Merge pull request nest#1573 from niltonlk/specify-rectify-rate

Add min_rate to specify a non-zero rectfying rate for rate neuron models with input noise (rate_neuron_ipn)

Author: heplesser

models/gauss_rate.h

@@ -83,8 +83,9 @@ transformers.
  g                 real    Gain parameter
  mu                real    Mean of the Gaussian gain function
  sigma             real    Standard deviation of Gaussian gain function
+ rectify_rate      real    Rectfying rate
  linear_summation  boolean Specifies type of non-linearity (see above)
- rectify_output    boolean Switch to restrict rate to values >= 0
+ rectify_output    boolean Switch to restrict rate to values >= rectify_rate
 =================  ======= ==============================================
 
 Note:

models/lin_rate.h

@@ -85,7 +85,8 @@ transformers.
  g_in            real    Linear factor in multiplicative coupling
  theta_ex        real    Shift in multiplicative coupling
  theta_in        real    Shift in multiplicative coupling
- rectify_output  boolean Switch to restrict rate to values >= 0
+ rectify_rate    real    Rectfying rate
+ rectify_output  boolean Switch to restrict rate to values >= rectify_rate
 ===============  ======= ==================================================
 
 

models/rate_neuron_ipn.h

@@ -178,14 +178,18 @@ class rate_neuron_ipn : public Archiving_Node
     /** Mean input.*/
     double mu_;
 
+    /** Minimum rate.*/
+    double rectify_rate_;
+
     /** Target of non-linearity.
         True (default): Gain function applied to linearly summed input.
         False: Gain function applied to each input before summation.
     **/
     bool linear_summation_;
 
     /** Should the rate be rectified?.
-        True: If the rate is negative it is set to zero after each time step.
+        True: If the rate is smaller than rectify_rate it is set to rectify_rate
+              after each time step.
         False (default): No rectification.
     **/
     bool rectify_output_;

models/rate_neuron_ipn_impl.h

@@ -68,6 +68,7 @@ nest::rate_neuron_ipn< TNonlinearities >::Parameters_::Parameters_()
   , lambda_( 1.0 ) // ms
   , sigma_( 1.0 )
   , mu_( 0.0 )
+  , rectify_rate_( 0.0 )
   , linear_summation_( true )
   , rectify_output_( false )
   , mult_coupling_( false )
@@ -94,6 +95,7 @@ nest::rate_neuron_ipn< TNonlinearities >::Parameters_::get( DictionaryDatum& d )
   def< double >( d, names::lambda, lambda_ );
   def< double >( d, names::sigma, sigma_ );
   def< double >( d, names::mu, mu_ );
+  def< double >( d, names::rectify_rate, rectify_rate_ );
   def< bool >( d, names::linear_summation, linear_summation_ );
   def< bool >( d, names::rectify_output, rectify_output_ );
   def< bool >( d, names::mult_coupling, mult_coupling_ );
@@ -110,6 +112,7 @@ nest::rate_neuron_ipn< TNonlinearities >::Parameters_::set( const DictionaryDatu
   updateValueParam< double >( d, names::tau, tau_, node );
   updateValueParam< double >( d, names::lambda, lambda_, node );
   updateValueParam< double >( d, names::mu, mu_, node );
+  updateValueParam< double >( d, names::rectify_rate, rectify_rate_, node );
   updateValueParam< double >( d, names::sigma, sigma_, node );
   updateValueParam< bool >( d, names::linear_summation, linear_summation_, node );
   updateValueParam< bool >( d, names::rectify_output, rectify_output_, node );
@@ -145,6 +148,10 @@ nest::rate_neuron_ipn< TNonlinearities >::Parameters_::set( const DictionaryDatu
   {
     throw BadProperty( "Noise parameter must not be negative." );
   }
+  if ( rectify_rate_ < 0 )
+  {
+    throw BadProperty( "Rectifying rate must not be negative." );
+  }
 }
 
 template < class TNonlinearities >
@@ -339,9 +346,9 @@ nest::rate_neuron_ipn< TNonlinearities >::update_( Time const& origin,
       S_.rate_ += V_.P2_ * H_in * ( delayed_rates_in + instant_rates_in );
     }
 
