From 7a085842f6c0379aa76a52d37f8550bdf7f35b21 Mon Sep 17 00:00:00 2001
From: Matthieu Zimmer <contact@matthieu-zimmer.net>
Date: Fri, 16 May 2014 19:24:17 +0200
Subject: [PATCH 1/3] portage to eigen3 seems ok

---
 af.hpp            |   9 ++--
 esn.hpp           |   6 +--
 esn_2.hpp         |   7 +--
 io_trait.hpp      |   4 --
 pf.hpp            |  14 ++----
 test_dnn.cpp      |  50 +++++++++---------
 test_dnn_ff.cpp   |  42 ++++++++--------
 test_hyper_nn.cpp | 126 +++++++++++++++++++++++-----------------------
 trait.hpp         |   2 -
 wscript           |  16 +++---
 10 files changed, 134 insertions(+), 142 deletions(-)

diff --git a/af.hpp b/af.hpp
index fb9b6aa..f98af91 100644
--- a/af.hpp
+++ b/af.hpp
@@ -36,6 +36,7 @@
 #define _NN_AF_HPP_
 
 #include "params.hpp"
+#include <sferes/stc.hpp>
 
 // classic activation functions
 namespace nn
@@ -59,7 +60,7 @@ namespace nn
   struct AfTanh : public Af<P>
   {
     typedef P params_t;
-    static const float lambda = 5.0f;
+    SFERES_CONST float lambda = 5.0f;
     AfTanh() { assert(trait<P>::size(this->_params) == 1); }
     float operator()(float p) const
     {
@@ -72,7 +73,7 @@ namespace nn
   struct AfTanhNoBias : public Af<P>
   {
     typedef params::Dummy params_t;
-    static const float lambda = 5.0f;
+    SFERES_CONST float lambda = 5.0f;
     AfTanhNoBias() { }
     float operator()(float p) const
     {
@@ -86,7 +87,7 @@ namespace nn
   struct AfSigmoidNoBias : public Af<>
   {
     typedef params::Dummy params_t;
-    static const float lambda = 5.0f;
+    SFERES_CONST float lambda = 5.0f;
     AfSigmoidNoBias() { }
     float operator()(float p) const { return 1.0 / (exp(-p * lambda) + 1); }
   protected:
@@ -96,7 +97,7 @@ namespace nn
   struct AfSigmoidBias : public Af<P>
   {
     typedef P params_t;
-    static const float lambda = 5.0f;
+    SFERES_CONST float lambda = 5.0f;
     AfSigmoidBias() { assert(this->_params.size() == 1); }
     float operator()(float p) const
     {
diff --git a/esn.hpp b/esn.hpp
index 42fdd1d..2e7b557 100644
--- a/esn.hpp
+++ b/esn.hpp
@@ -39,8 +39,8 @@
 #define _NN_ESN_HPP_
 
 #include <Eigen/Core>
-#include <Eigen/Array>
 #include <Eigen/QR> 
+#include <Eigen/Eigenvalues>
 
 #include <sferes/misc/rand.hpp>
 
@@ -93,8 +93,8 @@ namespace nn
 	  else
 	    conn(i, j) = 0.0f;
       // spectral radius
-      float max = (conn.eigenvalues().real().cwise().square()
-		   + conn.eigenvalues().imag().cwise().square()
+      float max = (conn.eigenvalues().real().array().square()
+		   + conn.eigenvalues().imag().array().square()
 		   ).maxCoeff();
       assert(max > 0);
       conn *= alpha / sqrtf(max);
diff --git a/esn_2.hpp b/esn_2.hpp
index ede5419..3a706a7 100644
--- a/esn_2.hpp
+++ b/esn_2.hpp
@@ -39,8 +39,9 @@
 #define _NN_ESN_HPP_
 
 #include <Eigen/Core>
-#include <Eigen/Array>
 #include <Eigen/QR> 
+#include <Eigen/Eigenvalues>
+
 
 #include <sferes/misc/rand.hpp>
 #include <sferes/misc.hpp>
@@ -164,8 +165,8 @@ namespace nn
 	if (sferes::misc::rand<float>() < alpha)
 	  conn(i, j) = sferes::misc::rand(-1.0f, 1.0f);
     // spectral radius
-    float max = (conn.eigenvalues().real().cwise().square()
-		 + conn.eigenvalues().imag().cwise().square()
+    float max = (conn.eigenvalues().real().array().square()
+		 + conn.eigenvalues().imag().array().square()
 		 ).maxCoeff();
     assert(max > 0);
     conn *= alpha / sqrtf(max);
diff --git a/io_trait.hpp b/io_trait.hpp
index 6e618b0..b44da2a 100644
--- a/io_trait.hpp
+++ b/io_trait.hpp
@@ -42,9 +42,7 @@
 #include <map>
 #include <valarray>
 
