Merge branch 'develop' into feature/fit-phys

.gitignore

@@ -31,6 +31,7 @@ lib/eigen_files.mk
 # CI builds
 ci-scripts/local/*
 
-# VS Code Studio stuff
-.vscode
-*.code-workspace
+# CLion stuff
+.idea/*
+CMakeLists.txt
+cmake-build-debug/*

.travis.yml

@@ -1,5 +1,9 @@
 language: cpp
 
+notifications:
+  email: false
+  slack: ukqcd:mQLXCtz8D2cg89xT8j1a4wku
+  
 cache:
   directories:
     - ci-scripts/local
@@ -8,32 +12,56 @@ cache:
 matrix:
   include:
     - os:        osx
-      osx_image: xcode10.1
+      osx_image: xcode7.2
       compiler: clang
     - os:        osx
-      osx_image: xcode10.1
+      osx_image: xcode7.2
       compiler: gcc
-      env: VERSION=-7
+      env: VERSION=-5
     - compiler: gcc
       addons:
         apt:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-7
+            - g++-4.9
+            - libgsl0-dev
             - flex
             - bison
-      env: VERSION=-7
+      env: VERSION=-4.9
+    - compiler: gcc
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - g++-5
+            - libgsl0-dev
+            - flex
+            - bison
+      env: VERSION=-5
     - compiler: clang
       addons:
         apt:
           sources:
             - ubuntu-toolchain-r-test
           packages:
-            - g++-7
+            - g++-4.8
+            - 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
+      env: CLANG_LINK=http://llvm.org/releases/3.6.0/clang+llvm-3.6.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
+    - compiler: clang
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - g++-4.8
+            - libgsl0-dev
+            - flex
+            - bison
+      env: CLANG_LINK=http://llvm.org/releases/3.7.0/clang+llvm-3.7.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz
 
 before_install:
   - export LATDIR=`pwd`
@@ -42,8 +70,9 @@ 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 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
+  - 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" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc5; fi
   
 install:
   - export CC=$CC$VERSION
@@ -56,8 +85,7 @@ install:
   - ./install-deps.sh `pwd`/local
   - cd ..
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export LD_LIBRARY_PATH=${LATDIR}/ci-scripts/local/lib:$LD_LIBRARY_PATH; fi
-  - if [[ "$CC" == "gcc-7" ]]; then export CXXFLAGS='-Wno-int-in-bool-context'; fi
 
 script:
   - cd ci-scripts
-  - ./install-latan.sh `pwd`/local
+  - ./install-latan.sh `pwd`/local $TRAVIS_OS_NAME

