Merge branch 'develop' into feature/fit-phys

.gitignore

@@ -35,7 +35,3 @@ ci-scripts/local/*
 .idea/*
 CMakeLists.txt
 cmake-build-debug/*
-
-# VS Code Studio stuff
-.vscode
-*.code-workspace

Readme.md

@@ -55,28 +55,6 @@ in the `ci-scripts` directory where `<prefix>` is where you want LatAnalyze (and
 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
-#### v3.3
-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
 Fix:
 * Wrong argument number check in `latan-resample`

ci-scripts/install-hdf5.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-NAME='hdf5-1.10.1'
+NAME='hdf5-1.8.16'
 
 if (( $# != 1 )); then
   echo "usage: `basename $0` <prefix> {osx|linux}" 1>&2
@@ -11,7 +11,7 @@ PREFIX=$1
 set -ex
 INITDIR=`pwd`
 cd local/build
-wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${NAME}/src/${NAME}.tar.gz
+wget http://www.hdfgroup.org/ftp/HDF5/releases/${NAME}/src/${NAME}.tar.gz
 tar -xzvf ${NAME}.tar.gz
 mkdir ${NAME}/build
 cd ${NAME}/build

configure.ac

@@ -2,7 +2,7 @@
 
 # Initialization
 AC_PREREQ([2.63])
-AC_INIT([LatAnalyze],[3.3],[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])

lib/Dataset.hpp

@@ -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/FFT.hpp

@@ -1,53 +0,0 @@
-/*
- * FFT.hpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2017 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/GslFFT.cpp

@@ -1,89 +0,0 @@
-/*
- * GslFFT.cpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2017 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/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)
-    {
-        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/GslFFT.hpp

@@ -1,57 +0,0 @@
-/*
- * GslFFT.hpp, part of LatAnalyze
- *
- * Copyright (C) 2013 - 2017 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/Mat.hpp>
-#include <LatAnalyze/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/GslQagsIntegrator.cpp

@@ -19,7 +19,6 @@
 
 #include <LatAnalyze/GslQagsIntegrator.hpp>
 #include <LatAnalyze/includes.hpp>
-#include <LatAnalyze/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/Makefile.am

@@ -31,7 +31,6 @@ libLatAnalyze_la_SOURCES = \
     FitInterface.cpp       \
     Function.cpp           \
     Global.cpp             \
-    GslFFT.cpp             \
     GslHybridRootFinder.cpp\
     GslMinimizer.cpp       \
     GslQagsIntegrator.cpp  \
@@ -60,12 +59,10 @@ libLatAnalyze_la_HEADERS = \
     Dataset.hpp            \
     Derivative.hpp         \
     Exceptions.hpp         \
-    FFT.hpp                \
     Function.hpp           \
     File.hpp               \
     FitInterface.hpp       \
     Global.hpp             \
-    GslFFT.hpp             \
     GslHybridRootFinder.hpp\
     GslMinimizer.hpp       \
     GslQagsIntegrator.hpp  \

lib/Math.hpp

@@ -72,9 +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();
+    const double pi = 3.1415926535897932384626433832795028841970;
+    const double e  = 2.7182818284590452353602874713526624977572;
 }
 
 

lib/MathInterpreter.cpp

@@ -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/TabFunction.cpp

@@ -29,11 +29,18 @@ using namespace Latan;
 // constructors ////////////////////////////////////////////////////////////////
 TabFunction::TabFunction(const DVec &x, const DVec &y,
                          const InterpType interpType)
+: interpType_(interpType)
 {
     setData(x, y);
-    setInterpolationType(interpType);
 }
 
+//TabFunction::TabFunction(const XYStatData &data, const Index i, const Index j,
+//                         const InterpType interpType)
+//: interpType_(interpType)
+//{
+//    setData(data, i, j);
+//}
+
 // access //////////////////////////////////////////////////////////////////////
 void TabFunction::setData(const DVec &x, const DVec &y)
 {
@@ -47,10 +54,10 @@ void TabFunction::setData(const DVec &x, const DVec &y)
     }
 }
 
-void TabFunction::setInterpolationType(const InterpType interpType)
-{
-    interpType_ = interpType;
-}
+//void TabFunction::setData(const XYStatData &data, const Index i, const Index j)
+//{
+//    setData(data.x(i), data.y(j));
+//}
 
 // function call ///////////////////////////////////////////////////////////////
 double TabFunction::operator()(const double *arg) const
@@ -147,6 +154,12 @@ DoubleFunction Latan::interpolate(const DVec &x, const DVec &y,
     return TabFunction(x, y, interpType).makeFunction();
 }
 
+//DoubleFunction Latan::interpolate(const XYStatData &data, const Index i,
+//                                  const Index j, const InterpType interpType)
+//{
+//    return TabFunction(data, i, j, interpType).makeFunction();
+//}
+
 map<double, double>::const_iterator TabFunction::nearest(const double x) const
 {
     map<double, double>::const_iterator ret;

lib/TabFunction.hpp

@@ -45,11 +45,13 @@ public:
     TabFunction(void) = default;
     TabFunction(const DVec &x, const DVec &y,
                 const InterpType interpType = InterpType::LINEAR);
+    //TabFunction(const XYStatData &data, const Index i = 0, const Index j = 0,
+    //            const InterpType interpType = InterpType::LINEAR);
     // destructor
     virtual ~TabFunction(void) = default;
     // access
     void setData(const DVec &x, const DVec &y);
-    void setInterpolationType(const InterpType interpType);
+    // void setData(const XYStatData &data, const Index i = 0, const Index j = 0);
     // function call
     double operator()(const double *arg) const;
     // factory
@@ -63,6 +65,9 @@ private:
 
