rename shape to kernel

WillemWybo · Oct 8, 2020 · 4a0fd44 · 4a0fd44
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diff --git a/doc/models_library/aeif_cond_alpha.rst b/doc/models_library/aeif_cond_alpha.rst
@@ -114,8 +114,8 @@ Source code
      end
      equations:
        function V_bounded mV = min(V_m,V_peak) # prevent exponential divergence
-       shape g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
-       shape g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
 
        /* Add functions to simplify the equation definition of V_m*/
        function exp_arg real = (V_bounded - V_th) / Delta_T

diff --git a/doc/models_library/aeif_cond_exp.rst b/doc/models_library/aeif_cond_exp.rst
@@ -120,8 +120,8 @@ Source code
      end
      equations:
        function V_bounded mV = min(V_m,V_peak) # prevent exponential divergence
-       shape g_in = exp(-1 / tau_syn_in * t)
-       shape g_ex = exp(-1 / tau_syn_ex * t)
+       kernel g_in = exp(-1 / tau_syn_in * t)
+       kernel g_ex = exp(-1 / tau_syn_ex * t)
 
        /* Add aliases to simplify the equation definition of V_m*/
        function exp_arg real = (V_bounded - V_th) / Delta_T

diff --git a/doc/models_library/hh_cond_exp_destexhe.rst b/doc/models_library/hh_cond_exp_destexhe.rst
@@ -154,8 +154,8 @@ Source code
      equations:
 
        /* synapses: exponential conductance*/
-       shape g_in = exp(-1 / tau_syn_in * t)
-       shape g_ex = exp(-1 / tau_syn_ex * t)
+       kernel g_in = exp(-1 / tau_syn_in * t)
+       kernel g_ex = exp(-1 / tau_syn_ex * t)
 
        /* Add aliases to simplify the equation definition of V_m*/
        function I_Na pA = g_Na * Act_m * Act_m * Act_m * Act_h * (V_m - E_Na)

diff --git a/doc/models_library/hh_cond_exp_traub.rst b/doc/models_library/hh_cond_exp_traub.rst
@@ -156,8 +156,8 @@ Source code
      equations:
 
        /* synapses: exponential conductance*/
-       shape g_in = exp(-1 / tau_syn_in * t)
-       shape g_ex = exp(-1 / tau_syn_ex * t)
+       kernel g_in = exp(-1 / tau_syn_in * t)
+       kernel g_ex = exp(-1 / tau_syn_ex * t)
 
        /* Add aliases to simplify the equation definition of V_m*/
        function I_Na pA = g_Na * Act_m * Act_m * Act_m * Act_h * (V_m - E_Na)

diff --git a/doc/models_library/hh_psc_alpha.rst b/doc/models_library/hh_psc_alpha.rst
@@ -142,8 +142,8 @@ Source code
      equations:
 
        /* synapses: alpha functions*/
-       shape I_syn_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
-       shape I_syn_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel I_syn_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel I_syn_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
        function I_syn_exc pA = convolve(I_syn_ex,spikeExc)
        function I_syn_inh pA = convolve(I_syn_in,spikeInh)
        function I_Na pA = g_Na * Act_m * Act_m * Act_m * Inact_h * (V_m - E_Na)

diff --git a/doc/models_library/iaf_chxk_2008.rst b/doc/models_library/iaf_chxk_2008.rst
@@ -113,8 +113,8 @@ Source code
 
      end
      equations:
-       shape g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
-       shape g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
        G_ahp__d'=(-2 / tau_ahp) * G_ahp__d - (1 / tau_ahp ** 2) * G_ahp
        function I_syn_exc pA = convolve(g_ex,spikesExc) * (V_m - E_ex)
        function I_syn_inh pA = convolve(g_in,spikesInh) * (V_m - E_in)

diff --git a/doc/models_library/iaf_cond_alpha.rst b/doc/models_library/iaf_cond_alpha.rst
@@ -108,8 +108,8 @@ Source code
        V_m mV = E_L # membrane potential
      end
      equations:
-       shape g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
-       shape g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
        function I_syn_exc pA = convolve(g_ex,spikeExc) * (V_m - E_ex)
        function I_syn_inh pA = convolve(g_in,spikeInh) * (V_m - E_in)
        function I_leak pA = g_L * (V_m - E_L)

