Updated the naming convention and switched to the Random_stream header

Data_Storage.h

@@ -1,32 +1,32 @@
 /*
-*	Copyright (c) 2015 Michael Schellenberger Costa
-*
-*	Permission is hereby granted, free of charge, to any person obtaining a copy
-*	of this software and associated documentation files (the "Software"), to deal
-*	in the Software without restriction, including without limitation the rights
-*	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-*	copies of the Software, and to permit persons to whom the Software is
-*	furnished to do so, subject to the following conditions:
-*
-*	The above copyright notice and this permission notice shall be included in
-*	all copies or substantial portions of the Software.
-*
-*	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-*	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-*	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-*	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-*	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-*	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-*	THE SOFTWARE.
-*
-*	AUTHORS:	Michael Schellenberger Costa: mschellenbergercosta@gmail.com
-*
-*	Based on:	A thalamocortical neural mass model of the EEG during NREM sleep and its response
-*               to auditory stimulation.
-*				M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born,
-*               T Martinetz, JC Claussen.
-*				PLoS Compuational Biology (in review)
-*/
+ *	Copyright (c) 2015 University of Lübeck
+ *
+ *	Permission is hereby granted, free of charge, to any person obtaining a copy
+ *	of this software and associated documentation files (the "Software"), to deal
+ *	in the Software without restriction, including without limitation the rights
+ *	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ *	copies of the Software, and to permit persons to whom the Software is
+ *	furnished to do so, subject to the following conditions:
+ *
+ *	The above copyright notice and this permission notice shall be included in
+ *	all copies or substantial portions of the Software.
+ *
+ *	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ *	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ *	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ *	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ *	THE SOFTWARE.
+ *
+ *	AUTHORS:	Michael Schellenberger Costa: mschellenbergercosta@gmail.com
+ *
+ *	Based on:	A thalamocortical neural mass model of the EEG during NREM sleep and its response
+ *				to auditory stimulation.
+ *				M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
+ *				JC Claussen.
+ *				PLoS Computational Biology In Review (in review).
+ */
 
 /****************************************************************************************************/
 /*									Functions for data storage										*/
@@ -37,26 +37,11 @@
 /****************************************************************************************************/
 /*											Save data												*/
 /****************************************************************************************************/
-inline void get_data(int counter, Thalamic_Column& Col,	double* Vt,	double* Vr,	double* ah) {
+void get_data(int counter, Thalamic_Column& Col,	double* Vt,	double* Vr,	double* ah) {
 	Vt 		[counter] = Col.Vt 		[0];
 	Vr 		[counter] = Col.Vr 		[0];
 	ah 		[counter] = Col.act_h 	();
 }
 /****************************************************************************************************/
 /*										 		end													*/
-/****************************************************************************************************/
-
-
-/****************************************************************************************************/
-/*									Create MATLAB data container									*/
-/****************************************************************************************************/
-mxArray* SetMexArray(int N, int M) {
-	mxArray* Array	= mxCreateDoubleMatrix(0, 0, mxREAL);
-    mxSetM(Array, N);
-    mxSetN(Array, M);
-    mxSetData(Array, mxMalloc(sizeof(double)*M*N));
-    return Array;
-}
-/****************************************************************************************************/
-/*										 		end													*/
-/****************************************************************************************************/
+/****************************************************************************************************/

NM_Thalamus.pro

@@ -3,17 +3,17 @@ CONFIG += console
 CONFIG -= app_bundle
 CONFIG -= qt
 
-TARGET   =  Thalamus.cpp
+TARGET = Thalamus.cpp
 
 SOURCES +=  Thalamic_Column.cpp \
-            Thalamus_mex.cpp    \
-            Thalamus.cpp
+	    Thalamus.cpp	\
+	    Thalamus_mex.cpp
 
-HEADERS +=  Data_Storage.h      \
-            ODE.h               \
-            Random_Stream.h     \
-            Stimulation.h       \
-            Thalamic_Column.h
+HEADERS +=  ODE.h		\
+	    Data_Storage.h	\
+	    Random_Stream.h	\
+	    Stimulation.h	\
+	    Thalamic_Column.h
 
 QMAKE_CXXFLAGS += -std=c++11 -O3
 

Plots.m

@@ -1,11 +1,11 @@
 % mex command is given by: 
-% mex CXXFLAGS="\$CXXFLAGS -std=c++11 -O3" Thalamus.cpp Thalamic_Column.cpp
+% mex CXXFLAGS="\$CXXFLAGS -std=c++11 -O3" Thalamus_mex.cpp Thalamic_Column.cpp
 
 function Plots(T)
 
 if nargin == 0
-    Con     	= [ 0.063;       % g_h
-                    0.02;       % g_LK_t
+    Con     	= [ 0.01;       % g_h
+                    0.05;       % g_LK
                     3;          % N_tr
                     5;          % N_rt
                     30];		% N_rr 
@@ -23,9 +23,9 @@ function Plots(T)
                     70;       	% duration of the stimulus      in ms
                     5;          % time between stimuli          in s    
                     1];         % time until stimuli after min 	in ms
-    T       	= 30;  		% duration of the simulation
+    T       	= 90;  		% duration of the simulation
 end
-[Vt, Vr, ah] = Thalamus(T, Con, var_stim);
+[Vt, Vr, ah] = Thalamus_mex(T, Con, var_stim);
 
