├── .gitignore ├── src ├── mutual_information │ ├── miutils.mexw64 │ ├── MIxnyn.exe │ ├── milca_2.exe │ ├── milca_2.ilk │ ├── milca_2.pdb │ ├── Project2.ilk │ ├── Project2.pdb │ ├── casting_test.mexw64 │ ├── casting_test.mexw64.pdb │ ├── README.md │ ├── MIhigherdim.m │ ├── casting_test.cpp │ ├── MIhigherdim.C │ ├── MIxnyn.C │ ├── fastfc_mi.cpp │ └── miutils.h ├── generalized_sync │ ├── fastfc_gs_ver2.mexw64 │ ├── README.md │ ├── fastfc_gs_ver2.c │ ├── fastfc_gs.c │ └── LICENSE ├── filter │ ├── README.md │ ├── fastfc_filt.c │ └── LICENSE ├── phase_sync │ ├── README.md │ ├── fastfc_wpli.c │ ├── fastfc_ps.c │ ├── fastfc_ps_filt.c │ └── LICENSE ├── networks │ ├── README.md │ ├── fastfc_strength_wu.c │ ├── fastfc_cluster_coef_wu.c │ ├── fastfc_cluster_coef_bu.c │ ├── fastfc_shortest_path_length_w.c │ ├── fastfc_betweenness_cent_w.c │ └── LICENSE └── README.md ├── fastfc_gs.mexw64 ├── fastfc_mi.mexw64 ├── fastfc_ps.mexw64 ├── libfftw3f-3.dll ├── fastfc_filt.mexw64 ├── fastfc_wpli.mexw64 ├── fastfc_gs_ver2.mexw64 ├── fastfc_strength_wu.mexw64 ├── fastfc_cluster_coef_bu.mexw64 ├── fastfc_cluster_coef_wu.mexw64 ├── fastfc_betweenness_cent_w.mexw64 ├── fastfc_shortest_path_length_w.mexw64 ├── .gitattributes ├── README.md ├── testing_fastFC.m └── LICENSE /.gitignore: -------------------------------------------------------------------------------- 1 | *.asv -------------------------------------------------------------------------------- /src/mutual_information/miutils.mexw64: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /fastfc_gs.mexw64: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/juangpc/FastFC/HEAD/fastfc_gs.mexw64 -------------------------------------------------------------------------------- /fastfc_mi.mexw64: 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-------------------------------------------------------------------------------- /src/mutual_information/casting_test.mexw64: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/juangpc/FastFC/HEAD/src/mutual_information/casting_test.mexw64 -------------------------------------------------------------------------------- /src/mutual_information/casting_test.mexw64.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/juangpc/FastFC/HEAD/src/mutual_information/casting_test.mexw64.pdb -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | # Auto detect text files and perform LF normalization 2 | * text=auto 3 | 4 | # These files are MEX compiled binary files and should be left untouched 5 | # (binary is a macro for -text -diff) 6 | *.mexw32 binary 7 | *.mexw64 binary 8 | *.mexa64 binary 9 | *.mexmaci64 binary 10 | 11 | # Standard to msysgit 12 | *.doc diff=astextplain 13 | *.DOC diff=astextplain 14 | *.docx diff=astextplain 15 | *.DOCX diff=astextplain 16 | *.dot diff=astextplain 17 | *.DOT diff=astextplain 18 | *.pdf diff=astextplain 19 | *.PDF diff=astextplain 20 | *.rtf diff=astextplain 21 | *.RTF diff=astextplain 22 | -------------------------------------------------------------------------------- /src/generalized_sync/README.md: -------------------------------------------------------------------------------- 1 | # FastFC 2 | Fast Functional Connectivity Toolbox. This toolbox implements efficient C computing of different FC indices. It does so through C-MEX external interface appi and within Matlab's development environment. 3 | # 4 | Development branch for Generalized Synchronization measures. 5 | 6 | S, H, M, L indices will be developed following descriptions from Daniel Chicharro's work (Chicharro et al 2009). 7 | 8 | S, H, M with a much faster and less memory demanding version (version2). It perfomrs this by avoiding andy sorting by using an ordered register filled online while measurements take place. 9 | 10 | Maybe some other implementations will be added. 11 | 12 | # Related research: 13 | Efficient computation of functional brain networks: towards real-time functional connectivity 14 | Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto -------------------------------------------------------------------------------- /src/filter/README.md: -------------------------------------------------------------------------------- 1 | # FastFC 2 | Fast Functional Connectivity Toolbox. This toolbox implements efficient C computing of different FC indices. It does so through C-MEX external interface appi and within Matlab's development environment. 3 | 4 | Development branch for Filtering with zero phase distortion. 5 | 6 | This branch contains the source-code for implementation of a zero phase distortion filtering procedure. 7 | 8 | All in a single file in order to help ports to other toolboxes. Matlab's MEX external interface has been used to connect Matlab's environment variables to this C function. 9 | 10 | fastFC_filt function is developed after matlab's filtfilt function. It implements a two passes FIR filtering with previous circular padding of the original signal. 11 | 12 | # Related research: 13 | Efficient computation of functional brain networks: towards real-time functional connectivity 14 | Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 15 | -------------------------------------------------------------------------------- /src/phase_sync/README.md: -------------------------------------------------------------------------------- 1 | # FastFC 2 | Fast Functional Connectivity Toolbox. This toolbox implements efficient C computing of different FC indices. It does so through C-MEX external interface appi and within Matlab's development environment. 3 | 4 | Development branch for Phase Connectivity measures. 5 | 6 | This branch contains the source-code for implementation of PLV, PLI, wPLI and the imaginary part of the Coherence measures. 7 | 8 | All in a single file in order to help ports to other toolboxes. Matlab's MEX external interface has been used to connect Matlab's environment variables to this C function. 9 | 10 | There is also a Phase Sync function version which implements FIR filtereing at the same time. However this version is not finished. There is aproblem with it and it blows matlab. 11 | 12 | # Related research: 13 | Efficient computation of functional brain networks: towards real-time functional connectivity 14 | Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto -------------------------------------------------------------------------------- /src/mutual_information/README.md: -------------------------------------------------------------------------------- 1 | # FastFC 2 | Fast Functional Connectivity Toolbox 3 | # 4 | This branch is only for developing of Mutual Information index. 5 | 6 | This implementation is built on top of MILCA implementation 7 | (see: http://www.ucl.ac.uk/ion/departments/sobell/Research/RLemon/MILCA/MILCA) 8 | 9 | Here you will find: 10 | 11 | - A modified version of binutils in order to be compatible with windows Visual Studio compatible version of binutils.cpp and binutils.h 12 | - A binary verson of MILCA but compiled directly with Visual Studio. 13 | - A Matlab version of Mutual Information index calculation which calls the binary program just preiously mentioned. 14 | - The source coude of a modified version of MILCA program but implemented so that it communicate with MATLAB through its external MEX interface, instead of through a text document. 15 | - A binary version of this last program, compiled with Visual Studio for Matlab in Windows 64bit systems. 16 | - Some other tools and tries that have been generated while development. See log for more details. 17 | 18 | # Related research: 19 | Efficient computation of functional brain networks: towards real-time functional connectivity 20 | Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 21 | -------------------------------------------------------------------------------- /src/networks/README.md: -------------------------------------------------------------------------------- 1 | # FastFC 2 | Fast Functional Connectivity Toolbox. This toolbox implements efficient C computing of different FC indices. It does so through C-MEX external interface appi and within Matlab's development environment. 3 | 4 | This branch is dedicated to the development of network indices, graph theoretic measures of FC adjacency matrices. 5 | Be aware autolinks are forbidden. Thus, adjacency matrices' principal diagonal must be zeroed. 6 | ## Contents 7 | - Clustering Coefficient for binary undirected networks. 8 | - Clustering Coefficient for weighted undirected networks. 9 | - Strength for weighted undirected networks. 10 | - Shortest path length for weighted networks (both directed and undirected). 11 | - Betweenness centrality for weighted networks (both directed and undirected). 12 | 13 | ## Future Development 14 | - Shortest path length could perform much better if the inversion of the adj. matrix could be done by thread parallelization. At the same time double to float transformation could take place. And continue there as the program does now. 15 | 16 | # Related research: 17 | Efficient computation of functional brain networks: towards real-time functional connectivity 18 | Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # FastFC 2 | 3 | Fast Functional Connectivity Toolbox. This toolbox implements efficient C computing of different FC indices. It does so through C-MEX external interface appi and within Matlab's development environment. The focus of FastFC is to be very small and easy to adapt to any existing toolbox within Matlab. 4 | 5 | This is the main release branch of the repo. It only includes the final executable files, a needed dll and an example script. Please see other branches for accesing source code for each set of functions. 6 | 7 | 'Hope it helps! 8 | 9 | # Related research: 10 | Efficient computation of functional brain networks: towards real-time functional connectivity 11 | Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 12 | 13 | # Installation 14 | The library has been implemented in standard C, although it uses OMP and FFTW (both open source projects). The only thing needed in order to use the functions is the FFTW dll which is included with the executables. 15 | 16 | # Filtering tool 17 | - Zero-phase distorsion FIR filtering. 18 | This filtering function has been built out of necessity. It closely resembles Matlab's filtfilt built-in function implementation. It performs an N-dimensional circular padding (N=filter order). 19 | 20 | # Functional Connectivity measures 21 | - Phase Synchronization measures: PLV, PLV's p-value, PLI, wPLI and imaginary part of the Coherence. 22 | - Mutual Information. (MILCA implementation). 23 | - Generalized Synchronization measures: S, H, M, L 24 | - Generalized Synchronization measrues (version 2. faster): S, H, M. 25 | 26 | # Complex Networks measures 27 | - Strength for weighted undirected networks. 28 | - Clustering Coefficient for binary undirected networks. 29 | - Clustering Coefficient for weighted undirected networks. 30 | - Shortest path length for weighted networks (both directed and undirected). 31 | - Betweenness centrality for weighted networks (both directed and undirected). 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /src/README.md: -------------------------------------------------------------------------------- 1 | # FastFC 2 | 3 | Fast Functional Connectivity Toolbox. This toolbox implements efficient C computing of different FC indices. It does so through C-MEX external interface appi and within Matlab's development environment. The focus of FastFC is to be very small and easy to adapt to any existing toolbox within Matlab. 4 | 5 | This is the development branch. It includes all the files writen during development of each index. Also object files for Visual Studio debugging and few other things. The C (all indices except MI) and C++ (for Mutual Information index) code can be found in the /src folder. 6 | 7 | 'Hope it helps! 8 | 9 | # Related research: 10 | Efficient computation of functional brain networks: towards real-time functional connectivity 11 | Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 12 | 13 | # Installation 14 | The library has been implemented in standard C, although it uses OMP and FFTW (both open source projects). The only thing needed in order to use the functions is the FFTW dll which is included with the executables. 15 | 16 | # Filtering tool 17 | - Zero-phase distorsion FIR filtering. 18 | This filtering function has been built out of necessity. It closely resembles Matlab's filtfilt built-in function implementation. It performs an N-dimensional circular padding (N=filter order). 19 | 20 | # Functional Connectivity measures 21 | - Phase Synchronization measures: PLV, PLV's p-value, PLI, wPLI and imaginary part of the Coherence. 22 | - Mutual Information. (MILCA implementation). 23 | - Generalized Synchronization measures: S, H, M, L 24 | - Generalized Synchronization measrues (version 2. faster): S, H, M. 25 | 26 | # Complex Networks measures 27 | - Strength for weighted undirected networks. 28 | - Clustering Coefficient for binary undirected networks. 29 | - Clustering Coefficient for weighted undirected networks. 30 | - Shortest path length for weighted networks (both directed and undirected). 31 | - Betweenness centrality for weighted networks (both directed and undirected). 32 | 33 | 34 | -------------------------------------------------------------------------------- /src/networks/fastfc_strength_wu.c: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (c) 2014-2015 Juan Garcia-Prieto Cuesta 3 | // 4 | // This file is part of Fast Functional Connectivity (FastFC) 5 | // 6 | // FastFC is free software: you can redistribute it and/or modify 7 | // it under the terms of the GNU General Public License as published by 8 | // the Free Software Foundation, either version 3 of the License, or 9 | // (at your option) any later version. 10 | // 11 | // FastFC is distributed in the hope that it will be useful, 12 | // but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | // GNU General Public License for more details. 15 | // 16 | // You should have received a copy of the GNU General Public License 17 | // along with FastFC. If not, see . 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | 32 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 33 | { 34 | int node_i,node_j; 35 | double *W,*S,s_aux; 36 | const int n_nodes=(int)mxGetM(prhs[0]); 37 | 38 | plhs[0]=mxCreateDoubleMatrix(1,n_nodes,mxREAL); 39 | W=(double*)mxGetPr(prhs[0]); 40 | S=(double*)mxGetPr(plhs[0]); 41 | 42 | #pragma omp parallel 43 | { 44 | #pragma omp for private(node_i,node_j) reduction(+:s_aux) 45 | for(node_i=0;node_i. 15 | %----------------------------------------------------------------------------------------- 16 | % Contacts: 17 | % 18 | % Harald Stoegbauer 19 | % Alexander Kraskov 20 | %----------------------------------------------------------------------------------------- 21 | % Please reference 22 | % 23 | % A. Kraskov, H. Stogbauer, and P. Grassberger, 24 | % Estimating mutual information. 25 | % Phys. Rev. E 69 (6) 066138, 2004 26 | % 27 | % in your published research. 28 | 29 | 30 | function miout=MIhigherdim(x,kneig,emb_dim,emb_tau) 31 | 32 | % Calculate MI value of any high-dimensional vector - to include also 33 | % dependencies in time use embedding dimension >1 (see[1], Fig 14) 34 | % (rectangular version) 35 | % x....input data mxn m...channelnummer n...sampling points m<1 (default is 1) 39 | 40 | %default-values 41 | if ~exist('kneig'), kneig=6; end 42 | if ~exist('emb_dim'), emb_dim=1; end 43 | if ~exist('emb_tau'), emb_tau=1; end 44 | 45 | [Nd,N]=size(x); 46 | 47 | 48 | if Nd>N 49 | zwsp=x; 50 | [Nd,N]=size(x); 51 | else 52 | zwsp=x'; 53 | end 54 | 55 | save('zwspMIhigh.txt','zwsp','-ascii') 56 | 57 | % execute C Programm 58 | [a unout]=system(['milca_2 zwspMIhigh.txt ',num2str(Nd),' ',num2str(emb_dim),' ',num2str(emb_tau),' ',num2str(N),' ',num2str(kneig)]); 59 | miout=str2num(unout); 60 | 61 | 62 | -------------------------------------------------------------------------------- /src/mutual_information/casting_test.cpp: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | // 4 | // __inline double fastabs(double x){ 5 | // unsigned long int *x_int=&x; 6 | // unsigned long int n=*x_int&0x7fffffff; 7 | // return (double)n; 8 | // } 9 | 10 | // 11 | // inline double fastabs(double x){ 12 | // float a =(float)x; 13 | // 14 | // unsigned int b = *reinterpret_cast(&a); 15 | // return (double) (b&0x7fffffff) ; 16 | // } 17 | // 18 | 19 | // inline double fastabs(double x){ 20 | // float x_f=(float)x; 21 | // unsigned int= 22 | // return (double&) (((unsigned int&)x_f)&0x7fffffff) ; 23 | // } 24 | // 25 | 26 | // double fastabs(double x){ 27 | // double x_abs=fabs(x); 28 | // double *ptr_x; 29 | // ptr_x=(double*)mxMalloc(2*sizeof(double)); 30 | // *ptr_x=x; 31 | // *(ptr_x+1)=0x7fffffffffffffff; 32 | // unsigned long int x_int=(((unsigned long int&)x)&0x7fff ffff ffff ffff); 33 | // //return (double&) x_int ; 34 | // return *(ptr_x+1); 35 | // } 36 | 37 | // double fastabs(double x) 38 | // { 39 | // double mask=9.2233720368547758e18; 40 | // unsigned long int xx=((unsigned long int&)x&(unsigned long int&)mask); 41 | // return (double&)xx; 42 | // } 43 | 44 | double fastabs(float x) 45 | { 46 | unsigned int int_x=((unsigned int&)x&0x7fffffff); 47 | return (double)(float&)int_x; 48 | } 49 | 50 | 51 | 52 | 53 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 54 | { 55 | // unsigned int int_in; 56 | double x; 57 | double in=mxGetScalar(prhs[0]); 58 | 59 | x=fastabs(in); 60 | 61 | plhs[0]=mxCreateDoubleScalar(x); 62 | 63 | } 64 | 65 | 66 | 67 | // 68 | // int_in=*(long int*)∈ 69 | // p_in=(long int*)∈ 70 | // // reinterpret_cast 71 | // // int_in_1=*p_in; 72 | // // int_in_2=3; 73 | // // 74 | // // int_in_1=int_in_1*int_in_2; 75 | // mexPrintf("\nsize of int: %d\n",sizeof(int)); 76 | // mexPrintf("\nsize of double: %d\n",sizeof(double)); 77 | // mexPrintf("\nsize of long int: %d\n",sizeof(long int)); 78 | // mexPrintf("\nsize of long long int: %d\n",sizeof(long long int)); 79 | // mexPrintf("\nsize of float: %d\n",sizeof(float)); 80 | // mexPrintf("\nsize of pointer to int: %d\n",sizeof(int*)); 81 | // mexPrintf("\nsize of pointer to double: %d\n",sizeof(double)); 82 | // mexPrintf("\nsize of pointer to long int: %d\n",sizeof(long int*)); 83 | // mexPrintf("\nsize of pointer to float: %d\n",sizeof(float*)); 84 | // 85 | 86 | // mexPrintf("\nint_in: %f\n",int_in); 87 | // mexPrintf("\np_in: %f\n\n",*p_in); 88 | 89 | 90 | -------------------------------------------------------------------------------- /src/networks/fastfc_cluster_coef_wu.c: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (c) 2014-2015 Juan Garcia-Prieto Cuesta 3 | // 4 | // This file is part of Fast Functional Connectivity (FastFC) 5 | // 6 | // FastFC is free software: you can redistribute it and/or modify 7 | // it under the terms of the GNU General Public License as published by 8 | // the Free Software Foundation, either version 3 of the License, or 9 | // (at your option) any later version. 