 DoubleFunction interpolate(const DVec &x, const DVec &y,
                            const InterpType interpType = InterpType::LINEAR);
+//DoubleFunction interpolate(const XYStatData &data, const Index i = 0,
+//                           const Index j = 0,
+//                           const InterpType interpType = InterpType::LINEAR);
 
 END_LATAN_NAMESPACE
 

physics/Makefile.am

@@ -6,10 +6,14 @@ if CXX_INTEL
 endif
 endif
 
-bin_PROGRAMS = latan-2pt-fit
+bin_PROGRAMS = latan-fit-2pt latan-fit-phys
 
-latan_2pt_fit_SOURCES  = 2pt-fit.cpp
-latan_2pt_fit_CXXFLAGS = $(COM_CXXFLAGS)
-latan_2pt_fit_LDFLAGS  = -L../lib/.libs -lLatAnalyze
+latan_fit_2pt_SOURCES  = fit-2pt.cpp
+latan_fit_2pt_CXXFLAGS = $(COM_CXXFLAGS)
+latan_fit_2pt_LDFLAGS  = -L../lib/.libs -lLatAnalyze
+
+latan_fit_phys_SOURCES  = fit-phys.cpp fit-phys-env.cpp
+latan_fit_phys_CXXFLAGS = $(COM_CXXFLAGS)
+latan_fit_phys_LDFLAGS  = -L../lib/.libs -lLatAnalyze
 
 ACLOCAL_AMFLAGS = -I .buildutils/m4

physics/fit-2pt.cpp

@@ -38,7 +38,7 @@ int main(int argc, char *argv[])
                   "singular value elimination threshold", "0.");
     opt.addOption("v", "verbosity", OptParser::OptType::value  , true,
                   "minimizer verbosity level (0|1|2)", "0");
-    opt.addOption("o", "output", OptParser::OptType::value  , true,
+    opt.addOption("o", "output"   , OptParser::OptType::value  , true,
                   "output file", "");
     opt.addOption("" , "uncorr"   , OptParser::OptType::trigger, true,
                   "only do the uncorrelated fit");