Makefile.am

@@ -1,5 +1,3 @@
 SUBDIRS = lib utils physics examples
 
-bin_SCRIPTS=latan-config
-
 ACLOCAL_AMFLAGS = -I .buildutils/m4

Readme.md

@@ -1,4 +1,5 @@
 # LatAnalyze 
+Contributors: Antonin Portelli, Matt Spraggs
 
 License: GNU General Public License v3
 
@@ -40,93 +41,22 @@ 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 only strict dependencies is the [GSL](http://www.gnu.org/software/gsl/).
+The strict dependencies are the [GSL](http://www.gnu.org/software/gsl/) and [LatCore](https://github.com/aportelli/LatCore).
 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>
+./install-latan.sh <prefix> {osx|linux}
 ``` 
-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.
+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).
 
-### 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).
+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`.
 
 ## History
-#### v3.5.1
-Various fixes and cleaning of outdated code.
-
-#### 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
-* Linear and constant models to the 2-point fitter
-
-Changes:
-* HDF5 is now a compulsory dependency
-
-Fixes:
-* Variance matrix computation fix.
-
-#### v3.3
-Additions:
-* Sample plot CL utility.
-* Infinity as a math constant.
-* Option to dump bootstrap sequence while resampling.
-* FFT through the GSL.
-
-Changes:
-* GSL integrator accepts infinite bounds.
-* `latan-sample-combine` accepts mixes of `DSample` and `DMatSample`.
-* More general `latan-sample-element` command.
-
-#### v3.2.2
-Additions:
-* The math interpreter supports `inf` for infinity.
-
-Changes:
-* Vector version of `setUnidimData`.
-
-Fixes:
-* Variance matrix computation fix.
-
 #### v3.2.1
-Fixes:
+Fix:
 * Wrong argument number check in `latan-resample`
 
 #### v3.2 (needs LatCore 1.1)

bootstrap.sh

@@ -2,5 +2,4 @@
 
 rm -rf .buildutils
 mkdir -p .buildutils/m4
-./update_eigen.sh eigen-3.3.8.tar.bz2
 autoreconf -fvi

ci-scripts/install-deps.sh

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

ci-scripts/install-gsl.sh

@@ -1,26 +0,0 @@
-#!/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 -P)
-mkdir -p ${PREFIX}
-cd ${PREFIX}
-PREFIX=$(pwd -P)
-cd ${INITDIR}/local/build
-wget http://ftpmirror.gnu.org/gsl/${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}

ci-scripts/install-hdf5.sh

@@ -1,20 +1,17 @@
 #!/usr/bin/env bash
 
-NAME='hdf5-1.10.5'
+NAME='hdf5-1.8.16'
 
 if (( $# != 1 )); then
-  echo "usage: `basename $0` <prefix>" 1>&2
+  echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
   exit 1
 fi
 PREFIX=$1
 
 set -ex
-INITDIR=$(pwd -P)
-mkdir -p ${PREFIX}
-cd ${PREFIX}
-PREFIX=$(pwd -P)
-cd ${INITDIR}/local/build
-wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${NAME}/src/${NAME}.tar.gz
+INITDIR=`pwd`
+cd local/build
+wget http://www.hdfgroup.org/ftp/HDF5/releases/${NAME}/src/${NAME}.tar.gz
 tar -xzvf ${NAME}.tar.gz
 mkdir ${NAME}/build
 cd ${NAME}/build

ci-scripts/install-latan.sh

@@ -1,22 +1,19 @@
 #!/usr/bin/env bash
 
-if (( $# != 1 )); then
-  echo "usage: `basename $0` <prefix>" 1>&2
+if (( $# != 2 )); then
+  echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
   exit 1
 fi
 PREFIX=$1
+OS=$2
 
 set -ex
-INITDIR=$(pwd -P)
-mkdir -p ${PREFIX}
-cd ${PREFIX}
-PREFIX=$(pwd -P)
-cd ${INITDIR}
 ./install-deps.sh ${PREFIX}
 cd ..
 ./bootstrap.sh
 mkdir -p build
 cd build
-../configure --prefix=${PREFIX} --with-minuit=${PREFIX} --with-nlopt=${PREFIX} --with-hdf5=${PREFIX} --with-gsl=${PREFIX} CXXFLAGS="${CXXFLAGS} -O3 -march=haswell -mtune=haswell"
+if [[ "$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='-O3 -march=native -mtune=native'
 make -j4
 make install

ci-scripts/install-latcore.sh

@@ -0,0 +1,25 @@
+#!/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}

ci-scripts/install-minuit.sh

@@ -3,17 +3,14 @@
 NAME='Minuit2-5.34.14'
 
 if (( $# != 1 )); then
-  echo "usage: `basename $0` <prefix>" 1>&2
+  echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
   exit 1
 fi
 PREFIX=$1
 
 set -ex
-INITDIR=$(pwd -P)
-mkdir -p ${PREFIX}
-cd ${PREFIX}
-PREFIX=$(pwd -P)
-cd ${INITDIR}/local/build
+INITDIR=`pwd`
+cd local/build
 wget http://www.cern.ch/mathlibs/sw/5_34_14/Minuit2/${NAME}.tar.gz
 tar -xzvf ${NAME}.tar.gz
 mkdir -p ${NAME}/build

ci-scripts/install-nlopt.sh

@@ -1,25 +1,21 @@
 #!/usr/bin/env bash
 
-NAME='2.6.1'
+NAME='nlopt-2.4.2'
 
 if (( $# != 1 )); then
-  echo "usage: `basename $0` <prefix>" 1>&2
+  echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
   exit 1
 fi
 PREFIX=$1
 
 set -ex
-INITDIR=$(pwd -P)
-mkdir -p ${PREFIX}
-cd ${PREFIX}
-PREFIX=$(pwd -P)
-cd ${INITDIR}/local/build
-wget https://github.com/stevengj/nlopt/archive/v${NAME}.tar.gz
-tar -xzvf v${NAME}.tar.gz
-NAME=nlopt-${NAME}
+INITDIR=`pwd`
+cd local/build
+wget http://ab-initio.mit.edu/nlopt/${NAME}.tar.gz
+tar -xzvf ${NAME}.tar.gz
 mkdir -p ${NAME}/build
 cd ${NAME}/build
-cmake -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_WITH_INSTALL_NAME_DIR=TRUE -DCMAKE_INSTALL_NAME_DIR="${PREFIX}/lib" ..
+../configure --prefix=${PREFIX} --with-cxx --without-guile --without-python --without-octave --without-matlab --with-pic
 make -j4 
 make install
 cd ${INITDIR}/local

configure.ac

@@ -2,13 +2,13 @@
 
 # Initialization
 AC_PREREQ([2.63])
-AC_INIT([LatAnalyze],[3.5.1],[antonin.portelli@me.com],[LatAnalyze])
+AC_INIT([LatAnalyze],[3.2.1-dev],[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 subdir-objects])
+AM_INIT_AUTOMAKE([1.11 -Wall -Werror foreign])
 AM_SILENT_RULES([yes])
 AC_CONFIG_HEADERS([config.h])
 AM_CONDITIONAL([HAVE_AM_MINOR_LE_11],
@@ -48,6 +48,14 @@ 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"])
+CFLAGS="$AM_CFLAGS $CFLAGS"
+CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
+LDFLAGS="$AM_LDFLAGS $LDFLAGS"
 
 # Get compilers informations
 AX_COMPILER_VENDOR
@@ -70,24 +78,24 @@ AC_DEFINE_UNQUOTED([GXX_VERSION],["$GXX_VERSION"],
 			[version of g++ that will compile the code])
 
 # Checks for libraries.
-CXXFLAGS_CPY=$CXXFLAGS
-LDFLAGS_CPY=$LDFLAGS
-CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
-LDFLAGS="$AM_LDFLAGS $LDFLAGS"
 AC_CHECK_LIB([m],[cos],[],[AC_MSG_ERROR([libm library not found])])
 AC_CHECK_LIB([gslcblas],[cblas_dgemm],[],
              [AC_MSG_ERROR([GSL CBLAS library not found])])
 AC_CHECK_LIB([gsl],[gsl_blas_dgemm],[],[AC_MSG_ERROR([GSL library not found])])
-AC_CHECK_LIB([nlopt],[nlopt_create],
+AC_CHECK_LIB([nlopt_cxx],[nlopt_create],
     [AC_DEFINE([HAVE_NLOPT],
     [1],
-    [Define to 1 if you have the `NLopt' library (-lnlopt).])]
+    [Define to 1 if you have the `NLopt' library (-lnlopt_cxx).])]
     [have_nlopt=true]
-    [LIBS="$LIBS -lnlopt"],[])
+    [LIBS="$LIBS -lnlopt_cxx"],[])
 AM_CONDITIONAL([HAVE_NLOPT], [test x$have_nlopt = xtrue])
 AC_CHECK_LIB([hdf5_cpp],[H5Fopen],
-    [LIBS="$LIBS -lhdf5_cpp -lhdf5"],
-    [AC_MSG_ERROR([HDF5 library not found])], [-lhdf5])
+    [AC_DEFINE([HAVE_HDF5],
+    [1],
+    [Define to 1 if you have the `HDF5' library (-lhdf5_cpp).])]
+    [have_hdf5=true]
+    [LIBS="$LIBS -lhdf5_cpp -lhdf5"],[],[-lhdf5])
+AM_CONDITIONAL([HAVE_HDF5], [test x$have_hdf5 = xtrue])
 SAVED_LDFLAGS=$LDFLAGS
 LDFLAGS="$LDFLAGS -lMinuit2"
 AC_MSG_CHECKING([for ROOT::Minuit2::BasicMinimumError in -lMinuit2]);
@@ -104,44 +112,35 @@ AC_LINK_IFELSE(
     [AC_MSG_RESULT([no])])
 AM_CONDITIONAL([HAVE_MINUIT], [test x$have_minuit = xtrue])
 LDFLAGS=$SAVED_LDFLAGS
-CXXFLAGS=$CXXFLAGS_CPY
-LDFLAGS=$LDFLAGS_CPY
+SAVED_LDFLAGS=$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
 
 # Checks for header files.
 AC_HEADER_STDC
 
-cwd=`pwd -P`; cd ${srcdir}; abs_srcdir=`pwd -P`; cd ${cwd}
-LATAN_CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
-LATAN_LDFLAGS="$AM_LDFLAGS $LDFLAGS"
-LATAN_LIBS=$LIBS
-LATAN_SHORT_SHA=`git rev-parse --short HEAD`
-LATAN_SHA=`git rev-parse HEAD`
-LATAN_BRANCH=`git rev-parse --abbrev-ref HEAD`
-AM_CXXFLAGS="-I${abs_srcdir}/lib $AM_CXXFLAGS"
-AM_CFLAGS="-I${abs_srcdir}/lib $AM_CFLAGS"
-CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
-LDFLAGS="$AM_LDFLAGS $LDFLAGS"
 AC_SUBST([LIBS])