10 | // 11 | // FastFC is distributed in the hope that it will be useful, 12 | // but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | // GNU General Public License for more details. 15 | // 16 | // You should have received a copy of the GNU General Public License 17 | // along with FastFC. If not, see . 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | #include 32 | 33 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 34 | { 35 | int *K,node_i,node_j,z; 36 | double *W,*W2,*C,cyc3,w2_aux; 37 | 38 | const int n_nodes=(int)mxGetM(prhs[0]); 39 | W=(double*)mxGetPr(prhs[0]); 40 | K=(int*)mxMalloc(n_nodes*sizeof(int)); 41 | W2=(double*)mxCalloc(n_nodes*n_nodes,sizeof(double)); 42 | plhs[0]=mxCreateDoubleMatrix(n_nodes,1,mxREAL); 43 | C=(double*)mxGetPr(plhs[0]); 44 | 45 | omp_set_num_threads(omp_get_num_procs()); 46 | #pragma omp parallel 47 | { 48 | #pragma omp for private(node_i,node_j,z) reduction(+:w2_aux) 49 | for(node_i=0;node_i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | 32 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 33 | { 34 | 35 | int *n_neis,*n_triangs,*neis,link_i,link_j,nei_i,nei_j; 36 | double *A,*C; 37 | 38 | const int n_links=(int)mxGetM(prhs[0]); 39 | 40 | A=(double*)mxGetPr(prhs[0]); 41 | 42 | neis=(int*)mxMalloc(n_links*(n_links-1)*sizeof(int)); 43 | n_neis=(int*)mxCalloc(n_links,sizeof(int)); 44 | n_triangs=(int*)mxCalloc(n_links,sizeof(int)); 45 | 46 | plhs[0]=mxCreateDoubleMatrix(n_links,1,mxREAL); 47 | C=(double*)mxGetPr(plhs[0]); 48 | 49 | omp_set_num_threads(omp_get_num_procs()); 50 | #pragma omp parallel 51 | { 52 | #pragma omp for private(link_i,link_j) 53 | for(link_i=0;link_i1) 72 | { 73 | C[link_i]=(double)n_triangs[link_i]/(n_neis[link_i]*(n_neis[link_i]-1)*.5); 74 | }else{ 75 | C[link_i]=0; 76 | } 77 | } 78 | } 79 | 80 | mxFree(neis); 81 | mxFree(n_neis); 82 | mxFree(n_triangs); 83 | 84 | } 85 | -------------------------------------------------------------------------------- /src/mutual_information/MIhigherdim.C: -------------------------------------------------------------------------------- 1 | // Copyright 2009 Alexander Kraskov, Harald Stoegbauer, Peter Grassberger 2 | //----------------------------------------------------------------------------------------- 3 | // This program is free software: you can redistribute it and/or modify 4 | // it under the terms of the GNU General Public License as published by 5 | // the Free Software Foundation, either version 3 of the License, or 6 | // (at your option) any later version. 7 | // 8 | // This program is distributed in the hope that it will be useful, 9 | // but WITHOUT ANY WARRANTY; without even the implied warranty of 10 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 11 | // GNU General Public License for more details. 12 | // 13 | // You should receive a copy of the GNU General Public License 14 | // along with this program. See also . 15 | //----------------------------------------------------------------------------------------- 16 | // Contacts: 17 | // 18 | // Harald Stoegbauer 19 | // Alexander Kraskov 20 | //----------------------------------------------------------------------------------------- 21 | // Please reference 22 | // 23 | // A. Kraskov, H. Stogbauer, and P. Grassberger, 24 | // Estimating mutual information. 25 | // Phys. Rev. E 69 (6) 066138, 2004 26 | // 27 | // in your published research. 28 | 29 | #define _CRT_SECURE_NO_WARNINGS 30 | 31 | #include 32 | #include 33 | #include 34 | #include 35 | #include 36 | #include 37 | 38 | #include "miutils.h" 39 | 40 | int main(int argc, char **argv) { 41 | 42 | FILE *fin; 43 | int i; 44 | double **x; 45 | double *min; 46 | double *max; 47 | double *psi; 48 | int K,N; 49 | int d; 50 | double mir; 51 | int dim,edim,tau; 52 | 53 | double s,me; 54 | double addnoise=-1; 55 | 56 | if (argc<7) { 57 | fprintf(stderr,"\nMutual Infomation (MI) k-nearest neighbours statistics (rectangular)\n\n"); 58 | fprintf(stderr,"Usage:\n%s <# points> <# neighbours> [addnoise]\n\n",argv[0]); 59 | fprintf(stderr,"Input:\n\t\ttext file with columns and <# points> rows\n"); 60 | fprintf(stderr,"\t\t\tnumber of columns in file\n"); 61 | fprintf(stderr,"\t\t\tembedding dimension\n"); 62 | fprintf(stderr,"\t\t\tembedding delay\n"); 63 | fprintf(stderr,"\t<# points>\tnumber of rows (length of characteristic vector)\n"); 64 | fprintf(stderr,"\t<# neighbours>\tnumber of the nearest neighbours for MI estimator\n"); 65 | fprintf(stderr,"\t[addnoise]\tnoise amplitude; default 1e-8\n"); 66 | fprintf(stderr,"\nOutput:\n"); 67 | fprintf(stderr,"\nMI\n"); 68 | fprintf(stderr,"\nContact: kraskov@its.caltech.edu\n"); 69 | exit(-1); 70 | } 71 | 72 | dim=atoi(argv[2]); 73 | edim=atoi(argv[3]); 74 | tau=atoi(argv[4]); 75 | N=atoi(argv[5]); 76 | K=atoi(argv[6]); 77 | if (argc==8) {addnoise=atof(argv[7]);} 78 | if (argc>=9) {fprintf(stderr,"Too many input arguments\n");exit(-1);} 79 | 80 | x=(double**)calloc(dim,sizeof(double*)); 81 | for (d=0;dmax[d]) max[d]=x[d][i]; 112 | } 113 | for (i=0;i. 16 | //----------------------------------------------------------------------------------------- 17 | // Contacts: 18 | // 19 | // Harald Stoegbauer 20 | // Alexander Kraskov 21 | //----------------------------------------------------------------------------------------- 22 | // Please reference 23 | // 24 | // A. Kraskov, H. Stogbauer, and P. Grassberger, 25 | // Estimating mutual information. 26 | // Phys. Rev. E 69 (6) 066138, 2004 27 | // 28 | // in your published research. 29 | 30 | 31 | #include 32 | #include 33 | #include 34 | #include 35 | #include 36 | #include 37 | 38 | #include "miutils.h" 39 | 40 | int main(int argc, char **argv) { 41 | 42 | FILE *fin; 43 | int i; 44 | double **x; 45 | double *scal; 46 | double *min; 47 | double *max; 48 | double *psi; 49 | int K,N; 50 | int d; 51 | double mir; 52 | int dimx,dimy; 53 | 54 | 55 | int BOX1; 56 | 57 | double s,me; 58 | double addnoise=-1; 59 | 60 | if (argc<6) { 61 | fprintf(stderr,"\nMutual Infomation (MI) k-nearest neighbours statistics (rectangular)\n\n"); 62 | fprintf(stderr,"Usage:\n%s <# points> <# neighbours> [addnoise]\n\n",argv[0]); 63 | fprintf(stderr,"Input:\n\t\ttext file with columns and <# points> rows\n"); 64 | fprintf(stderr,"\t\t\tnumber of columns for X (dimension of X)\n"); 65 | fprintf(stderr,"\t\t\tnumber of columns for Y (dimension of Y)\n"); 66 | fprintf(stderr,"\t<# points>\tnumber of rows (length of characteristic vector)\n"); 67 | fprintf(stderr,"\t<# neighbours>\tnumber of the nearest neighbours for MI estimator\n"); 68 | fprintf(stderr,"\t[addnoise]\tnoise amplitude; default 1e-8\n"); 69 | fprintf(stderr,"\nOutput:\n"); 70 | fprintf(stderr,"\nMI\n"); 71 | fprintf(stderr,"\nContact: kraskov@its.caltech.edu\n"); 72 | exit(-1); 73 | } 74 | 75 | 76 | 77 | dimx=atoi(argv[2]); 78 | dimy=atoi(argv[3]); 79 | N=atoi(argv[4]); 80 | K=atoi(argv[5]); 81 | if (argc==7) {addnoise=atof(argv[6]);} 82 | if (argc>=8) {fprintf(stderr,"Too many input arguments\n");exit(-1);} 83 | 84 | x=(double**)calloc(dimx+dimy,sizeof(double*)); 85 | for (d=0;dmax[d]) max[d]=x[d][i]; 117 | } 118 | for (i=0;i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | 30 | // Copyright 2009 Alexander Kraskov, Harald Stoegbauer, Peter Grassberger 31 | //----------------------------------------------------------------------------------------- 32 | // This program is free software: you can redistribute it and/or modify 33 | // it under the terms of the GNU General Public License as published by 34 | // the Free Software Foundation, either version 3 of the License, or 35 | // (at your option) any later version. 36 | // 37 | // This program is distributed in the hope that it will be useful, 38 | // but WITHOUT ANY WARRANTY; without even the implied warranty of 39 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 40 | // GNU General Public License for more details. 41 | // 42 | // You should receive a copy of the GNU General Public License 43 | // along with this program. See also . 44 | //----------------------------------------------------------------------------------------- 45 | // Contacts: 46 | // 47 | // Harald Stoegbauer 48 | // Alexander Kraskov 49 | //----------------------------------------------------------------------------------------- 50 | // Please reference 51 | // 52 | // A. Kraskov, H. Stogbauer, and P. Grassberger, 53 | // Estimating mutual information. 54 | // Phys. Rev. E 69 (6) 066138, 2004 55 | // 56 | // in your published research. 57 | */ 58 | #define _CRT_SECURE_NO_WARNINGS 59 | 60 | #include 61 | #include 62 | #include 63 | 64 | #include 65 | #include 66 | #include 67 | #include 68 | #include 69 | #include 70 | 71 | #include "miutils.h" 72 | 73 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 74 | { 75 | int N,edim,tau,K,n_sensors,sensor_i,sensor_j,i,d,n_threads; 76 | const int dim=2; 77 | double addnoise=-1; 78 | double *data,**x;//*min,*max; 79 | double *psi; 80 | // double s,me; 81 | double *out_mi,*mi,mi_value; 82 | 83 | 84 | data=(double*)mxGetPr(prhs[0]); 85 | N=(int)mxGetM(prhs[0]); 86 | n_sensors=(int)mxGetN(prhs[0]); 87 | edim=(int)mxGetScalar(prhs[1]); 88 | tau=(int)mxGetScalar(prhs[2]); 89 | K=(int)mxGetScalar(prhs[3]); 90 | const int n_indexes=n_sensors*n_sensors; 91 | n_threads=omp_get_num_procs(); 92 | 93 | 94 | if (nrhs<4) 95 | mexErrMsgIdAndTxt("MATLAB:trial_mi_milca","Not enough input arguments\n"); 96 | if (nrhs==6) 97 | addnoise=mxGetScalar(prhs[4]); 98 | if (nrhs>6) 99 | mexErrMsgIdAndTxt("MATLAB:trial_mi_milca","Too many input arguments\n"); 100 | 101 | x=(double**)mxMalloc(dim*sizeof(double*)); 102 | 103 | for (d=0;d. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | 30 | #include 31 | #include 32 | #include 33 | 34 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 35 | { 36 | int sensor_i,thread_i; 37 | mwSize i; 38 | float *b,**x; 39 | double *x_d,*b_d,*y; 40 | fftwf_complex **fft_x,*fft_b; 41 | fftwf_plan p_r2c,p_c2r; 42 | 43 | const mwSize l_b=(mwSize)mxGetN(prhs[0]); 44 | const mwSize n_samples=(mwSize)mxGetM(prhs[1]); 45 | const int n_sensors=(int)mxGetN(prhs[1]); 46 | const int mode=(int)mxGetScalar(prhs[2]); 47 | const int n_threads=omp_get_num_procs(); 48 | const mwSize l_p=n_samples+2*(l_b-1); 49 | const float n_factor=(float)1./l_p; 50 | 51 | b_d=(double*)mxGetPr(prhs[0]); 52 | x_d=(double*)mxGetPr(prhs[1]); 53 | 54 | b=(float*)mxMalloc(l_p*sizeof(float)); 55 | x=(float**)mxMalloc(n_threads*sizeof(float*)); 56 | fft_x=(fftwf_complex**)mxMalloc(n_threads*sizeof(fftwf_complex*)); 57 | fft_b=(fftwf_complex*)fftwf_malloc(l_p*sizeof(fftwf_complex)); 58 | 59 | plhs[0]=mxCreateDoubleMatrix(n_samples,n_sensors,mxREAL); 60 | y=(double*)mxGetPr(plhs[0]); 61 | 62 | for(thread_i=0;thread_i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | #include 32 | 33 | #define INF (float)mxGetInf(); 34 | 35 | typedef struct _node{ 36 | int val; 37 | struct _node* prev; 38 | struct _node* next; 39 | }node; 40 | 41 | node * flush_node(int i,node * list,int n,node * list_init) 42 | { 43 | if(i==list->val) 44 | return list->next; 45 | if(i==n-1) 46 | return list; 47 | else{ 48 | list_init[i].prev->next=list_init[i].next; 49 | list_init[i].next->prev=list_init[i].prev; 50 | return list; 51 | } 52 | } 53 | 54 | node * init_nodes(int n,node * list) 55 | { 56 | int i=0; 57 | list->val=i; 58 | list->prev=NULL; 59 | list->next=&list[1]; 60 | for(i=1;ival*n+inode]val]) 116 | { 117 | D_i[node_i->val]=D_i[inode]+(float)L[node_i->val*n+inode]; 118 | B_i[node_i->val]=B_i[inode]+1; 119 | } 120 | node_i=node_i->next; 121 | } 122 | node_i=nodes; 123 | min_d=D_i[node_i->val]; 124 | min_node=node_i->val; 125 | for(i=0;ival]val]; 130 | min_node=node_i->val; 131 | } 132 | node_i=node_i->next; 133 | } 134 | inode=min_node; 135 | nodes=flush_node(min_node,nodes,n,nodes_init[th_i]); 136 | l_nodes--; 137 | } 138 | } 139 | } 140 | 141 | plhs[0]=mxCreateDoubleMatrix(n,n,mxREAL); 142 | plhs[1]=mxCreateDoubleMatrix(n,n,mxREAL); 143 | 144 | //copiar resultado en D_d 145 | #pragma omp parallel sections private(i) 146 | { 147 | #pragma omp section 148 | { 149 | D_d=(double*)mxGetPr(plhs[0]); 150 | for(i=0;i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | #include 32 | #include 33 | 34 | #define _2PI 6.283185307179586 35 | 36 | void calc_hamm_win(float*w,int wl) 37 | { 38 | int i; 39 | const int wlh=(wl%2)? wl/2:(wl+1)/2; 40 | const float k=(float)_2PI/(wl-1); 41 | for(i=0;i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | #include 32 | 33 | #define INF (float)mxGetInf(); 34 | 35 | typedef struct _node{ 36 | int inode; 37 | int val; 38 | struct _node* prev; 39 | struct _node* next; 40 | }node; 41 | 42 | node * flush_node(int n,int i,node * list,node * list_init) 43 | { 44 | if(i==list->val) 45 | return list->next; 46 | if(i==n-1) 47 | return list; 48 | else{ 49 | list_init[i].prev->next=list_init[i].next; 50 | list_init[i].next->prev=list_init[i].prev; 51 | return list; 52 | } 53 | } 54 | 55 | node * init_nodes(int n,int inode,node * list) 56 | { 57 | int i=0; 58 | list->inode=inode; 59 | list->val=i; 60 | list->prev=NULL; 61 | list->next=&list[1]; 62 | for(i=1;ival*n+inode]val]) 173 | { 174 | D_i[node_i->val]=D_i[inode]+(float)L[node_i->val*n+inode]; 175 | B_i[node_i->val]=B_i[inode]+1; 176 | node_i->inode=inode; 177 | } 178 | node_i=node_i->next; 179 | } 180 | node_i=nodes; 181 | min_d=D_i[node_i->val]; 182 | min_node=node_i->val; 183 | min_node_prev=node_i->inode; 184 | for(i=0;ival]val]; 189 | min_node=node_i->val; 190 | min_node_prev=node_i->inode; 191 | } 192 | node_i=node_i->next; 193 | } 194 | inode=min_node; 195 | nodes=flush_node(n,min_node,nodes,nodes_init[th_i]); 196 | push_node2path(n,min_node_prev,inode,path[th_i]); 197 | l_nodes--; 198 | } 199 | 200 | count_path(n,n_i,Betw,path[th_i],itinerary[th_i]); 201 | } 202 | } 203 | 204 | plhs[0]=mxCreateDoubleMatrix(n,n,mxREAL); 205 | plhs[1]=mxCreateDoubleMatrix(n,n,mxREAL); 206 | plhs[2]=mxCreateDoubleMatrix(n,1,mxREAL); 207 | 208 | #pragma omp parallel sections private(i) 209 | { 210 | #pragma omp section 211 | { 212 | D_d=(double*)mxGetPr(plhs[0]); 213 | for(i=0;i 32 | #include 33 | #include 34 | #include 35 | 36 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 37 | { 38 | int sensor_i,sensor_j; 39 | mwSize sample_i,first_samp_sensor_i,f_i; 40 | mwIndex i; 41 | float *x_f,*x_f_i,*x_f_j,*adj_plv,*adj_pli,*pval_plv,plv_i, 42 | sum_cos,sum_sin,sum_sin_sign,phi,sin_phi; 43 | double *x_d,*out_plv,*out_pli,*out_pval; 44 | fftwf_complex *a,*h; 45 | fftwf_plan p_r2c, p_c2c; 46 | 47 | const mwSize n_samples=(mwSize)mxGetM(prhs[0]); 48 | const int n_sensors=(int)mxGetN(prhs[0]); 49 | const mwSize n_elements=n_samples*(mwSize)n_sensors; 50 | const int is_even=(n_samples%2)? 0:1; 51 | const mwSize n_f=n_samples/2+((is_even)? 0:1); 52 | const float factor_n=(float)1.0/n_samples; 53 | const mwSize n_indexes=n_sensors*n_sensors; 54 | const mwSize init_sample=(int)mxGetScalar(prhs[1]); 55 | const int n_threads=omp_get_num_procs(); 56 | const mwSize last_sample=n_samples-init_sample; 57 | const mwSize n_samples_eff=n_samples-2*init_sample; 58 | const int mode=(int)mxGetScalar(prhs[2]); 59 | 60 | x_d=(double*)mxGetPr(prhs[0]); 61 | 62 | x_f=(float*)mxMalloc(n_elements*sizeof(float)); 63 | h=(fftwf_complex*)fftwf_malloc(n_elements*sizeof(fftwf_complex)); 64 | a=(fftwf_complex*)fftwf_malloc(n_elements*sizeof(fftwf_complex)); 65 | 66 | if (mode==3) 67 | { 68 | p_r2c=fftwf_plan_dft_r2c_1d(n_samples,x_f,h,FFTW_EXHAUSTIVE); 69 | p_c2c=fftwf_plan_dft_1d(n_samples,h,a,FFTW_BACKWARD,FFTW_EXHAUSTIVE); 70 | } 71 | else if (mode==3) 72 | { 73 | p_r2c=fftwf_plan_dft_r2c_1d(n_samples,x_f,h,FFTW_PATIENT); 74 | p_c2c=fftwf_plan_dft_1d(n_samples,h,a,FFTW_BACKWARD,FFTW_PATIENT); 75 | } 76 | else if (mode==3) 77 | { 78 | p_r2c=fftwf_plan_dft_r2c_1d(n_samples,x_f,h,FFTW_MEASURE); 79 | p_c2c=fftwf_plan_dft_1d(n_samples,h,a,FFTW_BACKWARD,FFTW_MEASURE); 80 | } 81 | else 82 | { 83 | p_r2c=fftwf_plan_dft_r2c_1d(n_samples,x_f,h,FFTW_ESTIMATE); 84 | p_c2c=fftwf_plan_dft_1d(n_samples,h,a,FFTW_BACKWARD,FFTW_ESTIMATE); 85 | } 86 | 87 | omp_set_num_threads(n_threads); 88 | #pragma omp parallel 89 | { 90 | #pragma omp for private(sensor_i,sample_i,first_samp_sensor_i,f_i) 91 | for(sensor_i=0;sensor_i0.0)-(sin_phi<0.0); 156 | } 157 | sum_cos/=n_samples_eff; 158 | sum_sin/=n_samples_eff; 159 | 160 | plv_i=sqrtf(sum_cos*sum_cos+sum_sin*sum_sin); 161 | adj_pli[sensor_j+(n_sensors*sensor_i)]=fabsf(sum_sin_sign/n_samples_eff); 162 | adj_plv[sensor_j+(n_sensors*sensor_i)]=plv_i; 163 | pval_plv[sensor_j+(n_sensors*sensor_i)]= 164 | expf(sqrtf((float)(1+4*n_samples_eff)+4.0*(float)n_samples_eff*(float)n_samples_eff*(1.0-plv_i*plv_i))-(float)(1+2*n_samples_eff)); 165 | 166 | adj_plv[sensor_i+(n_sensors*sensor_j)]=plv_i; 167 | adj_pli[sensor_i+(n_sensors*sensor_j)]=adj_pli[sensor_j+(n_sensors*sensor_i)]; 168 | pval_plv[sensor_i+(n_sensors*sensor_j)]=pval_plv[sensor_j+(n_sensors*sensor_i)]; 169 | 170 | } 171 | } 172 | } 173 | 174 | mxFree(x_f); 175 | 176 | plhs[0]=mxCreateDoubleMatrix(n_sensors,n_sensors,mxREAL); 177 | plhs[1]=mxCreateDoubleMatrix(n_sensors,n_sensors,mxREAL); 178 | plhs[2]=mxCreateDoubleMatrix(n_sensors,n_sensors,mxREAL); 179 | 180 | 181 | #pragma omp parallel sections private(i) 182 | { 183 | #pragma omp section 184 | { 185 | out_plv=(double*)mxGetPr(plhs[0]); 186 | for(i=0;i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | #include 32 | #include 33 | 34 | #define INF (float)mxGetInf(); 35 | 36 | typedef struct neighbour{ 37 | int index; 38 | float dist; 39 | }neighbour; 40 | 41 | int cmp(const void *a,const void *b) 42 | { 43 | return (((neighbour*)a)->dist < ((neighbour*)b)->dist)? 