physics/fit-phys-env.cpp

@@ -0,0 +1,509 @@
+#include "fit-phys-env.hpp"
+#include <LatCore/XmlReader.hpp>
+#include <LatAnalyze/CompiledModel.hpp>
+#include <LatAnalyze/Io.hpp>
+
+#define DRATIO(a,b) static_cast<double>(a)/static_cast<double>(b)
+
+using namespace std;
+using namespace Latan;
+
+void FitEnv::reset(void)
+{
+    nT_.clear();
+    nL_.clear();
+    variable_.clear();
+    varData_.clear();
+    varName_.clear();
+    varScalePow_.clear();
+    quantity_.clear();
+    quData_.clear();
+    quName_.clear();
+    ensemble_.clear();
+    point_.clear();
+    macro_.clear();
+    scaleVar_ = nullptr;
+}
+
+Index FitEnv::getVarIndex(const string name)
+{
+    if (name == "nT")
+    {
+        return 0;
+    }
+    else if (name == "nL")
+    {
+        return 1;
+    }
+    else
+    {
+        auto it = variable_.find(name);
+        
+        if (it != variable_.end())
+        {
+            return it->second.index;
+        }
+        else
+        {
+            LATAN_ERROR(Range, "no variable with name '" + name + "'");
+        }
+    }
+}
+
+string FitEnv::getVarName(const Index i)
+{
+    if (i < static_cast<Index>(varName_.size()))
+    {
+        return varName_[i];
+    }
+    else
+    {
+        LATAN_ERROR(Range, "no variable with index " + strFrom(i));
+    }
+}
+
+Index FitEnv::getQuIndex(const string name)
+{
+    auto it = quantity_.find(name);
+    
+    if (it != quantity_.end())
+    {
+        return it->second.index;
+    }
+    else
+    {
+        LATAN_ERROR(Range, "no quantity with name '" + name + "'");
+    }
+}
+
+string FitEnv::getQuName(const Index i)
+{
+    if (i < static_cast<Index>(quName_.size()))
+    {
+        return quName_[i];
+    }
+    else
+    {
+        LATAN_ERROR(Range, "no variable with index " + strFrom(i));
+    }
+}
+
+DVec FitEnv::getPhyPt(void)
+{
+    DVec phyPt(varName_.size());
+    
+    for (unsigned int i = 0; i < varName_.size(); ++i)
+    {
+        phyPt(i) = variable_[varName_[i]].physVal;
+    }
+    
+    return phyPt;
+}
+
+vector<const DoubleModel *> FitEnv::getModels(void)
+{
+    vector<const DoubleModel *> m;
+    
+    for (auto &q: quantity_)
+    {
+        m.push_back(&q.second.model);
+    }
+    
+    return m;
+}
+
+#define XGFV(type, ...) XmlReader::getFirstValue<type>(node, __VA_ARGS__)
+
+void FitEnv::parseXml(const string paramFileName)
+{
+    XmlReader                paramFile(paramFileName);
+    const XmlNode            *node = nullptr;
+    set<unsigned int>        nTs, nLs;
+    map<string, set<string>> varFileNames, quFileNames;
+    
+    reset();
+    nSample_ = paramFile.getFirstValue<Index>("nSample");
+    scale_   = paramFile.getFirstValue<string>("scale");
+    
+    // macros
+    if (paramFile.hasNode("macros", "macro"))
+    {
+        node = paramFile.getFirstNode("macros", "macro");
+        while (node)
+        {
+            macro_[XGFV(string, "symbol")] = XGFV(string, "value");
+            node                           = paramFile.getNextSameNode(node);
+        }
+    }
+    
+    // ensembles
+    node = paramFile.getFirstNode("ensembles", "ensemble");
+    while (node)
+    {
+        string   name, spacing;
+        Ensemble ens;
+        
+        name            = XGFV(string, "name");
+        ens.nT          = XGFV(unsigned int, "nT");
+        ens.nL          = XGFV(unsigned int, "nL");
+        ensemble_[name] = ens;
+        node            = paramFile.getNextSameNode(node);
+        nTs.insert(ens.nT);
+        nLs.insert(ens.nL);
+    }
+    
+    // fit variables
+    {
+        string  name;
+        VarInfo var;
+        
+        name            = "T";
+        var.physVal     = HUGE_VAL;
+        var.dim         = -1;
+        variable_[name] = var;
+    }
+    {
+        string  name;
+        VarInfo var;
+        
+        name            = "L";
+        var.physVal     = HUGE_VAL;
+        var.dim         = -1;
+        variable_[name] = var;
+    }
+    node = paramFile.getFirstNode("variables", "variable");
+    while (node)
+    {
+        string  name;
+        VarInfo var;
+        
+        name            = XGFV(string, "name");
+        var.physVal     = XGFV(double, "physical");
+        var.dim         = XGFV(int, "dim");
+        variable_[name] = var;
+        if (name == scale_)
+        {
+            scaleVar_ = &(variable_[name]);
+        }
+        node = paramFile.getNextSameNode(node);
+    }
+    if (!scaleVar_)
+    {
+        LATAN_ERROR(Definition, "scaling variable '" + scale_
+                    + "' not defined");
+    }
+    for (auto &v: variable_)
+    {
+        v.second.index = varName_.size();
+        varName_.push_back(v.first);
+    }
+    for (auto &v: variable_)
+    {
+        varScalePow_.push_back(DRATIO(v.second.dim, scaleVar_->dim));
+    }
+    
+    // fitted quantities
+    node = paramFile.getFirstNode("quantities", "quantity");
+    while (node)
+    {
+        string           name, code = "";
+        Index            nPar;
+        QuInfo           q;
+        DoubleModel      m;
+        shared_ptr<DVec> buf(new DVec(varName_.size()));
+        
+        name            = XGFV(string, "name");
+        nPar            = XGFV(Index, "model", "nPar");
+        q.dim           = XGFV(int, "dim");
+        for (auto &v: variable_)
+        {
+            code += v.first + " = x_" + strFrom(v.second.index) + "; ";
+            code += v.first + "_phy = " + strFrom(v.second.physVal) + "; ";
+        }
+        code           += XGFV(string, "model", "code");
+        DEBUG_VAR(code);
+        m               = compile(code, variable_.size(), nPar);
+        auto wrap       = [m, buf, this, q](const double *x, const double *p)
+        {
+            double s = x[scaleVar_->index];
+            
+            for (unsigned int i = 0; i < varScalePow_.size(); ++i)
+            {
+                if (i != scaleVar_->index)
+                {
+                    (*buf)(i) = x[i]*pow(s, varScalePow_[i]);
+                }
+                else
+                {
+                    (*buf)(i) = x[i];
+                }
+            }
+            
+            return pow(s, -DRATIO(q.dim, scaleVar_->dim))*m(buf->data(), p);
+        };
+        q.model.setFunction(wrap, m.getNArg(), m.getNPar());
+        quantity_[name] = q;
+        node            = paramFile.getNextSameNode(node);
+    }
+    for (auto &q: quantity_)
+    {
+        q.second.index = quName_.size();
+        quName_.push_back(q.first);
+    }
+    
+    // data points
+    node = paramFile.getFirstNode("points", "point");
+    while (node)
+    {
+        string ensemble, fileName;
+        Point  point;
+        
+        ensemble = XGFV(string, "ensemble");
+        auto it  = ensemble_.find(ensemble);
+        if (it == ensemble_.end())
+        {
+            LATAN_ERROR(Parsing, "unknown ensemble '" + ensemble + "'");
+        }
+        macro_["_ensemble_"] = ensemble;
+        point.isActive       = XGFV(bool, "active");
+        point.ensemble       = &(it->second);
+        for (auto &v: variable_)
+        {
+            if (v.first == "T")
+            {
