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NM_TC/TC_mex.cpp
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Nov 9, 2015 @miscco Updated the code with correct license.
1 /*
2 * Copyright (c) 2015 University of Lübeck
3 *
4 * Permission is hereby granted, free of charge, to any person obtaining a copy
5 * of this software and associated documentation files (the "Software"), to deal
6 * in the Software without restriction, including without limitation the rights
7 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
8 * copies of the Software, and to permit persons to whom the Software is
9 * furnished to do so, subject to the following conditions:
10 *
11 * The above copyright notice and this permission notice shall be included in
12 * all copies or substantial portions of the Software.
13 *
14 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
15 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
16 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
17 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
18 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
19 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
20 * THE SOFTWARE.
21 *
22 * AUTHORS: Michael Schellenberger Costa: mschellenbergercosta@gmail.com
23 *
24 * Based on: A thalamocortical neural mass model of the EEG during NREM sleep and its response
25 * to auditory stimulation.
26 * M Schellenberger Costa, A Weigenand, H-VV Ngo, L Marshall, J Born, T Martinetz,
27 * JC Claussen.
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28 * PLoS Computational Biology http://dx.doi.org/10.1371/journal.pcbi.1005022
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29 */
30
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31 /******************************************************************************/
32 /* Implementation of the simulation as MATLAB routine (mex compiler) */
33 /* mex command is given by: */
34 /* mex CXXFLAGS="\$CXXFLAGS -std=c++11 -O3" TC_mex.cpp Cortical_Column.cpp */
35 /* Thalamic_Column.cpp */
36 /******************************************************************************/
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37 #include "mex.h"
38 #include "matrix.h"
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39
40 #include <iterator>
41 #include <vector>
42
43 #include "Cortical_Column.h"
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44 #include "Data_Storage.h"
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45 #include "ODE.h"
46 #include "Stimulation.h"
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47 #include "Thalamic_Column.h"
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48 mxArray* GetMexArray(int N, int M);
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49 mxArray* get_marker(Stim &stim);
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50
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51 /******************************************************************************/
52 /* Fixed simulation settings */
53 /******************************************************************************/
54 extern const int onset = 20; /* Time until data is stored in s */
55 extern const int res = 1E4; /* Number of iteration steps per s */
56 extern const int red = 1E2; /* Number of iterations steps not saved */
57 extern const double dt = 1E3/res; /* Duration of a time step in ms */
58 extern const double h = sqrt(dt); /* Square root of dt for SRK iteration */
59
60 /******************************************************************************/
61 /* Simulation routine */
62 /* lhs defines outputs */
63 /* rhs defines inputs */
64 /******************************************************************************/
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65 void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
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66 /* Initialize the seeder */
67 srand(time(NULL));
68
69 /* Fetch inputs */
70 const int T = (int) (mxGetScalar(prhs[0])); /* Duration of simulation in s */
71 const int Time = (T+onset)*res; /* Total number of iteration steps */
72 double* Param_Cortex = mxGetPr (prhs[1]); /* Parameters of cortical module */
73 double* Param_Thalamus = mxGetPr (prhs[2]); /* Parameters of thalamic module */
74 double* Connections = mxGetPr (prhs[3]); /* Connectivity values C <-> T */
75 double* var_stim = mxGetPr (prhs[4]); /* Parameters of stimulation protocol */
76
77 /* Initialize the populations */
78 Cortical_Column Cortex = Cortical_Column(Param_Cortex, Connections);
79 Thalamic_Column Thalamus = Thalamic_Column(Param_Thalamus, Connections);
80
81 /* Link both modules */
82 Cortex.get_Thalamus(Thalamus);
83 Thalamus.get_Cortex(Cortex);
84
85 /* Initialize the stimulation protocol */
86 Stim Stimulation(Cortex, Thalamus, var_stim);
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87
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88 /* Create data containers */
89 std::vector<mxArray*> dataArray;
90 dataArray.reserve(4);
91 dataArray.push_back(GetMexArray(1, T*res/red)); // Vt
92 dataArray.push_back(GetMexArray(1, T*res/red)); // Vr
93 dataArray.push_back(GetMexArray(1, T*res/red)); // Ca
94 dataArray.push_back(GetMexArray(1, T*res/red)); // act_h
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95
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96 /* Pointer to the data blocks */
97 std::vector<double*> dataPointer;
98 dataPointer.reserve(dataArray.size());
99 for (auto &dataptr : dataArray) {
100 dataPointer.push_back(mxGetPr(dataptr));
101 }
102
103 /* Simulation */
104 int count = 0;
105 for (unsigned t=0; t < Time; ++t) {
106 ODE (Cortex, Thalamus);
107 Stimulation.check_stim(t);
108 if(t >= onset*res && t%red == 0){
109 get_data(count, Cortex, Thalamus, dataPointer);
110 ++count;
111 }
112 }
113
114 /* Return the data containers */
115 nlhs = dataArray.size()+1;
116 for (auto &dataptr : dataArray) {
117 plhs[std::distance(&dataptr, dataArray.data())] = dataptr;
118 }
119 plhs[dataArray.size()] = get_marker(Stimulation);
120
121 return;
122 }
123
124 /******************************************************************************/
125 /* Create MATLAB data containers */
126 /******************************************************************************/
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127 mxArray* GetMexArray(int N, int M) {
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128 mxArray* Array = mxCreateDoubleMatrix(0, 0, mxREAL);
129 mxSetM(Array, N);
130 mxSetN(Array, M);
131 {mxSetData(Array, mxMalloc(sizeof(double)*M*N));}
132 return Array;
133 }
134
135 mxArray* get_marker(Stim &stim) {
136 extern const int red;
137 mxArray* marker = mxCreateDoubleMatrix(0, 0, mxREAL);
138 mxSetM(marker, 1);
139 mxSetN(marker, stim.marker_stimulation.size());
140 mxSetData(marker, mxMalloc(sizeof(double)*stim.marker_stimulation.size()));
141 double* Pr_Marker = mxGetPr(marker);
142 unsigned counter = 0;
143 /* Division by res transforms marker time from dt to sampling rate */
144 for(auto & elem : stim.marker_stimulation) {
145 Pr_Marker[counter++] = elem/red;
146 }
147 return marker;
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148 }