44 | -1:(((neighbour*)a)->dist > ((neighbour*)b)->dist); 45 | } 46 | 47 | void init_knn(const int n_sensors,const int n_states,const int k, 48 | neighbour * k_nn) 49 | { 50 | int sensor_i,state_i,k_i; 51 | for(sensor_i=0;sensor_iW) 62 | { 63 | if(*k_ind)&(abs(i-j)>W)) 66 | k_i++; 67 | for(k_ii=*k_in;k_ii>k_i;k_ii--) 68 | k_nn[k_ii]=k_nn[k_ii-1]; 69 | 70 | k_nn[k_i].dist=d; 71 | k_nn[k_i].index=j; 72 | *k_in+=1; 73 | } else if(k_nn[k_i].dist>d) { 74 | k_i++; 75 | while((k_id)) 76 | k_i++; 77 | for(k_ii=0;k_ii. 15 | % 16 | % ------------------------------------------ 17 | % Please consider citing our work: 18 | % 19 | % Efficient computation of functional brain networks: towards real-time functional connectivity 20 | % Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 21 | % 22 | % ------------------------------------------ 23 | % Contact: Juan Garcia-Prieto juangpc (at) gmail.com 24 | % ------------------------------------------ 25 | % 26 | 27 | 28 | %% FastFC testing script 29 | 30 | % configure number of sensors and samples 31 | n_samples=1000; 32 | n_sensors=100; 33 | x=randn(n_samples,n_sensors); % remember columnwise matrix of each sensor. 34 | 35 | %% 36 | fprintf('\n\n *** FastFC testing script *** \n\n\n'); 37 | fprintf(' This function is intended to check the correct installation of FastFC.\n'); 38 | fprintf(' While it helps understanding how different functions can be used.\n\n'); 39 | fprintf([' The testing setup will be a set of ' num2str(n_samples) ' samples and ' num2str(n_sensors) ' sensors.\n']); 40 | fprintf(' IMPORTANT: sensors must be stored as columns in the input data.\n\n\n'); 41 | 42 | %% testing FastFC filtering function 43 | fprintf(' Starting Zero Phase Distortion filtering test:\n') 44 | b=fir1(ceil(n_samples/5),[0.0160 0.0240],'bandpass',hamming(ceil(n_samples/5)+1),'scale'); 45 | 46 | % y=fastfc_filt(filter,data,mode) 47 | % Input parameters: 48 | % filter = row vector with filter denominator coefficients. 49 | % data = column matrix with data to be filtered. Each sensor should be each column. 50 | % mode = mode for FFT scheduling 51 | % mode = 0 , execute fastest but suboptimal. 52 | % mode = 1 , execute fast but in a suboptimal algorithm. 53 | % mode = 2 , execute slower the first time, but consider possible faster algorithms. 54 | % mode = 3 , execute slowest the first time, but consider the fastest algorithm. 55 | % Output parameters: 56 | % y = array the same size of data, with each column corresponding to each filtered column of data. 57 | 58 | y_filtfilt=filtfilt(b,1,x); 59 | tic; 60 | y_filtfilt=filtfilt(b,1,x); 61 | t_filtfilt=toc; 62 | y_fastfc=fastfc_filt(b,x,1); %this first call takes longer for optimization purposes. 63 | tic;y_fastfc=fastfc_filt(b,x,1);t_fastfc=toc; 64 | fprintf(' New filtfilt version called ''fastfc_filt'' is working properly.\n'); 65 | fprintf([' FastFC is ' num2str(t_filtfilt/t_fastfc) ' times faster than Matlab''s filtfilt.\n\n']); 66 | 67 | %% Testing Phase Synchronization function 68 | fprintf(' Starting Phase Synchronization test:\n'); 69 | 70 | % [plv,pval_plv,pli,wpli]=fastfc_ps(data,samples_to_discard,mode) 71 | % 72 | % Input parameters: 73 | % data = data (sensors by columns). 74 | % samples_to_discard = samples to discard at the beginning and samples to discard at the end of the phase signals. i.e. To discard 200 samples at the beginning and 200 samples at the end of each sensor, samples_to_discard should equal 200. 75 | % mode = 0 -> execute fastest but suboptimal. 76 | % mode = 1 -> execute fast but in a suboptimal algorithm. 77 | % mode = 2 -> execute slower the first time, but consider possible faster algorithms. 78 | % mode = 3 -> execute slowest the first time, but consider the fastest algorithm. 79 | % Output parameters: 80 | % plv = Phase Locking Value Functional Connectivity matrix. 81 | % pval_plv = pvalue for each index of the PLV matrix. 82 | % pli = Phase Locking Index Functional Connectivity matrix. 83 | % wPli = weighted Phase Locking Functional Connectivity matrix. 84 | 85 | tic;[plv,pval_plv,pli]=fastfc_ps(x,n_samples*.1,1);t_ps1=toc; 86 | tic;[wpli,imc]=fastfc_wpli(x);t_ps2=toc; 87 | 88 | fprintf(' Function ''fastfc_ps'' is working properly.\n'); 89 | fprintf(' FastFC calculation of Phase Synch. indices: PLV and PLI took: %.03f seconds.\n',t_ps1); 90 | fprintf(' FastFC calculation of Phase Synch. indices: PLI, wPLI and ImC took: %.03f seconds.\n\n',t_ps2); 91 | 92 | %% Testing Mutual Info 93 | fprintf(' Starting Mutual Information test:\n'); 94 | 95 | % [mi]=fastfc_mi(data,emb_dim,tau,k); 96 | % Input parameters: 97 | % data = eeg data (sensors by columns). 98 | % emb_dim = embedding dimensions to consider 99 | % tau = time lag to consider for embedding 100 | % k = number of neighbours to consider 101 | % Output parameters: 102 | % mi = Mutual Information Functional Connectivity matrix 103 | 104 | emb_dim=3; 105 | tau=2; 106 | k=4; 107 | tic;[mi]=fastfc_mi(x,emb_dim,tau,k);t_mi=toc; 108 | 109 | fprintf(' Function ''fastfc_mi'' is working properly.\n'); 110 | fprintf(' FastFC calculation of Mutual Information index took: %.03f seconds.\n\n',t_mi); 111 | 112 | %% Testing Generalized Synchronization 113 | fprintf(' Starting Generalized Synchronization test:\n'); 114 | 115 | % [S,H,M,L]=fastfc_gs(data,emb_dim,tau,k,w,states_eff_step) 116 | % 117 | % Input parameters: 118 | % data = eeg data (sensors by columns). 119 | % emb_dim = embedding dimension 120 | % tau = time lag for embedding 121 | % k = number of neighbours to consider 122 | % w = window correction for neighbour finding 123 | % states_eff_step = state-space down sampling to consider when calculating distances 124 | % Output parameters: 125 | % S, H, M and L = Functional Connectivity matrices for each index. 126 | 127 | emb_dim=3; 128 | tau=2; 129 | k=4; 130 | w=20; 131 | states_eff_step=1; 132 | 133 | tic;[S,H,M,L]=fastfc_gs(x,emb_dim,tau,k,w,states_eff_step);t_gs=toc; 134 | 135 | fprintf(' Function ''fastfc_gs'' is working properly.\n'); 136 | fprintf(' FastFC calculation of Generalized Synchronization indices: S, H, M, and L took: %0.2f seconds.\n\n',t_gs); 137 | 138 | %% Testing Strength 139 | fprintf(' Starting Strength test:\n'); 140 | 141 | A=randn(n_sensors); 142 | A(1:n_sensors+1:end)=0; 143 | 144 | % [S]=fastfc_strength_wu(A) 145 | % 146 | % Input parameters: 147 | % A = adjacency matrix of real values between 0 and 1, with zeroed principal diagonal elements. 148 | % Output parameters: 149 | % C = a row matrix where every value represents the Strength of each node. 150 | 151 | tic;[St]=fastfc_strength_wu(A);t_S=toc; 152 | 153 | fprintf(' Function ''fastfc_strength_wu'' is working properly.'); 154 | fprintf(' FastFC calculation of Strength index took: %0.4f seconds.\n\n',t_S); 155 | 156 | %% Testing Clustering Coefficient 157 | fprintf(' Starting Clustering Coefficient test:\n'); 158 | 159 | A=randn(n_sensors); 160 | A(1:n_sensors+1:end)=0; 161 | 162 | % [C]=fastfc_cluster_coef_wu(A) 163 | % 164 | % Input parameters: 165 | % A = adjacency matrix of nodes by nodes. Values between 0 and 1. Principal diagonal is zero. 166 | % Output parameters: 167 | % C= column matrix where every value represents the Clustering Coefficient of each node. 168 | 169 | tic;[C]=fastfc_cluster_coef_wu(A);t_C=toc; 170 | 171 | fprintf(' Function ''fastfc_cluster_coef_wu'' is working properly.\n'); 172 | fprintf(' FastFC calculation of Clustering Coefficient index took: %0.4f seconds.\n\n',t_C); 173 | 174 | %% Testing Shortest Path Length 175 | fprintf(' Starting Shortest Path Lenght test:\n'); 176 | 177 | A=randn(n_sensors); 178 | A(1:n_sensors+1:end)=0; 179 | W=(A.^-1); 180 | 181 | % [D,L]=fastfc_shortest_path_length_w(W) 182 | % 183 | % Input parameters: 184 | % W = directed or undirected weighted connection length matrix.Typically W is obtained by inverting each element in the Functional Connectivity matrix, transforming therefore between weights to length. 185 | % Output parameters: 186 | % D = distance matrix between nodes (shortest weighted path). 187 | % L = number of edges in each shortest weighted path. 188 | 189 | tic;[Dst,Ln]=fastfc_shortest_path_length_w(W);t_L=toc; 190 | 191 | fprintf(' Function ''fastfc_shortest_path_length_w'' is working properly.\n'); 192 | fprintf(' FastFC calculation of Shortest Path Length index took: %0.4f seconds.\n\n',t_L); 193 | 194 | %% Testing Betweenness Centrality 195 | fprintf(' Starting Betweenness Centrality test:\n'); 196 | 197 | A=randn(n_sensors); 198 | A(1:n_sensors+1:end)=0; 199 | W=(A.^-1); 200 | 201 | % [D,L,BC]=fastfc_betweenness_cent_w(W) 202 | % 203 | % Input parameters: 204 | % W = directed or undirected connection-length matrix. 205 | % Output parameters: 206 | % D = distance matrix between nodes (shortest weighted path). 207 | % L = number of edges in each shortest weighted path. 208 | % BC = node Betweenness Centrality for each node in the network. 209 | 210 | tic;[D,L,B]=fastfc_betweenness_cent_w(W);t_B=toc; 211 | 212 | fprintf(' Function ''fastfc_shortest_path_length_w'' is working properly.\n'); 213 | fprintf(' FastFC calculation of Shortest Path Length index took: %0.4f seconds.\n\n',t_B); 214 | 215 | %% Final 216 | fprintf(' ............ Fast FC is working rock solid. Thanks! ..............\n\n') 217 | fprintf(' This file is part of Fast Functional Connectivity (FastFC) ---> http://juangpc.github.io/FastFC\n'); 218 | fprintf(' Please consider helping by citing our work\n\n\n'); 219 | 220 | -------------------------------------------------------------------------------- /src/generalized_sync/fastfc_gs.c: -------------------------------------------------------------------------------- 1 | // 2 | // Copyright (c) 2014-2015 Juan Garcia-Prieto Cuesta 3 | // 4 | // This file is part of Fast Functional Connectivity (FastFC) 5 | // 6 | // FastFC is free software: you can redistribute it and/or modify 7 | // it under the terms of the GNU General Public License as published by 8 | // the Free Software Foundation, either version 3 of the License, or 9 | // (at your option) any later version. 10 | // 11 | // FastFC is distributed in the hope that it will be useful, 12 | // but WITHOUT ANY WARRANTY; without even the implied warranty of 13 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14 | // GNU General Public License for more details. 15 | // 16 | // You should have received a copy of the GNU General Public License 17 | // along with FastFC. If not, see . 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | #include 32 | 33 | struct neighbor{ 34 | int index; 35 | float dist; 36 | }; 37 | 38 | int comp(const void *a,const void *b) 39 | { 40 | return ((*(struct neighbor *)a).dist<(*(struct neighbor *)b).dist)? 41 | -1: 42 | ((*(struct neighbor *)a).dist>(*(struct neighbor *)b).dist); 43 | } 44 | 45 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 46 | { 47 | 48 | //call 49 | // shml(trial(by columns),emb_d,tau, k , w_emb , states_eff_step, 50 | // (0) (1) (2) (3) (4) (5) 51 | 52 | int state_eff_i,state_i,state_j,tau_i,n_states,n_states_eff,n_indexes, 53 | actual_state,k_in,index_i,sensor_i,sensor_j; 54 | float *mean_d_nn,*mean_d,*adj_s,*adj_h,*adj_m,*adj_l, 55 | dist_diff,dist_sum_1,dist_sum_2,cum_dist_sum_1, 56 | cum_sum_s,cum_sum_h,cum_sum_m,cum_sum_l, 57 | g_i,g_i_g_ik,mean_rank_dist,mean_cond_dist; 58 | double *data,*data_i,*out_s,*out_h,*out_m,*out_l; 59 | struct neighbor *emb_dist,*emb_dist_i,*emb_dist_ord,*emb_dist_ord_i, 60 | *knn,*knn_i,this_neighbor; 61 | 62 | const int n_samples=(int)mxGetM(prhs[0]); 63 | const int n_sensors=(int)mxGetN(prhs[0]); 64 | const int emb_d=(int)mxGetScalar(prhs[1]); 65 | const int tau=(int)mxGetScalar(prhs[2]); 66 | const int k=(int)mxGetScalar(prhs[3]); 67 | const int w_emb=(int)mxGetScalar(prhs[4]); 68 | const int states_eff_step=(int)mxGetScalar(prhs[5]); 69 | const int n_threads=omp_get_num_procs(); 70 | 71 | n_states=n_samples-(tau*(emb_d-1)); 72 | n_states_eff=n_states/states_eff_step; 73 | n_indexes=n_sensors*n_sensors; 74 | g_i=((float)n_states)/2; 75 | g_i_g_ik=g_i-(((float)k+1)/2); 76 | 77 | data=(double*)mxGetPr(prhs[0]); 78 | 79 | emb_dist=(struct neighbor*)mxMalloc(n_states_eff*n_states*n_sensors*sizeof(struct neighbor)); 80 | emb_dist_ord=(struct neighbor*)mxMalloc(n_states_eff*n_states*n_sensors*sizeof(struct neighbor)); 81 | mean_d=(float*)mxMalloc(n_states_eff*n_sensors*sizeof(float)); 82 | mean_d_nn=(float*)mxMalloc(n_states_eff*n_sensors*sizeof(float)); 83 | knn=(struct neighbor*)mxMalloc(n_states_eff*k*n_sensors*sizeof(struct neighbor)); 84 | 85 | omp_set_num_threads(n_threads); 86 | 87 | for(sensor_i=0;sensor_iw_emb) 126 | { 127 | knn_i[k_in+state_eff_i*k].index=this_neighbor.index; 128 | knn_i[k_in+state_eff_i*k].dist=this_neighbor.dist; 129 | dist_sum_2+=this_neighbor.dist; 130 | k_in++; 131 | } 132 | state_i++; 133 | } 134 | mean_d_nn[state_eff_i+sensor_i*n_states_eff]=dist_sum_2/(float)k; 135 | } 136 | } 137 | } 138 | 139 | adj_s=(float*)mxMalloc(n_indexes*sizeof(float)); 140 | adj_h=(float*)mxMalloc(n_indexes*sizeof(float)); 141 | adj_m=(float*)mxMalloc(n_indexes*sizeof(float)); 142 | adj_l=(float*)mxMalloc(n_indexes*sizeof(float)); 143 | 144 | for(sensor_i=0;sensor_i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | #include 30 | #include 31 | #include 32 | #include 33 | 34 | void mexFunction(int nlhs,mxArray *plhs[],int nrhs,const mxArray *prhs[]) 35 | { 36 | int i,s_i,s_j,th_i; 37 | float *b,*x,*adj_plv,*pval_plv,*adj_pli,*adj_wpli,phi,sin_phi,plv_i; 38 | float sum_cos=0; 39 | float sum_sin=0; 40 | float sum_sin_sign=0; 41 | float sum_abs_sin=0; 42 | 43 | double *x_d,*b_d,*out_plv,*out_pli,*out_wpli,*out_pval; 44 | fftwf_complex *fft_b,**h,**a; 45 | fftwf_plan p_r2c_1,p_r2c_2,p_c2r,p_c2c; 46 | 47 | const int n_samples=(int)mxGetM(prhs[0]); 48 | const int n_sensors=(int)mxGetN(prhs[0]); 49 | const int init_sample=(int)mxGetScalar(prhs[1]); 50 | const int l_b=(int)mxGetN(prhs[2]); 51 | const int mode=(int)mxGetScalar(prhs[3]); 52 | const int n_threads=1;//omp_get_num_procs(); 53 | 54 | const int n_indexes=n_sensors*n_sensors; 55 | const int n_samples_eff=n_samples-2*init_sample; 56 | const int l_p=n_samples+2*(l_b-1); 57 | const int is_even=(n_samples%2)?0:1; 58 | const int n_f=n_samples/2+((is_even)?0:1); 59 | const float factor_n_l_p=(float)1./l_p; 60 | const float factor_n_ns=(float)1./n_samples; 61 | const float factor_n_eff=(float)1./n_samples_eff; 62 | 63 | x_d=(double*)mxGetPr(prhs[0]); 64 | b_d=(double*)mxGetPr(prhs[2]); 65 | 66 | b=(float*)fftwf_malloc(l_p*sizeof(float)); 67 | fft_b=(fftwf_complex*)fftwf_malloc(l_p*sizeof(fftwf_complex)); 68 | 69 | x=(float*)mxMalloc(l_p*n_sensors*sizeof(float)); 70 | h=(fftwf_complex**)mxMalloc(n_threads*sizeof(fftwf_complex*)); 71 | a=(fftwf_complex**)mxMalloc(n_threads*sizeof(fftwf_complex*)); 72 | 73 | for(th_i=0;th_i0.0)-(sin_phi<0.0); 212 | sum_abs_sin+=fabsf(sin_phi); 213 | } 214 | sum_cos*=factor_n_eff; 215 | sum_sin*=factor_n_eff; 216 | 217 | plv_i=sqrtf(sum_cos*sum_cos+sum_sin*sum_sin); 218 | adj_pli[s_j+(n_sensors*s_i)]=fabsf(sum_sin_sign/n_samples_eff); 219 | adj_wpli[s_j+(n_sensors*s_i)]=(fabsf(sum_sin)*n_samples_eff)/sum_abs_sin; 220 | adj_plv[s_j+(n_sensors*s_i)]=plv_i; 221 | pval_plv[s_j+(n_sensors*s_i)]=expf( 222 | sqrtf((float)(1+4*n_samples_eff)+ 223 | (float)4.0*n_samples_eff*n_samples_eff*((float)1.0-plv_i*plv_i)) 224 | -(1+2*n_samples_eff)); 225 | 226 | adj_plv[s_i+(n_sensors*s_j)]=plv_i; 227 | adj_pli[s_i+(n_sensors*s_j)]=adj_pli[s_j+(n_sensors*s_i)]; 228 | adj_wpli[s_i+(n_sensors*s_j)]=adj_wpli[s_j+(n_sensors*s_i)]; 229 | pval_plv[s_i+(n_sensors*s_j)]=pval_plv[s_j+(n_sensors*s_i)]; 230 | 231 | } 232 | } 233 | } 234 | 235 | mxFree(x); 236 | 237 | plhs[0]=mxCreateDoubleMatrix(n_sensors,n_sensors,mxREAL); 238 | plhs[1]=mxCreateDoubleMatrix(n_sensors,n_sensors,mxREAL); 239 | plhs[2]=mxCreateDoubleMatrix(n_sensors,n_sensors,mxREAL); 240 | plhs[3]=mxCreateDoubleMatrix(n_sensors,n_sensors,mxREAL); 241 | 242 | 243 | #pragma omp parallel sections private(i) 244 | { 245 | #pragma omp section 246 | { 247 | out_plv=(double*)mxGetPr(plhs[0]); 248 | for(i=0;i. 18 | // 19 | // ------------------------------------------------------- 20 | // Please consider citing our work: 21 | // 22 | // Efficient computation of functional brain networks: towards real-time functional connectivity 23 | // Frontiers in Neuroinformatics (2017) García-Prieto Juan, Bajo Ricardo, Pereda Ernesto 24 | // 25 | // ------------------------------------------------------- 26 | // Contact: Juan Garcia-Prieto juangpc (at) gmail.com 27 | // ------------------------------------------------------- 28 | // 29 | 30 | /* Copyright 2009 Alexander Kraskov, Harald Stoegbauer, Peter Grassberger 31 | //----------------------------------------------------------------------------------------- 32 | // This program is free software: you can redistribute it and/or modify 33 | // it under the terms of the GNU General Public License as published by 34 | // the Free Software Foundation, either version 3 of the License, or 35 | // (at your option) any later version. 36 | // 37 | // This program is distributed in the hope that it will be useful, 38 | // but WITHOUT ANY WARRANTY; without even the implied warranty of 39 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 40 | // GNU General Public License for more details. 