+                fileName = strFrom(point.ensemble->nT);
+            }
+            else if (v.first == "L")
+            {
+                fileName = strFrom(point.ensemble->nL);
+            }
+            else
+            {
+                fileName = macroSubst(XGFV(string, v.first));
+            }
+            point.fileName[v.first] = fileName;
+            varFileNames[v.first].insert(fileName);
+        }
+        for (auto &q: quantity_)
+        {
+            fileName                = macroSubst(XGFV(string, q.first));
+            point.fileName[q.first] = fileName;
+            quFileNames[q.first].insert(fileName);
+        }
+        point_.push_back(point);
+        node = paramFile.getNextSameNode(node);
+    }
+    macro_.erase("_ensemble_");
+    
+    // compute data indices
+    for (auto &v: varFileNames)
+    {
+        varData_.push_back(vector<Data>());
+        for (auto &f: v.second)
+        {
+            Data d;
+            
+            d.fileName            = f;
+            varIndex_[v.first][f] = varData_.back().size();
+            varData_.back().push_back(d);
+        }
+    }
+    for (auto &q: quFileNames)
+    {
+        quData_.push_back(vector<Data>());
+        for (auto &f: q.second)
+        {
+            Data d;
+            
+            d.fileName           = f;
+            quIndex_[q.first][f] = quData_.back().size();
+            quData_.back().push_back(d);
+        }
+    }
+    
+    // compute point coordinates
+    for (auto &p: point_)
+    {
+        p.coord.resize(varName_.size());
+        for (unsigned int i = 0; i < varName_.size(); ++i)
+        {
+            p.coord[i] = varIndex_[varName_[i]][p.fileName[varName_[i]]];
+        }
+    }
+}
+
+#undef XGFV
+
+std::string FitEnv::macroSubst(const std::string str) const
+{
+    std::string res = str, pat;
+    
+    for (auto &m: macro_)
+    {
+        pat      = "@" + m.first + "@";
+        auto pos = res.find(pat);
+        
+        if (pos != string::npos)
+        {
+            res.replace(pos, pat.size(), m.second);
+        }
+    }
+    
+    return res;
+}
+
+void FitEnv::load(void)
+{
+    for (unsigned int i = 0; i < varName_.size(); ++i)
+    {
+        auto &v = varData_[i];
+        
+        if ((varName_[i] == "T") or (varName_[i] == "L"))
+        {
+            for (auto &d: v)
+            {
+                d.value.resize(nSample_);
+                d.value.fill(strTo<double>(d.fileName));
+            }
+        }
+        else
+        {
+            for (auto &d: v)
+            {
+                d.value = Io::load<DSample>(d.fileName);
+                if (d.value.size() != nSample_)
+                {
+                    LATAN_ERROR(Size, "sample loaded from file '" + d.fileName
+                                + "' has a wrong number of element (expected "
+                                + strFrom(nSample_) + ", got "
+                                + strFrom(d.value.size()) + ")");
+                }
+            }
+        }
+        
+    }
+    for (auto &q: quData_)
+    {
+        for (auto &d: q)
+        {
+            d.value = Io::load<DSample>(d.fileName);
+            if (d.value.size() != nSample_)
+            {
+                LATAN_ERROR(Size, "sample loaded from file '" + d.fileName
+                            + "' has a wrong number of element (expected "
+                            + strFrom(nSample_) + ", got "
+                            + strFrom(d.value.size()) + ")");
+            }
+        }
+    }
+
+}
+
+XYSampleData FitEnv::generateData(const bool phyUnits, const bool corr)
+{
+    XYSampleData  data(nSample_);
+    Index         k, k1, k2, ind;
+    const Index   sInd = getVarIndex(scale_);
+    DSample       scale, tmp;
+    int           dim;
+    const int     sDim = scaleVar_->dim;
+    
+    // add dimensions
+    for (unsigned int i = 0; i < varName_.size(); ++i)
+    {
+        data.addXDim(varData_[i].size(), varName_[i],
+                     ((varName_[i] == "T") or (varName_[i] == "L")));
+    }
+    for (auto &q: quName_)
+    {
+        data.addYDim(q);
+    }
+    // add data
+    for (auto &p: point_)
+    {
+        k     = data.dataIndex(p.coord);
+        scale = varData_[sInd][varIndex_[scale_][p.fileName[scale_]]].value;
+        for (unsigned int i = 0; i < varName_.size(); ++i)
+        {
+            ind = varIndex_[varName_[i]][p.fileName[varName_[i]]];
+            dim = variable_[varName_[i]].dim;
+            tmp = varData_[i][ind].value;
+            if (phyUnits and (varName_[i] != scale_))
+            {
+                FOR_STAT_ARRAY(tmp, s)
+                {
+                    tmp[s] *= pow(scale[s], DRATIO(dim, sDim));
+                }
+            }
+            data.x(p.coord[i], i) = tmp;
+        }
+        for (unsigned int j = 0; j < quName_.size(); ++j)
+        {
+            ind = quIndex_[quName_[j]][p.fileName[quName_[j]]];
+            dim = quantity_[quName_[j]].dim;
+            tmp = quData_[j][ind].value;
+            if (phyUnits)
+            {
+                FOR_STAT_ARRAY(tmp, s)
+                {
+                    tmp[s] *= pow(scale[s], DRATIO(dim, sDim));
+                }
+            }
+            data.y(k, j) = tmp;
+        }
+    }
+    // add correlations
+    if (corr)
+    {
+        for (unsigned int p1 = 0; p1 < point_.size(); ++p1)
+        for (unsigned int p2 = p1; p2 < point_.size(); ++p2)
+        {
+            if (point_[p1].ensemble == point_[p2].ensemble)
+            {
+                k1 = data.dataIndex(point_[p1].coord);
+                k2 = data.dataIndex(point_[p2].coord);
+                for (unsigned int i1 = 0; i1 < varName_.size(); ++i1)
+                for (unsigned int i2 = i1; i2 < varName_.size(); ++i2)
+                {
+                    data.assumeXXCorrelated(true, point_[p1].coord[i1], i1,
+                                            point_[p2].coord[i2], i2);
+                }
+                for (unsigned int j1 = 0; j1 < quName_.size(); ++j1)
+                for (unsigned int j2 = j1; j2 < quName_.size(); ++j2)
+                {
+                    data.assumeYYCorrelated(true, k1, j1, k2, j2);
+                }
+                for (unsigned int i = 0; i < varName_.size(); ++i)
+                for (unsigned int j = 0; j < quName_.size(); ++j)
+                {
+                    data.assumeXYCorrelated(true, point_[p1].coord[i], i, k2, j);
+                    data.assumeXYCorrelated(true, point_[p2].coord[i], i, k1, j);
+                }
+            }
+        }
+    }
+    
+    return data;
+}
+
+ostream & operator<<(ostream &out, FitEnv &f)
+{
+    for (unsigned int i = 0; i < f.varName_.size(); ++i)
+    {
+        out << f.varName_[i] << ":" << endl;
+        for (auto &d: f.varData_[i])
+        {
+            out << "  * " << d.fileName << endl;
+        }
+    }
+    for (unsigned int i = 0; i < f.quName_.size(); ++i)
+    {
+        out << f.quName_[i] << ":" << endl;
+        for (auto &d: f.quData_[i])
+        {
+            out << "  * " << d.fileName << endl;
+        }
+    }
+    
+    return out;
+}

