData.hpp
if HAVE_MINUIT
libLatAnalyze_la_SOURCES += MinuitMinimizer.cpp
libLatAnalyze_la_HEADERS += MinuitMinimizer.hpp
libLatAnalyze_la_SOURCES += Numerical/MinuitMinimizer.cpp
HPPFILES += Numerical/MinuitMinimizer.hpp
endif
if HAVE_NLOPT
libLatAnalyze_la_SOURCES += NloptMinimizer.cpp
libLatAnalyze_la_HEADERS += NloptMinimizer.hpp
libLatAnalyze_la_SOURCES += Numerical/NloptMinimizer.cpp
HPPFILES += Numerical/NloptMinimizer.hpp
endif
libLatAnalyze_la_CXXFLAGS = $(COM_CXXFLAGS)
libLatAnalyze_la_LIBADD = libLexers.la
if HAVE_AM_MINOR_LE_11
AsciiParser.hpp: AsciiParser.ypp
$(AM_V_YACC) $(YACC) -o AsciiParser.cpp --defines=AsciiParser.hpp $<
Io/AsciiParser.hpp: Io/AsciiParser.ypp
$(AM_V_YACC) $(YACC) -o Io/AsciiParser.cpp --defines=Io/AsciiParser.hpp $<
MathParser.hpp: MathParser.ypp
$(AM_V_YACC) $(YACC) -o MathParser.cpp --defines=MathParser.hpp $<
Core/MathParser.hpp: Core/MathParser.ypp
$(AM_V_YACC) $(YACC) -o Core/MathParser.cpp --defines=Core/MathParser.hpp $<
endif
BUILT_SOURCES = AsciiParser.hpp MathParser.hpp
BUILT_SOURCES = Io/AsciiParser.hpp Core/MathParser.hpp
CLEANFILES = \
MathLexer.cpp \
AsciiLexer.cpp \
AsciiParser.cpp\
AsciiParser.hpp\
MathParser.cpp \
MathParser.hpp
CLEANFILES = \
Core/MathLexer.cpp \
Core/MathParser.cpp\
Core/MathParser.hpp\
Io/AsciiLexer.cpp \
Io/AsciiParser.cpp \
Io/AsciiParser.hpp
nobase_dist_pkginclude_HEADERS = $(HPPFILES) $(eigen_files) Io/Xml/tinyxml2.hpp
ACLOCAL_AMFLAGS = -I .buildutils/m4

4
lib/Derivative.cpp → lib/Numerical/Derivative.cpp
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@@ -17,9 +17,9 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Derivative.hpp>
#include <LatAnalyze/Numerical/Derivative.hpp>
#include <LatAnalyze/includes.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Core/Math.hpp>
using namespace std;
using namespace Latan;

2
lib/Derivative.hpp → lib/Numerical/Derivative.hpp
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@@ -21,7 +21,7 @@
#define Latan_Derivative_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Functional/Function.hpp>
BEGIN_LATAN_NAMESPACE

0
lib/FFT.hpp → lib/Numerical/FFT.hpp
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2
lib/GslFFT.cpp → lib/Numerical/GslFFT.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/GslFFT.hpp>
#include <LatAnalyze/Numerical/GslFFT.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

4
lib/GslFFT.hpp → lib/Numerical/GslFFT.hpp
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@@ -21,8 +21,8 @@
#define Latan_GslFFT_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/FFT.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Numerical/FFT.hpp>
#include <gsl/gsl_fft_complex.h>
BEGIN_LATAN_NAMESPACE

2
lib/GslHybridRootFinder.cpp → lib/Numerical/GslHybridRootFinder.cpp
View File

@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/GslHybridRootFinder.hpp>
#include <LatAnalyze/Numerical/GslHybridRootFinder.hpp>
#include <LatAnalyze/includes.hpp>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_multiroots.h>

2
lib/GslHybridRootFinder.hpp → lib/Numerical/GslHybridRootFinder.hpp
View File

@@ -21,7 +21,7 @@
#define Latan_GslHybridRootFinder_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/RootFinder.hpp>
#include <LatAnalyze/Numerical/RootFinder.hpp>
#include <gsl/gsl_multiroots.h>
BEGIN_LATAN_NAMESPACE

4
lib/GslMinimizer.cpp → lib/Numerical/GslMinimizer.cpp
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@@ -17,9 +17,9 @@
* along with LatAnalyze. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/GslMinimizer.hpp>
#include <LatAnalyze/Numerical/GslMinimizer.hpp>
#include <LatAnalyze/includes.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Core/Math.hpp>
#include <gsl/gsl_multimin.h>
#include <gsl/gsl_blas.h>