diff --git a/doc/models_library/iaf_cond_exp.rst b/doc/models_library/iaf_cond_exp.rst
@@ -97,8 +97,8 @@ Source code
        V_m mV = E_L # membrane potential
      end
      equations:
-       shape g_in = exp(-t / tau_syn_in) # inputs from the inh conductance
-       shape g_ex = exp(-t / tau_syn_ex) # inputs from the exc conductance
+       kernel g_in = exp(-t / tau_syn_in) # inputs from the inh conductance
+       kernel g_ex = exp(-t / tau_syn_ex) # inputs from the exc conductance
        function I_syn_exc pA = convolve(g_ex,spikeExc) * (V_m - E_ex)
        function I_syn_inh pA = convolve(g_in,spikeInh) * (V_m - E_in)
        function I_leak pA = g_L * (V_m - E_L)

diff --git a/doc/models_library/iaf_cond_exp_sfa_rr.rst b/doc/models_library/iaf_cond_exp_sfa_rr.rst
@@ -118,8 +118,8 @@ Source code
        g_rr nS = 0nS # inputs from the rr conductance
      end
      equations:
-       shape g_in = exp(-t / tau_syn_in) # inputs from the inh conductance
-       shape g_ex = exp(-t / tau_syn_ex) # inputs from the exc conductance
+       kernel g_in = exp(-t / tau_syn_in) # inputs from the inh conductance
+       kernel g_ex = exp(-t / tau_syn_ex) # inputs from the exc conductance
        g_sfa'=-g_sfa / tau_sfa
        g_rr'=-g_rr / tau_rr
        function I_syn_exc pA = convolve(g_ex,spikesExc) * (V_m - E_ex)

diff --git a/doc/models_library/iaf_psc_alpha.rst b/doc/models_library/iaf_psc_alpha.rst
@@ -8,8 +8,8 @@ Description
 +++++++++++
 
 iaf_psc_alpha is an implementation of a leaky integrate-and-fire model
-with alpha-function shaped synaptic currents. Thus, synaptic currents
-and the resulting post-synaptic potentials have a finite rise time.
+with alpha-kernel synaptic currents. Thus, synaptic currents and the
+resulting post-synaptic potentials have a finite rise time.
 
 The threshold crossing is followed by an absolute refractory period
 during which the membrane potential is clamped to the resting potential.
@@ -149,9 +149,9 @@ Source code
        function V_m mV = V_abs + E_L # Membrane potential.
      end
      equations:
-       shape I_shape_in = pA * (e / tau_syn_in) * t * exp(-1 / tau_syn_in * t)
-       shape I_shape_ex = pA * (e / tau_syn_ex) * t * exp(-1 / tau_syn_ex * t)
-       function I pA = convolve(I_shape_in,in_spikes) + convolve(I_shape_ex,ex_spikes) + I_e + I_stim
+       kernel I_kernel_in = pA * (e / tau_syn_in) * t * exp(-1 / tau_syn_in * t)
+       kernel I_kernel_ex = pA * (e / tau_syn_ex) * t * exp(-1 / tau_syn_ex * t)
+       function I pA = convolve(I_kernel_in,in_spikes) + convolve(I_kernel_ex,ex_spikes) + I_e + I_stim
        V_abs'=-1 / Tau * V_abs + 1 / C_m * I
      end
 
@@ -209,4 +209,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2020-05-27 18:26:45.061053
+   Generated at 2020-05-27 18:26:45.061053
diff --git a/doc/models_library/iaf_psc_delta.rst b/doc/models_library/iaf_psc_delta.rst
@@ -1,7 +1,7 @@
 iaf_psc_delta
 #############
 
-iaf_psc_delta - Current-based leaky integrate-and-fire neuron model with delta-shaped post-synaptic currents
+iaf_psc_delta - Current-based leaky integrate-and-fire neuron model with delta-kernel post-synaptic currents
 
 
 Description
@@ -124,7 +124,7 @@ Source code
        function V_m mV = V_abs + E_L # Membrane potential.
      end
      equations:
-       shape G = delta(t,tau_m)
+       kernel G = delta(t,tau_m)
        V_abs'=-1 / tau_m * V_abs + 1 / C_m * (convolve(G,spikes) + I_e + I_stim)
      end
 
@@ -195,4 +195,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2020-05-27 18:26:45.171065
+   Generated at 2020-05-27 18:26:45.171065
diff --git a/doc/models_library/iaf_psc_exp.rst b/doc/models_library/iaf_psc_exp.rst
@@ -8,7 +8,7 @@ Description
 +++++++++++
 
 iaf_psc_exp is an implementation of a leaky integrate-and-fire model
-with exponential shaped postsynaptic currents (PSCs) according to [1]_.
+with exponential kernel postsynaptic currents (PSCs) according to [1]_.
 Thus, postsynaptic currents have an infinitely short rise time.
 