physics/fit-phys-env.hpp

@@ -0,0 +1,82 @@
+#ifndef fit_phys_env_hpp_
+#define fit_phys_env_hpp_
+
+#include <LatAnalyze/MatSample.hpp>
+#include <LatAnalyze/Model.hpp>
+#include <LatAnalyze/XYSampleData.hpp>
+
+class FitEnv
+{
+public:
+    // fit variable info
+    struct VarInfo
+    {
+        double       physVal;
+        int          dim;
+        Latan::Index index;
+    };
+    // fitted quantity info
+    struct QuInfo
+    {
+        Latan::DoubleModel model;
+        int                dim;
+        Latan::Index       index;
+    };
+    // ensemble
+    struct Ensemble
+    {
+        unsigned int  nT, nL;
+    };
+    // point
+    struct Point
+    {
+        bool                               isActive{true};
+        const Ensemble                     *ensemble{nullptr};
+        std::map<std::string, std::string> fileName;
+        std::vector<Latan::Index>          coord;
+    };
+    // data container
+    struct Data
+    {
+        std::string    fileName;
+        Latan::DSample value;
+    };
+    // table types
+    typedef std::vector<std::vector<Data>> DataTable;
+    typedef std::map<std::string, std::map<std::string, unsigned int>>
+            IndexTable;
+public:
+    FitEnv(void)          = default;
+    virtual ~FitEnv(void) = default;
+    void                reset(void);
+    Latan::Index        getVarIndex(const std::string name);
+    std::string         getVarName(const Latan::Index i);
+    Latan::Index        getQuIndex(const std::string name);
+    std::string         getQuName(const Latan::Index i);
+    Latan::DVec         getPhyPt(void);
+    std::vector<const Latan::DoubleModel *> getModels(void);
+    void                parseXml(const std::string paramFileName);
+    std::string         macroSubst(const std::string str) const;
+    void                load(void);
+    Latan::XYSampleData generateData(const bool phyUnits, const bool corr);
+    friend std::ostream & operator<<(std::ostream &out, FitEnv &f);
+private:
+    Latan::Index                       nSample_;
+    std::string                        scale_;
+    std::vector<unsigned int>          nT_, nL_;
+    DataTable                          varData_, quData_;
+    IndexTable                         varIndex_, quIndex_;
+    std::map<std::string, VarInfo>     variable_;
+    VarInfo                            *scaleVar_{nullptr};
+    std::vector<std::string>           varName_;
+    std::vector<double>                varScalePow_;
+    std::map<std::string, QuInfo>      quantity_;
+    std::vector<std::string>           quName_;
+    std::map<std::string, Ensemble>    ensemble_;
+    std::vector<Point>                 point_;
+    std::map<std::string, std::string> macro_;
+};
+
+std::ostream & operator<<(std::ostream &out, FitEnv &f);
+
+#endif // fit_phys_env_hpp_

physics/fit-phys.cpp

@@ -0,0 +1,77 @@
+#include <LatAnalyze/Io.hpp>
+#include <LatAnalyze/MinuitMinimizer.hpp>
+#include <LatAnalyze/NloptMinimizer.hpp>
+#include <LatAnalyze/Plot.hpp>
+#include "fit-phys-env.hpp"
+
+using namespace std;
+using namespace Latan;
+
+int main(int argc, char *argv[])
+{
+    // parse arguments /////////////////////////////////////////////////////////
+    string paramFileName;
+    
+    if (argc != 2)
+    {
+        cerr << "usage: " << argv[0] << " <parameter file>" << endl;
+        
+        return EXIT_FAILURE;
+    }
+    paramFileName = argv[1];
+    
+    // parse XML & load data ///////////////////////////////////////////////////
+    FitEnv env;
+    
+    env.parseXml(paramFileName);
+    env.load();
+    
+    XYSampleData uncorrData = env.generateData(false, false);
+    XYSampleData corrData   = env.generateData(false, true);
+    
+    cout << "DATA SUMMARY" << endl;
+    cout << "============" << endl;
+    cout << env << uncorrData << endl;
+    
+    // fit /////////////////////////////////////////////////////////////////////
+    auto v = env.getModels();
+    SampleFitResult fit;
+    MinuitMinimizer min1, min2;
+    vector<Minimizer *> min{&min1, &min2};
+    DVec            init(v[0]->getNPar());
+    
+    min1.setVerbosity(Minimizer::Verbosity::Normal);
+    min2.setVerbosity(Minimizer::Verbosity::Normal);
+    min1.setMaxIteration(1000000);
+    min1.setPrecision(1.0e-3);
+    min2.setMaxIteration(1000000);
+    min2.setPrecision(1.0e-5);
+    init.fill(1.0);
+    fit = uncorrData.fit(min, init, v);
+    fit.print();
+    init = fit[central].block(0, 0, init.size(), 1);
+    fit = corrData.fit(min2, init, v);
+    fit.print();
+    
+//    init = fit[central].block(0, 0, v[0]->getNPar(), 1);
+//    min1.setVerbosity(Minimizer::Verbosity::Normal);
+//    fit = corrData.fit(min1, init, v);
+    
+    // plot ////////////////////////////////////////////////////////////////////
+//    Plot p;
+//    DVec phyPt = env.getPhyPt();
+//    phyPt(env.getVarIndex("a")) = 1.;
+//    XYSampleData projData = uncorrData.getPartialResiduals(fit, phyPt, env.getVarIndex("M_Ds"));
+//    
+//    p << PlotPredBand(fit.getModel(_).bind(env.getVarIndex("M_Ds"), phyPt), 0., 3.);
+//    p << PlotData(projData.getData(), env.getVarIndex("M_Ds"), 0);
+//    p.display();
+//    p.reset();
+//    projData = uncorrData.getPartialResiduals(fit, phyPt, env.getVarIndex("a"));
+//    p << PlotPredBand(fit.getModel(_).bind(env.getVarIndex("a"), phyPt), 0., 1.);
+//    p << PlotData(projData.getData(), env.getVarIndex("a"), 0);
+//    p.display();
+//    p.reset();
+    
+    return EXIT_SUCCESS;
+}