-AC_SUBST([AM_CXXFLAGS])
+AC_SUBST([AM_CFLAGS])
 AC_SUBST([AM_LDFLAGS])
-AC_SUBST([LATAN_CXXFLAGS])
-AC_SUBST([LATAN_LDFLAGS])
-AC_SUBST([LATAN_LIBS])
-AC_SUBST([LATAN_SHA])
-AC_SUBST([LATAN_BRANCH])
 
-AC_CONFIG_FILES([latan-config], [chmod +x latan-config])
-AC_CONFIG_FILES([Makefile])
-AC_CONFIG_FILES([lib/Makefile])
-AC_CONFIG_FILES([utils/Makefile])
-AC_CONFIG_FILES([physics/Makefile])
-AC_CONFIG_FILES([examples/Makefile])
+AC_CONFIG_FILES([Makefile lib/Makefile utils/Makefile physics/Makefile 
+                 examples/Makefile])
 AC_OUTPUT
 
 echo "*********************************************"
 echo "* ${PACKAGE_NAME} v${VERSION}" build options
 echo "*********************************************"
 echo "* C++ compiler     : $CXX"
+echo "* HDF5 support     : `test x$HAVE_HDF5_TRUE = 'x'   && echo yes \
+                                                          || echo no`"
 echo "* Minuit minimizers: `test x$HAVE_MINUIT_TRUE = 'x' && echo yes \
                                                           || echo no`"
 echo "* NLopt minimizers : `test x$HAVE_NLOPT_TRUE = 'x'  && echo yes \

examples/Makefile.am

@@ -17,7 +17,6 @@ noinst_PROGRAMS =           \
     exMathInterpreter       \
     exMin                   \
     exPlot                  \
-    exPValue                \
     exRand                  \
     exRootFinder
 
@@ -61,10 +60,6 @@ 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

examples/exCompiledDoubleFunction.cpp

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

examples/exDerivative.cpp

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

examples/exFit.cpp

@@ -1,10 +1,10 @@
 #include <iostream>
 #include <cmath>
-#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>
+#include <LatAnalyze/CompiledModel.hpp>
+#include <LatAnalyze/Io.hpp>
+#include <LatAnalyze/GslMinimizer.hpp>
+#include <LatAnalyze/Plot.hpp>
+#include <LatAnalyze/XYStatData.hpp>
 
 using namespace std;
 using namespace Latan;

examples/exFitSample.cpp

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

examples/exIntegrator.cpp

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

examples/exInterp.cpp

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

examples/exMat.cpp

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

examples/exMathInterpreter.cpp

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

examples/exMin.cpp

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

examples/exPValue.cpp

@@ -1,23 +0,0 @@
-#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;
-}

examples/exPlot.cpp

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

examples/exRand.cpp

@@ -1,15 +1,11 @@
-#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>
+#include <LatAnalyze/Io.hpp>
+#include <LatAnalyze/CompiledFunction.hpp>
+#include <LatAnalyze/Plot.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)
@@ -40,24 +36,5 @@ 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;
 }

examples/exRootFinder.cpp

@@ -1,5 +1,5 @@
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Numerical/GslHybridRootFinder.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/GslHybridRootFinder.hpp>
 
 using namespace std;
 using namespace Latan;
@@ -7,8 +7,8 @@ using namespace Latan;
 int main(void)
 {
     constexpr double a = 1., b = 10.;
-    DoubleFunction f1([](const double *x){return a*(1.-x[0]);}, 2);
-    DoubleFunction f2([](const double *x){return b*(x[1]-x[0]*x[0]);}, 2);
+    DoubleFunction f1([a](const double *x){return a*(1.-x[0]);}, 2);
+    DoubleFunction f2([b](const double *x){return b*(x[1]-x[0]*x[0]);}, 2);
     vector<DoubleFunction *> system = {&f1, &f2};
     GslHybridRootFinder solve;
     DVec init(2), x;

latan-config.in

@@ -1,79 +0,0 @@
-#! /bin/sh
-
-prefix=@prefix@
-exec_prefix=@exec_prefix@
-includedir=@includedir@
-
-usage()
-{
-  cat <<EOF
-Usage: latan-config [OPTION]
-
-Known values for OPTION are:
-
-  --prefix     show LatAnalyze installation prefix
-  --cxxflags   print pre-processor and compiler flags
-  --ldflags    print library linking flags
-  --libs       print library linking information
-  --help       display this help and exit
-  --version    output version information
-  --git        print git revision
-
-EOF
-  
-  exit $1
-}
-
-if test $# -eq 0; then
-  usage 1
-fi
-
-cflags=false
-libs=false
-
-while test $# -gt 0; do
-  case "$1" in
-    -*=*) optarg=`echo "$1" | sed 's/[-_a-zA-Z0-9]*=//'` ;;
-    *) optarg= ;;
-  esac
-  
-  case "$1" in
-    --prefix)
-      echo $prefix
-    ;;
-    
-    --version)
-      echo @VERSION@
-      exit 0
-    ;;
-    
-    --git)
-      echo "@LATAN_BRANCH@ @LATAN_SHA@"
-      exit 0
-    ;;
-    
-    --help)
-      usage 0
-    ;;
-    
-    --cxxflags)
-      echo @LATAN_CXXFLAGS@
-    ;;
-    
-    --ldflags)
-      echo @LATAN_LDFLAGS@
-    ;;
-    
-    --libs)
-      echo @LIBS@
-    ;;
-    
-    *)
-      usage
-      exit 1
-    ;;
-  esac
-  shift
-done
-
-exit 0

lib/AsciiFile.cpp

@@ -1,7 +1,7 @@
 /*
  * AsciiFile.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Io/AsciiFile.hpp>
+#include <LatAnalyze/AsciiFile.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/AsciiFile.hpp

@@ -1,7 +1,7 @@
 /*
  * AsciiFile.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,10 +21,10 @@
 #define Latan_AsciiFile_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Io/File.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
-#include <LatAnalyze/Statistics/MatSample.hpp>
-#include <LatAnalyze/Core/ParserState.hpp>
+#include <LatAnalyze/File.hpp>
+#include <LatAnalyze/Mat.hpp>
+#include <LatAnalyze/MatSample.hpp>
+#include <LatAnalyze/ParserState.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/AsciiLexer.lpp

@@ -1,7 +1,7 @@
 /*
  * AsciiLexer.lpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -25,7 +25,7 @@
 %option yylineno
 
 %{
-	#include <LatAnalyze/Io/AsciiFile.hpp>
+	#include <LatAnalyze/AsciiFile.hpp>
 	#include "AsciiParser.hpp"
     
     using namespace std;

lib/AsciiParser.ypp

@@ -1,7 +1,7 @@
 /*
  * AsciiParser.ypp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -19,9 +19,9 @@
 
 %{
     #include <LatAnalyze/Global.hpp>
-	#include <LatAnalyze/Io/AsciiFile.hpp>
-    #include <LatAnalyze/Core/Mat.hpp>
-    #include <LatAnalyze/Statistics/MatSample.hpp>
+	#include <LatAnalyze/AsciiFile.hpp>
+    #include <LatAnalyze/Mat.hpp>
+    #include <LatAnalyze/MatSample.hpp>
 
     using namespace std;
     using namespace Latan;

lib/CompiledFunction.cpp

@@ -1,7 +1,7 @@
 /*
  * CompiledFunction.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,8 +17,8 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Functional/CompiledFunction.hpp>
-#include <LatAnalyze/Core/Math.hpp>
+#include <LatAnalyze/CompiledFunction.hpp>
+#include <LatAnalyze/Math.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/CompiledFunction.hpp

@@ -1,7 +1,7 @@
 /*
  * CompiledFunction.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define	Latan_CompiledFunction_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Core/MathInterpreter.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/MathInterpreter.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/CompiledModel.cpp

@@ -1,7 +1,7 @@
 /*
  * CompiledModel.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,8 +17,8 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Functional/CompiledModel.hpp>
-#include <LatAnalyze/Core/Math.hpp>
+#include <LatAnalyze/CompiledModel.hpp>
+#include <LatAnalyze/Math.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/CompiledModel.hpp

@@ -1,7 +1,7 @@
 /*
  * CompiledModel.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define Latan_CompiledModel_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Model.hpp>
-#include <LatAnalyze/Core/MathInterpreter.hpp>
+#include <LatAnalyze/Model.hpp>
+#include <LatAnalyze/MathInterpreter.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/Core/Eigen.hpp

@@ -1,123 +0,0 @@
-/*
- * Eigen.hpp, part of LatAnalyze 3
- *
- * Copyright (C) 2013 - 2020 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