41 | // 42 | // You should receive a copy of the GNU General Public License 43 | // along with this program. See also . 44 | //----------------------------------------------------------------------------------------- 45 | // Contacts: 46 | // 47 | // Harald Stoegbauer 48 | // Alexander Kraskov 49 | //----------------------------------------------------------------------------------------- 50 | // Please reference 51 | // 52 | // A. Kraskov, H. Stogbauer, and P. Grassberger, 53 | // Estimating mutual information. 54 | // Phys. Rev. E 69 (6) 066138, 2004 55 | // 56 | // in your published research. 57 | */ 58 | 59 | void make_box1(double *x, int N, double scal, int bs, 60 | int *box, int *lis, int *mxi); 61 | /* make one-dimensional box 62 | input 63 | x - input sequence 64 | N - length of the input sequence 65 | scal - renormalization factor, scal=#boxes/(max(x)-min(x)) 66 | bs - #boxes 67 | output 68 | box - each element of the array is ordinary number of the last point in the box 69 | lis - each element of the array is ordinary number of the previous points in the box or -1 70 | mxi - accumulative number of the points in the box 71 | */ 72 | void make_box2(double **x, int dim, int N, int comp1, int comp2, int bs, int inveps, 73 | int **box, int *lis); 74 | /* uses comp1 and comp2 component for two-dimensional grid */ 75 | /* make two-dimensional box !!! changing the order of the points 76 | input 77 | x - two-dimensional input sequence 78 | dim - dimension of x 79 | N - length of the input sequence 80 | comp1 - first component for two dimensional grid 81 | comp2 - second component for two dimensional grid 82 | bs - #boxes 83 | inveps - box size 84 | output 85 | box - each element of the array is ordinary number of the last point in the box 86 | lis - each element of the array is ordinary number of the previous points in the box or -1 87 | */ 88 | void make_box2ind(double **x, int dim, int N, int comp1, int comp2, int bs, int inveps, 89 | int *ind, int **box, int *lis); 90 | /* make two-dimensional box !!! changing the order of the points, but saving the order in ind 91 | input 92 | x - dim-dimensional input sequence 93 | dim - dimension of input sequence 94 | N - length of the input sequence 95 | comp1 - first component for creating grid 96 | comp2 - first component for creating grid 97 | bs - #boxes 98 | inveps - box size 99 | output 100 | ind - index of original data 101 | box - each element of the array is ordinary number of the last point in the box 102 | lis - each element of the array is ordinary number of the previous points in the box or -1 103 | */ 104 | int neiE1(double *x, int i, double scal, int bs, double eps, int *box, int *lis, int *mxi); 105 | /* searching for neighbors of point i in eps-neighborhood in one dimension 106 | input 107 | x - one-dimensional input sequence 108 | i - current point 109 | scal - renormalization factor, scal=#boxes/(max(x)-min(x)) 110 | bs - #boxes 111 | eps - neighborhood 112 | box - each element of the array is ordinary number of the last point in the box 113 | lis - each element of the array is ordinary number of the previous points in the box or -1 114 | mxi - accumulative number of the points in the box 115 | output 116 | number of neighbors 117 | */ 118 | int neiE(double **x, int i, int comp1, int comp2, int dim, int bs, double epsgrid, double eps, int **box, int *lis); 119 | /* searching for neighbors of point i in eps-neighborhood in dim dimension 120 | input 121 | x - dim-dimensional input sequence 122 | i - current point 123 | dim -dimension on input sequence 124 | comp1 - 125 | comp2 - 126 | bs - #boxes 127 | epsgrid - size of the grid 128 | eps - neighborhood 129 | box - each element of the array is ordinary number of the last point in the box 130 | lis - each element of the array is ordinary number of the previous points in the box or -1 131 | output 132 | number of neighbors 133 | */ 134 | void neiEK(double **x, int i, int comp1, int comp2, int dim, int K, 135 | int bs, double epsgrid, double *eps, int **box, int *lis, 136 | int *nx); 137 | /* searching for neighbors of point i in eps-neighborhood in dim dimension for K 138 | input 139 | x - dim-dimensional input sequence 140 | i - current point 141 | dim -dimension on input sequence 142 | K - max number of neighbors 143 | comp1 - 144 | comp2 - 145 | bs - #boxes 146 | epsgrid - size of the grid 147 | eps - neighborhood 148 | box - each element of the array is ordinary number of the last point in the box 149 | lis - each element of the array is ordinary number of the previous points in the box or -1 150 | output 151 | nx - number of neighbors 152 | */ 153 | 154 | 155 | void neiK(double **x, int dim, int comp1, int comp2, int i, 156 | int bs, double epsgrid, int K, int **box, int *lis, 157 | int *nn); 158 | /* searching for K neighbors of point i in dim dimension 159 | input 160 | x - dim-dimensional input sequence 161 | dim - dimension of x 162 | comp1 - first component for two dimensional grid 163 | comp2 - second component for two dimensional grid 164 | i - current point 165 | bs - #boxes 166 | epsgrid - size of the grid 167 | box - each element of the array is ordinary number of the last point in the box 168 | lis - each element of the array is ordinary number of the previous points in the box or -1 169 | output 170 | nn - indices of K neighbors 171 | */ 172 | 173 | //void neiK(double **x, int i, int bs, double epsgrid, int K, int **box, int *lis, 174 | // int *nn); 175 | /* searching for K neighbours of point i in two dimension 176 | input 177 | x - 2-dimensional input sequence 178 | i - current point 179 | bs - #boxes 180 | epsgrid - size of the grid 181 | box - each element of the array is ordinary number of the last point in the box 182 | lis - each element of the array is ordinary number of the previous points in the box or -1 183 | output 184 | nn - indices of K neighbors 185 | */ 186 | void mi2(double **x, int N, int K, 187 | double *psi, 188 | double *scal, 189 | double *mic, double *mir); 190 | void mi2c(double **x, int N, int K, 191 | double *psi, 192 | double *scal, 193 | double *mic); 194 | void mi2r(double **x, int N, int K, 195 | double *psi, 196 | double *scal, 197 | double *mir); 198 | void mi2r_(double **x, int N, int K, 199 | double *psi, 200 | double *scal, 201 | double *mir); 202 | 203 | void red(double **x, int dim, int N, int K, 204 | double *psi, 205 | double *scal, 206 | double *mic, double *mir); 207 | void redc(double **x, int dim, int N, int K, 208 | double *psi, 209 | double *scal, 210 | double *mic); 211 | void redr(double **x, int dim, int N, int K, 212 | double *psi, 213 | double *scal, 214 | double *mir); 215 | void redr_embed(double **x, int dim, int edim, int tau, int N, int K, 216 | double *psi, 217 | double *mir); 218 | void mi_xnyn(double **x, int dimx, int dimy, int N, int K, 219 | double *psi, 220 | double *scal, 221 | double *mic, double *mir); 222 | /* 223 | calculating of mutual information between vectors, only for one K 224 | 225 | input 226 | x - (dimx+dimy)-dimensional input 227 | dimx - dimension of vector x 228 | dimy - dimension of vector y 229 | N - length of vectors 230 | K - max number of neighbors 231 | psi - digamma function 232 | scal - scale for one dimensional box (BOX1/(max-min)) 233 | output 234 | mic - cubic method 235 | mir - rectange method 236 | */ 237 | void mic_xnyn(double **x, int dimx, int dimy, int N, int K, 238 | double *psi, 239 | double *scal, 240 | double *mic); 241 | void mir_xnyn(double **x, int dimx, int dimy, int N, int K, 242 | double *psi, 243 | double *scal, 244 | double *mir); 245 | 246 | 247 | 248 | void redK(double **x, int dim, int N, int K, 249 | double *psi, 250 | double *scal, 251 | double *mi_cr); 252 | /* 253 | calculating of redundancy 254 | 255 | input 256 | x - dim-dimensional input 257 | dim - dimension 258 | N - length of vectors 259 | K - max number of neighbors 260 | psi - digamma function 261 | scal - scale for one dimensional box (BOX1/(max-min)) 262 | output 263 | mi_cr - MI using cubic and rectangle method for different K 264 | array contains the values of mutual information [cub_k1,rec_k1,cub_k2,rec_k2,...,cub_kK,rec_kK] 265 | */ 266 | 267 | void mi2K(double **x, int N, int K, 268 | double *psi, 269 | double *scal, 270 | double *mi_cr); 271 | /* 272 | calculating of mutual information 273 | 274 | input 275 | x - two-dimensional input 276 | N - length of vectors 277 | K - max number of neighbors 278 | psi - digamma function 279 | scal - scale for one dimensional box (BOX1/(max-min)) 280 | output 281 | mi_cr - MI using cubic and rectangle method for different K 282 | array contains the values of mutual information [cub_k1,rec_k1,cub_k2,rec_k2,...,cub_kK,rec_kK] 283 | */ 284 | 285 | void mi_xnynK(double **x, int dimx, int dimy, int N, int K, 286 | double *psi, 287 | double *scal, 288 | double *mi_cr); 289 | void mi_xnynKembed(double **x, int dim, int N, int K, 290 | double **xx, double **yy, 291 | int **boxx, int *lisx, int *indx, 292 | int **boxy, int *lisy, int *indy, 293 | double *psi, 294 | double *mi_cr); 295 | 296 | 297 | void mi2h(double **x, int N, int K, 298 | double *psi, 299 | double *scal, 300 | double *mic, double *mir, double *hc, double *hr); 301 | 302 | 303 | void mi_embed(double **x, int dim, int N, int K, float *mi_cr, 304 | double *psi, double *phi, double minx, double maxx, double miny, double maxy); 305 | 306 | 307 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 2, June 1991 3 | 4 | Copyright (C) 1989, 1991 Free Software Foundation, Inc., 5 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 6 | Everyone is permitted to copy and distribute verbatim copies 7 | of this license document, but changing it is not allowed. 8 | 9 | Preamble 10 | 11 | The licenses for most software are designed to take away your 12 | freedom to share and change it. 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Our General Public Licenses are designed to make sure that you 23 | have the freedom to distribute copies of free software (and charge for 24 | this service if you wish), that you receive source code or can get it 25 | if you want it, that you can change the software or use pieces of it 26 | in new free programs; and that you know you can do these things. 27 | 28 | To protect your rights, we need to make restrictions that forbid 29 | anyone to deny you these rights or to ask you to surrender the rights. 30 | These restrictions translate to certain responsibilities for you if you 31 | distribute copies of the software, or if you modify it. 32 | 33 | For example, if you distribute copies of such a program, whether 34 | gratis or for a fee, you must give the recipients all the rights that 35 | you have. You must make sure that they, too, receive or can get the 36 | source code. And you must show them these terms so they know their 37 | rights. 38 | 39 | We protect your rights with two steps: (1) copyright the software, and 40 | (2) offer you this license which gives you legal permission to copy, 41 | distribute and/or modify the software. 42 | 43 | Also, for each author's protection and ours, we want to make certain 44 | that everyone understands that there is no warranty for this free 45 | software. If the software is modified by someone else and passed on, we 46 | want its recipients to know that what they have is not the original, so 47 | that any problems introduced by others will not reflect on the original 48 | authors' reputations. 49 | 50 | Finally, any free program is threatened constantly by software 51 | patents. We wish to avoid the danger that redistributors of a free 52 | program will individually obtain patent licenses, in effect making the 53 | program proprietary. To prevent this, we have made it clear that any 54 | patent must be licensed for everyone's free use or not licensed at all. 55 | 56 | The precise terms and conditions for copying, distribution and 57 | modification follow. 58 | 59 | GNU GENERAL PUBLIC LICENSE 60 | TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 61 | 62 | 0. This License applies to any program or other work which contains 63 | a notice placed by the copyright holder saying it may be distributed 64 | under the terms of this General Public License. The "Program", below, 65 | refers to any such program or work, and a "work based on the Program" 66 | means either the Program or any derivative work under copyright law: 67 | that is to say, a work containing the Program or a portion of it, 68 | either verbatim or with modifications and/or translated into another 69 | language. (Hereinafter, translation is included without limitation in 70 | the term "modification".) Each licensee is addressed as "you". 71 | 72 | Activities other than copying, distribution and modification are not 73 | covered by this License; they are outside its scope. The act of 74 | running the Program is not restricted, and the output from the Program 75 | is covered only if its contents constitute a work based on the 76 | Program (independent of having been made by running the Program). 77 | Whether that is true depends on what the Program does. 78 | 79 | 1. You may copy and distribute verbatim copies of the Program's 80 | source code as you receive it, in any medium, provided that you 81 | conspicuously and appropriately publish on each copy an appropriate 82 | copyright notice and disclaimer of warranty; keep intact all the 83 | notices that refer to this License and to the absence of any warranty; 84 | and give any other recipients of the Program a copy of this License 85 | along with the Program. 86 | 87 | You may charge a fee for the physical act of transferring a copy, and 88 | you may at your option offer warranty protection in exchange for a fee. 89 | 90 | 2. You may modify your copy or copies of the Program or any portion 91 | of it, thus forming a work based on the Program, and copy and 92 | distribute such modifications or work under the terms of Section 1 93 | above, provided that you also meet all of these conditions: 94 | 95 | a) You must cause the modified files to carry prominent notices 96 | stating that you changed the files and the date of any change. 97 | 98 | b) You must cause any work that you distribute or publish, that in 99 | whole or in part contains or is derived from the Program or any 100 | part thereof, to be licensed as a whole at no charge to all third 101 | parties under the terms of this License. 102 | 103 | c) If the modified program normally reads commands interactively 104 | when run, you must cause it, when started running for such 105 | interactive use in the most ordinary way, to print or display an 106 | announcement including an appropriate copyright notice and a 107 | notice that there is no warranty (or else, saying that you provide 108 | a warranty) and that users may redistribute the program under 109 | these conditions, and telling the user how to view a copy of this 110 | License. (Exception: if the Program itself is interactive but 111 | does not normally print such an announcement, your work based on 112 | the Program is not required to print an announcement.) 113 | 114 | These requirements apply to the modified work as a whole. If 115 | identifiable sections of that work are not derived from the Program, 116 | and can be reasonably considered independent and separate works in 117 | themselves, then this License, and its terms, do not apply to those 118 | sections when you distribute them as separate works. But when you 119 | distribute the same sections as part of a whole which is a work based 120 | on the Program, the distribution of the whole must be on the terms of 121 | this License, whose permissions for other licensees extend to the 122 | entire whole, and thus to each and every part regardless of who wrote it. 123 | 124 | Thus, it is not the intent of this section to claim rights or contest 125 | your rights to work written entirely by you; rather, the intent is to 126 | exercise the right to control the distribution of derivative or 127 | collective works based on the Program. 128 | 129 | In addition, mere aggregation of another work not based on the Program 130 | with the Program (or with a work based on the Program) on a volume of 131 | a storage or distribution medium does not bring the other work under 132 | the scope of this License. 133 | 134 | 3. You may copy and distribute the Program (or a work based on it, 135 | under Section 2) in object code or executable form under the terms of 136 | Sections 1 and 2 above provided that you also do one of the following: 137 | 138 | a) Accompany it with the complete corresponding machine-readable 139 | source code, which must be distributed under the terms of Sections 140 | 1 and 2 above on a medium customarily used for software interchange; or, 141 | 142 | b) Accompany it with a written offer, valid for at least three 143 | years, to give any third party, for a charge no more than your 144 | cost of physically performing source distribution, a complete 145 | machine-readable copy of the corresponding source code, to be 146 | distributed under the terms of Sections 1 and 2 above on a medium 147 | customarily used for software interchange; or, 148 | 149 | c) Accompany it with the information you received as to the offer 150 | to distribute corresponding source code. (This alternative is 151 | allowed only for noncommercial distribution and only if you 152 | received the program in object code or executable form with such 153 | an offer, in accord with Subsection b above.) 154 | 155 | The source code for a work means the preferred form of the work for 156 | making modifications to it. For an executable work, complete source 157 | code means all the source code for all modules it contains, plus any 158 | associated interface definition files, plus the scripts used to 159 | control compilation and installation of the executable. However, as a 160 | special exception, the source code distributed need not include 161 | anything that is normally distributed (in either source or binary 162 | form) with the major components (compiler, kernel, and so on) of the 163 | operating system on which the executable runs, unless that component 164 | itself accompanies the executable. 