From baed3234927f825824d948095938be8c225662f1 Mon Sep 17 00:00:00 2001
From: rgast <rgast@cbs.mpg.de>
Date: Wed, 10 Jul 2019 13:11:21 +0200
Subject: [PATCH] Finished backend version that can be merged with the master
 branch.

---
 .../jansen_rit/simple_jansenrit.yaml          | 68 ++++++++++++++++---
 pyrates/backend/funcs.py                      |  2 +-
 2 files changed, 59 insertions(+), 11 deletions(-)

diff --git a/model_templates/jansen_rit/simple_jansenrit.yaml b/model_templates/jansen_rit/simple_jansenrit.yaml
index 2d2a7902..c59168f7 100755
--- a/model_templates/jansen_rit/simple_jansenrit.yaml
+++ b/model_templates/jansen_rit/simple_jansenrit.yaml
@@ -25,25 +25,62 @@ PRO:
     V_thr:
       default: 6e-3
 
-RPO:
+JRC_op:
   base: OperatorTemplate
   equations:
-    - 'd/dt * PSP = PSP_t'
-    - 'd/dt * PSP_t =  h/tau * (sigmoid(V_in, m_max, r, V_thr) + u) - (1./tau)^2. * PSP - 2. * 1./tau * PSP_t'
+    - 'd/dt * PSP_ein = PSP_t_ein'
+    - 'd/dt * PSP_t_ein =  h_e*c_pc_ein/tau_e * sigmoid((PSP_pc_e + PSP_pc_i), m_max, r, V_thr) - (1./tau_e)^2. * PSP_ein - (2./tau_e) * PSP_t_ein'
+    - 'd/dt * PSP_iin = PSP_t_iin'
+    - 'd/dt * PSP_t_iin =  h_e*c_pc_iin/tau_e * sigmoid((PSP_pc_e + PSP_pc_i), m_max, r, V_thr) - (1./tau_e)^2. * PSP_iin - (2./tau_e) * PSP_t_iin'
+    - 'd/dt * PSP_pc_e = PSP_t_pc_e'
+    - 'd/dt * PSP_t_pc_e =  h_e/tau_e * (c_ein_pc*sigmoid(PSP_ein, m_max, r, V_thr) + u) - (1./tau_e)^2. * PSP_pc_e - (2./tau_e) * PSP_t_pc_e'
+    - 'd/dt * PSP_pc_i = PSP_t_pc_i'
+    - 'd/dt * PSP_t_pc_i =  h_i*c_iin_pc/tau_i * sigmoid(PSP_iin, m_max, r, V_thr) - (1./tau_i)^2. * PSP_pc_i - (2./tau_i) * PSP_t_pc_i'
+    - 'PSP_pc = PSP_pc_e + PSP_pc_i'
   variables:
-    h:
+    h_e:
       default: 3.25e-3
-    tau:
+    tau_e:
       default: 10e-3
+    h_i:
+      default: -22e-3
+    tau_i:
+      default: 20e-3
     u:
       default: placeholder
-    V_in:
-      default: input
-      in_var: PSP
-    PSP:
+    PSP_ein:
+      default: variable
+    PSP_t_ein:
+      default: variable
+    PSP_iin:
+      default: variable
+    PSP_t_iin:
+      default: variable
+    PSP_pc:
       default: output
-    PSP_t:
+    PSP_pc_e:
+      default: variable
+    PSP_t_pc_e:
+      default: variable
+    PSP_pc_i:
+      default: variable
+    PSP_t_pc_i:
       default: variable
+    m_max:
+      default: 5.
+    r:
+      default: 560.
+    V_thr:
+      default: 6e-3
+    c_ein_pc:
+      default: 108.0
+    c_iin_pc:
+      default: 33.75
+    c_pc_ein:
+      default: 135.0
+    c_pc_iin:
+      default: 33.75
+
 
 RPO_e_pc:
   base: OperatorTemplate
@@ -98,6 +135,11 @@ RPO_i:
     PSP_t:
       default: variable
 
+JRC_pop:
+  base: NodeTemplate
+  operators:
+    - JRC_op
+
 PC:
   base: NodeTemplate
   operators:
@@ -133,3 +175,9 @@ JRC:
     - [PC/PRO/m_out, EIN/RPO_e/m_in, DummyEdge, {weight: 135.}]
     - [EIN/PRO/m_out, PC/RPO_e_pc/m_in, DummyEdge, {weight: 108.}]
     - [IIN/PRO/m_out, PC/RPO_i/m_in, DummyEdge, {weight: 33.75}]
+
+JRC_simple:
+  base: CircuitTemplate
+  nodes:
+    JRC: JRC_pop
+  edges:
diff --git a/pyrates/backend/funcs.py b/pyrates/backend/funcs.py
index 025747f9..c32f429d 100644
--- a/pyrates/backend/funcs.py
+++ b/pyrates/backend/funcs.py
@@ -41,7 +41,7 @@
 # function definitions
 ######################
 
-def pr_sigmoid(x, scaling=1., steepness=1.0, offset=0.):
+def pr_sigmoid(x, scaling=1.0, steepness=1.0, offset=0.0):
     return scaling/(1. + np.exp(steepness*(offset-x)))