lib/Core/EigenPlugin.hpp

@@ -1,60 +0,0 @@
-/*
- * 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();
-}

lib/Core/OptParser.cpp

@@ -1,299 +0,0 @@
-/*
- * 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;
-}

lib/Core/OptParser.hpp

@@ -1,103 +0,0 @@
-/*
- * 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_

lib/Core/Utilities.cpp

@@ -1,137 +0,0 @@
-/*
- * Utilities.cpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2020 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());
-}

lib/Core/Utilities.hpp

@@ -1,250 +0,0 @@
-/*
- * Utilities.hpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2020 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_

lib/Core/stdincludes.hpp

@@ -1,56 +0,0 @@
-/*
- * stdincludes.hpp, part of LatAnalyze 3
- *
- * Copyright (C) 2013 - 2020 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_

lib/Dataset.hpp

@@ -1,7 +1,7 @@
 /*
  * Dataset.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define Latan_Dataset_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Io/File.hpp>
-#include <LatAnalyze/Statistics/StatArray.hpp>
+#include <LatAnalyze/File.hpp>
+#include <LatAnalyze/StatArray.hpp>
 
 BEGIN_LATAN_NAMESPACE
 
@@ -47,8 +47,6 @@ public:
     // resampling
     Sample<T> bootstrapMean(const Index nSample, const SeedType seed);
     Sample<T> bootstrapMean(const Index nSample);
-    void      dumpBootstrapSeq(std::ostream &out, const Index nSample,
-                               const SeedType seed);
 private:
     // mean from pointer vector for resampling
     void ptVectorMean(T &m, const std::vector<const T *> &v);
@@ -116,23 +114,6 @@ Sample<T> Dataset<T>::bootstrapMean(const Index nSample)
     return bootstrapMean(nSample, rd());
 }
 
-template <typename T>
-void Dataset<T>::dumpBootstrapSeq(std::ostream &out, const Index nSample,
-                                  const SeedType seed)
-{
-    std::mt19937                         gen(seed);
-    std::uniform_int_distribution<Index> dis(0, this->size() - 1);
-
-    for (Index i = 0; i < nSample; ++i)
-    {
-        for (unsigned int j = 0; j < this->size(); ++j)
-        {
-            out << dis(gen) << " " << std::endl;
-        }
-        out << std::endl;
-    }
-}
-
 template <typename T>
 void Dataset<T>::ptVectorMean(T &m, const std::vector<const T *> &v)
 {

lib/Derivative.cpp

@@ -1,7 +1,7 @@
 /*
  * Derivative.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,9 +17,9 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Numerical/Derivative.hpp>
+#include <LatAnalyze/Derivative.hpp>
 #include <LatAnalyze/includes.hpp>
-#include <LatAnalyze/Core/Math.hpp>
+#include <LatAnalyze/Math.hpp>
 
 using namespace std;
 using namespace Latan;

lib/Derivative.hpp

@@ -1,7 +1,7 @@
 /*
  * Derivative.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,7 +21,7 @@
 #define Latan_Derivative_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
+#include <LatAnalyze/Function.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/Exceptions.cpp

@@ -1,7 +1,7 @@
 /*
  * Exceptions.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Core/Exceptions.hpp>
+#include <LatAnalyze/Exceptions.hpp>
 #include <LatAnalyze/includes.hpp>
 
 #ifndef ERR_SUFF

lib/Exceptions.hpp

@@ -1,7 +1,7 @@
 /*
  * Exceptions.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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

lib/File.cpp

@@ -1,7 +1,7 @@
 /*
  * File.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Io/File.hpp>
+#include <LatAnalyze/File.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/File.hpp

@@ -1,7 +1,7 @@
 /*
  * File.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,9 +21,9 @@
 #define	Latan_File_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Io/IoObject.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
-#include <LatAnalyze/Statistics/MatSample.hpp>
+#include <LatAnalyze/IoObject.hpp>
+#include <LatAnalyze/Mat.hpp>
+#include <LatAnalyze/MatSample.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/FitInterface.cpp

@@ -1,7 +1,7 @@
 /*
  * FitInterface.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Statistics/FitInterface.hpp>
+#include <LatAnalyze/FitInterface.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;
@@ -200,7 +200,6 @@ double FitInterface::getSvdTolerance(void) const
 void FitInterface::setSvdTolerance(const double &tol)
 {
     svdTol_ = tol;
-    scheduleLayoutInit();
 }
 
 VarName & FitInterface::xName(void)

lib/FitInterface.hpp

@@ -1,7 +1,7 @@
 /*
  * FitInterface.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,7 +21,7 @@
 #define Latan_FitInterface_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
+#include <LatAnalyze/Mat.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/Function.cpp

@@ -1,7 +1,7 @@
 /*
  * Function.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Functional/Function.hpp>
+#include <LatAnalyze/Function.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;
@@ -111,20 +111,6 @@ 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
@@ -179,26 +165,6 @@ 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
 {

lib/Function.hpp

@@ -1,7 +1,7 @@
 /*
  * Function.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define	Latan_Function_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
-#include <LatAnalyze/Statistics/MatSample.hpp>
+#include <LatAnalyze/Mat.hpp>
+#include <LatAnalyze/MatSample.hpp>
 
 BEGIN_LATAN_NAMESPACE
 
@@ -52,12 +52,9 @@ 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);

lib/Global.cpp

@@ -1,7 +1,7 @@
 /*
  * Global.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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

lib/Global.hpp

@@ -1,7 +1,7 @@
 /*
  * Global.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -20,27 +20,13 @@
 #ifndef Latan_Global_hpp_
 #define	Latan_Global_hpp_
 
-#include <LatAnalyze/Core/stdincludes.hpp>
+#include <LatCore/LatCore.hpp>
 
 #define BEGIN_LATAN_NAMESPACE \
-namespace Latan {
+namespace Latan {\
+using namespace LatCore;
 #define END_LATAN_NAMESPACE }
 
-// macro utilities
-#define unique_arg(...) __VA_ARGS__
-#define DEBUG_VAR(x) std::cout << #x << "= "  << x << std::endl
-#define DEBUG_MAT(m) std::cout << #m << "=\n" << m << std::endl
-
-// attribute to switch off unused warnings with gcc
-#ifdef __GNUC__
-#define __dumb __attribute__((unused))
-#else
-#define __dumb
-#endif
-
-// max length for paths
-#define MAX_PATH_LENGTH 512u
-
 BEGIN_LATAN_NAMESPACE
 
 // Placeholder type ////////////////////////////////////////////////////////////
@@ -61,8 +47,6 @@ namespace Env
 
 END_LATAN_NAMESPACE
 
-#include <LatAnalyze/Core/Eigen.hpp>
-#include <LatAnalyze/Core/Exceptions.hpp>
-#include <LatAnalyze/Core/Utilities.hpp>
+#include <LatAnalyze/Exceptions.hpp>
 
 #endif // Latan_Global_hpp_

lib/GslHybridRootFinder.cpp

@@ -1,7 +1,7 @@
 /*
  * GslHybridRootFinder.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Numerical/GslHybridRootFinder.hpp>
+#include <LatAnalyze/GslHybridRootFinder.hpp>
 #include <LatAnalyze/includes.hpp>
 #include <gsl/gsl_vector.h>
 #include <gsl/gsl_multiroots.h>

lib/GslHybridRootFinder.hpp

@@ -1,7 +1,7 @@
 /*
  * GslHybridRootFinder.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,7 +21,7 @@
 #define Latan_GslHybridRootFinder_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Numerical/RootFinder.hpp>
+#include <LatAnalyze/RootFinder.hpp>
 #include <gsl/gsl_multiroots.h>
 
 BEGIN_LATAN_NAMESPACE

lib/GslMinimizer.cpp

@@ -1,7 +1,7 @@
 /*
  * GslMinimizer.cpp, part of LatAnalyze
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * Copyright (C) 2013 - 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
@@ -17,9 +17,9 @@
  * along with LatAnalyze.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Numerical/GslMinimizer.hpp>
+#include <LatAnalyze/GslMinimizer.hpp>
 #include <LatAnalyze/includes.hpp>
-#include <LatAnalyze/Core/Math.hpp>
+#include <LatAnalyze/Math.hpp>
 #include <gsl/gsl_multimin.h>
 #include <gsl/gsl_blas.h>
 

lib/GslMinimizer.hpp

@@ -1,7 +1,7 @@