165 | 166 | If distribution of executable or object code is made by offering 167 | access to copy from a designated place, then offering equivalent 168 | access to copy the source code from the same place counts as 169 | distribution of the source code, even though third parties are not 170 | compelled to copy the source along with the object code. 171 | 172 | 4. You may not copy, modify, sublicense, or distribute the Program 173 | except as expressly provided under this License. Any attempt 174 | otherwise to copy, modify, sublicense or distribute the Program is 175 | void, and will automatically terminate your rights under this License. 176 | However, parties who have received copies, or rights, from you under 177 | this License will not have their licenses terminated so long as such 178 | parties remain in full compliance. 179 | 180 | 5. You are not required to accept this License, since you have not 181 | signed it. However, nothing else grants you permission to modify or 182 | distribute the Program or its derivative works. These actions are 183 | prohibited by law if you do not accept this License. Therefore, by 184 | modifying or distributing the Program (or any work based on the 185 | Program), you indicate your acceptance of this License to do so, and 186 | all its terms and conditions for copying, distributing or modifying 187 | the Program or works based on it. 188 | 189 | 6. Each time you redistribute the Program (or any work based on the 190 | Program), the recipient automatically receives a license from the 191 | original licensor to copy, distribute or modify the Program subject to 192 | these terms and conditions. You may not impose any further 193 | restrictions on the recipients' exercise of the rights granted herein. 194 | You are not responsible for enforcing compliance by third parties to 195 | this License. 196 | 197 | 7. If, as a consequence of a court judgment or allegation of patent 198 | infringement or for any other reason (not limited to patent issues), 199 | conditions are imposed on you (whether by court order, agreement or 200 | otherwise) that contradict the conditions of this License, they do not 201 | excuse you from the conditions of this License. If you cannot 202 | distribute so as to satisfy simultaneously your obligations under this 203 | License and any other pertinent obligations, then as a consequence you 204 | may not distribute the Program at all. For example, if a patent 205 | license would not permit royalty-free redistribution of the Program by 206 | all those who receive copies directly or indirectly through you, then 207 | the only way you could satisfy both it and this License would be to 208 | refrain entirely from distribution of the Program. 209 | 210 | If any portion of this section is held invalid or unenforceable under 211 | any particular circumstance, the balance of the section is intended to 212 | apply and the section as a whole is intended to apply in other 213 | circumstances. 214 | 215 | It is not the purpose of this section to induce you to infringe any 216 | patents or other property right claims or to contest validity of any 217 | such claims; this section has the sole purpose of protecting the 218 | integrity of the free software distribution system, which is 219 | implemented by public license practices. Many people have made 220 | generous contributions to the wide range of software distributed 221 | through that system in reliance on consistent application of that 222 | system; it is up to the author/donor to decide if he or she is willing 223 | to distribute software through any other system and a licensee cannot 224 | impose that choice. 225 | 226 | This section is intended to make thoroughly clear what is believed to 227 | be a consequence of the rest of this License. 228 | 229 | 8. If the distribution and/or use of the Program is restricted in 230 | certain countries either by patents or by copyrighted interfaces, the 231 | original copyright holder who places the Program under this License 232 | may add an explicit geographical distribution limitation excluding 233 | those countries, so that distribution is permitted only in or among 234 | countries not thus excluded. In such case, this License incorporates 235 | the limitation as if written in the body of this License. 236 | 237 | 9. The Free Software Foundation may publish revised and/or new versions 238 | of the General Public License from time to time. Such new versions will 239 | be similar in spirit to the present version, but may differ in detail to 240 | address new problems or concerns. 241 | 242 | Each version is given a distinguishing version number. If the Program 243 | specifies a version number of this License which applies to it and "any 244 | later version", you have the option of following the terms and conditions 245 | either of that version or of any later version published by the Free 246 | Software Foundation. If the Program does not specify a version number of 247 | this License, you may choose any version ever published by the Free Software 248 | Foundation. 249 | 250 | 10. If you wish to incorporate parts of the Program into other free 251 | programs whose distribution conditions are different, write to the author 252 | to ask for permission. For software which is copyrighted by the Free 253 | Software Foundation, write to the Free Software Foundation; we sometimes 254 | make exceptions for this. Our decision will be guided by the two goals 255 | of preserving the free status of all derivatives of our free software and 256 | of promoting the sharing and reuse of software generally. 257 | 258 | NO WARRANTY 259 | 260 | 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY 261 | FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN 262 | OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES 263 | PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED 264 | OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 265 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS 266 | TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE 267 | PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, 268 | REPAIR OR CORRECTION. 269 | 270 | 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 271 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR 272 | REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, 273 | INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 274 | OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED 275 | TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY 276 | YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER 277 | PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE 278 | POSSIBILITY OF SUCH DAMAGES. 279 | 280 | END OF TERMS AND CONDITIONS 281 | 282 | How to Apply These Terms to Your New Programs 283 | 284 | If you develop a new program, and you want it to be of the greatest 285 | possible use to the public, the best way to achieve this is to make it 286 | free software which everyone can redistribute and change under these terms. 287 | 288 | To do so, attach the following notices to the program. It is safest 289 | to attach them to the start of each source file to most effectively 290 | convey the exclusion of warranty; and each file should have at least 291 | the "copyright" line and a pointer to where the full notice is found. 292 | 293 | {description} 294 | Copyright (C) {year} {fullname} 295 | 296 | This program is free software; you can redistribute it and/or modify 297 | it under the terms of the GNU General Public License as published by 298 | the Free Software Foundation; either version 2 of the License, or 299 | (at your option) any later version. 300 | 301 | This program is distributed in the hope that it will be useful, 302 | but WITHOUT ANY WARRANTY; without even the implied warranty of 303 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 304 | GNU General Public License for more details. 305 | 306 | You should have received a copy of the GNU General Public License along 307 | with this program; if not, write to the Free Software Foundation, Inc., 308 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 309 | 310 | Also add information on how to contact you by electronic and paper mail. 311 | 312 | If the program is interactive, make it output a short notice like this 313 | when it starts in an interactive mode: 314 | 315 | Gnomovision version 69, Copyright (C) year name of author 316 | Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 317 | This is free software, and you are welcome to redistribute it 318 | under certain conditions; type `show c' for details. 319 | 320 | The hypothetical commands `show w' and `show c' should show the appropriate 321 | parts of the General Public License. Of course, the commands you use may 322 | be called something other than `show w' and `show c'; they could even be 323 | mouse-clicks or menu items--whatever suits your program. 324 | 325 | You should also get your employer (if you work as a programmer) or your 326 | school, if any, to sign a "copyright disclaimer" for the program, if 327 | necessary. Here is a sample; alter the names: 328 | 329 | Yoyodyne, Inc., hereby disclaims all copyright interest in the program 330 | `Gnomovision' (which makes passes at compilers) written by James Hacker. 331 | 332 | {signature of Ty Coon}, 1 April 1989 333 | Ty Coon, President of Vice 334 | 335 | This General Public License does not permit incorporating your program into 336 | proprietary programs. If your program is a subroutine library, you may 337 | consider it more useful to permit linking proprietary applications with the 338 | library. If this is what you want to do, use the GNU Lesser General 339 | Public License instead of this License. 340 | 341 | -------------------------------------------------------------------------------- /src/filter/LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 2, June 1991 3 | 4 | Copyright (C) 1989, 1991 Free Software Foundation, Inc., 5 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 6 | Everyone is permitted to copy and distribute verbatim copies 7 | of this license document, but changing it is not allowed. 8 | 9 | Preamble 10 | 11 | The licenses for most software are designed to take away your 12 | freedom to share and change it. By contrast, the GNU General Public 13 | License is intended to guarantee your freedom to share and change free 14 | software--to make sure the software is free for all its users. This 15 | General Public License applies to most of the Free Software 16 | Foundation's software and to any other program whose authors commit to 17 | using it. (Some other Free Software Foundation software is covered by 18 | the GNU Lesser General Public License instead.) You can apply it to 19 | your programs, too. 20 | 21 | When we speak of free software, we are referring to freedom, not 22 | price. Our General Public Licenses are designed to make sure that you 23 | have the freedom to distribute copies of free software (and charge for 24 | this service if you wish), that you receive source code or can get it 25 | if you want it, that you can change the software or use pieces of it 26 | in new free programs; and that you know you can do these things. 27 | 28 | To protect your rights, we need to make restrictions that forbid 29 | anyone to deny you these rights or to ask you to surrender the rights. 30 | These restrictions translate to certain responsibilities for you if you 31 | distribute copies of the software, or if you modify it. 32 | 33 | For example, if you distribute copies of such a program, whether 34 | gratis or for a fee, you must give the recipients all the rights that 35 | you have. You must make sure that they, too, receive or can get the 36 | source code. And you must show them these terms so they know their 37 | rights. 38 | 39 | We protect your rights with two steps: (1) copyright the software, and 40 | (2) offer you this license which gives you legal permission to copy, 41 | distribute and/or modify the software. 42 | 43 | Also, for each author's protection and ours, we want to make certain 44 | that everyone understands that there is no warranty for this free 45 | software. If the software is modified by someone else and passed on, we 46 | want its recipients to know that what they have is not the original, so 47 | that any problems introduced by others will not reflect on the original 48 | authors' reputations. 49 | 50 | Finally, any free program is threatened constantly by software 51 | patents. We wish to avoid the danger that redistributors of a free 52 | program will individually obtain patent licenses, in effect making the 53 | program proprietary. To prevent this, we have made it clear that any 54 | patent must be licensed for everyone's free use or not licensed at all. 55 | 56 | The precise terms and conditions for copying, distribution and 57 | modification follow. 58 | 59 | GNU GENERAL PUBLIC LICENSE 60 | TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 61 | 62 | 0. This License applies to any program or other work which contains 63 | a notice placed by the copyright holder saying it may be distributed 64 | under the terms of this General Public License. The "Program", below, 65 | refers to any such program or work, and a "work based on the Program" 66 | means either the Program or any derivative work under copyright law: 67 | that is to say, a work containing the Program or a portion of it, 68 | either verbatim or with modifications and/or translated into another 69 | language. (Hereinafter, translation is included without limitation in 70 | the term "modification".) Each licensee is addressed as "you". 71 | 72 | Activities other than copying, distribution and modification are not 73 | covered by this License; they are outside its scope. The act of 74 | running the Program is not restricted, and the output from the Program 75 | is covered only if its contents constitute a work based on the 76 | Program (independent of having been made by running the Program). 77 | Whether that is true depends on what the Program does. 78 | 79 | 1. You may copy and distribute verbatim copies of the Program's 80 | source code as you receive it, in any medium, provided that you 81 | conspicuously and appropriately publish on each copy an appropriate 82 | copyright notice and disclaimer of warranty; keep intact all the 83 | notices that refer to this License and to the absence of any warranty; 84 | and give any other recipients of the Program a copy of this License 85 | along with the Program. 86 | 87 | You may charge a fee for the physical act of transferring a copy, and 88 | you may at your option offer warranty protection in exchange for a fee. 89 | 90 | 2. You may modify your copy or copies of the Program or any portion 91 | of it, thus forming a work based on the Program, and copy and 92 | distribute such modifications or work under the terms of Section 1 93 | above, provided that you also meet all of these conditions: 94 | 95 | a) You must cause the modified files to carry prominent notices 96 | stating that you changed the files and the date of any change. 97 | 98 | b) You must cause any work that you distribute or publish, that in 99 | whole or in part contains or is derived from the Program or any 100 | part thereof, to be licensed as a whole at no charge to all third 101 | parties under the terms of this License. 102 | 103 | c) If the modified program normally reads commands interactively 104 | when run, you must cause it, when started running for such 105 | interactive use in the most ordinary way, to print or display an 106 | announcement including an appropriate copyright notice and a 107 | notice that there is no warranty (or else, saying that you provide 108 | a warranty) and that users may redistribute the program under 109 | these conditions, and telling the user how to view a copy of this 110 | License. (Exception: if the Program itself is interactive but 111 | does not normally print such an announcement, your work based on 112 | the Program is not required to print an announcement.) 113 | 114 | These requirements apply to the modified work as a whole. If 115 | identifiable sections of that work are not derived from the Program, 116 | and can be reasonably considered independent and separate works in 117 | themselves, then this License, and its terms, do not apply to those 118 | sections when you distribute them as separate works. But when you 119 | distribute the same sections as part of a whole which is a work based 120 | on the Program, the distribution of the whole must be on the terms of 121 | this License, whose permissions for other licensees extend to the 122 | entire whole, and thus to each and every part regardless of who wrote it. 123 | 124 | Thus, it is not the intent of this section to claim rights or contest 125 | your rights to work written entirely by you; rather, the intent is to 126 | exercise the right to control the distribution of derivative or 127 | collective works based on the Program. 128 | 129 | In addition, mere aggregation of another work not based on the Program 130 | with the Program (or with a work based on the Program) on a volume of 131 | a storage or distribution medium does not bring the other work under 132 | the scope of this License. 