-#ifdef EIGEN2_ENABLED
 #include <Eigen/Core>
-#endif
 
 namespace nn
 {
@@ -57,7 +55,6 @@ namespace nn
     typedef std::valarray<T> vector_t;
   };
 
-#ifdef EIGEN2_ENABLED
   // go with eigen with float (TODO : double)
   template<>
   struct io_trait<float>
@@ -67,7 +64,6 @@ namespace nn
     static vector_t zero(size_t k) { return Eigen::VectorXf::Zero(k); }
 
   };
-#endif
 
   template<>
   struct io_trait<std::pair<float, float> >
diff --git a/pf.hpp b/pf.hpp
index fb14ab4..cf9aa8f 100644
--- a/pf.hpp
+++ b/pf.hpp
@@ -38,6 +38,7 @@
 
 #include <cstdlib>
 #include <sferes/misc/rand.hpp>
+#include <sferes/stc.hpp>
 
 #include "params.hpp"
 #include "trait.hpp"
@@ -86,12 +87,7 @@ namespace nn
        //_w_cache.dot(inputs)<<std::endl;
       if (inputs.size() == 0)
         return 0.0f;
-#ifdef EIGEN2_ENABLED
-      return _w_cache.dot(inputs);
-#else
- #warning "No eigen2 -> no vectorization of pwfsum"
-      return (_w_cache * inputs).sum();
-#endif
+      return inputs.dot(_w_cache);
     }
     protected:
       trait<float>::vector_t _w_cache;
@@ -112,9 +108,9 @@ namespace nn
   {
     typedef std::pair<float, float> weight_t;
     typedef P params_t;
-    static const float dt = 0.01;
-    static const float a_r = 20.0f;
-    static const float a_x = 20.0f;
+    SFERES_CONST float dt = 0.01;
+    SFERES_CONST float a_r = 20.0f;
+    SFERES_CONST float a_x = 20.0f;
     void set_r(float r) { _r = r; }
     void set_x(float x) { _x = x; }
     void set_omega(float o) { _omega = o; }
diff --git a/test_dnn.cpp b/test_dnn.cpp
index 8c8c5a4..0ccdd4c 100644
--- a/test_dnn.cpp
+++ b/test_dnn.cpp
@@ -112,39 +112,39 @@ struct Params
 {
   struct evo_float
   {
-    static const float mutation_rate = 0.1f;
-    static const float cross_rate = 0.1f;
-    static const mutation_t mutation_type = polynomial;
-    static const cross_over_t cross_over_type = sbx;
-    static const float eta_m = 15.0f;
-    static const float eta_c = 15.0f;
+    SFERES_CONST float mutation_rate = 0.1f;
+    SFERES_CONST float cross_rate = 0.1f;
+    SFERES_CONST mutation_t mutation_type = polynomial;
+    SFERES_CONST cross_over_t cross_over_type = sbx;
+    SFERES_CONST float eta_m = 15.0f;
+    SFERES_CONST float eta_c = 15.0f;
   };
   struct parameters
   {
     // maximum value of parameters
-    static const float min = -5.0f;
+    SFERES_CONST float min = -5.0f;
     // minimum value
-    static const float max = 5.0f;
+    SFERES_CONST float max = 5.0f;
   };
   struct dnn
   {
-    static const size_t nb_inputs	= 4;
-    static const size_t nb_outputs	= 1;
-    static const size_t min_nb_neurons	= 4;
-    static const size_t max_nb_neurons	= 5;
-    static const size_t min_nb_conns	= 100;
-    static const size_t max_nb_conns	= 101;
-    static const float  max_weight	= 2.0f;
-    static const float  max_bias	= 2.0f;
-
-    static const float m_rate_add_conn	= 1.0f;
-    static const float m_rate_del_conn	= 1.0f;
-    static const float m_rate_change_conn = 1.0f;
-    static const float m_rate_add_neuron  = 1.0f;
-    static const float m_rate_del_neuron  = 1.0f;
-
-    static const int io_param_evolving = true;
-    static const init_t init = random_topology;
+    SFERES_CONST size_t nb_inputs	= 4;
+    SFERES_CONST size_t nb_outputs	= 1;
+    SFERES_CONST size_t min_nb_neurons	= 4;
+    SFERES_CONST size_t max_nb_neurons	= 5;
+    SFERES_CONST size_t min_nb_conns	= 100;
+    SFERES_CONST size_t max_nb_conns	= 101;
+    SFERES_CONST float  max_weight	= 2.0f;
+    SFERES_CONST float  max_bias	= 2.0f;
+
+    SFERES_CONST float m_rate_add_conn	= 1.0f;
+    SFERES_CONST float m_rate_del_conn	= 1.0f;
+    SFERES_CONST float m_rate_change_conn = 1.0f;
+    SFERES_CONST float m_rate_add_neuron  = 1.0f;
+    SFERES_CONST float m_rate_del_neuron  = 1.0f;
+
+    SFERES_CONST int io_param_evolving = true;
+    SFERES_CONST init_t init = random_topology;
   };
 };
 