 /*
  * GslMinimizer.hpp, part of LatAnalyze
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * Copyright (C) 2013 - 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
@@ -21,9 +21,9 @@
 #define Latan_GslMinimizer_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Numerical/Derivative.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Numerical/Minimizer.hpp>
+#include <LatAnalyze/Derivative.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/Minimizer.hpp>
 #include <gsl/gsl_vector.h>
 
 BEGIN_LATAN_NAMESPACE

lib/GslQagsIntegrator.cpp

@@ -1,7 +1,7 @@
 /*
  * GslQagsIntegrator.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,9 +17,8 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Numerical/GslQagsIntegrator.hpp>
+#include <LatAnalyze/GslQagsIntegrator.hpp>
 #include <LatAnalyze/includes.hpp>
-#include <LatAnalyze/Core/Math.hpp>
 
 using namespace std;
 using namespace Latan;
@@ -56,26 +55,9 @@ double GslQagsIntegrator::operator()(const DoubleFunction &f, const double xMin,
     
     gslF.function = fWrap;
     gslF.params   = reinterpret_cast<void *>(&const_cast<DoubleFunction &>(f));
-    if ((xMin > -Math::inf) and (xMax < Math::inf))
-    {
-        gsl_integration_qags(&gslF, xMin, xMax, 0.0, precision_, limit_,
-                             workspace_, &result, &error_);
-    }
-    else if (xMax < Math::inf)
-    {
-        gsl_integration_qagil(&gslF, xMax, 0.0, precision_, limit_,
-                              workspace_, &result, &error_);
-    }
-    else if (xMin > -Math::inf)
-    {
-        gsl_integration_qagiu(&gslF, xMin, 0.0, precision_, limit_,
-                              workspace_, &result, &error_);
-    }
-    else
-    {
-        gsl_integration_qagi(&gslF, 0.0, precision_, limit_,
-                             workspace_, &result, &error_);
-    }
+    
+    gsl_integration_qags(&gslF, xMin, xMax, 0.0, precision_, limit_, workspace_,
+                         &result, &error_);
     
     return result;
 }

lib/GslQagsIntegrator.hpp

@@ -1,7 +1,7 @@
 /*
  * GslQagsIntegrator.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define Latan_GslQagsIntegrator_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Numerical/Integrator.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/Integrator.hpp>
 #include <gsl/gsl_integration.h>
 
 BEGIN_LATAN_NAMESPACE

lib/Hdf5File.cpp

@@ -1,7 +1,7 @@
 /*
  * Hdf5File.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli, Matt Spraggs
+ * Copyright (C) 2013 - 2016 Antonin Portelli, Matt Spraggs
  *
  * 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
@@ -17,8 +17,8 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Io/Hdf5File.hpp>
-#include <LatAnalyze/Io/IoObject.hpp>
+#include <LatAnalyze/Hdf5File.hpp>
+#include <LatAnalyze/IoObject.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/Hdf5File.hpp

@@ -1,7 +1,7 @@
 /*
  * Hdf5File.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli, Matt Spraggs
+ * Copyright (C) 2013 - 2016 Antonin Portelli, Matt Spraggs
  *
  * 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
@@ -21,9 +21,9 @@
 #define Latan_Hdf5File_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Io/File.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
-#include <LatAnalyze/Statistics/MatSample.hpp>
+#include <LatAnalyze/File.hpp>
+#include <LatAnalyze/Mat.hpp>
+#include <LatAnalyze/MatSample.hpp>
 #include <H5Cpp.h>
 
 BEGIN_LATAN_NAMESPACE

lib/Histogram.cpp

@@ -1,7 +1,7 @@
 /*
  * Histogram.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Statistics/Histogram.hpp>
+#include <LatAnalyze/Histogram.hpp>
 #include <LatAnalyze/includes.hpp>
 #include <gsl/gsl_histogram.h>
 #include <gsl/gsl_sf.h>

lib/Histogram.hpp

@@ -1,7 +1,7 @@
 /*
  * Histogram.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,7 +21,7 @@
 #define Latan_Histogram_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Statistics/StatArray.hpp>
+#include <LatAnalyze/StatArray.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/Integrator.hpp

@@ -1,7 +1,7 @@
 /*
  * Integrator.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,7 +21,7 @@
 #define Latan_Integrator_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
+#include <LatAnalyze/Function.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/Io.cpp

@@ -1,7 +1,7 @@
 /*
  * Io.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,10 +17,12 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Io/Io.hpp>
+#include <LatAnalyze/Io.hpp>
 #include <LatAnalyze/includes.hpp>
-#include <LatAnalyze/Io/AsciiFile.hpp>
-#include <LatAnalyze/Io/Hdf5File.hpp>
+#include <LatAnalyze/AsciiFile.hpp>
+#ifdef HAVE_HDF5
+#include <LatAnalyze/Hdf5File.hpp>
+#endif
 
 using namespace std;
 using namespace Latan;
@@ -40,10 +42,12 @@ unique_ptr<File> Io::open(const std::string &fileName, const unsigned int mode)
     {
         return unique_ptr<File>(new AsciiFile(fileName, mode));
     }
+#ifdef HAVE_HDF5
     else if (ext == "h5")
     {
         return unique_ptr<File>(new Hdf5File(fileName, mode));
     }
+#endif
     else
     {
         LATAN_ERROR(Io, "unknown file extension '" + ext + "'");

lib/Io.hpp

@@ -1,7 +1,7 @@
 /*
  * Io.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,7 +21,7 @@
 #define Latan_Io_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Io/File.hpp>
+#include <LatAnalyze/File.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/Io/BinReader.cpp

@@ -1,81 +0,0 @@
-/*
- * 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;
-}

lib/Io/BinReader.hpp

@@ -1,196 +0,0 @@
-/*
- * 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_

lib/Io/XmlReader.cpp

@@ -1,84 +0,0 @@
-/*
- * XmlReader.cpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2020 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;
-    }
-}

lib/Io/XmlReader.hpp

@@ -1,235 +0,0 @@
-/*
- * XmlReader.hpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2020 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_

lib/IoObject.hpp

@@ -1,7 +1,7 @@
 /*
  * IoObject.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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

lib/Makefile.am

@@ -7,15 +7,13 @@ if CXX_INTEL
 endif
 endif
 
-include eigen_files.mk
-
 AM_LFLAGS = -olex.yy.c
-AM_YFLAGS = -y -d -Wno-yacc -Wno-deprecated
+AM_YFLAGS = -d
 
 lib_LTLIBRARIES    = libLatAnalyze.la
 noinst_LTLIBRARIES = libLexers.la
 
-libLexers_la_SOURCES  = Io/AsciiLexer.lpp Core/MathLexer.lpp
+libLexers_la_SOURCES  = AsciiLexer.lpp MathLexer.lpp
 if CXX_GNU
     libLexers_la_CXXFLAGS = $(COM_CXXFLAGS) -Wno-unused-parameter -Wno-unused-function -Wno-deprecated-register
 else
@@ -23,121 +21,100 @@ else
 endif
 
 libLatAnalyze_la_SOURCES = \
-    includes.hpp                     \
+    AsciiFile.cpp          \
+    AsciiParser.ypp        \
+    CompiledFunction.cpp   \
+    CompiledModel.cpp      \
+    Derivative.cpp         \
+    Exceptions.cpp         \
+    File.cpp               \
+    FitInterface.cpp       \
+    Function.cpp           \
     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             \
-    Physics/CorrelatorFitter.cpp     \
-    Physics/EffectiveMass.cpp        \
-    Statistics/FitInterface.cpp      \
-    Statistics/Histogram.cpp         \
-    Statistics/Random.cpp            \
-    Statistics/StatArray.cpp         \
-    Statistics/XYSampleData.cpp      \
-    Statistics/XYStatData.cpp        \
+    GslHybridRootFinder.cpp\
+    GslMinimizer.cpp       \
+    GslQagsIntegrator.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         \
 	../config.h
 libLatAnalyze_ladir = $(pkgincludedir)
-HPPFILES =                           \
+libLatAnalyze_la_HEADERS = \
+    AsciiFile.hpp          \
+    CompiledFunction.hpp   \
+    CompiledModel.hpp      \
+    Dataset.hpp            \
+    Derivative.hpp         \
+    Exceptions.hpp         \
+    Function.hpp           \
+    File.hpp               \
+    FitInterface.hpp       \
     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             \
-    Physics/CorrelatorFitter.hpp     \
