Major cleanup and code modernization

Data_Storage.h

@@ -20,28 +20,17 @@
  *	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).
  */
 
-/****************************************************************************************************/
-/*									Functions for data storage										*/
-/****************************************************************************************************/
+/******************************************************************************/
+/*                        Functions for data storage                          */
+/******************************************************************************/
 #pragma once
+#include <vector>
 #include "Thalamic_Column.h"
 
-/****************************************************************************************************/
-/*											Save data												*/
-/****************************************************************************************************/
-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 	();
+void get_data(unsigned counter, Thalamic_Column& Thalamus, std::vector<double*> pData) {
+    pData[0][counter] = Thalamus.Vt 		[0];
+    pData[0][counter] = Thalamus.Vr 		[0];
+    pData[0][counter] = Thalamus.act_h 	();
 }
-/****************************************************************************************************/
-/*										 		end													*/
-/****************************************************************************************************/

NM_Thalamus.pro

@@ -6,14 +6,17 @@ CONFIG -= qt
 TARGET = Thalamus.cpp
 
 SOURCES +=  Thalamic_Column.cpp \
-	    Thalamus.cpp	\
-	    Thalamus_mex.cpp
+			Thalamus.cpp	\
+			Thalamus_mex.cpp
 
 HEADERS +=  Data_Storage.h	\
-	    ODE.h		\
-	    Random_Stream.h	\
-	    Thalamic_Column.h
-
-QMAKE_CXXFLAGS += -std=c++11 -O3
+			ODE.h		\
+			Random_Stream.h	\
+			Thalamic_Column.h
 
 SOURCES -= Thalamus_mex.cpp
+
+QMAKE_CXXFLAGS += -std=c++11
+QMAKE_CXXFLAGS_RELEASE -= -O1
+QMAKE_CXXFLAGS_RELEASE -= -O2
+QMAKE_CXXFLAGS_RELEASE *= -O3

Random_Stream.h

@@ -23,58 +23,35 @@
  *              Stefanie Gareis: gareis@inb.uni-luebeck.de
  */
 
-/****************************************************************************************************/
-/*                                       Random number streams                                      */
-/****************************************************************************************************/
+/******************************************************************************/
+/*                          Random number streams                             */
+/******************************************************************************/
 #pragma once
 #include <random>
 
-/****************************************************************************************************/
-/*									Struct for normal distribution                                  */
-/****************************************************************************************************/
-struct random_stream_normal
-{
-    /* Random number engine: Mersenne-Twister */
+class random_stream_normal {
+public:
+    explicit random_stream_normal(double mean, double stddev)
+    : mt(rand()), norm_dist(mean, stddev) {}
+    explicit random_stream_normal(double mean, double stddev, double seed)
+    : mt(seed), norm_dist(mean, stddev) {}
+
+    double operator ()(void) { return norm_dist(mt); }
+private:
     std::mt19937_64                     mt;
-    /* Random number generator: Normal-distribution */
     std::normal_distribution<double>    norm_dist;
-
-    /* Constructors */
-    random_stream_normal(){}
-    random_stream_normal(double mean, double stddev)
-    : mt(rand()) , norm_dist(mean, stddev)
-    {}
-
-    /* Overwrites the function-call operator "( )" */
-    double operator( )(void) {
-        return norm_dist(mt);
-    }
 };
-/****************************************************************************************************/
-/*										 		end													*/
-/****************************************************************************************************/
 
-/****************************************************************************************************/
-/*									Struct for uniform int distribution                             */
-/****************************************************************************************************/
-struct random_stream_uniform_int
-{
-    /* Random number engine: Mersenne-Twister */
+class random_stream_uniform_int {
+public:
+    explicit random_stream_uniform_int(int lower_bound, int upper_bound)
+    : mt(rand()), uniform_dist(lower_bound, upper_bound) {}
+    explicit random_stream_uniform_int(int lower_bound, int upper_bound, double seed)
+    : mt(seed), uniform_dist(lower_bound, upper_bound) {}
+
+    double operator ()(void) { return uniform_dist(mt); }
+private:
     std::mt19937_64                     mt;
-    /* Random number generator: Uniform integer-distribution */
     std::uniform_int_distribution<>     uniform_dist;
-
-    /* Constructors */
-    random_stream_uniform_int(){}
-    random_stream_uniform_int(double lower_bound, double upper_bound)
-    : mt(rand()) , uniform_dist(lower_bound, upper_bound)
-    {}
-
-    /* Overwrites the function-call operator "( )" */
-    double operator( )(void) {
-        return uniform_dist(mt);
-    }
 };
-/****************************************************************************************************/
-/*										 		end													*/
-/****************************************************************************************************/
+