diff --git a/test_dnn_ff.cpp b/test_dnn_ff.cpp
index 6a116fe..1c253fe 100644
--- a/test_dnn_ff.cpp
+++ b/test_dnn_ff.cpp
@@ -60,37 +60,37 @@ struct Params
 {
   struct evo_float
   {
-    static const float mutation_rate = 0.1f;
-    static const float cross_rate = 0.1f;
-    static const mutation_t mutation_type = polynomial;
-    static const cross_over_t cross_over_type = sbx;
-    static const float eta_m = 15.0f;
-    static const float eta_c = 15.0f;
+    SFERES_CONST float mutation_rate = 0.1f;
+    SFERES_CONST float cross_rate = 0.1f;
+    SFERES_CONST mutation_t mutation_type = polynomial;
+    SFERES_CONST cross_over_t cross_over_type = sbx;
+    SFERES_CONST float eta_m = 15.0f;
+    SFERES_CONST float eta_c = 15.0f;
   };
   struct parameters
   {
     // maximum value of parameters
-    static const float min = -5.0f;
+    SFERES_CONST float min = -5.0f;
     // minimum value
-    static const float max = 5.0f;
+    SFERES_CONST float max = 5.0f;
   };
   struct dnn
   {
-    static const size_t nb_inputs	= 4;
-    static const size_t nb_outputs	= 2;
-    static const size_t min_nb_neurons	= 4;
-    static const size_t max_nb_neurons	= 5;
-    static const size_t min_nb_conns	= 100;
-    static const size_t max_nb_conns	= 101;
+    SFERES_CONST size_t nb_inputs	= 4;
+    SFERES_CONST size_t nb_outputs	= 2;
+    SFERES_CONST size_t min_nb_neurons	= 4;
+    SFERES_CONST size_t max_nb_neurons	= 5;
+    SFERES_CONST size_t min_nb_conns	= 100;
+    SFERES_CONST size_t max_nb_conns	= 101;
 
-    static const float m_rate_add_conn	= 1.0f;
-    static const float m_rate_del_conn	= 0.1f;
-    static const float m_rate_change_conn = 1.0f;
-    static const float m_rate_add_neuron  = 1.0f;
-    static const float m_rate_del_neuron  = 1.0f;
+    SFERES_CONST float m_rate_add_conn	= 1.0f;
+    SFERES_CONST float m_rate_del_conn	= 0.1f;
+    SFERES_CONST float m_rate_change_conn = 1.0f;
+    SFERES_CONST float m_rate_add_neuron  = 1.0f;
+    SFERES_CONST float m_rate_del_neuron  = 1.0f;
 
-    static const int io_param_evolving = true;
-    static const init_t init = ff;
+    SFERES_CONST int io_param_evolving = true;
+    SFERES_CONST init_t init = ff;
   };
 };
 
diff --git a/test_hyper_nn.cpp b/test_hyper_nn.cpp
index 62cde61..35388ed 100644
--- a/test_hyper_nn.cpp
+++ b/test_hyper_nn.cpp
@@ -52,30 +52,30 @@ struct Params1
 {
   struct dnn
   {
-    static const size_t nb_inputs = 3;
-    static const size_t nb_outputs = 1;
+    SFERES_CONST size_t nb_inputs = 3;
+    SFERES_CONST size_t nb_outputs = 1;
 