-    Physics/EffectiveMass.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
+    GslHybridRootFinder.hpp\
+    GslMinimizer.hpp       \
+    GslQagsIntegrator.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
+if HAVE_HDF5
+    libLatAnalyze_la_SOURCES += Hdf5File.cpp
+    libLatAnalyze_la_HEADERS += Hdf5File.hpp
+endif
 if HAVE_MINUIT
-    libLatAnalyze_la_SOURCES += Numerical/MinuitMinimizer.cpp
-    HPPFILES += Numerical/MinuitMinimizer.hpp
+    libLatAnalyze_la_SOURCES += MinuitMinimizer.cpp
+    libLatAnalyze_la_HEADERS += MinuitMinimizer.hpp
 endif
 if HAVE_NLOPT
-    libLatAnalyze_la_SOURCES += Numerical/NloptMinimizer.cpp
-    HPPFILES += Numerical/NloptMinimizer.hpp
+    libLatAnalyze_la_SOURCES += NloptMinimizer.cpp
+    libLatAnalyze_la_HEADERS += NloptMinimizer.hpp
 endif
 libLatAnalyze_la_CXXFLAGS = $(COM_CXXFLAGS)
 libLatAnalyze_la_LIBADD   = libLexers.la
 
 if HAVE_AM_MINOR_LE_11
-Io/AsciiParser.hpp: Io/AsciiParser.ypp
-	$(AM_V_YACC) $(YACC) -o Io/AsciiParser.cpp --defines=Io/AsciiParser.hpp $<
+AsciiParser.hpp: AsciiParser.ypp
+	$(AM_V_YACC) $(YACC) -o AsciiParser.cpp --defines=AsciiParser.hpp $<
 
-Core/MathParser.hpp: Core/MathParser.ypp
-	$(AM_V_YACC) $(YACC) -o Core/MathParser.cpp --defines=Core/MathParser.hpp $<
+MathParser.hpp: MathParser.ypp
+	$(AM_V_YACC) $(YACC) -o MathParser.cpp --defines=MathParser.hpp $<
 endif
 
-BUILT_SOURCES = Io/AsciiParser.hpp Core/MathParser.hpp
+BUILT_SOURCES = AsciiParser.hpp 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
+    MathLexer.cpp  \
+    AsciiLexer.cpp \
+    AsciiParser.cpp\
+    AsciiParser.hpp\
+    MathParser.cpp \
+    MathParser.hpp
 
 ACLOCAL_AMFLAGS = -I .buildutils/m4

lib/Mat.cpp

@@ -1,7 +1,7 @@
 /*
  * Mat.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Core/Mat.hpp>
+#include <LatAnalyze/Mat.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/Mat.hpp

@@ -1,7 +1,7 @@
 /*
  * Mat.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,7 +21,11 @@
 #define Latan_Mat_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Io/IoObject.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)
 
 BEGIN_LATAN_NAMESPACE
 

lib/MatSample.hpp

@@ -1,7 +1,7 @@
 /*
  * MatSample.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define Latan_MatSample_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
-#include <LatAnalyze/Statistics/StatArray.hpp>
+#include <LatAnalyze/Mat.hpp>
+#include <LatAnalyze/StatArray.hpp>
 
 BEGIN_LATAN_NAMESPACE
 
@@ -228,7 +228,7 @@ Index MatSample<T>::BlockTemplate<S>::getNCol(void) const
 // assignement operators ///////////////////////////////////////////////////////
 template <typename T>
 template <class S>
-typename MatSample<T>::template BlockTemplate<S> &
+MatSample<T>::BlockTemplate<S> &
 MatSample<T>::BlockTemplate<S>::operator=(const S &sample)
 {
     FOR_STAT_ARRAY(sample_, s)
@@ -241,7 +241,7 @@ MatSample<T>::BlockTemplate<S>::operator=(const S &sample)
 
 template <typename T>
 template <class S>
-typename MatSample<T>::template BlockTemplate<S> &
+MatSample<T>::BlockTemplate<S> &
 MatSample<T>::BlockTemplate<S>::operator=(const S &&sample)
 {
     *this = sample;

lib/Math.cpp

@@ -1,7 +1,7 @@
 /*
  * Math.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Core/Math.hpp>
+#include <LatAnalyze/Math.hpp>
 #include <LatAnalyze/includes.hpp>
 #include <gsl/gsl_cdf.h>
 
@@ -107,14 +107,8 @@ 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);

lib/Math.hpp

@@ -1,7 +1,7 @@
 /*
  * Math.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define	Latan_Math_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Core/MathInterpreter.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/MathInterpreter.hpp>
 
 BEGIN_LATAN_NAMESPACE
 
@@ -72,10 +72,8 @@ namespace MATH_NAMESPACE
     DMat varToCorr(const DMat &var);
     
     // Constants
-    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();
+    const double pi = 3.1415926535897932384626433832795028841970;
+    const double e  = 2.7182818284590452353602874713526624977572;
 }
 
 
@@ -153,7 +151,6 @@ DECL_STD_FUNC(fabs)
 namespace MATH_NAMESPACE
 {
     extern DoubleFunction chi2PValue;
-    extern DoubleFunction chi2Ccdf;
 }
 
 END_LATAN_NAMESPACE

lib/MathInterpreter.cpp

@@ -1,7 +1,7 @@
 /*
  * MathInterpreter.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,9 +17,9 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Core/MathInterpreter.hpp>
+#include <LatAnalyze/MathInterpreter.hpp>
 #include <LatAnalyze/includes.hpp>
-#include <LatAnalyze/Core/Math.hpp>
+#include <LatAnalyze/Math.hpp>
 
 using namespace std;
 using namespace Latan;
@@ -690,7 +690,7 @@ void MathInterpreter::compile(RunContext &context)
         if (root_)
         {
             context.addVariable("pi", Math::pi);
-            context.addVariable("inf", Math::inf);
+            context.addVariable("inf", HUGE_VAL);
             ADD_STDMATH_FUNCS(context);
             root_->compile(program_, context);
             for (unsigned int i = 0; i < program_.size(); ++i)

lib/MathInterpreter.hpp

@@ -1,7 +1,7 @@
 /*
  * MathInterpreter.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -20,9 +20,9 @@
 #ifndef Latan_MathInterpreter_hpp_
 #define	Latan_MathInterpreter_hpp_
 
-#include <LatAnalyze/Functional/Function.hpp>
+#include <LatAnalyze/Function.hpp>
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Core/ParserState.hpp>
+#include <LatAnalyze/ParserState.hpp>
 
 #define MAXIDLENGTH 256
 

lib/MathLexer.lpp

@@ -1,7 +1,7 @@
 /*
  * MathLexer.lpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -25,7 +25,7 @@
 %option yylineno
 
 %{
-    #include <LatAnalyze/Core/MathInterpreter.hpp>
+    #include <LatAnalyze/MathInterpreter.hpp>
     #include "MathParser.hpp"
     
     using namespace std;

lib/MathParser.ypp

@@ -1,7 +1,7 @@
 /*
  * MathParser.ypp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -19,7 +19,7 @@
 
 %{
     #include <LatAnalyze/Global.hpp>
-	#include <LatAnalyze/Core/MathInterpreter.hpp>
+	#include <LatAnalyze/MathInterpreter.hpp>
 
     using namespace std;
     using namespace Latan;

lib/Minimizer.cpp

@@ -1,7 +1,7 @@
 /*
  * Minimizer.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Numerical/Minimizer.hpp>
+#include <LatAnalyze/Minimizer.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/Minimizer.hpp

@@ -1,7 +1,7 @@
 /*
  * Minimizer.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,9 +21,9 @@
 #define Latan_Minimizer_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
-#include <LatAnalyze/Numerical/Solver.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/Mat.hpp>
+#include <LatAnalyze/Solver.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/MinuitMinimizer.cpp

@@ -1,7 +1,7 @@
 /*
  * MinuitMinimizer.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Numerical/MinuitMinimizer.hpp>
+#include <LatAnalyze/MinuitMinimizer.hpp>
 #include <LatAnalyze/includes.hpp>
 #include <Minuit2/Minuit2Minimizer.h>
 #include <Math/Functor.h>

lib/MinuitMinimizer.hpp

@@ -1,7 +1,7 @@
 /*
  * MinuitMinimizer.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define Latan_MinuitMinimizer_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Numerical/Minimizer.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/Minimizer.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/Model.cpp

@@ -1,7 +1,7 @@
 /*
  * Model.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Functional/Model.hpp>
+#include <LatAnalyze/Model.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/Model.hpp

@@ -1,7 +1,7 @@
 /*
  * Model.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,8 +21,8 @@
 #define Latan_Model_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/Mat.hpp>
 
 BEGIN_LATAN_NAMESPACE
 

lib/NloptMinimizer.cpp

@@ -1,7 +1,7 @@
 /*
  * NloptMinimizer.cpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -17,7 +17,7 @@
  * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include <LatAnalyze/Numerical/NloptMinimizer.hpp>
+#include <LatAnalyze/NloptMinimizer.hpp>
 #include <LatAnalyze/includes.hpp>
 
 using namespace std;

