General code cleanup.

Removed dependency on boost libraries.
miscco · 1cba4bc319c9ce517108b6226c5f05aa41c477b8 · miscco committed Dec 29, 2015 · Dec 29, 2015 · 1cba4bc
1 parent c8fb6e6
commit 1cba4bc319c9ce517108b6226c5f05aa41c477b8
diff --git a/Cortical_Column.cpp b/Cortical_Column.cpp
@@ -44,10 +44,10 @@ void Cortical_Column::set_RNG(void) {
 	/* Create RNG for each stream */
 	for (int i=0; i<N; ++i){
 		/* Add the RNG for I_{l}*/
-		MTRands.push_back({ENG(rand()), DIST (0.0, dphi*dt)});
+        MTRands.push_back(random_stream_normal(0.0, dphi*dt));
 
 		/* Add the RNG for I_{l,0} */
-		MTRands.push_back({ENG(rand()), DIST (0.0, dt)});
+        MTRands.push_back(random_stream_normal(0.0, dt));
 
 		/* Get the random number for the first iteration */
 		Rand_vars.push_back(MTRands[2*i]());
diff --git a/Cortical_Column.h b/Cortical_Column.h
@@ -34,23 +34,10 @@
 #pragma once
 #include <cmath>
 #include <vector>
-#include <boost/random/mersenne_twister.hpp>
-#include <boost/random/normal_distribution.hpp>
-#include <boost/random/variate_generator.hpp>
+#include "Random_Stream.h"
 #include "Thalamic_Column.h"
 using std::vector;
-
 class Thalamic_Column;
-/****************************************************************************************************/
-/*										Typedefs for RNG											*/
-/****************************************************************************************************/
-typedef boost::mt11213b                    	ENG;    /* Mersenne Twister		*/
-typedef boost::normal_distribution<double>	DIST;   /* Normal Distribution	*/
-typedef boost::variate_generator<ENG,DIST> 	GEN;    /* Variate generator	*/
-/****************************************************************************************************/
-/*										 		end			 										*/
-/****************************************************************************************************/
-
 
 /****************************************************************************************************/
 /*									Macro for vector initialization									*/
@@ -131,7 +118,7 @@ class Cortical_Column {
 					x		= _INIT(0.0);		/* derivative of y									*/
 
 	/* Random number generators */
-	vector<GEN>		MTRands;
+    vector<random_stream_normal> MTRands;
 
 	/* Container for noise */
 	vector<double>	Rand_vars;
diff --git a/saves.h → Data_Storage.h b/saves.h → Data_Storage.h
diff --git a/NM_TC.pro b/NM_TC.pro
@@ -6,15 +6,16 @@ CONFIG -= qt
 TARGET = TC.cpp
 
 SOURCES +=  Cortical_Column.cpp \
-	    TC.cpp \
-	    TC_mex.cpp \
+            TC.cpp              \
+            TC_mex.cpp          \
 	    Thalamic_Column.cpp
 
-HEADERS +=  Cortical_Column.h \
-	    ODE.h \
-	    saves.h \
-	    Stimulation.h \
-	    Thalamic_Column.h
+HEADERS +=  Cortical_Column.h   \
+            Data_Storage.h      \
+            ODE.h               \
+            Random_Stream.h     \
+            Stimulation.h       \
+            Thalamic_Column.h
 
 QMAKE_CXXFLAGS += -std=c++11 -O3
 
diff --git a/Random_Stream.h b/Random_Stream.h
@@ -0,0 +1,81 @@
+/*
+ *	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                                      */
+/****************************************************************************************************/
+#pragma once
+#include <random>
+
+/****************************************************************************************************/
+/*									Struct for normal distribution                                  */
+/****************************************************************************************************/
+struct random_stream_normal
+{
+    /* Random number engine: Mersenne-Twister */
+    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 */
+    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													*/
+/****************************************************************************************************/
diff --git a/Stimulation.h b/Stimulation.h
@@ -32,19 +32,11 @@
 /*								Implementation of the stimulation protocol							*/
 /****************************************************************************************************/
 #pragma once
-#include <boost/random/uniform_int_distribution.hpp>
+#include "Random_Stream.h"
 #include "Cortical_Column.h"
 #include "Thalamic_Column.h"
 
 /****************************************************************************************************/
-/*										Typedefs for RNG											*/
-/****************************************************************************************************/
-typedef boost::random::uniform_int_distribution<>		DIST_int;   /* Uniform integer distribution	*/
-/****************************************************************************************************/
-/*										 		end			 										*/
-/****************************************************************************************************/
-
-/****************************************************************************************************/
 /*											Stimulation object										*/
 /****************************************************************************************************/
 class Stim {
@@ -151,11 +143,10 @@ class Stim {
 	Thalamic_Column* Thalamus;
 
 	/* Data containers */
-	vector<int>		marker_stimulation;
+    std::vector<int> marker_stimulation;
 