133 | 134 | 3. You may copy and distribute the Program (or a work based on it, 135 | under Section 2) in object code or executable form under the terms of 136 | Sections 1 and 2 above provided that you also do one of the following: 137 | 138 | a) Accompany it with the complete corresponding machine-readable 139 | source code, which must be distributed under the terms of Sections 140 | 1 and 2 above on a medium customarily used for software interchange; or, 141 | 142 | b) Accompany it with a written offer, valid for at least three 143 | years, to give any third party, for a charge no more than your 144 | cost of physically performing source distribution, a complete 145 | machine-readable copy of the corresponding source code, to be 146 | distributed under the terms of Sections 1 and 2 above on a medium 147 | customarily used for software interchange; or, 148 | 149 | c) Accompany it with the information you received as to the offer 150 | to distribute corresponding source code. (This alternative is 151 | allowed only for noncommercial distribution and only if you 152 | received the program in object code or executable form with such 153 | an offer, in accord with Subsection b above.) 154 | 155 | The source code for a work means the preferred form of the work for 156 | making modifications to it. For an executable work, complete source 157 | code means all the source code for all modules it contains, plus any 158 | associated interface definition files, plus the scripts used to 159 | control compilation and installation of the executable. However, as a 160 | special exception, the source code distributed need not include 161 | anything that is normally distributed (in either source or binary 162 | form) with the major components (compiler, kernel, and so on) of the 163 | operating system on which the executable runs, unless that component 164 | itself accompanies the executable. 165 | 166 | If distribution of executable or object code is made by offering 167 | access to copy from a designated place, then offering equivalent 168 | access to copy the source code from the same place counts as 169 | distribution of the source code, even though third parties are not 170 | compelled to copy the source along with the object code. 171 | 172 | 4. You may not copy, modify, sublicense, or distribute the Program 173 | except as expressly provided under this License. Any attempt 174 | otherwise to copy, modify, sublicense or distribute the Program is 175 | void, and will automatically terminate your rights under this License. 176 | However, parties who have received copies, or rights, from you under 177 | this License will not have their licenses terminated so long as such 178 | parties remain in full compliance. 179 | 180 | 5. You are not required to accept this License, since you have not 181 | signed it. However, nothing else grants you permission to modify or 182 | distribute the Program or its derivative works. These actions are 183 | prohibited by law if you do not accept this License. Therefore, by 184 | modifying or distributing the Program (or any work based on the 185 | Program), you indicate your acceptance of this License to do so, and 186 | all its terms and conditions for copying, distributing or modifying 187 | the Program or works based on it. 188 | 189 | 6. Each time you redistribute the Program (or any work based on the 190 | Program), the recipient automatically receives a license from the 191 | original licensor to copy, distribute or modify the Program subject to 192 | these terms and conditions. You may not impose any further 193 | restrictions on the recipients' exercise of the rights granted herein. 194 | You are not responsible for enforcing compliance by third parties to 195 | this License. 196 | 197 | 7. If, as a consequence of a court judgment or allegation of patent 198 | infringement or for any other reason (not limited to patent issues), 199 | conditions are imposed on you (whether by court order, agreement or 200 | otherwise) that contradict the conditions of this License, they do not 201 | excuse you from the conditions of this License. If you cannot 202 | distribute so as to satisfy simultaneously your obligations under this 203 | License and any other pertinent obligations, then as a consequence you 204 | may not distribute the Program at all. For example, if a patent 205 | license would not permit royalty-free redistribution of the Program by 206 | all those who receive copies directly or indirectly through you, then 207 | the only way you could satisfy both it and this License would be to 208 | refrain entirely from distribution of the Program. 209 | 210 | If any portion of this section is held invalid or unenforceable under 211 | any particular circumstance, the balance of the section is intended to 212 | apply and the section as a whole is intended to apply in other 213 | circumstances. 214 | 215 | It is not the purpose of this section to induce you to infringe any 216 | patents or other property right claims or to contest validity of any 217 | such claims; this section has the sole purpose of protecting the 218 | integrity of the free software distribution system, which is 219 | implemented by public license practices. Many people have made 220 | generous contributions to the wide range of software distributed 221 | through that system in reliance on consistent application of that 222 | system; it is up to the author/donor to decide if he or she is willing 223 | to distribute software through any other system and a licensee cannot 224 | impose that choice. 225 | 226 | This section is intended to make thoroughly clear what is believed to 227 | be a consequence of the rest of this License. 228 | 229 | 8. If the distribution and/or use of the Program is restricted in 230 | certain countries either by patents or by copyrighted interfaces, the 231 | original copyright holder who places the Program under this License 232 | may add an explicit geographical distribution limitation excluding 233 | those countries, so that distribution is permitted only in or among 234 | countries not thus excluded. In such case, this License incorporates 235 | the limitation as if written in the body of this License. 236 | 237 | 9. The Free Software Foundation may publish revised and/or new versions 238 | of the General Public License from time to time. Such new versions will 239 | be similar in spirit to the present version, but may differ in detail to 240 | address new problems or concerns. 241 | 242 | Each version is given a distinguishing version number. If the Program 243 | specifies a version number of this License which applies to it and "any 244 | later version", you have the option of following the terms and conditions 245 | either of that version or of any later version published by the Free 246 | Software Foundation. If the Program does not specify a version number of 247 | this License, you may choose any version ever published by the Free Software 248 | Foundation. 249 | 250 | 10. If you wish to incorporate parts of the Program into other free 251 | programs whose distribution conditions are different, write to the author 252 | to ask for permission. For software which is copyrighted by the Free 253 | Software Foundation, write to the Free Software Foundation; we sometimes 254 | make exceptions for this. Our decision will be guided by the two goals 255 | of preserving the free status of all derivatives of our free software and 256 | of promoting the sharing and reuse of software generally. 257 | 258 | NO WARRANTY 259 | 260 | 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY 261 | FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN 262 | OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES 263 | PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED 264 | OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 265 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS 266 | TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE 267 | PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, 268 | REPAIR OR CORRECTION. 269 | 270 | 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 271 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR 272 | REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, 273 | INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 274 | OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED 275 | TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY 276 | YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER 277 | PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE 278 | POSSIBILITY OF SUCH DAMAGES. 279 | 280 | END OF TERMS AND CONDITIONS 281 | 282 | How to Apply These Terms to Your New Programs 283 | 284 | If you develop a new program, and you want it to be of the greatest 285 | possible use to the public, the best way to achieve this is to make it 286 | free software which everyone can redistribute and change under these terms. 287 | 288 | To do so, attach the following notices to the program. It is safest 289 | to attach them to the start of each source file to most effectively 290 | convey the exclusion of warranty; and each file should have at least 291 | the "copyright" line and a pointer to where the full notice is found. 292 | 293 | {description} 294 | Copyright (C) {year} {fullname} 295 | 296 | This program is free software; you can redistribute it and/or modify 297 | it under the terms of the GNU General Public License as published by 298 | the Free Software Foundation; either version 2 of the License, or 299 | (at your option) any later version. 300 | 301 | This program is distributed in the hope that it will be useful, 302 | but WITHOUT ANY WARRANTY; without even the implied warranty of 303 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 304 | GNU General Public License for more details. 305 | 306 | You should have received a copy of the GNU General Public License along 307 | with this program; if not, write to the Free Software Foundation, Inc., 308 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 309 | 310 | Also add information on how to contact you by electronic and paper mail. 311 | 312 | If the program is interactive, make it output a short notice like this 313 | when it starts in an interactive mode: 314 | 315 | Gnomovision version 69, Copyright (C) year name of author 316 | Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 317 | This is free software, and you are welcome to redistribute it 318 | under certain conditions; type `show c' for details. 319 | 320 | The hypothetical commands `show w' and `show c' should show the appropriate 321 | parts of the General Public License. Of course, the commands you use may 322 | be called something other than `show w' and `show c'; they could even be 323 | mouse-clicks or menu items--whatever suits your program. 324 | 325 | You should also get your employer (if you work as a programmer) or your 326 | school, if any, to sign a "copyright disclaimer" for the program, if 327 | necessary. Here is a sample; alter the names: 328 | 329 | Yoyodyne, Inc., hereby disclaims all copyright interest in the program 330 | `Gnomovision' (which makes passes at compilers) written by James Hacker. 331 | 332 | {signature of Ty Coon}, 1 April 1989 333 | Ty Coon, President of Vice 334 | 335 | This General Public License does not permit incorporating your program into 336 | proprietary programs. If your program is a subroutine library, you may 337 | consider it more useful to permit linking proprietary applications with the 338 | library. If this is what you want to do, use the GNU Lesser General 339 | Public License instead of this License. 340 | 341 | -------------------------------------------------------------------------------- /src/networks/LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 2, June 1991 3 | 4 | Copyright (C) 1989, 1991 Free Software Foundation, Inc., 5 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 6 | Everyone is permitted to copy and distribute verbatim copies 7 | of this license document, but changing it is not allowed. 8 | 9 | Preamble 10 | 11 | The licenses for most software are designed to take away your 12 | freedom to share and change it. By contrast, the GNU General Public 13 | License is intended to guarantee your freedom to share and change free 14 | software--to make sure the software is free for all its users. This 15 | General Public License applies to most of the Free Software 16 | Foundation's software and to any other program whose authors commit to 17 | using it. (Some other Free Software Foundation software is covered by 18 | the GNU Lesser General Public License instead.) You can apply it to 19 | your programs, too. 20 | 21 | When we speak of free software, we are referring to freedom, not 22 | price. Our General Public Licenses are designed to make sure that you 23 | have the freedom to distribute copies of free software (and charge for 24 | this service if you wish), that you receive source code or can get it 25 | if you want it, that you can change the software or use pieces of it 26 | in new free programs; and that you know you can do these things. 27 | 28 | To protect your rights, we need to make restrictions that forbid 29 | anyone to deny you these rights or to ask you to surrender the rights. 30 | These restrictions translate to certain responsibilities for you if you 31 | distribute copies of the software, or if you modify it. 32 | 33 | For example, if you distribute copies of such a program, whether 34 | gratis or for a fee, you must give the recipients all the rights that 35 | you have. You must make sure that they, too, receive or can get the 36 | source code. And you must show them these terms so they know their 37 | rights. 38 | 39 | We protect your rights with two steps: (1) copyright the software, and 40 | (2) offer you this license which gives you legal permission to copy, 41 | distribute and/or modify the software. 42 | 43 | Also, for each author's protection and ours, we want to make certain 44 | that everyone understands that there is no warranty for this free 45 | software. If the software is modified by someone else and passed on, we 46 | want its recipients to know that what they have is not the original, so 47 | that any problems introduced by others will not reflect on the original 48 | authors' reputations. 49 | 50 | Finally, any free program is threatened constantly by software 51 | patents. We wish to avoid the danger that redistributors of a free 52 | program will individually obtain patent licenses, in effect making the 53 | program proprietary. To prevent this, we have made it clear that any 54 | patent must be licensed for everyone's free use or not licensed at all. 55 | 56 | The precise terms and conditions for copying, distribution and 57 | modification follow. 58 | 59 | GNU GENERAL PUBLIC LICENSE 60 | TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 61 | 62 | 0. This License applies to any program or other work which contains 63 | a notice placed by the copyright holder saying it may be distributed 64 | under the terms of this General Public License. The "Program", below, 65 | refers to any such program or work, and a "work based on the Program" 66 | means either the Program or any derivative work under copyright law: 67 | that is to say, a work containing the Program or a portion of it, 68 | either verbatim or with modifications and/or translated into another 69 | language. (Hereinafter, translation is included without limitation in 70 | the term "modification".) Each licensee is addressed as "you". 71 | 72 | Activities other than copying, distribution and modification are not 73 | covered by this License; they are outside its scope. The act of 74 | running the Program is not restricted, and the output from the Program 75 | is covered only if its contents constitute a work based on the 76 | Program (independent of having been made by running the Program). 77 | Whether that is true depends on what the Program does. 78 | 79 | 1. You may copy and distribute verbatim copies of the Program's 80 | source code as you receive it, in any medium, provided that you 81 | conspicuously and appropriately publish on each copy an appropriate 82 | copyright notice and disclaimer of warranty; keep intact all the 83 | notices that refer to this License and to the absence of any warranty; 84 | and give any other recipients of the Program a copy of this License 85 | along with the Program. 86 | 87 | You may charge a fee for the physical act of transferring a copy, and 88 | you may at your option offer warranty protection in exchange for a fee. 89 | 90 | 2. You may modify your copy or copies of the Program or any portion 91 | of it, thus forming a work based on the Program, and copy and 92 | distribute such modifications or work under the terms of Section 1 93 | above, provided that you also meet all of these conditions: 94 | 95 | a) You must cause the modified files to carry prominent notices 96 | stating that you changed the files and the date of any change. 97 | 98 | b) You must cause any work that you distribute or publish, that in 99 | whole or in part contains or is derived from the Program or any 100 | part thereof, to be licensed as a whole at no charge to all third 101 | parties under the terms of this License. 102 | 103 | c) If the modified program normally reads commands interactively 104 | when run, you must cause it, when started running for such 105 | interactive use in the most ordinary way, to print or display an 106 | announcement including an appropriate copyright notice and a 107 | notice that there is no warranty (or else, saying that you provide 108 | a warranty) and that users may redistribute the program under 109 | these conditions, and telling the user how to view a copy of this 110 | License. (Exception: if the Program itself is interactive but 111 | does not normally print such an announcement, your work based on 112 | the Program is not required to print an announcement.) 113 | 114 | These requirements apply to the modified work as a whole. If 115 | identifiable sections of that work are not derived from the Program, 116 | and can be reasonably considered independent and separate works in 117 | themselves, then this License, and its terms, do not apply to those 118 | sections when you distribute them as separate works. But when you 119 | distribute the same sections as part of a whole which is a work based 120 | on the Program, the distribution of the whole must be on the terms of 121 | this License, whose permissions for other licensees extend to the 122 | entire whole, and thus to each and every part regardless of who wrote it. 123 | 124 | Thus, it is not the intent of this section to claim rights or contest 125 | your rights to work written entirely by you; rather, the intent is to 126 | exercise the right to control the distribution of derivative or 127 | collective works based on the Program. 