lib/NloptMinimizer.hpp

@@ -1,7 +1,7 @@
 /*
  * NloptMinimizer.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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
@@ -21,9 +21,9 @@
 #define Latan_NloptMinimizer_hpp_
 
 #include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Numerical/Derivative.hpp>
-#include <LatAnalyze/Functional/Function.hpp>
-#include <LatAnalyze/Numerical/Minimizer.hpp>
+#include <LatAnalyze/Derivative.hpp>
+#include <LatAnalyze/Function.hpp>
+#include <LatAnalyze/Minimizer.hpp>
 #include <nlopt.hpp>
 
 BEGIN_LATAN_NAMESPACE

lib/Numerical/FFT.hpp

@@ -1,53 +0,0 @@
-/*
- * FFT.hpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2020 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 Latan_FFT_hpp_
-#define Latan_FFT_hpp_
-
-#include <LatAnalyze/Global.hpp>
-
-BEGIN_LATAN_NAMESPACE
-
-/******************************************************************************
- *                             FFT abstract class                             *
- ******************************************************************************/
-
-class FFT
-{
-public:
-    enum
-    {
-      Forward  = 0,
-      Backward = 1
-    };
-public:
-  // constructor
-  FFT(void) = default;
-  FFT(const Index size);
-  // destructor
-  virtual ~FFT(void) = default;
-  // size
-  virtual void resize(const Index size) = 0;
-  // FFT
-  virtual void operator()(CMat &x, const unsigned int dir = FFT::Forward) = 0;
-};
-
-END_LATAN_NAMESPACE
-
-#endif // Latan_FFT_hpp_

lib/Numerical/GslFFT.cpp

@@ -1,90 +0,0 @@
-/*
- * GslFFT.cpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2020 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/Numerical/GslFFT.hpp>
-#include <LatAnalyze/includes.hpp>
-
-using namespace std;
-using namespace Latan;
-
-/******************************************************************************
- *                           GslFFT implementation                            *
- ******************************************************************************/
-// constructor /////////////////////////////////////////////////////////////////
-GslFFT::GslFFT(const Index size)
-{
-    resize(size);
-}
-
-// destructor //////////////////////////////////////////////////////////////////
-GslFFT::~GslFFT(void)
-{
-    clear();
-}
-
-// size ////////////////////////////////////////////////////////////////////////
-void GslFFT::resize(const Index size)
-{
-    if (size_ != size)
-    {
-        clear();
-        size_      = size;
-        wavetable_ = gsl_fft_complex_wavetable_alloc(size_);
-        workspace_ = gsl_fft_complex_workspace_alloc(size_);
-    }
-}
-
-// fft /////////////////////////////////////////////////////////////////////////
-void GslFFT::operator()(CMat &x, const unsigned int dir)
-{
-    if (x.size() != size_)
-    {
-        LATAN_ERROR(Size, "wrong input vector size");
-    }
-    else
-    {
-        switch (dir)
-        {
-            case FFT::Forward:
-                gsl_fft_complex_forward((double *)x.data(), 1, size_,
-                                        wavetable_, workspace_);
-                break;
-            case FFT::Backward:
-                gsl_fft_complex_backward((double *)x.data(), 1, size_,
-                                         wavetable_, workspace_);
-                break;
-            default:
-                LATAN_ERROR(Argument, "invalid FT direction");
-                break;
-        }
-    }
-}
-
-// destroy GSL objects /////////////////////////////////////////////////////////
-void GslFFT::clear(void)
-{
-    if (!wavetable_)
-    {
-        gsl_fft_complex_wavetable_free(wavetable_);
-    }
-    if (!workspace_)
-    {
-        gsl_fft_complex_workspace_free(workspace_);
-    }
-}

lib/Numerical/GslFFT.hpp

@@ -1,57 +0,0 @@
-/*
- * GslFFT.hpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2020 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 Latan_GslFFT_hpp_
-#define Latan_GslFFT_hpp_
-
-#include <LatAnalyze/Global.hpp>
-#include <LatAnalyze/Core/Mat.hpp>
-#include <LatAnalyze/Numerical/FFT.hpp>
-#include <gsl/gsl_fft_complex.h>
-
-BEGIN_LATAN_NAMESPACE
-
-/******************************************************************************
- *                                 GSL FFT                                    *
- ******************************************************************************/
-
-class GslFFT: public FFT
-{
-public:
-    // constructors
-    GslFFT(void) = default;
-    GslFFT(const Index size);
-    // destructor
-    virtual ~GslFFT(void);
-    // size
-    void resize(const Index size);
-    // fft
-    virtual void operator()(CMat &x, const unsigned int dir = FFT::Forward);
-private:
-    // destroy GSL objects
-    void clear(void);
-private:
-    Index                     size_{0};
-    gsl_fft_complex_wavetable *wavetable_{nullptr};
-    gsl_fft_complex_workspace *workspace_{nullptr};
-};
-
-END_LATAN_NAMESPACE
-
-#endif // Latan_GslFFT_hpp_

lib/ParserState.hpp

@@ -1,7 +1,7 @@
 /*
  * ParserState.hpp, part of LatAnalyze 3
  *
- * Copyright (C) 2013 - 2020 Antonin Portelli
+ * 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

lib/Physics/CorrelatorFitter.cpp

@@ -1,417 +0,0 @@
-/*
- * CorrelatorFitter.cpp, part of LatAnalyze 3
- *
- * Copyright (C) 2013 - 2020 Antonin Portelli
- *
- * LatAnalyze 3 is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * LatAnalyze 3 is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <LatAnalyze/Physics/CorrelatorFitter.hpp>
-#include <LatAnalyze/includes.hpp>
-
-using namespace std;
-using namespace Latan;
-
-/******************************************************************************
- *                           Correlator models                                *
- ******************************************************************************/
-DoubleModel CorrelatorModels::makeExpModel(const Index nState)
-{
-    DoubleModel mod;
-
-    mod.setFunction([nState](const double *x, const double *p)
-    {
-        double res = 0.;
-
-        for (unsigned int i = 0; i < nState; ++i)
-        {
-            res += p[2*i + 1]*exp(-p[2*i]*x[0]);
-        }
-
-        return res;
-    }, 1, 2*nState);
-    for (unsigned int i = 0; i < nState; ++i)
-    {
-        mod.parName().setName(2*i, "E_" + strFrom(i));
-        mod.parName().setName(2*i + 1, "Z_" + strFrom(i));
-    }
-
-    return mod;
-}
-
-DoubleModel CorrelatorModels::makeCoshModel(const Index nState, const Index nt)
-{
-    DoubleModel mod;
-
-    mod.setFunction([nState, nt](const double *x, const double *p)
-    {
-        double res = 0.;
-
-        for (unsigned int i = 0; i < nState; ++i)
-        {
-            res += p[2*i + 1]*(exp(-p[2*i]*x[0]) + exp(-p[2*i]*(nt - x[0])));
-        }
-
-        return res;
-    }, 1, 2*nState);
-    for (unsigned int i = 0; i < nState; ++i)
-    {
-        mod.parName().setName(2*i, "E_" + strFrom(i));
-        mod.parName().setName(2*i + 1, "Z_" + strFrom(i));
-    }
-
-    return mod;
-}
-
-DoubleModel CorrelatorModels::makeSinhModel(const Index nState, const Index nt)
-{
-    DoubleModel mod;
-
-    mod.setFunction([nState, nt](const double *x, const double *p)
-    {
-        double res = 0.;
-
-        for (unsigned int i = 0; i < nState; ++i)
-        {
-            res += p[2*i + 1]*(exp(-p[2*i]*x[0]) - exp(-p[2*i]*(nt - x[0])));
-        }
-
-        return res;
-    }, 1, 2*nState);
-    for (unsigned int i = 0; i < nState; ++i)
-    {
-        mod.parName().setName(2*i, "E_" + strFrom(i));
-        mod.parName().setName(2*i + 1, "Z_" + strFrom(i));
-    }
-
-    return mod;
-}
-
-DoubleModel CorrelatorModels::makeConstModel(void)
-{
-    DoubleModel mod;
-
-    mod.setFunction([](const double *x __dumb, const double *p __dumb)
-    {
-        return p[0];
-    }, 1, 1);
-    mod.parName().setName(0, "cst");
-
-    return mod;
-}
-
-DoubleModel CorrelatorModels::makeLinearModel(void)
-{
-    DoubleModel mod;
-
-    mod.setFunction([](const double *x, const double *p)
-    {
-        return p[1] + p[0]*x[0];
-    }, 1, 2);
-
-    return mod;