 L        = max(size(Vt));
 timeaxis = linspace(0,T,L);

Random_Stream.h

@@ -1,32 +1,27 @@
 /*
-*	Copyright (c) 2015 Michael Schellenberger Costa
-*
-*	Permission is hereby granted, free of charge, to any person obtaining a copy
-*	of this software and associated documentation files (the "Software"), to deal
-*	in the Software without restriction, including without limitation the rights
-*	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-*	copies of the Software, and to permit persons to whom the Software is
-*	furnished to do so, subject to the following conditions:
-*
-*	The above copyright notice and this permission notice shall be included in
-*	all copies or substantial portions of the Software.
-*
-*	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-*	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-*	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-*	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-*	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-*	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-*	THE SOFTWARE.
-*
-*	AUTHORS:	Michael Schellenberger Costa: mschellenbergercosta@gmail.com
-*
-*	Based on:	A thalamocortical neural mass model of the EEG during NREM sleep and its response
-*               to auditory stimulation.
-*				M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born,
-*               T Martinetz, JC Claussen.
-*				PLoS Compuational Biology (in review)
-*/
+ *	Copyright (c) 2015 University of Lübeck
+ *
+ *	Permission is hereby granted, free of charge, to any person obtaining a copy
+ *	of this software and associated documentation files (the "Software"), to deal
+ *	in the Software without restriction, including without limitation the rights
+ *	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ *	copies of the Software, and to permit persons to whom the Software is
+ *	furnished to do so, subject to the following conditions:
+ *
+ *	The above copyright notice and this permission notice shall be included in
+ *	all copies or substantial portions of the Software.
+ *
+ *	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ *	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ *	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ *	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ *	THE SOFTWARE.
+ *
+ *	AUTHORS:	Michael Schellenberger Costa: mschellenbergercosta@gmail.com
+ *              Stefanie Gareis: gareis@inb.uni-luebeck.de
+ */
 
 /****************************************************************************************************/
 /*                                       Random number streams                                      */

Stimulation.h

@@ -1,32 +1,32 @@
 /*
-*	Copyright (c) 2015 Michael Schellenberger Costa
-*
-*	Permission is hereby granted, free of charge, to any person obtaining a copy
-*	of this software and associated documentation files (the "Software"), to deal
-*	in the Software without restriction, including without limitation the rights
-*	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-*	copies of the Software, and to permit persons to whom the Software is
-*	furnished to do so, subject to the following conditions:
-*
-*	The above copyright notice and this permission notice shall be included in
-*	all copies or substantial portions of the Software.
-*
-*	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-*	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-*	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-*	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-*	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-*	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-*	THE SOFTWARE.
-*
-*	AUTHORS:	Michael Schellenberger Costa: mschellenbergercosta@gmail.com
-*
-*	Based on:	A thalamocortical neural mass model of the EEG during NREM sleep and its response
-*               to auditory stimulation.
-*				M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born,
-*               T Martinetz, JC Claussen.
-*				PLoS Compuational Biology (in review)
-*/
+ *	Copyright (c) 2015 University of Lübeck
+ *
+ *	Permission is hereby granted, free of charge, to any person obtaining a copy
+ *	of this software and associated documentation files (the "Software"), to deal
+ *	in the Software without restriction, including without limitation the rights
+ *	to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ *	copies of the Software, and to permit persons to whom the Software is
+ *	furnished to do so, subject to the following conditions:
+ *
+ *	The above copyright notice and this permission notice shall be included in
+ *	all copies or substantial portions of the Software.
+ *
+ *	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ *	IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *	FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ *	AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *	LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ *	OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ *	THE SOFTWARE.
+ *
+ *	AUTHORS:	Michael Schellenberger Costa: mschellenbergercosta@gmail.com
+ *
+ *	Based on:	A thalamocortical neural mass model of the EEG during NREM sleep and its response
+ *				to auditory stimulation.
+ *				M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
+ *				JC Claussen.
+ *				PLoS Computational Biology In Review (in review).
+ */
 
 /****************************************************************************************************/
 /*								Implementation of the stimulation protocol							*/
@@ -117,9 +117,9 @@ class Stim {
 	/* Create MATLAB container for marker storage */
 	mxArray* get_marker(void) {
 		mxArray* Marker	= mxCreateDoubleMatrix(0, 0, mxREAL);
-	    mxSetM(Marker, 1);
-	    mxSetN(Marker, marker_stimulation.size());
-	    mxSetData(Marker, mxMalloc(sizeof(double)*marker_stimulation.size()));
+		mxSetM(Marker, 1);
+		mxSetN(Marker, marker_stimulation.size());
+		mxSetData(Marker, mxMalloc(sizeof(double)*marker_stimulation.size()));
 		double* Pr_Marker	= mxGetPr(Marker);
 		for(unsigned i=0; i<marker_stimulation.size(); ++i) {
 			Pr_Marker[i] = marker_stimulation[i];