utils/Makefile.am

@@ -10,8 +10,6 @@ bin_PROGRAMS =            \
     latan-sample-combine  \
     latan-sample-element  \
     latan-sample-fake     \
-    latan-sample-ft       \
-    latan-sample-plot     \
     latan-sample-plot-corr\
     latan-sample-read     \
     latan-resample
@@ -28,18 +26,10 @@ latan_sample_fake_SOURCES  = sample-fake.cpp
 latan_sample_fake_CXXFLAGS = $(COM_CXXFLAGS)
 latan_sample_fake_LDFLAGS  = -L../lib/.libs -lLatAnalyze
 
-latan_sample_ft_SOURCES  = sample-ft.cpp
-latan_sample_ft_CXXFLAGS = $(COM_CXXFLAGS)
-latan_sample_ft_LDFLAGS  = -L../lib/.libs -lLatAnalyze
-
 latan_sample_plot_corr_SOURCES  = sample-plot-corr.cpp
 latan_sample_plot_corr_CXXFLAGS = $(COM_CXXFLAGS)
 latan_sample_plot_corr_LDFLAGS  = -L../lib/.libs -lLatAnalyze
 
-latan_sample_plot_SOURCES  = sample-plot.cpp
-latan_sample_plot_CXXFLAGS = $(COM_CXXFLAGS)
-latan_sample_plot_LDFLAGS  = -L../lib/.libs -lLatAnalyze
-
 latan_sample_read_SOURCES  = sample-read.cpp
 latan_sample_read_CXXFLAGS = $(COM_CXXFLAGS)
 latan_sample_read_LDFLAGS  = -L../lib/.libs -lLatAnalyze

utils/resample.cpp

@@ -39,7 +39,7 @@ int main(int argc, char *argv[])
 {
     // argument parsing ////////////////////////////////////////////////////////
     OptParser     opt;
-    bool          parsed, dumpBoot;
+    bool          parsed;
     random_device rd;
     SeedType      seed = rd();
     string        manFileName, nameFileName, outDirName;
@@ -56,8 +56,6 @@ int main(int argc, char *argv[])
                   "output directory", ".");
     opt.addOption("f", "format"    , OptParser::OptType::value,   true,
                   "output file format", DEF_FMT);
-    opt.addOption("d", "dump-boot" , OptParser::OptType::trigger, true,
-                  "dump bootstrap sequence");
     opt.addOption("" , "help"      , OptParser::OptType::trigger, true,
                   "show this help message and exit");
     parsed = opt.parse(argc, argv);
@@ -77,7 +75,6 @@ int main(int argc, char *argv[])
     }
     ext          = opt.optionValue("f");
     outDirName   = opt.optionValue("o");
-    dumpBoot     = opt.gotOption("d");
     manFileName  = opt.getArgs()[0];
     nameFileName = opt.getArgs()[1];
     
@@ -127,15 +124,6 @@ int main(int argc, char *argv[])
         
         cout << '\r' << ProgressBar(i + 1, name.size());
         data[name[i]].bin(binSize);
-        if ((i == 0) and dumpBoot)
-        {
-            ofstream file(outDirName + "/" + manFileName + ".bootseq");
-
-            file << "# bootstrap sequences" << endl;
-            file << "# manifest file: " << manFileName << endl;
-            file << "#      bin size: " << binSize << endl;
-            data[name[i]].dumpBootstrapSeq(file, nSample, seed);
-        }
         s = data[name[i]].bootstrapMean(nSample, seed);
         Io::save<DMatSample>(s, outDirName + "/" + outFileName,
                              File::Mode::write, outFileName);

utils/sample-combine.cpp

@@ -25,21 +25,14 @@ using namespace std;
 using namespace Latan;
 
 template <typename T>
-static void loadAndCheck(vector<T> &sample __dumb,
-                         const vector<string> &fileName __dumb)
+static void loadAndCheck(vector<T> &sample, const vector<string> &fileName)
 {
-    abort();
-}
-
-template <>
-void loadAndCheck(vector<DSample> &sample, const vector<string> &fileName)
-{
-    const unsigned int n = static_cast<unsigned int>(sample.size());
+    const unsigned int n = sample.size();
     Index              nSample = 0;
     
     for (unsigned int i = 0; i < n; ++i)
     {
-        sample[i] = Io::load<DSample>(fileName[i]);
+        sample[i] = Io::load<T>(fileName[i]);
         if (i == 0)
         {
             nSample = sample[i].size();
@@ -53,62 +46,6 @@ void loadAndCheck(vector<DSample> &sample, const vector<string> &fileName)
     }
 }
 