-}
-
-CorrelatorModels::ModelPar CorrelatorModels::parseModel(const string s)
-{
-    smatch   sm;
-    ModelPar par;
-
-    if (regex_match(s, sm, regex("exp([0-9]+)")))
-    {
-        par.type   = CorrelatorType::exp;
-        par.nState = strTo<Index>(sm[1].str());
-    }
-    else if (regex_match(s, sm, regex("cosh([0-9]+)")))
-    {
-        par.type   = CorrelatorType::cosh;
-        par.nState = strTo<Index>(sm[1].str());
-    }
-    else if (regex_match(s, sm, regex("sinh([0-9]+)")))
-    {
-        par.type   = CorrelatorType::sinh;
-        par.nState = strTo<Index>(sm[1].str());
-    }
-    else if (s == "linear")
-    {
-        par.type   = CorrelatorType::linear;
-        par.nState = 1;
-    }
-    else if (s == "cst")
-    {
-        par.type   = CorrelatorType::cst;
-        par.nState = 1;
-    }
-    else
-    {
-        par.type   = CorrelatorType::undefined;
-        par.nState = 0;
-    }
-
-    return par;
-}
-
-DoubleModel CorrelatorModels::makeModel(const CorrelatorModels::ModelPar par,
-                                        const Index nt)
-{
-    switch (par.type)
-    {
-    case CorrelatorType::undefined:
-        LATAN_ERROR(Argument, "correlator type is undefined");
-        break;
-    case CorrelatorType::exp:
-        return makeExpModel(par.nState);
-        break;
-    case CorrelatorType::cosh:
-        return makeCoshModel(par.nState, nt);
-        break;
-    case CorrelatorType::sinh:
-        return makeSinhModel(par.nState, nt);
-        break;
-    case CorrelatorType::linear:
-        return makeLinearModel();
-        break;
-    case CorrelatorType::cst:
-        return makeConstModel();
-        break;
-    }
-}
-
-DVec CorrelatorModels::parameterGuess(const DMatSample &corr, 
-                                      const ModelPar par)
-{
-    DVec  init;
-    Index nt = corr[central].size();
-
-    switch (par.type)
-    {
-    case CorrelatorType::undefined:
-        LATAN_ERROR(Argument, "correlator type is undefined");
-        break;
-    case CorrelatorType::exp:
-    case CorrelatorType::cosh:
-    case CorrelatorType::sinh:
-        init.resize(2*par.nState);
-        init(0) = log(corr[central](nt/4)/corr[central](nt/4 + 1));
-        init(1) = corr[central](nt/4)/(exp(-init(0)*nt/4));
-        for (Index p = 2; p < init.size(); p += 2)
-        {
-            init(p)     = 2*init(p - 2);
-            init(p + 1) = init(p - 1)/2.;
-        }
-        break;
-    case CorrelatorType::linear:
-        init.resize(2);
-        init(0) = corr[central](nt/4) - corr[central](nt/4 + 1, 0);
-        init(1) = corr[central](nt/4, 0) + nt/4*init(0);
-        break;
-    case CorrelatorType::cst:
-        init.resize(1);
-        init(0) = corr[central](nt/4);
-        break;
-    default:
-        break;
-    }
-
-    return init;
-}
-
-/******************************************************************************
- *                         Correlator utilities                               *
- ******************************************************************************/
-DMatSample CorrelatorUtils::shift(const DMatSample &c, const Index ts)
-{
-    if (ts != 0)
-    {
-        const Index nt  = c[central].rows();
-        DMatSample  buf = c;
-
-        FOR_STAT_ARRAY(buf, s)
-        {
-            for (Index t = 0; t < nt; ++t)
-            {
-                buf[s]((t - ts + nt)%nt) = c[s](t);
-            }
-        }
-
-        return buf;
-    }
-    else
-    {
-        return c;
-    }
-}
-
-DMatSample CorrelatorUtils::fold(const DMatSample &c)
-{
-    const Index nt  = c[central].rows();
-    DMatSample  buf = c;
-
-    FOR_STAT_ARRAY(buf, s)
-    {
-        for (Index t = 0; t < nt; ++t)
-        {
-            buf[s](t) = 0.5*(c[s](t) + c[s]((nt - t) % nt));
-        }
-    }
-
-    return buf;
-}
-
-DMatSample CorrelatorUtils::fourierTransform(const DMatSample &c, FFT &fft, 
-                                             const unsigned int dir)
-{
-    const Index nSample   = c.size();
-    const Index nt        = c[central].rows();
-    bool        isComplex = (c[central].cols() > 1);
-    CMatSample  buf(nSample, nt, 1);
-    DMatSample  out(nSample, nt, 2);
-
-    fft.resize(nt);
-    FOR_STAT_ARRAY(buf, s)
-    {
-        buf[s].real() = c[s].col(0);
-        if (isComplex)
-        {
-            buf[s].imag() = c[s].col(1);
-        }
-        else
-        {
-            buf[s].imag() = DVec::Constant(nt, 0.);
-        }
-        fft(buf[s], dir);
-        out[s].col(0) = buf[s].real();
-        out[s].col(1) = buf[s].imag();
-    }
-
-    return out;    
-}
-
-/******************************************************************************
- *                      CorrelatorFitter implementation                       *
- ******************************************************************************/
-// constructors ////////////////////////////////////////////////////////////////
-CorrelatorFitter::CorrelatorFitter(const DMatSample &corr)
-{
-    setCorrelator(corr);
-}
-
-CorrelatorFitter::CorrelatorFitter(const std::vector<DMatSample> &corr)
-{
-    setCorrelators(corr);
-}
-
-// access //////////////////////////////////////////////////////////////////////
-XYSampleData & CorrelatorFitter::data(void)
-{
-    return *data_;
-}
-
-void CorrelatorFitter::setCorrelator(const DMatSample &corr)
-{
-    std::vector<DMatSample> vec;
-
-    vec.push_back(corr);
-    setCorrelators(vec);
-}   
-
-void CorrelatorFitter::setCorrelators(const std::vector<DMatSample> &corr)
-{
-    Index                           nSample = corr[0].size();
-    DMatSample                      tVec(nSample);
-    std::vector<const DMatSample *> ptVec;
-
-    nt_ = corr[0][central].rows();
-    tVec.fill(DVec::LinSpaced(nt_, 0, nt_ - 1));
-    for (auto &c: corr)
-    {
-        ptVec.push_back(&c);
-    }
-    data_.reset(new XYSampleData(corr[0].size()));
-    data_->addXDim(nt_, "t/a", true);
-    for (unsigned int i = 0; i < corr.size(); ++i)
-    {
-        data_->addYDim("C_" + strFrom(i) + "(t)");
-    }
-    data_->setUnidimData(tVec, ptVec);
-    model_.resize(corr.size());
-    range_.resize(corr.size(), make_pair(0, nt_ - 1));
-    thinning_.resize(corr.size(), 1);
-}
-
-void CorrelatorFitter::setModel(const DoubleModel &model, const Index i)
-{
-    model_[i] = model;
-}
-
-const DoubleModel & CorrelatorFitter::getModel(const Index i) const
-{
-    return model_.at(i);
-}
-
-void CorrelatorFitter::setFitRange(const Index tMin, const Index tMax, 
-                                   const Index i)
-{
-    range_[i] = make_pair(tMin, tMax);
-    refreshRanges();
-}
-
-void CorrelatorFitter::setCorrelation(const bool isCorrelated, const Index i, 
-                                      const Index j)
-{
-    data_->assumeYYCorrelated(isCorrelated, i, j);
-}
-
-DMat CorrelatorFitter::getVarianceMatrix(void) const
-{
-    return data_->getFitVarMat();
-}
-
-void CorrelatorFitter::setThinning(const Index thinning, const Index i)
-{
-    thinning_[i] = thinning;
-    refreshRanges();
-}
-
-// fit functions ///////////////////////////////////////////////////////////////
-SampleFitResult CorrelatorFitter::fit(Minimizer &minimizer, const DVec &init)
-{
-    vector<Minimizer *> vecPt = {&minimizer};
-
-    return fit(vecPt, init);
-}
-
-SampleFitResult CorrelatorFitter::fit(vector<Minimizer *> &minimizer,
-                                      const DVec &init)
-{
-    vector<const DoubleModel *> vecPt(model_.size());
-    
-    for (unsigned int i = 0; i < model_.size(); ++i)
-    {
-        vecPt[i] = &(model_[i]);
-    }
-
-    return data_->fit(minimizer, init, vecPt);
-}
-
-// internal function to refresh fit ranges /////////////////////////////////////
-void CorrelatorFitter::refreshRanges(void)
-{
-    for (unsigned int i = 0; i < range_.size(); ++i)
-    for (Index t = 0; t < nt_; ++t)
-    {
-        data_->fitPoint((t >= range_[i].first) and (t <= range_[i].second)
-                         and ((t - range_[i].first) % thinning_[i] == 0), t);
-    }
-}