 The threshold crossing is followed by an absolute refractory period (t_ref)
@@ -108,9 +108,9 @@ Source code
        function V_m mV = V_abs + E_L # Membrane potential.
      end
      equations:
-       shape I_shape_in = exp(-t / tau_syn_in)
-       shape I_shape_ex = exp(-t / tau_syn_ex)
-       function I_syn pA = convolve(I_shape_in,in_spikes) + convolve(I_shape_ex,ex_spikes)
+       kernel I_kernel_in = exp(-t / tau_syn_in)
+       kernel I_kernel_ex = exp(-t / tau_syn_ex)
+       function I_syn pA = convolve(I_kernel_in,in_spikes) + convolve(I_kernel_ex,ex_spikes)
        V_abs'=-V_abs / tau_m + (I_syn + I_e + I_stim) / C_m
      end
 
@@ -164,4 +164,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2020-05-27 18:26:44.688938
+   Generated at 2020-05-27 18:26:44.688938
diff --git a/doc/models_library/iaf_psc_exp_htum.rst b/doc/models_library/iaf_psc_exp_htum.rst
@@ -8,7 +8,7 @@ Description
 +++++++++++
 
 iaf_psc_exp_htum is an implementation of a leaky integrate-and-fire model
-with exponential shaped postsynaptic currents (PSCs) according to [1]_.
+with exponential kernel postsynaptic currents (PSCs) according to [1]_.
 The postsynaptic currents have an infinitely short rise time.
 In particular, this model allows setting an absolute and relative
 refractory time separately, as required by [1]_.
@@ -118,9 +118,9 @@ Source code
        V_m mV = 0.0mV # Membrane potential
      end
      equations:
-       shape I_shape_in = exp(-1 / tau_syn_in * t)
-       shape I_shape_ex = exp(-1 / tau_syn_ex * t)
-       function I_syn pA = convolve(I_shape_in,in_spikes) + convolve(I_shape_ex,ex_spikes)
+       kernel I_kernel_in = exp(-1 / tau_syn_in * t)
+       kernel I_kernel_ex = exp(-1 / tau_syn_ex * t)
+       function I_syn pA = convolve(I_kernel_in,in_spikes) + convolve(I_kernel_ex,ex_spikes)
        V_m'=-V_m / tau_m + (I_syn + I_e + I_stim) / C_m
      end
 
@@ -206,4 +206,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2020-05-27 18:26:44.972470
+   Generated at 2020-05-27 18:26:44.972470
diff --git a/doc/models_library/izhikevich_psc_alpha.rst b/doc/models_library/izhikevich_psc_alpha.rst
@@ -1,7 +1,7 @@
 izhikevich_psc_alpha
 ####################
 
-izhikevich_psc_alpha - Detailed Izhikevich neuron model with alpha-shaped post-synaptic current
+izhikevich_psc_alpha - Detailed Izhikevich neuron model with alpha-kernel post-synaptic current
 
 
 Description
@@ -21,7 +21,7 @@ The dynamics are given by:
    &\;\;\;\; V_m \text{ is set to } c
    &\;\;\;\; U_m \text{ is incremented by } d
 
-On each spike arrival, the membrane potential feels an alpha-shaped current of the form:
+On each spike arrival, the membrane potential feels an alpha-kernel current of the form:
 
 .. math::
 
@@ -119,8 +119,8 @@ Source code
      equations:
 
        /* synapses: alpha functions*/
-       shape I_syn_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
-       shape I_syn_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel I_syn_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel I_syn_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
        function I_syn_exc pA = convolve(I_syn_ex,spikesExc)
        function I_syn_inh pA = convolve(I_syn_in,spikesInh)
        V_m'=(k * (V_m - V_r) * (V_m - V_t) - U_m + I_e + I_stim + I_syn_inh + I_syn_exc) / C_m
@@ -181,4 +181,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2020-05-27 18:26:44.646052
+   Generated at 2020-05-27 18:26:44.646052
diff --git a/doc/models_library/mat2_psc_exp.rst b/doc/models_library/mat2_psc_exp.rst
@@ -8,7 +8,7 @@ Description
 +++++++++++
 
 mat2_psc_exp is an implementation of a leaky integrate-and-fire model
-with exponential shaped postsynaptic currents (PSCs). Thus, postsynaptic
+with exponential kernel postsynaptic currents (PSCs). Thus, postsynaptic
 currents have an infinitely short rise time.
 