6
lib/GslMinimizer.hpp → lib/Numerical/GslMinimizer.hpp
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@@ -21,9 +21,9 @@
#define Latan_GslMinimizer_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Derivative.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Minimizer.hpp>
#include <LatAnalyze/Numerical/Derivative.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Numerical/Minimizer.hpp>
#include <gsl/gsl_vector.h>
BEGIN_LATAN_NAMESPACE

4
lib/GslQagsIntegrator.cpp → lib/Numerical/GslQagsIntegrator.cpp
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@@ -17,9 +17,9 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/GslQagsIntegrator.hpp>
#include <LatAnalyze/Numerical/GslQagsIntegrator.hpp>
#include <LatAnalyze/includes.hpp>
#include <LatAnalyze/Math.hpp>
#include <LatAnalyze/Core/Math.hpp>
using namespace std;
using namespace Latan;

4
lib/GslQagsIntegrator.hpp → lib/Numerical/GslQagsIntegrator.hpp
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@@ -21,8 +21,8 @@
#define Latan_GslQagsIntegrator_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Integrator.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Numerical/Integrator.hpp>
#include <gsl/gsl_integration.h>
BEGIN_LATAN_NAMESPACE

2
lib/Integrator.hpp → lib/Numerical/Integrator.hpp
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@@ -21,7 +21,7 @@
#define Latan_Integrator_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Functional/Function.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/Minimizer.cpp → lib/Numerical/Minimizer.cpp
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@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Minimizer.hpp>
#include <LatAnalyze/Numerical/Minimizer.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

6
lib/Minimizer.hpp → lib/Numerical/Minimizer.hpp
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@@ -21,9 +21,9 @@
#define Latan_Minimizer_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/Solver.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Core/Mat.hpp>
#include <LatAnalyze/Numerical/Solver.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/MinuitMinimizer.cpp → lib/Numerical/MinuitMinimizer.cpp
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@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/MinuitMinimizer.hpp>
#include <LatAnalyze/Numerical/MinuitMinimizer.hpp>
#include <LatAnalyze/includes.hpp>
#include <Minuit2/Minuit2Minimizer.h>
#include <Math/Functor.h>

4
lib/MinuitMinimizer.hpp → lib/Numerical/MinuitMinimizer.hpp
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@@ -21,8 +21,8 @@
#define Latan_MinuitMinimizer_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Minimizer.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Numerical/Minimizer.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/NloptMinimizer.cpp → lib/Numerical/NloptMinimizer.cpp
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@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/NloptMinimizer.hpp>
#include <LatAnalyze/Numerical/NloptMinimizer.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

6
lib/NloptMinimizer.hpp → lib/Numerical/NloptMinimizer.hpp
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@@ -21,9 +21,9 @@
#define Latan_NloptMinimizer_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Derivative.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Minimizer.hpp>
#include <LatAnalyze/Numerical/Derivative.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Numerical/Minimizer.hpp>
#include <nlopt.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/RootFinder.cpp → lib/Numerical/RootFinder.cpp
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@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/RootFinder.hpp>
#include <LatAnalyze/Numerical/RootFinder.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

4
lib/RootFinder.hpp → lib/Numerical/RootFinder.hpp
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@@ -21,8 +21,8 @@
#define Latan_RootFinder_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/Function.hpp>
#include <LatAnalyze/Solver.hpp>
#include <LatAnalyze/Functional/Function.hpp>
#include <LatAnalyze/Numerical/Solver.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/Solver.cpp → lib/Numerical/Solver.cpp
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@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Solver.hpp>
#include <LatAnalyze/Numerical/Solver.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

0
lib/Solver.hpp → lib/Numerical/Solver.hpp
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4
lib/Dataset.hpp → lib/Statistics/Dataset.hpp
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@@ -21,8 +21,8 @@
#define Latan_Dataset_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/File.hpp>
#include <LatAnalyze/StatArray.hpp>
#include <LatAnalyze/Io/File.hpp>
#include <LatAnalyze/Statistics/StatArray.hpp>
BEGIN_LATAN_NAMESPACE

2
lib/FitInterface.cpp → lib/Statistics/FitInterface.cpp
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@@ -17,7 +17,7 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/FitInterface.hpp>
#include <LatAnalyze/Statistics/FitInterface.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;

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