Small bugfixes and cleanup.

Plots.m

@@ -1,5 +1,5 @@
 % mex command is given by: 
-% mex CXXFLAGS="\$CXXFLAGS -std=gnu++0x -fpermissive" Thalamus.cpp Thalamic_Colum.cpp
+% mex CXXFLAGS="\$CXXFLAGS -std=gnu++0x -fpermissive" Thalamus.cpp Thalamic_Column.cpp
 
 function Plots(T, onset)
 

Stimulation.h

@@ -69,7 +69,7 @@ class Stim {
 	// stimulation strength
 	double strength = 0.0;
 
-	// inter stimulus intervall
+	// inter stimulus interval
 	int ISI = 0;
 
 	// onset until stimulation starts

Thalamic_Column.cpp

@@ -51,27 +51,27 @@ double Thalamic_Column::get_Qr	(int N) const{
 // excitatory input to TC population
 double Thalamic_Column::I_et	(int N) const{
 	_SWITCH((Vt)(Phi_tt))
-	double psi = g_AMPA * var_Phi_tt * (var_Vt - V_rev_e);
+	double psi = g_AMPA * var_Phi_tt * (var_Vt - E_AMPA);
 	return psi;
 }
 
 // inhibitory input to TC population
 double Thalamic_Column::I_it	(int N) const{
 	_SWITCH((Vt)(Phi_rt))
-	double psi = g_GABA * var_Phi_rt * (var_Vt - V_rev_i);
+	double psi = g_GABA * var_Phi_rt * (var_Vt - E_GABA);
 	return psi;
 }
 // excitatory input to RE population
 double Thalamic_Column::I_er	(int N) const{
 	_SWITCH((Vr)(Phi_tr))
-	double psi = g_AMPA * var_Phi_tr * (var_Vr - V_rev_e);
+	double psi = g_AMPA * var_Phi_tr * (var_Vr - E_AMPA);
 	return psi;
 }
 
 // inhibitory input to RE population
 double Thalamic_Column::I_ir	(int N) const{
 	_SWITCH((Vr)(Phi_rr))
-	double psi = g_GABA * var_Phi_rr * (var_Vr - V_rev_i);
+	double psi = g_GABA * var_Phi_rr * (var_Vr - E_GABA);
 	return psi;
 }
 /****************************************************************************************************/

Thalamic_Column.h

@@ -50,6 +50,9 @@ class Thalamic_Column {
 	// Initialize the RNGs
 	void 	set_RNG		(void);
 
+	// change the strength of input
+	void	set_input	(double I) {input = I;}
+
 	// Firing rates
 	double 	get_Qt		(int) const;
 	double 	get_Qr		(int) const;

Thalamus.cpp

@@ -37,14 +37,15 @@ void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
 
 	// Fetch inputs
 	const int T				= (int) (mxGetScalar(prhs[0]));
-	double* Connectivity	= mxGetPr (prhs[1]);
+	const int Time 			= (T+onset)*res;
+	double* Param_Thalamus	= mxGetPr (prhs[1]);
 	double* var_stim	 	= mxGetPr (prhs[2]);
 
 	// Initializing the populations;
-	Thalamic_Column Thalamus(Connectivity);
+	Thalamic_Column Thalamus(Param_Thalamus);
 
 	// Initialize the stimulation protocol
-	Stim	Stimulation(Thalamus, Var_Stim);
+	Stim	Stimulation(Thalamus, var_stim);
 
 	// setting up the data containers
 	mxArray* Vt		= SetMexArray(1, T*red);

parameters.h

@@ -78,8 +78,8 @@
 /*										reversal potentials											*/
 /****************************************************************************************************/
 // synaptic inputs in mV
-#define V_rev_e  	0
-#define V_rev_i  	-70
+#define E_AMPA  	0
+#define E_GABA  	-70
 
 // Leak current
 #define E_L_t		-70