-    static const float m_rate_add_conn = 1.0f;
-    static const float m_rate_del_conn = 0.3f;
-    static const float m_rate_change_conn = 1.0f;
-    static const float m_rate_add_neuron = 1.0f;
-    static const float m_rate_del_neuron = 0.2f;
+    SFERES_CONST float m_rate_add_conn = 1.0f;
+    SFERES_CONST float m_rate_del_conn = 0.3f;
+    SFERES_CONST float m_rate_change_conn = 1.0f;
+    SFERES_CONST float m_rate_add_neuron = 1.0f;
+    SFERES_CONST float m_rate_del_neuron = 0.2f;
 
-    static const init_t init = ff;
+    SFERES_CONST init_t init = ff;
   };
   struct evo_float
   {
-    static const float mutation_rate = 0.1f;
-    static const float cross_rate = 0.1f;
-    static const mutation_t mutation_type = polynomial;
-    static const cross_over_t cross_over_type = sbx;
-    static const float eta_m = 15.0f;
-    static const float eta_c = 15.0f;
+    SFERES_CONST float mutation_rate = 0.1f;
+    SFERES_CONST float cross_rate = 0.1f;
+    SFERES_CONST mutation_t mutation_type = polynomial;
+    SFERES_CONST cross_over_t cross_over_type = sbx;
+    SFERES_CONST float eta_m = 15.0f;
+    SFERES_CONST float eta_c = 15.0f;
   };
   struct parameters
   {
-    static const float min = -2.0f;
-    static const float max = 2.0f;
+    SFERES_CONST float min = -2.0f;
+    SFERES_CONST float max = 2.0f;
   };
 
   struct cppn
@@ -84,18 +84,18 @@ struct Params1
     struct sampled
     {
       SFERES_ARRAY(float, values, 0, 1, 2);
-      static const float mutation_rate = 0.1f;
-      static const float cross_rate = 0.25f;
-      static const bool ordered = false;
+      SFERES_CONST float mutation_rate = 0.1f;
+      SFERES_CONST float cross_rate = 0.25f;
+      SFERES_CONST bool ordered = false;
     };
     struct evo_float
     {
-      static const float mutation_rate = 0.1f;
-      static const float cross_rate = 0.1f;
-      static const mutation_t mutation_type = polynomial;
-      static const cross_over_t cross_over_type = sbx;
-      static const float eta_m = 15.0f;
-      static const float eta_c = 15.0f;
+      SFERES_CONST float mutation_rate = 0.1f;
+      SFERES_CONST float cross_rate = 0.1f;
+      SFERES_CONST mutation_t mutation_type = polynomial;
+      SFERES_CONST cross_over_t cross_over_type = sbx;
+      SFERES_CONST float eta_m = 15.0f;
+      SFERES_CONST float eta_c = 15.0f;
     };
   };
 };
@@ -105,34 +105,34 @@ struct Params2
 {
   struct dnn
   {
-    static const size_t nb_inputs = 4;
-    static const size_t nb_outputs = 1;
-
-    static const float m_rate_add_conn = 1.0f;
-    static const float m_rate_del_conn = 0.3f;
-    static const float m_rate_change_conn = 1.0f;
-    static const float m_rate_add_neuron = 1.0f;
-    static const float m_rate_del_neuron = 0.2f;
-
-    static const float weight_sigma = 0.5f;
-    static const float vect_sigma = 0.5f;
-    static const float m_rate_weight = 1.0f;
-    static const float m_rate_fparams = 1.0f;
-    static const init_t init = ff;
+    SFERES_CONST size_t nb_inputs = 4;
+    SFERES_CONST size_t nb_outputs = 1;
+
+    SFERES_CONST float m_rate_add_conn = 1.0f;
+    SFERES_CONST float m_rate_del_conn = 0.3f;
+    SFERES_CONST float m_rate_change_conn = 1.0f;
+    SFERES_CONST float m_rate_add_neuron = 1.0f;
+    SFERES_CONST float m_rate_del_neuron = 0.2f;
+
+    SFERES_CONST float weight_sigma = 0.5f;
+    SFERES_CONST float vect_sigma = 0.5f;
+    SFERES_CONST float m_rate_weight = 1.0f;
+    SFERES_CONST float m_rate_fparams = 1.0f;
+    SFERES_CONST init_t init = ff;
   };
   struct evo_float
   {
-    static const float mutation_rate = 0.1f;
-    static const float cross_rate = 0.1f;
-    static const mutation_t mutation_type = polynomial;
-    static const cross_over_t cross_over_type = sbx;
-    static const float eta_m = 15.0f;
-    static const float eta_c = 15.0f;
+    SFERES_CONST float mutation_rate = 0.1f;
+    SFERES_CONST float cross_rate = 0.1f;
+    SFERES_CONST mutation_t mutation_type = polynomial;
+    SFERES_CONST cross_over_t cross_over_type = sbx;
+    SFERES_CONST float eta_m = 15.0f;
+    SFERES_CONST float eta_c = 15.0f;
   };
   struct parameters
   {
-    static const float min = -2.0f;
-    static const float max = 2.0f;
+    SFERES_CONST float min = -2.0f;
+    SFERES_CONST float max = 2.0f;
   };
 