128 | 129 | In addition, mere aggregation of another work not based on the Program 130 | with the Program (or with a work based on the Program) on a volume of 131 | a storage or distribution medium does not bring the other work under 132 | the scope of this License. 133 | 134 | 3. You may copy and distribute the Program (or a work based on it, 135 | under Section 2) in object code or executable form under the terms of 136 | Sections 1 and 2 above provided that you also do one of the following: 137 | 138 | a) Accompany it with the complete corresponding machine-readable 139 | source code, which must be distributed under the terms of Sections 140 | 1 and 2 above on a medium customarily used for software interchange; or, 141 | 142 | b) Accompany it with a written offer, valid for at least three 143 | years, to give any third party, for a charge no more than your 144 | cost of physically performing source distribution, a complete 145 | machine-readable copy of the corresponding source code, to be 146 | distributed under the terms of Sections 1 and 2 above on a medium 147 | customarily used for software interchange; or, 148 | 149 | c) Accompany it with the information you received as to the offer 150 | to distribute corresponding source code. (This alternative is 151 | allowed only for noncommercial distribution and only if you 152 | received the program in object code or executable form with such 153 | an offer, in accord with Subsection b above.) 154 | 155 | The source code for a work means the preferred form of the work for 156 | making modifications to it. For an executable work, complete source 157 | code means all the source code for all modules it contains, plus any 158 | associated interface definition files, plus the scripts used to 159 | control compilation and installation of the executable. However, as a 160 | special exception, the source code distributed need not include 161 | anything that is normally distributed (in either source or binary 162 | form) with the major components (compiler, kernel, and so on) of the 163 | operating system on which the executable runs, unless that component 164 | itself accompanies the executable. 165 | 166 | If distribution of executable or object code is made by offering 167 | access to copy from a designated place, then offering equivalent 168 | access to copy the source code from the same place counts as 169 | distribution of the source code, even though third parties are not 170 | compelled to copy the source along with the object code. 171 | 172 | 4. You may not copy, modify, sublicense, or distribute the Program 173 | except as expressly provided under this License. Any attempt 174 | otherwise to copy, modify, sublicense or distribute the Program is 175 | void, and will automatically terminate your rights under this License. 176 | However, parties who have received copies, or rights, from you under 177 | this License will not have their licenses terminated so long as such 178 | parties remain in full compliance. 179 | 180 | 5. You are not required to accept this License, since you have not 181 | signed it. However, nothing else grants you permission to modify or 182 | distribute the Program or its derivative works. These actions are 183 | prohibited by law if you do not accept this License. Therefore, by 184 | modifying or distributing the Program (or any work based on the 185 | Program), you indicate your acceptance of this License to do so, and 186 | all its terms and conditions for copying, distributing or modifying 187 | the Program or works based on it. 188 | 189 | 6. Each time you redistribute the Program (or any work based on the 190 | Program), the recipient automatically receives a license from the 191 | original licensor to copy, distribute or modify the Program subject to 192 | these terms and conditions. You may not impose any further 193 | restrictions on the recipients' exercise of the rights granted herein. 194 | You are not responsible for enforcing compliance by third parties to 195 | this License. 196 | 197 | 7. If, as a consequence of a court judgment or allegation of patent 198 | infringement or for any other reason (not limited to patent issues), 199 | conditions are imposed on you (whether by court order, agreement or 200 | otherwise) that contradict the conditions of this License, they do not 201 | excuse you from the conditions of this License. If you cannot 202 | distribute so as to satisfy simultaneously your obligations under this 203 | License and any other pertinent obligations, then as a consequence you 204 | may not distribute the Program at all. For example, if a patent 205 | license would not permit royalty-free redistribution of the Program by 206 | all those who receive copies directly or indirectly through you, then 207 | the only way you could satisfy both it and this License would be to 208 | refrain entirely from distribution of the Program. 209 | 210 | If any portion of this section is held invalid or unenforceable under 211 | any particular circumstance, the balance of the section is intended to 212 | apply and the section as a whole is intended to apply in other 213 | circumstances. 214 | 215 | It is not the purpose of this section to induce you to infringe any 216 | patents or other property right claims or to contest validity of any 217 | such claims; this section has the sole purpose of protecting the 218 | integrity of the free software distribution system, which is 219 | implemented by public license practices. Many people have made 220 | generous contributions to the wide range of software distributed 221 | through that system in reliance on consistent application of that 222 | system; it is up to the author/donor to decide if he or she is willing 223 | to distribute software through any other system and a licensee cannot 224 | impose that choice. 225 | 226 | This section is intended to make thoroughly clear what is believed to 227 | be a consequence of the rest of this License. 228 | 229 | 8. If the distribution and/or use of the Program is restricted in 230 | certain countries either by patents or by copyrighted interfaces, the 231 | original copyright holder who places the Program under this License 232 | may add an explicit geographical distribution limitation excluding 233 | those countries, so that distribution is permitted only in or among 234 | countries not thus excluded. In such case, this License incorporates 235 | the limitation as if written in the body of this License. 236 | 237 | 9. The Free Software Foundation may publish revised and/or new versions 238 | of the General Public License from time to time. Such new versions will 239 | be similar in spirit to the present version, but may differ in detail to 240 | address new problems or concerns. 241 | 242 | Each version is given a distinguishing version number. If the Program 243 | specifies a version number of this License which applies to it and "any 244 | later version", you have the option of following the terms and conditions 245 | either of that version or of any later version published by the Free 246 | Software Foundation. If the Program does not specify a version number of 247 | this License, you may choose any version ever published by the Free Software 248 | Foundation. 249 | 250 | 10. If you wish to incorporate parts of the Program into other free 251 | programs whose distribution conditions are different, write to the author 252 | to ask for permission. For software which is copyrighted by the Free 253 | Software Foundation, write to the Free Software Foundation; we sometimes 254 | make exceptions for this. Our decision will be guided by the two goals 255 | of preserving the free status of all derivatives of our free software and 256 | of promoting the sharing and reuse of software generally. 257 | 258 | NO WARRANTY 259 | 260 | 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY 261 | FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN 262 | OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES 263 | PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED 264 | OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 265 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS 266 | TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE 267 | PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, 268 | REPAIR OR CORRECTION. 269 | 270 | 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 271 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR 272 | REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, 273 | INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 274 | OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED 275 | TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY 276 | YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER 277 | PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE 278 | POSSIBILITY OF SUCH DAMAGES. 279 | 280 | END OF TERMS AND CONDITIONS 281 | 282 | How to Apply These Terms to Your New Programs 283 | 284 | If you develop a new program, and you want it to be of the greatest 285 | possible use to the public, the best way to achieve this is to make it 286 | free software which everyone can redistribute and change under these terms. 287 | 288 | To do so, attach the following notices to the program. It is safest 289 | to attach them to the start of each source file to most effectively 290 | convey the exclusion of warranty; and each file should have at least 291 | the "copyright" line and a pointer to where the full notice is found. 292 | 293 | {description} 294 | Copyright (C) {year} {fullname} 295 | 296 | This program is free software; you can redistribute it and/or modify 297 | it under the terms of the GNU General Public License as published by 298 | the Free Software Foundation; either version 2 of the License, or 299 | (at your option) any later version. 300 | 301 | This program is distributed in the hope that it will be useful, 302 | but WITHOUT ANY WARRANTY; without even the implied warranty of 303 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 304 | GNU General Public License for more details. 305 | 306 | You should have received a copy of the GNU General Public License along 307 | with this program; if not, write to the Free Software Foundation, Inc., 308 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 309 | 310 | Also add information on how to contact you by electronic and paper mail. 311 | 312 | If the program is interactive, make it output a short notice like this 313 | when it starts in an interactive mode: 314 | 315 | Gnomovision version 69, Copyright (C) year name of author 316 | Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 317 | This is free software, and you are welcome to redistribute it 318 | under certain conditions; type `show c' for details. 319 | 320 | The hypothetical commands `show w' and `show c' should show the appropriate 321 | parts of the General Public License. Of course, the commands you use may 322 | be called something other than `show w' and `show c'; they could even be 323 | mouse-clicks or menu items--whatever suits your program. 324 | 325 | You should also get your employer (if you work as a programmer) or your 326 | school, if any, to sign a "copyright disclaimer" for the program, if 327 | necessary. Here is a sample; alter the names: 328 | 329 | Yoyodyne, Inc., hereby disclaims all copyright interest in the program 330 | `Gnomovision' (which makes passes at compilers) written by James Hacker. 331 | 332 | {signature of Ty Coon}, 1 April 1989 333 | Ty Coon, President of Vice 334 | 335 | This General Public License does not permit incorporating your program into 336 | proprietary programs. If your program is a subroutine library, you may 337 | consider it more useful to permit linking proprietary applications with the 338 | library. If this is what you want to do, use the GNU Lesser General 339 | Public License instead of this License. 340 | 341 | -------------------------------------------------------------------------------- /src/phase_sync/LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 2, June 1991 3 | 4 | Copyright (C) 1989, 1991 Free Software Foundation, Inc., 5 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 6 | Everyone is permitted to copy and distribute verbatim copies 7 | of this license document, but changing it is not allowed. 8 | 9 | Preamble 10 | 11 | The licenses for most software are designed to take away your 12 | freedom to share and change it. By contrast, the GNU General Public 13 | License is intended to guarantee your freedom to share and change free 14 | software--to make sure the software is free for all its users. This 15 | General Public License applies to most of the Free Software 16 | Foundation's software and to any other program whose authors commit to 17 | using it. (Some other Free Software Foundation software is covered by 18 | the GNU Lesser General Public License instead.) You can apply it to 19 | your programs, too. 20 | 21 | When we speak of free software, we are referring to freedom, not 22 | price. Our General Public Licenses are designed to make sure that you 23 | have the freedom to distribute copies of free software (and charge for 24 | this service if you wish), that you receive source code or can get it 25 | if you want it, that you can change the software or use pieces of it 26 | in new free programs; and that you know you can do these things. 27 | 28 | To protect your rights, we need to make restrictions that forbid 29 | anyone to deny you these rights or to ask you to surrender the rights. 30 | These restrictions translate to certain responsibilities for you if you 31 | distribute copies of the software, or if you modify it. 32 | 33 | For example, if you distribute copies of such a program, whether 34 | gratis or for a fee, you must give the recipients all the rights that 35 | you have. You must make sure that they, too, receive or can get the 36 | source code. And you must show them these terms so they know their 37 | rights. 38 | 39 | We protect your rights with two steps: (1) copyright the software, and 40 | (2) offer you this license which gives you legal permission to copy, 41 | distribute and/or modify the software. 42 | 43 | Also, for each author's protection and ours, we want to make certain 44 | that everyone understands that there is no warranty for this free 45 | software. If the software is modified by someone else and passed on, we 46 | want its recipients to know that what they have is not the original, so 47 | that any problems introduced by others will not reflect on the original 48 | authors' reputations. 49 | 50 | Finally, any free program is threatened constantly by software 51 | patents. We wish to avoid the danger that redistributors of a free 52 | program will individually obtain patent licenses, in effect making the 53 | program proprietary. To prevent this, we have made it clear that any 54 | patent must be licensed for everyone's free use or not licensed at all. 55 | 56 | The precise terms and conditions for copying, distribution and 57 | modification follow. 58 | 59 | GNU GENERAL PUBLIC LICENSE 60 | TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 61 | 62 | 0. This License applies to any program or other work which contains 63 | a notice placed by the copyright holder saying it may be distributed 64 | under the terms of this General Public License. The "Program", below, 65 | refers to any such program or work, and a "work based on the Program" 66 | means either the Program or any derivative work under copyright law: 67 | that is to say, a work containing the Program or a portion of it, 68 | either verbatim or with modifications and/or translated into another 69 | language. (Hereinafter, translation is included without limitation in 70 | the term "modification".) Each licensee is addressed as "you". 71 | 72 | Activities other than copying, distribution and modification are not 73 | covered by this License; they are outside its scope. The act of 74 | running the Program is not restricted, and the output from the Program 75 | is covered only if its contents constitute a work based on the 76 | Program (independent of having been made by running the Program). 77 | Whether that is true depends on what the Program does. 78 | 79 | 1. You may copy and distribute verbatim copies of the Program's 80 | source code as you receive it, in any medium, provided that you 81 | conspicuously and appropriately publish on each copy an appropriate 82 | copyright notice and disclaimer of warranty; keep intact all the 83 | notices that refer to this License and to the absence of any warranty; 84 | and give any other recipients of the Program a copy of this License 85 | along with the Program. 86 | 87 | You may charge a fee for the physical act of transferring a copy, and 88 | you may at your option offer warranty protection in exchange for a fee. 89 | 90 | 2. You may modify your copy or copies of the Program or any portion 91 | of it, thus forming a work based on the Program, and copy and 92 | distribute such modifications or work under the terms of Section 1 93 | above, provided that you also meet all of these conditions: 94 | 95 | a) You must cause the modified files to carry prominent notices 96 | stating that you changed the files and the date of any change. 97 | 98 | b) You must cause any work that you distribute or publish, that in 99 | whole or in part contains or is derived from the Program or any 100 | part thereof, to be licensed as a whole at no charge to all third 101 | parties under the terms of this License. 