-    if ( P_.rectify_output_ and S_.rate_ < 0 )
+    if ( P_.rectify_output_ and S_.rate_ < P_.rectify_rate_ )
     {
-      S_.rate_ = 0;
+      S_.rate_ = P_.rectify_rate_;
     }
 
     if ( called_from_wfr_update )

models/rate_neuron_opn_impl.h

@@ -114,15 +114,15 @@ nest::rate_neuron_opn< TNonlinearities >::Parameters_::set( const DictionaryDatu
   if ( updateValueParam< double >( d, names::mean, mu_, node ) )
   {
     LOG( M_WARNING,
-      "rate_neuron_ipn< TNonlinearities >::Parameters_::set",
+      "rate_neuron_opn< TNonlinearities >::Parameters_::set",
       "The parameter mean has been renamed to mu. Please use the new "
       "name from now on." );
   }
 
   if ( updateValueParam< double >( d, names::std, sigma_, node ) )
   {
     LOG( M_WARNING,
-      "rate_neuron_ipn< TNonlinearities >::Parameters_::set",
+      "rate_neuron_opn< TNonlinearities >::Parameters_::set",
       "The parameter std has been renamed to sigma. Please use the new "
       "name from now on." );
   }

models/sigmoid_rate.h

@@ -81,8 +81,9 @@ transformers.
  g                  real    Gain parameter
  beta               real    Slope parameter
  theta              real    Threshold
+ rectify_rate       real    Rectfying rate
  linear_summation   boolean Specifies type of non-linearity (see above)
- rectify_output     boolean Switch to restrict rate to values >= 0
+ rectify_output     boolean Switch to restrict rate to values >= rectify_rate
 ==================  ======= ==============================================
 
 Note:

models/sigmoid_rate_gg_1998.h

@@ -75,8 +75,9 @@ transformers.
  mu                 real    Mean input
  sigma              real    Noise parameter
  g                  real    Gain parameter
+ rectify_rate       real    Rectfying rate
  linear_summation   boolean Specifies type of non-linearity (see above)
- rectify_output     boolean Switch to restrict rate to values >= 0
+ rectify_output     boolean Switch to restrict rate to values >= rectify_rate
 ==================  ======= ==============================================
 
 

models/tanh_rate.h

@@ -75,8 +75,9 @@ transformers.
  sigma              real    Noise parameter
  g                  real    Gain parameter
  theta              real    Threshold
+ rectify_rate       real    Rectfying rate
  linear_summation   boolean Specifies type of non-linearity (see above)
- rectify_output     boolean Switch to restrict rate to values >= 0
+ rectify_output     boolean Switch to restrict rate to values >= rectify_rate
 ==================  ======= ==============================================
 
 Note:

models/threshold_lin_rate.h

@@ -86,8 +86,9 @@ transformers.
  g                  real    Gain parameter
  alpha              real    Second Threshold
  theta              real    Threshold
+ rectify_rate       real    Rectfying rate
  linear_summation   boolean Specifies type of non-linearity (see above)
- rectify_output     boolean Switch to restrict rate to values >= 0
+ rectify_output     boolean Switch to restrict rate to values >= rectify_rate
 ==================  ======= ==============================================
 
 References

nestkernel/nest_names.cpp

@@ -348,6 +348,7 @@ const Name recordables( "recordables" );
 const Name recorder( "recorder" );
 const Name recording_backends( "recording_backends" );
 const Name rectify_output( "rectify_output" );
+const Name rectify_rate( "rectify_rate" );
 const Name refractory_input( "refractory_input" );
 const Name registered( "registered" );
 const Name relative_amplitude( "relative_amplitude" );

nestkernel/nest_names.h

@@ -369,6 +369,7 @@ extern const Name recordables;
 extern const Name recorder;
 extern const Name recording_backends;
 extern const Name rectify_output;
+extern const Name rectify_rate;
 extern const Name refractory_input;
 extern const Name registered;
 extern const Name relative_amplitude;