   struct cppn
@@ -141,18 +141,18 @@ struct Params2
     struct sampled
     {
       SFERES_ARRAY(float, values, 0, 1, 2);
-      static const float mutation_rate = 0.1f;
-      static const float cross_rate = 0.25f;
-      static const bool ordered = false;
+      SFERES_CONST float mutation_rate = 0.1f;
+      SFERES_CONST float cross_rate = 0.25f;
+      SFERES_CONST bool ordered = false;
     };
     struct evo_float
     {
-      static const float mutation_rate = 0.1f;
-      static const float cross_rate = 0.1f;
-      static const mutation_t mutation_type = polynomial;
-      static const cross_over_t cross_over_type = sbx;
-      static const float eta_m = 15.0f;
-      static const float eta_c = 15.0f;
+      SFERES_CONST float mutation_rate = 0.1f;
+      SFERES_CONST float cross_rate = 0.1f;
+      SFERES_CONST mutation_t mutation_type = polynomial;
+      SFERES_CONST cross_over_t cross_over_type = sbx;
+      SFERES_CONST float eta_m = 15.0f;
+      SFERES_CONST float eta_c = 15.0f;
     };
   };
   struct hyper_nn
@@ -168,13 +168,13 @@ struct Params2
                  );
     SFERES_ARRAY(float, weights, -1, 0, 1);
     SFERES_ARRAY(float, bias, -1, 0, 1);
-    static const size_t nb_inputs = 2;
-    static const size_t nb_outputs = 1;
-    static const size_t nb_hidden = 4;
-    static const size_t nb_pfparams = 0;
-    static const size_t nb_afparams = 1;
-    static const float conn_threshold = 0.2f;
-    static const float max_y = 10.0f;
+    SFERES_CONST size_t nb_inputs = 2;
+    SFERES_CONST size_t nb_outputs = 1;
+    SFERES_CONST size_t nb_hidden = 4;
+    SFERES_CONST size_t nb_pfparams = 0;
+    SFERES_CONST size_t nb_afparams = 1;
+    SFERES_CONST float conn_threshold = 0.2f;
+    SFERES_CONST float max_y = 10.0f;
     typedef nn::Neuron<nn::PfWSum<>,
                        nn::AfTanh<nn::params::Vectorf<1> > > neuron_t;
     typedef nn::Connection<> connection_t;
diff --git a/trait.hpp b/trait.hpp
index 75e1a91..c28d473 100644
--- a/trait.hpp
+++ b/trait.hpp
@@ -42,9 +42,7 @@
 #include <map>
 #include <valarray>
 
-#ifdef EIGEN2_ENABLED
 #include <Eigen/Core>
-#endif
 
 #include "params.hpp"
 
diff --git a/wscript b/wscript
index a118948..60d34ff 100644
--- a/wscript
+++ b/wscript
@@ -48,7 +48,7 @@ def build(bld):
     test_nn.source = 'test_nn.cpp'
     test_nn.includes = '. ../../'
     test_nn.uselib_local = ''
-    test_nn.uselib = 'EIGEN2 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK'
+    test_nn.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK'
     test_nn.target = 'test_nn'
     test_nn.unit_test = 1
 
@@ -56,7 +56,7 @@ def build(bld):
     test_dnn.source = 'test_dnn.cpp'
     test_dnn.includes = '. ../../'
     test_dnn.uselib_local = 'sferes2'
-    test_dnn.uselib = 'EIGEN2 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
+    test_dnn.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
     test_dnn.target = 'test_dnn'
     test_dnn.unit_test = 1
 
@@ -64,7 +64,7 @@ def build(bld):
     test_mlp.source = 'test_mlp.cpp'
     test_mlp.includes = '. ../../'
     test_mlp.uselib_local = 'sferes2'
-    test_mlp.uselib = 'EIGEN2 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
+    test_mlp.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
     test_mlp.target = 'test_mlp'
     test_mlp.unit_test = 1
 