 The threshold is lifted when the neuron is fired and then decreases in a
@@ -121,12 +121,12 @@ Source code
 
      end
      equations:
-       shape I_shape_in = exp(-1 / tau_syn_in * t)
-       shape I_shape_ex = exp(-1 / tau_syn_ex * t)
+       kernel I_kernel_in = exp(-1 / tau_syn_in * t)
+       kernel I_kernel_ex = exp(-1 / tau_syn_ex * t)
 
        /* V_th_alpha_1' = -V_th_alpha_1/tau_1*/
        /* V_th_alpha_2' = -V_th_alpha_2/tau_2*/
-       function I_syn pA = convolve(I_shape_in,in_spikes) + convolve(I_shape_ex,ex_spikes)
+       function I_syn pA = convolve(I_kernel_in,in_spikes) + convolve(I_kernel_ex,ex_spikes)
        V_abs'=-V_abs / tau_m + (I_syn + I_e + I_stim) / C_m
      end
 
@@ -194,4 +194,4 @@ Characterisation
 
 .. footer::
 
-   Generated at 2020-05-27 18:26:45.498666
+   Generated at 2020-05-27 18:26:45.498666
diff --git a/doc/models_library/terub_gpe.rst b/doc/models_library/terub_gpe.rst
@@ -184,11 +184,11 @@ Source code
 
        /* synapses: alpha functions*/
        /* alpha function for the g_in*/
-       shape g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
        /* alpha function for the g_ex*/
 
        /* alpha function for the g_ex*/
-       shape g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
 
        /* V dot -- synaptic input are currents, inhib current is negative*/
        V_m'=(-(I_Na + I_K + I_L + I_T + I_Ca + I_ahp) * pA + I_e + I_stim + I_ex_mod * pA + I_in_mod * pA) / C_m

diff --git a/doc/models_library/terub_stn.rst b/doc/models_library/terub_stn.rst
@@ -199,11 +199,11 @@ Source code
 
        /* synapses: alpha functions*/
        /* alpha function for the g_in*/
-       shape g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel g_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
        /* alpha function for the g_ex*/
 
        /* alpha function for the g_ex*/
-       shape g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel g_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
      end
 
      parameters:

diff --git a/doc/models_library/traub_psc_alpha.rst b/doc/models_library/traub_psc_alpha.rst
@@ -122,8 +122,8 @@ Source code
      equations:
 
        /* synapses: alpha functions*/
-       shape I_syn_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
-       shape I_syn_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
+       kernel I_syn_in = (e / tau_syn_in) * t * exp(-t / tau_syn_in)
+       kernel I_syn_ex = (e / tau_syn_ex) * t * exp(-t / tau_syn_ex)
        function I_syn_exc pA = convolve(I_syn_ex,spikeExc)
        function I_syn_inh pA = convolve(I_syn_in,spikeInh)
        function I_Na pA = g_Na * Act_m * Act_m * Act_m * Inact_h * (V_m - E_Na)

diff --git a/doc/models_library/wb_cond_exp.rst b/doc/models_library/wb_cond_exp.rst
@@ -118,8 +118,8 @@ Source code
      equations:
 
        /* synapses: exponential conductance*/
-       shape g_in = exp(-1.0 / tau_syn_in * t)
-       shape g_ex = exp(-1.0 / tau_syn_ex * t)
+       kernel g_in = exp(-1.0 / tau_syn_in * t)
+       kernel g_ex = exp(-1.0 / tau_syn_ex * t)
    recordable    function I_syn_exc pA = convolve(g_ex,spikeExc) * (V_m - E_ex)
    recordable    function I_syn_inh pA = convolve(g_in,spikeInh) * (V_m - E_in)
        function alpha_n 1/ms = -0.05 / (ms * mV) * (V_m + 34.0mV) / (exp(-0.1 * (V_m + 34.0mV)) - 1.0)