Cleaned up the code.

Needs minor parameter fixing for figures.
miscco · 429e8eb0af7375053f3b438bdd1c60053a3ca3c0 · miscco committed Jun 18, 2014 · Jun 18, 2014 · 429e8eb
1 parent 2708625
commit 429e8eb0af7375053f3b438bdd1c60053a3ca3c0
Unified Split

Showing with 20 additions and 23 deletions.

+1 −1 Cortical_Column.h

+7 −7 Plots.m

+2 −4 Stimulation.h

+7 −7 TC.cpp

+1 −2 Thalamic_Column.cpp

+2 −2 Thalamic_Column.h
diff --git a/Cortical_Column.h b/Cortical_Column.h
@@ -152,7 +152,7 @@ class Cortical_Column {
 	const double 	gamma_i		= 58.6E-3;
 
 	/* Axonal flux time constant */
-	const double 	nu			= 120E-3;
+	const double 	nu			= 60E-3;
 
 	/* Conductivities in mS/cm^-2 */
 	/* Leak */
diff --git a/Plots.m b/Plots.m
@@ -17,10 +17,10 @@ function Plots(T)
                     1.33;       % g_KNa
                     60E-3];     % dphi
 
-    Connectivity= [2;           % N_et
-               	   2;           % N_er
-                   5;           % N_te
-                   5];          % N_ti    
+    Connectivity= [3;           % N_et
+               	   3;           % N_er
+                   15;           % N_te
+                   20];          % N_ti    
 
     % stimulation parameters
     % first number is the mode of stimulation
@@ -30,9 +30,9 @@ function Plots(T)
     % 3 == phase dependend down state
     
     var_stim    = [ 0;          % mode of stimulation
-                    0;          % strength of the stimulus      in Hz (spikes per second)
-                    0;       	% duration of the stimulus      in ms
-                    0;          % time between stimuli          in s    
+                    30;          % strength of the stimulus      in Hz (spikes per second)
+                    50;       	% duration of the stimulus      in ms
+                    5;          % time between stimuli          in s    
                     0];         % time until stimuli after min 	in ms
 
     T       	= 30;           % duration of the simulation
diff --git a/Stimulation.h b/Stimulation.h
@@ -195,15 +195,13 @@ class Stim {
 	}
 
 private:
-
-	/* Stimulation parameters */
 	/* Stimulation strength */
 	double strength 	= 0.0;
 
 	/* Duration of the stimulation */
 	int duration 		= 500;
 
-	/* Inter stimulus intervall in case of periodic stimulation */
+	/* Inter-stimulus-interval in case of periodic stimulation */
 	int ISI				= 5E4;
 
 	/* Threshold for phase dependent stimulation */
@@ -229,7 +227,7 @@ class Stim {
 	/* Minimum found */
 	bool minimum_found		= false;
 
-	/* Onset in timesteps to correct the given time of the markers */
+	/* Onset in time steps to correct the given time of the markers */
 	int correction			= 10000;
 
 	/* Counter for stimulation duration */
diff --git a/TC.cpp b/TC.cpp
@@ -20,13 +20,13 @@
 *	THE SOFTWARE.
 */
 
-/********************************************************************************************************/
-/* 	Implementation of the simulation as MATLAB routine (mex compiler)									*/
-/* 	mex command is given by:																			*/
-/* 	mex CXXFLAGS="\$CXXFLAGS -std=gnu++0x -fpermissive" TC.cpp Cortical_Column.cpp Thalamic_Column.cpp	*/
-/*	The Simulation requires the following boost libraries:	Preprocessor								*/
-/*															Random										*/
-/********************************************************************************************************/
+/****************************************************************************************************/
+/* 	Implementation of the simulation as MATLAB routine (mex compiler)								*/
+/* 	mex command is given by:																		*/
+/* 	mex CXXFLAGS="\$CXXFLAGS -std=c++0x" TC.cpp Cortical_Column.cpp Thalamic_Column.cpp				*/
+/*	The Simulation requires the following boost libraries:	Preprocessor							*/
+/*															Random									*/
+/****************************************************************************************************/
 #include <ctime>
 #include "mex.h"
 #include "matrix.h"
diff --git a/Thalamic_Column.cpp b/Thalamic_Column.cpp
@@ -249,8 +249,7 @@ void Thalamic_Column::set_RK (int N) {
 	_SWITCH((Ca)
 			(Phi_tt)(Phi_tr)(Phi_rt)(Phi_rr)(phi)
 			(x_tt)	(x_tr)	(x_rt)	(x_rr)	(y)
-			(h_T_t)	(h_T_r)
-			(m_h)	(m_h2)	(P_h))
+			(h_T_t)	(h_T_r)	(m_h)	(m_h2)	(P_h))
 	Vt	  	[N] = dt*(-(I_L_t(N) + I_et(N) + I_it(N))/tau_t - (I_LK_t(N) + I_T_t(N) + I_h(N)));
 	Vr	  	[N] = dt*(-(I_L_r(N) + I_er(N) + I_ir(N))/tau_r - (I_LK_r(N) + I_T_r(N)));
 	Ca		[N] = dt*(alpha_Ca * I_T_t(N) - (var_Ca - Ca_0)/tau_Ca);
diff --git a/Thalamic_Column.h b/Thalamic_Column.h
@@ -165,7 +165,7 @@ class Thalamic_Column {
 	const double 	gamma_i		= 58.6E-3;
 
 	/* axonal flux time constant */
-	const double 	nu			= 120E-3;
+	const double 	nu			= 60E-3;
 
 	/* Conductivities in mS/cm^-2 */
 	/* Leak current */
@@ -216,7 +216,7 @@ class Thalamic_Column {
 
 	/* Noise parameters in ms^-1 */
 	const double 	mphi		= 0E-3;
-	const double	dphi		= 10E-3;;
+	const double	dphi		= 20E-3;;
 	double			input		= 0.0;