@@ -72,7 +72,7 @@ def build(bld):
     test_esn.source = 'test_esn.cpp'
     test_esn.includes = '. ../../'
     test_esn.uselib_local = 'sferes2'
-    test_esn.uselib = 'EIGEN2 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
+    test_esn.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
     test_esn.target = 'test_esn'
     test_esn.unit_test = 1
 
@@ -80,7 +80,7 @@ def build(bld):
     test_esn.source = 'test_hyper_nn.cpp'
     test_esn.includes = '. ../../'
     test_esn.uselib_local = 'sferes2'
-    test_esn.uselib = 'EIGEN2 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
+    test_esn.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
     test_esn.target = 'test_hyper_nn'
     test_esn.unit_test = 1
 
@@ -89,7 +89,7 @@ def build(bld):
     test_esn.source = 'test_dnn_ff.cpp'
     test_esn.includes = '. ../../'
     test_esn.uselib_local = 'sferes2'
-    test_esn.uselib = 'EIGEN2 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
+    test_esn.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
     test_esn.target = 'test_dnn_ff'
     test_esn.unit_test = 1
 
@@ -99,7 +99,7 @@ def build(bld):
     test_osc.source = 'test_osc.cpp'
     test_osc.includes = '. ../../'
     test_osc.uselib_local = 'sferes2'
-    test_osc.uselib = 'EIGEN2 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
+    test_osc.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
     test_osc.target = 'test_osc'
     test_osc.unit_test = 1
 
@@ -108,6 +108,6 @@ def build(bld):
     bench_nn.source = 'bench_nn.cpp'
     bench_nn.includes = '. ../../'
     bench_nn.uselib_local = 'sferes2'
-    bench_nn.uselib = 'EIGEN2 BOOST_GRAPH BOOST'
+    bench_nn.uselib = 'EIGEN3 BOOST_GRAPH BOOST'
     bench_nn.target = 'bench_nn'
 

From 329bac65f25961d8d994d1e56f6559869c7a18e4 Mon Sep 17 00:00:00 2001
From: Matthieu Zimmer <contact@matthieu-zimmer.net>
Date: Fri, 23 May 2014 17:25:14 +0200
Subject: [PATCH 2/3] fix merge

---
 af.hpp       | 2 --
 esn_2.hpp    | 5 ++---
 io_trait.hpp | 2 ++
 pf.hpp       | 1 -
 trait.hpp    | 1 +
 5 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/af.hpp b/af.hpp
index 4966cca..2db9d93 100644
--- a/af.hpp
+++ b/af.hpp
@@ -36,7 +36,6 @@
 #define _NN_AF_HPP_
 
 #include "params.hpp"
-#include <sferes/stc.hpp>
 
 // classic activation functions
 namespace nn
@@ -73,7 +72,6 @@ namespace nn
   struct AfTanhNoBias : public Af<P>
   {
     typedef params::Dummy params_t;
-    SFERES_CONST float lambda = 5.0f;
     BOOST_STATIC_CONSTEXPR float lambda = 5.0f;
     AfTanhNoBias() { }
     float operator()(float p) const
diff --git a/esn_2.hpp b/esn_2.hpp
index 3a706a7..cfc98e9 100644
--- a/esn_2.hpp
+++ b/esn_2.hpp
@@ -42,7 +42,6 @@
 #include <Eigen/QR> 
 #include <Eigen/Eigenvalues>
 
-
 #include <sferes/misc/rand.hpp>
 #include <sferes/misc.hpp>
 
@@ -165,8 +164,8 @@ namespace nn
 	if (sferes::misc::rand<float>() < alpha)
 	  conn(i, j) = sferes::misc::rand(-1.0f, 1.0f);
     // spectral radius
-    float max = (conn.eigenvalues().real().array().square()
-		 + conn.eigenvalues().imag().array().square()
+    float max = (conn.eigenvalues().real().cwise().square()
+		 + conn.eigenvalues().imag().cwise().square()
 		 ).maxCoeff();
     assert(max > 0);
     conn *= alpha / sqrtf(max);
diff --git a/io_trait.hpp b/io_trait.hpp
index c813a85..58b3d74 100644
--- a/io_trait.hpp
+++ b/io_trait.hpp
@@ -44,6 +44,7 @@
 