-template <>
-void loadAndCheck(vector<DMatSample> &sample, const vector<string> &fileName)
-{
-    const unsigned int n = static_cast<unsigned int>(sample.size());
-    Index              nSample = 0;
-    set<unsigned int>  failed;
-    bool               gotSize = false;
-    Index              nRow = 0, nCol = 0;
-    
-    for (unsigned int i = 0; i < n; ++i)
-    {
-        try
-        {
-            sample[i] = Io::load<DMatSample>(fileName[i]);
-            if (!gotSize)
-            {
-                nSample = sample[i].size();
-                nRow    = sample[i][central].rows();
-                nCol    = sample[i][central].cols();
-                gotSize = true;
-            }
-        }
-        catch (Exceptions::Definition)
-        {
-            failed.insert(i);
-        }
-    }
-    for (unsigned int i: failed)
-    {
-        DSample buf;
-        
-        buf = Io::load<DSample>(fileName[i]);
-        sample[i].resize(nSample);
-        FOR_STAT_ARRAY(sample[i], s)
-        {
-            sample[i][s] = DMat::Constant(nRow, nCol, buf[s]);
-        }
-    }
-    for (unsigned int i = 0; i < n; ++i)
-    {
-        if (sample[i].size() != nSample)
-        {
-            cerr << "error: number of sample mismatch (between '";
-            cerr << fileName[0] << "' and '" << fileName[i] << "')" << endl;
-            abort();
-        }
-        if ((sample[i][central].rows() != nRow) and
-            (sample[i][central].cols() != nCol))
-        {
-            cerr << "error: matrix size mismatch (between '";
-            cerr << fileName[0] << "' and '" << fileName[i] << "')" << endl;
-            abort();
-        }
-    }
-}
-
 template <typename T>
 static void combine(const string &outFileName __dumb,
                     const vector<T> &sample __dumb, const string &code __dumb)
@@ -120,7 +57,7 @@ template <>
 void combine(const string &outFileName, const vector<DSample> &sample,
              const string &code)
 {
-    const unsigned int n = static_cast<unsigned int>(sample.size());
+    const unsigned int n = sample.size();
     DoubleFunction     f = compile(code, n);
     DSample            result(sample[0]);
     DVec               buf(n);
@@ -150,7 +87,7 @@ template <>
 void combine(const string &outFileName, const vector<DMatSample> &sample,
              const string &code)
 {
-    const unsigned int n = static_cast<unsigned int>(sample.size());
+    const unsigned int n = sample.size();
     DoubleFunction     f = compile(code, n);
     DVec               buf(n);
     DMatSample         result(sample[0]);

utils/sample-element.cpp

@@ -1,103 +1,39 @@
-/*
- * sample-element.cpp, part of LatAnalyze 3
- *
- * 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
- * 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 <iostream>
+#include <string>
 
-#include <LatCore/OptParser.hpp>
 #include <LatAnalyze/Io.hpp>
 #include <LatAnalyze/MatSample.hpp>
 
-using namespace std;
-using namespace Latan;
 
 int main(int argc, char* argv[])
 {
-    // argument parsing ////////////////////////////////////////////////////////
-    OptParser opt;
-    bool      parsed;
-    string    inFilename, outFilename;
-    Index     r, c, nr, nc;
+    using namespace std;
+    using namespace Latan;
 
-    opt.addOption("r", "row",    OptParser::OptType::value  , false,
-                  "row");
-    opt.addOption("c", "col",    OptParser::OptType::value  , false,
-                  "column");
-    opt.addOption("" , "nrow",   OptParser::OptType::value  , true,
-                  "number of rows (default: 1)", "1");
-    opt.addOption("" , "ncol",   OptParser::OptType::value  , true,
-                  "number of columns (default: 1)", "1");
-    opt.addOption("o", "output", OptParser::OptType::value  , true,
-                  "output file name (default: result not saved)", "");
-    opt.addOption("" , "help"  , OptParser::OptType::trigger, true,
-                  "show this help message and exit");
-    parsed = opt.parse(argc, argv);
-    if (!parsed or (opt.getArgs().size() != 1) or opt.gotOption("help"))
-    {
-        cerr << "usage: " << argv[0];
-        cerr << " <options> <input file>" << endl;
-        cerr << endl << "Possible options:" << endl << opt << endl;
-        
-        return EXIT_FAILURE;
+    if (argc != 4 and argc != 5) {
+        cout << "Usage: " << argv[0] << " <input filename> <row> <column> ";
+        cout << "[output filename]" << endl;
+        return -1;
     }
-    inFilename  = opt.getArgs()[0];
-    outFilename = opt.optionValue("o");
-    r           = opt.optionValue<Index>("r");
-    c           = opt.optionValue<Index>("c");
-    nr          = opt.optionValue<Index>("nrow");
-    nc          = opt.optionValue<Index>("ncol");
 
-    // Data extraction /////////////////////////////////////////////////////////
-    auto inputData = Io::load<DMatSample>(inFilename);
+    string inFileName = argv[1];
+    auto row = strTo<Index>(argv[2]);
+    auto col = strTo<Index>(argv[3]);
+    string outFileName = (argc == 5) ? argv[4] : "";
 