 	/* Random number generator in case of semi-periodic stimulation */
-	ENG				Generator;
-	DIST_int		Uniform_Distribution;
+    random_stream_uniform_int Rand_Uniform;
 };
 /****************************************************************************************************/
 /*										 		end													*/
@@ -205,10 +196,7 @@ void Stim::setup (double* var_stim) {
 		/* If ISI is random create RNG */
 		if (ISI_range != 0){
 			/* Create the generator */
-			Generator = ENG(rand());
-
-			/* Combine RNG with distribution */
-			Uniform_Distribution = DIST_int(ISI-ISI_range, ISI+ISI_range);
+            Rand_Uniform = random_stream_uniform_int(ISI-ISI_range, ISI+ISI_range);
 		}
 	} else {
 		/* In case of phase dependent stimulation, time_to_stim is the time from minimum detection to start of stimulation */
@@ -246,7 +234,7 @@ void Stim::check_stim	(int time) {
 			}
 			/* After last stimulus in event update the timer with respect to (random) ISI*/
 			else {
-				time_to_stimuli += (ISI_range==0)? ISI : Uniform_Distribution(Generator);
+                time_to_stimuli += (ISI_range==0)? ISI : Rand_Uniform();
 
 				/* Reset the stimulus counter for next stimulation event */
 				count_stimuli = 1;
diff --git a/TC.cpp b/TC.cpp
@@ -30,12 +30,9 @@
 
 /****************************************************************************************************/
 /*		Main file for compilation tests																*/
-/*		The Simulation requires the following boost libraries:	Random								*/
 /****************************************************************************************************/
 #include <iostream>
 #include <ctime>
-#include "Cortical_Column.h"
-#include "Thalamic_Column.h"
 #include "ODE.h"
 
 
diff --git a/TC_mex.cpp b/TC_mex.cpp
@@ -32,16 +32,13 @@
 /* 	Implementation of the simulation as MATLAB routine (mex compiler)								*/
 /* 	mex command is given by:																		*/
 /* 	mex CXXFLAGS="\$CXXFLAGS -std=c++11" TC_mex.cpp Cortical_Column.cpp Thalamic_Column.cpp			*/
-/*	The Simulation requires the following boost libraries:	Random									*/
 /****************************************************************************************************/
 #include <ctime>
 #include "mex.h"
 #include "matrix.h"
-#include "Cortical_Column.h"
+#include "Data_Storage.h"
 #include "ODE.h"
-#include "saves.h"
 #include "Stimulation.h"
-#include "Thalamic_Column.h"
 mxArray* GetMexArray(int N, int M);
 
 /****************************************************************************************************/
diff --git a/Thalamic_Column.cpp b/Thalamic_Column.cpp
@@ -44,8 +44,8 @@ void Thalamic_Column::set_RNG(void) {
 	/* Create RNG for each stream */
 	for (int i=0; i<N; ++i){
 		/* Add the RNG for I_{l} and I_{l,0}*/
-		MTRands.push_back({ENG(rand()), DIST (0.0, dphi*dt)});
-		MTRands.push_back({ENG(rand()), DIST (0.0, dt)});
+        MTRands.push_back(random_stream_normal(0.0, dphi*dt));
+        MTRands.push_back(random_stream_normal(0.0, dt));
 
 		/* Get the random number for the first iteration */
 		Rand_vars.push_back(MTRands[2*i]());
diff --git a/Thalamic_Column.h b/Thalamic_Column.h
@@ -34,26 +34,12 @@
 #pragma once
 #include <cmath>
 #include <vector>
-#include <boost/random/mersenne_twister.hpp>
-#include <boost/random/normal_distribution.hpp>
-#include <boost/random/variate_generator.hpp>
+#include "Random_Stream.h"
 #include "Cortical_Column.h"
 using std::vector;
-
 class Cortical_Column;
 
 /****************************************************************************************************/
-/*										Typedefs for RNG											*/
-/****************************************************************************************************/
-typedef boost::mt11213b                    	ENG;    /* Mersenne Twister		*/
-typedef boost::normal_distribution<double>	DIST;   /* Normal Distribution	*/
-typedef boost::variate_generator<ENG,DIST> 	GEN;    /* Variate generator	*/
-/****************************************************************************************************/
-/*										 		end			 										*/
-/****************************************************************************************************/
-
-
-/****************************************************************************************************/
 /*									Macro for vector initialization									*/
 /****************************************************************************************************/
 #ifndef _INIT
@@ -158,7 +144,7 @@ class Thalamic_Column {
 					m_h2	= _INIT(0.0);		/* activation 	of h   channel bound with protein 	*/
 
 	/* Random number generators */
-	vector<GEN>		MTRands;
+    vector<random_stream_normal> MTRands;
 
 	/* Container for noise */
 	vector<double>	Rand_vars;