 #ifdef EIGEN3_ENABLED
 #include <Eigen/Core>
+#endif
 
 namespace nn
 {
@@ -66,6 +67,7 @@ namespace nn
     static vector_t zero(size_t k) { return Eigen::VectorXf::Zero(k); }
 
   };
+#endif
 
   template<>
   struct io_trait<std::pair<float, float> >
diff --git a/pf.hpp b/pf.hpp
index 9280815..28efce7 100644
--- a/pf.hpp
+++ b/pf.hpp
@@ -38,7 +38,6 @@
 
 #include <cstdlib>
 #include <sferes/misc/rand.hpp>
-#include <sferes/stc.hpp>
 
 #include "params.hpp"
 #include "trait.hpp"
diff --git a/trait.hpp b/trait.hpp
index 4f3d0cf..e5afa56 100644
--- a/trait.hpp
+++ b/trait.hpp
@@ -44,6 +44,7 @@
 
 #ifdef EIGEN3_ENABLED
 #include <Eigen/Core>
+#endif
 
 #include "params.hpp"
 

From 09ca77d267f094348a80f0932c03eac77cdac1ec Mon Sep 17 00:00:00 2001
From: Matthieu Zimmer <contact@matthieu-zimmer.net>
Date: Fri, 23 May 2014 19:25:34 +0200
Subject: [PATCH 3/3] io boost test

---
 test_dnn_ff_io.cpp | 142 +++++++++++++++++++++++++++++++++++++++++++++
 wscript            |  11 +++-
 2 files changed, 152 insertions(+), 1 deletion(-)
 create mode 100644 test_dnn_ff_io.cpp