-    if ((nr == 1) and (nc == 1))
+    auto inputData = Io::load<DMatSample>(inFileName);
+    cout << scientific;
+    cout << "central value:\n" << inputData[central](row, col) << endl;
+    cout << "standard deviation:\n";
+    cout << inputData.variance().cwiseSqrt()(row, col) << endl;
+
+    if (not outFileName.empty())
     {
         DSample outputData(inputData.size());
-        
-        FOR_STAT_ARRAY(inputData, s)
-        {
-            outputData[s] = inputData[s](r, c);
+        FOR_STAT_ARRAY(inputData, s) {
+            outputData[s] = inputData[s](row, col);
         }
 
-        cout << scientific;
-        cout << "central value:\n" << outputData[central] << endl;
-        cout << "standard deviation:\n";
-        cout << sqrt(outputData.variance()) << endl;
-        if (not outFilename.empty())
-        {
-            Io::save(outputData, outFilename);
+        Io::save(outputData, outFileName);
     }
-    }
-    else
-    {
-        DMatSample outputData(inputData.size(), nr, nc);
-        
-        FOR_STAT_ARRAY(inputData, s)
-        {
-            outputData[s] = inputData[s].block(r, c, nr, nc);
-        }
-        cout << scientific;
-        cout << "central value:\n" << outputData[central] << endl;
-        cout << "standard deviation:\n";
-        cout << outputData.variance().cwiseSqrt() << endl;
-        if (not outFilename.empty())
-        {
-            Io::save(outputData, outFilename);
-        }
-    }
-
-    return EXIT_SUCCESS;
 }

utils/sample-ft.cpp

@@ -1,94 +0,0 @@
-/*
- * sample-ft.cpp, part of LatAnalyze 3
- *
- * Copyright (C) 2013 - 2016 Antonin Portelli
- *
- * LatAnalyze 3 is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * LatAnalyze 3 is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <LatCore/OptParser.hpp>
-#include <LatAnalyze/GslFFT.hpp>
-#include <LatAnalyze/Io.hpp>
-
-using namespace std;
-using namespace Latan;
-
-int main(int argc, char *argv[])
-{
-    // argument parsing ////////////////////////////////////////////////////////
-    OptParser    opt;
-    bool         parsed;
-    string       inFilename, outFilename;
-    unsigned int dir = FFT::Forward;
-    
-    opt.addOption("o", "output", OptParser::OptType::value  , true,
-                  "output file name (default: result not saved)", "");
-    opt.addOption("b", "backward", OptParser::OptType::trigger, true,
-                  "backward Fourier transform (forward by default)");
-    opt.addOption("" , "help"  , OptParser::OptType::trigger, true,
-                  "show this help message and exit");
-    parsed = opt.parse(argc, argv);
-    if (!parsed or (opt.getArgs().size() != 1) or opt.gotOption("help"))
-    {
-        cerr << "usage: " << argv[0];
-        cerr << " <options> <input file>" << endl;
-        cerr << endl << "Possible options:" << endl << opt << endl;
-        
-        return EXIT_FAILURE;
-    }
-    inFilename  = opt.getArgs()[0];
-    outFilename = opt.optionValue("o");
-    if (opt.gotOption("b"))
-    {
-        dir = FFT::Backward;
-    }
-    
-    // Fourier transform ///////////////////////////////////////////////////////
-    DMatSample in          = Io::load<DMatSample>(inFilename);
-    Index      nSample     = in.size(), l = in[central].rows();
-    bool       isInComplex = (in[central].cols() > 1);
-    CMatSample res(nSample, l, 1);
-    DMatSample out(nSample, l, 2);
-    GslFFT     ft(l);
-    
-    cout << "-- computing Fourier transform..." << endl;
-    FOR_STAT_ARRAY(in, s)
-    {
-        res[s].real() = in[s].col(0);
-        if (isInComplex)
-        {
-            res[s].imag() = in[s].col(1);
-        }
-        else
-        {
-            res[s].imag() = DVec::Constant(l, 0.);
-        }
-        ft(res[s], dir);
-        out[s].col(0) = res[s].real();
-        out[s].col(1) = res[s].imag();
-    }
-    
-    // output /////////////////////////////////////////////////////////////////
-    cout << scientific;
-    cout << "central value:\n"      << out[central];
-    cout << endl;
-    cout << "standard deviation:\n" << out.variance().cwiseSqrt();
-    cout << endl;
-    if (!outFilename.empty())
-    {
-        Io::save<DMatSample>(out, outFilename);
-    }
-    
-    return EXIT_SUCCESS;
-}

utils/sample-plot.cpp

@@ -1,51 +0,0 @@
-/*
- * sample-plot.cpp, part of LatAnalyze 3
- *
- * Copyright (C) 2013 - 2016 Antonin Portelli
- *
- * LatAnalyze 3 is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * LatAnalyze 3 is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <LatAnalyze/Io.hpp>
-#include <LatAnalyze/Math.hpp>
-#include <LatAnalyze/Plot.hpp>
-
-using namespace std;
-using namespace Latan;
-using namespace Math;
-
-int main(int argc, char *argv[])
-{
-    string xFileName, yFileName;
-    
-    if (argc != 3)
-    {
-        cerr << "usage: " << argv[0] << " <x sample> <y sample>" << endl;
-        
-        return EXIT_FAILURE;
-    }
-    xFileName = argv[1];
-    yFileName = argv[2];
-    
-    Plot p;
-    DMatSample x, y;
-    
-    x = Io::load<DMatSample>(xFileName);
-    y = Io::load<DMatSample>(yFileName);
-    
-    p << PlotData(x, y);
-    p.display();
-    
-    return EXIT_SUCCESS;
-}