diff --git a/test_dnn_ff_io.cpp b/test_dnn_ff_io.cpp
new file mode 100644
index 0000000..0cc8d47
--- /dev/null
+++ b/test_dnn_ff_io.cpp
@@ -0,0 +1,142 @@
+//| This file is a part of the sferes2 framework.
+//| Copyright 2009, ISIR / Universite Pierre et Marie Curie (UPMC)
+//| Main contributor(s): Jean-Baptiste Mouret, mouret@isir.fr
+//|
+//| This software is a computer program whose purpose is to facilitate
+//| experiments in evolutionary computation and evolutionary robotics.
+//| 
+//| This software is governed by the CeCILL license under French law
+//| and abiding by the rules of distribution of free software.  You
+//| can use, modify and/ or redistribute the software under the terms
+//| of the CeCILL license as circulated by CEA, CNRS and INRIA at the
+//| following URL "http://www.cecill.info".
+//| 
+//| As a counterpart to the access to the source code and rights to
+//| copy, modify and redistribute granted by the license, users are
+//| provided only with a limited warranty and the software's author,
+//| the holder of the economic rights, and the successive licensors
+//| have only limited liability.
+//|
+//| In this respect, the user's attention is drawn to the risks
+//| associated with loading, using, modifying and/or developing or
+//| reproducing the software by the user in light of its specific
+//| status of free software, that may mean that it is complicated to
+//| manipulate, and that also therefore means that it is reserved for
+//| developers and experienced professionals having in-depth computer
+//| knowledge. Users are therefore encouraged to load and test the
+//| software's suitability as regards their requirements in conditions
+//| enabling the security of their systems and/or data to be ensured
+//| and, more generally, to use and operate it in the same conditions
+//| as regards security.
+//|
+//| The fact that you are presently reading this means that you have
+//| had knowledge of the CeCILL license and that you accept its terms.
+
+#define BOOST_TEST_DYN_LINK 
+#define BOOST_TEST_MODULE dnn_ff
+
+#include <boost/archive/xml_oarchive.hpp>
+#include <boost/archive/xml_iarchive.hpp>
+#include <boost/archive/binary_oarchive.hpp>
+#include <boost/archive/binary_iarchive.hpp>
+
+#include <boost/test/unit_test.hpp>
+#include <boost/serialization/nvp.hpp>
+#include <iostream>
+#include <cmath>
+#include <algorithm>
+#include <boost/graph/depth_first_search.hpp>
+
+#include <sferes/fit/fitness.hpp>
+#include <sferes/gen/evo_float.hpp>
+#include <sferes/phen/parameters.hpp>
+#include "gen_dnn_ff.hpp"
+#include "phen_dnn.hpp"
+
+using namespace sferes;
+using namespace sferes::gen::dnn;
+using namespace sferes::gen::evo_float;
+using boost::archive::xml_oarchive;
+using boost::archive::xml_iarchive;
+using boost::serialization::make_nvp;
+
+struct Params
+{
+  struct evo_float
+  {
+    SFERES_CONST float mutation_rate = 0.1f;
+    SFERES_CONST float cross_rate = 0.1f;
+    SFERES_CONST mutation_t mutation_type = polynomial;
+    SFERES_CONST cross_over_t cross_over_type = sbx;
+    SFERES_CONST float eta_m = 15.0f;
+    SFERES_CONST float eta_c = 15.0f;
+  };
+  struct parameters
+  {
+    // maximum value of parameters
+    SFERES_CONST float min = -5.0f;
+    // minimum value
+    SFERES_CONST float max = 5.0f;
+  };
+  struct dnn
+  {
+    SFERES_CONST size_t nb_inputs	= 4;
+    SFERES_CONST size_t nb_outputs	= 1;
+    SFERES_CONST size_t min_nb_neurons	= 4;
+    SFERES_CONST size_t max_nb_neurons	= 5;
+    SFERES_CONST size_t min_nb_conns	= 100;
+    SFERES_CONST size_t max_nb_conns	= 101;
+
+    SFERES_CONST float m_rate_add_conn	= 1.0f;
+    SFERES_CONST float m_rate_del_conn	= 0.1f;
+    SFERES_CONST float m_rate_change_conn = 1.0f;
+    SFERES_CONST float m_rate_add_neuron  = 1.0f;
+    SFERES_CONST float m_rate_del_neuron  = 1.0f;
+
+    SFERES_CONST int io_param_evolving = true;
+    SFERES_CONST init_t init = ff;
+  };
+};
+
+BOOST_AUTO_TEST_CASE(direct_nn_ff_io)
+{
+  srand(time(0));
+  typedef phen::Parameters<gen::EvoFloat<1, Params>, fit::FitDummy<>, Params> weight_t;
+  typedef phen::Parameters<gen::EvoFloat<1, Params>, fit::FitDummy<>, Params> bias_t;
+  typedef nn::PfWSum<weight_t> pf_t;
+  typedef nn::AfSigmoidBias<bias_t> af_t; 
+  typedef nn::Neuron<pf_t, af_t> neuron_t;
+  typedef nn::Connection<weight_t> connection_t;
+  typedef gen::DnnFF<neuron_t, connection_t, Params> gen_t;
+  typedef phen::Dnn<gen_t, fit::FitDummy<Params>, Params> phen_t;
+  phen_t i;
+  i.random();
+  i.develop();
+  std::vector<float> in(Params::dnn::nb_inputs, 0);
+  for(int i=0;i<Params::dnn::nb_inputs;i++)
+    in[i] = misc::rand<float>(0, 1);
+  i.nn().step(in);
+  float output1 = i.nn().get_neuron_output(0);
+  i.show(std::cout);
+  
+  std::ofstream ofs("/tmp/nn.xml");
+  xml_oarchive xml(ofs);
+  xml << make_nvp("test", i);
+  ofs.close();
+  
+  
+  phen_t* i2 = new phen_t;
+  std::ifstream inputFile("/tmp/nn.xml");
+  xml_iarchive xml2(inputFile);
+  xml2 >> make_nvp("test", *i2);
+  inputFile.close();
+  
+  i2->develop();
+  i2->nn().step(in);
+  float output2 = i2->nn().get_neuron_output(0);
+  i2->show(std::cout);
+  
+  std::cout << output1 << " " << output2;
+  BOOST_CHECK_EQUAL(output1, output2);
+}
+
diff --git a/wscript b/wscript
index 60d34ff..5b2db92 100644
--- a/wscript
+++ b/wscript
@@ -92,7 +92,16 @@ def build(bld):
     test_esn.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
     test_esn.target = 'test_dnn_ff'
     test_esn.unit_test = 1
-
+    
+    
+    test_esn = bld.new_task_gen('cxx', 'program')
+    test_esn.source = 'test_dnn_ff_io.cpp'
+    test_esn.includes = '. ../../'
+    test_esn.uselib_local = 'sferes2'
+    test_esn.uselib = 'EIGEN3 BOOST BOOST_GRAPH BOOST_UNIT_TEST_FRAMEWORK BOOST_SERIALIZATION'
+    test_esn.target = 'test_dnn_ff_io'
+    test_esn.unit_test = 1
+    
 
 
     test_osc = bld.new_task_gen('cxx', 'program')