102 | 103 | c) If the modified program normally reads commands interactively 104 | when run, you must cause it, when started running for such 105 | interactive use in the most ordinary way, to print or display an 106 | announcement including an appropriate copyright notice and a 107 | notice that there is no warranty (or else, saying that you provide 108 | a warranty) and that users may redistribute the program under 109 | these conditions, and telling the user how to view a copy of this 110 | License. (Exception: if the Program itself is interactive but 111 | does not normally print such an announcement, your work based on 112 | the Program is not required to print an announcement.) 113 | 114 | These requirements apply to the modified work as a whole. If 115 | identifiable sections of that work are not derived from the Program, 116 | and can be reasonably considered independent and separate works in 117 | themselves, then this License, and its terms, do not apply to those 118 | sections when you distribute them as separate works. But when you 119 | distribute the same sections as part of a whole which is a work based 120 | on the Program, the distribution of the whole must be on the terms of 121 | this License, whose permissions for other licensees extend to the 122 | entire whole, and thus to each and every part regardless of who wrote it. 123 | 124 | Thus, it is not the intent of this section to claim rights or contest 125 | your rights to work written entirely by you; rather, the intent is to 126 | exercise the right to control the distribution of derivative or 127 | collective works based on the Program. 128 | 129 | In addition, mere aggregation of another work not based on the Program 130 | with the Program (or with a work based on the Program) on a volume of 131 | a storage or distribution medium does not bring the other work under 132 | the scope of this License. 133 | 134 | 3. You may copy and distribute the Program (or a work based on it, 135 | under Section 2) in object code or executable form under the terms of 136 | Sections 1 and 2 above provided that you also do one of the following: 137 | 138 | a) Accompany it with the complete corresponding machine-readable 139 | source code, which must be distributed under the terms of Sections 140 | 1 and 2 above on a medium customarily used for software interchange; or, 141 | 142 | b) Accompany it with a written offer, valid for at least three 143 | years, to give any third party, for a charge no more than your 144 | cost of physically performing source distribution, a complete 145 | machine-readable copy of the corresponding source code, to be 146 | distributed under the terms of Sections 1 and 2 above on a medium 147 | customarily used for software interchange; or, 148 | 149 | c) Accompany it with the information you received as to the offer 150 | to distribute corresponding source code. (This alternative is 151 | allowed only for noncommercial distribution and only if you 152 | received the program in object code or executable form with such 153 | an offer, in accord with Subsection b above.) 154 | 155 | The source code for a work means the preferred form of the work for 156 | making modifications to it. For an executable work, complete source 157 | code means all the source code for all modules it contains, plus any 158 | associated interface definition files, plus the scripts used to 159 | control compilation and installation of the executable. However, as a 160 | special exception, the source code distributed need not include 161 | anything that is normally distributed (in either source or binary 162 | form) with the major components (compiler, kernel, and so on) of the 163 | operating system on which the executable runs, unless that component 164 | itself accompanies the executable. 165 | 166 | If distribution of executable or object code is made by offering 167 | access to copy from a designated place, then offering equivalent 168 | access to copy the source code from the same place counts as 169 | distribution of the source code, even though third parties are not 170 | compelled to copy the source along with the object code. 171 | 172 | 4. You may not copy, modify, sublicense, or distribute the Program 173 | except as expressly provided under this License. Any attempt 174 | otherwise to copy, modify, sublicense or distribute the Program is 175 | void, and will automatically terminate your rights under this License. 176 | However, parties who have received copies, or rights, from you under 177 | this License will not have their licenses terminated so long as such 178 | parties remain in full compliance. 179 | 180 | 5. You are not required to accept this License, since you have not 181 | signed it. However, nothing else grants you permission to modify or 182 | distribute the Program or its derivative works. These actions are 183 | prohibited by law if you do not accept this License. Therefore, by 184 | modifying or distributing the Program (or any work based on the 185 | Program), you indicate your acceptance of this License to do so, and 186 | all its terms and conditions for copying, distributing or modifying 187 | the Program or works based on it. 188 | 189 | 6. Each time you redistribute the Program (or any work based on the 190 | Program), the recipient automatically receives a license from the 191 | original licensor to copy, distribute or modify the Program subject to 192 | these terms and conditions. You may not impose any further 193 | restrictions on the recipients' exercise of the rights granted herein. 194 | You are not responsible for enforcing compliance by third parties to 195 | this License. 196 | 197 | 7. If, as a consequence of a court judgment or allegation of patent 198 | infringement or for any other reason (not limited to patent issues), 199 | conditions are imposed on you (whether by court order, agreement or 200 | otherwise) that contradict the conditions of this License, they do not 201 | excuse you from the conditions of this License. If you cannot 202 | distribute so as to satisfy simultaneously your obligations under this 203 | License and any other pertinent obligations, then as a consequence you 204 | may not distribute the Program at all. For example, if a patent 205 | license would not permit royalty-free redistribution of the Program by 206 | all those who receive copies directly or indirectly through you, then 207 | the only way you could satisfy both it and this License would be to 208 | refrain entirely from distribution of the Program. 209 | 210 | If any portion of this section is held invalid or unenforceable under 211 | any particular circumstance, the balance of the section is intended to 212 | apply and the section as a whole is intended to apply in other 213 | circumstances. 214 | 215 | It is not the purpose of this section to induce you to infringe any 216 | patents or other property right claims or to contest validity of any 217 | such claims; this section has the sole purpose of protecting the 218 | integrity of the free software distribution system, which is 219 | implemented by public license practices. Many people have made 220 | generous contributions to the wide range of software distributed 221 | through that system in reliance on consistent application of that 222 | system; it is up to the author/donor to decide if he or she is willing 223 | to distribute software through any other system and a licensee cannot 224 | impose that choice. 225 | 226 | This section is intended to make thoroughly clear what is believed to 227 | be a consequence of the rest of this License. 228 | 229 | 8. If the distribution and/or use of the Program is restricted in 230 | certain countries either by patents or by copyrighted interfaces, the 231 | original copyright holder who places the Program under this License 232 | may add an explicit geographical distribution limitation excluding 233 | those countries, so that distribution is permitted only in or among 234 | countries not thus excluded. In such case, this License incorporates 235 | the limitation as if written in the body of this License. 236 | 237 | 9. The Free Software Foundation may publish revised and/or new versions 238 | of the General Public License from time to time. Such new versions will 239 | be similar in spirit to the present version, but may differ in detail to 240 | address new problems or concerns. 241 | 242 | Each version is given a distinguishing version number. If the Program 243 | specifies a version number of this License which applies to it and "any 244 | later version", you have the option of following the terms and conditions 245 | either of that version or of any later version published by the Free 246 | Software Foundation. If the Program does not specify a version number of 247 | this License, you may choose any version ever published by the Free Software 248 | Foundation. 249 | 250 | 10. If you wish to incorporate parts of the Program into other free 251 | programs whose distribution conditions are different, write to the author 252 | to ask for permission. For software which is copyrighted by the Free 253 | Software Foundation, write to the Free Software Foundation; we sometimes 254 | make exceptions for this. Our decision will be guided by the two goals 255 | of preserving the free status of all derivatives of our free software and 256 | of promoting the sharing and reuse of software generally. 257 | 258 | NO WARRANTY 259 | 260 | 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY 261 | FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN 262 | OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES 263 | PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED 264 | OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 265 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS 266 | TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE 267 | PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, 268 | REPAIR OR CORRECTION. 269 | 270 | 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 271 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR 272 | REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, 273 | INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 274 | OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED 275 | TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY 276 | YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER 277 | PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE 278 | POSSIBILITY OF SUCH DAMAGES. 279 | 280 | END OF TERMS AND CONDITIONS 281 | 282 | How to Apply These Terms to Your New Programs 283 | 284 | If you develop a new program, and you want it to be of the greatest 285 | possible use to the public, the best way to achieve this is to make it 286 | free software which everyone can redistribute and change under these terms. 287 | 288 | To do so, attach the following notices to the program. It is safest 289 | to attach them to the start of each source file to most effectively 290 | convey the exclusion of warranty; and each file should have at least 291 | the "copyright" line and a pointer to where the full notice is found. 292 | 293 | {description} 294 | Copyright (C) {year} {fullname} 295 | 296 | This program is free software; you can redistribute it and/or modify 297 | it under the terms of the GNU General Public License as published by 298 | the Free Software Foundation; either version 2 of the License, or 299 | (at your option) any later version. 300 | 301 | This program is distributed in the hope that it will be useful, 302 | but WITHOUT ANY WARRANTY; without even the implied warranty of 303 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 304 | GNU General Public License for more details. 305 | 306 | You should have received a copy of the GNU General Public License along 307 | with this program; if not, write to the Free Software Foundation, Inc., 308 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 309 | 310 | Also add information on how to contact you by electronic and paper mail. 311 | 312 | If the program is interactive, make it output a short notice like this 313 | when it starts in an interactive mode: 314 | 315 | Gnomovision version 69, Copyright (C) year name of author 316 | Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 317 | This is free software, and you are welcome to redistribute it 318 | under certain conditions; type `show c' for details. 319 | 320 | The hypothetical commands `show w' and `show c' should show the appropriate 321 | parts of the General Public License. Of course, the commands you use may 322 | be called something other than `show w' and `show c'; they could even be 323 | mouse-clicks or menu items--whatever suits your program. 324 | 325 | You should also get your employer (if you work as a programmer) or your 326 | school, if any, to sign a "copyright disclaimer" for the program, if 327 | necessary. Here is a sample; alter the names: 328 | 329 | Yoyodyne, Inc., hereby disclaims all copyright interest in the program 330 | `Gnomovision' (which makes passes at compilers) written by James Hacker. 331 | 332 | {signature of Ty Coon}, 1 April 1989 333 | Ty Coon, President of Vice 334 | 335 | This General Public License does not permit incorporating your program into 336 | proprietary programs. If your program is a subroutine library, you may 337 | consider it more useful to permit linking proprietary applications with the 338 | library. If this is what you want to do, use the GNU Lesser General 339 | Public License instead of this License. 340 | 341 | -------------------------------------------------------------------------------- /src/generalized_sync/LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 2, June 1991 3 | 4 | Copyright (C) 1989, 1991 Free Software Foundation, Inc., 5 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 6 | Everyone is permitted to copy and distribute verbatim copies 7 | of this license document, but changing it is not allowed. 8 | 9 | Preamble 10 | 11 | The licenses for most software are designed to take away your 12 | freedom to share and change it. By contrast, the GNU General Public 13 | License is intended to guarantee your freedom to share and change free 14 | software--to make sure the software is free for all its users. This 15 | General Public License applies to most of the Free Software 16 | Foundation's software and to any other program whose authors commit to 17 | using it. (Some other Free Software Foundation software is covered by 18 | the GNU Lesser General Public License instead.) You can apply it to 19 | your programs, too. 20 | 21 | When we speak of free software, we are referring to freedom, not 22 | price. Our General Public Licenses are designed to make sure that you 23 | have the freedom to distribute copies of free software (and charge for 24 | this service if you wish), that you receive source code or can get it 25 | if you want it, that you can change the software or use pieces of it 26 | in new free programs; and that you know you can do these things. 27 | 28 | To protect your rights, we need to make restrictions that forbid 29 | anyone to deny you these rights or to ask you to surrender the rights. 30 | These restrictions translate to certain responsibilities for you if you 31 | distribute copies of the software, or if you modify it. 32 | 33 | For example, if you distribute copies of such a program, whether 34 | gratis or for a fee, you must give the recipients all the rights that 35 | you have. You must make sure that they, too, receive or can get the 36 | source code. And you must show them these terms so they know their 37 | rights. 38 | 39 | We protect your rights with two steps: (1) copyright the software, and 40 | (2) offer you this license which gives you legal permission to copy, 41 | distribute and/or modify the software. 42 | 43 | Also, for each author's protection and ours, we want to make certain 44 | that everyone understands that there is no warranty for this free 45 | software. If the software is modified by someone else and passed on, we 46 | want its recipients to know that what they have is not the original, so 47 | that any problems introduced by others will not reflect on the original 48 | authors' reputations. 49 | 50 | Finally, any free program is threatened constantly by software 51 | patents. We wish to avoid the danger that redistributors of a free 52 | program will individually obtain patent licenses, in effect making the 53 | program proprietary. To prevent this, we have made it clear that any 54 | patent must be licensed for everyone's free use or not licensed at all. 55 | 56 | The precise terms and conditions for copying, distribution and 57 | modification follow. 58 | 59 | GNU GENERAL PUBLIC LICENSE 60 | TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 61 | 62 | 0. This License applies to any program or other work which contains 63 | a notice placed by the copyright holder saying it may be distributed 64 | under the terms of this General Public License. The "Program", below, 65 | refers to any such program or work, and a "work based on the Program" 66 | means either the Program or any derivative work under copyright law: 67 | that is to say, a work containing the Program or a portion of it, 68 | either verbatim or with modifications and/or translated into another 69 | language. (Hereinafter, translation is included without limitation in 70 | the term "modification".) Each licensee is addressed as "you". 71 | 72 | Activities other than copying, distribution and modification are not 73 | covered by this License; they are outside its scope. The act of 74 | running the Program is not restricted, and the output from the Program 75 | is covered only if its contents constitute a work based on the 76 | Program (independent of having been made by running the Program). 77 | Whether that is true depends on what the Program does. 78 | 79 | 1. You may copy and distribute verbatim copies of the Program's 80 | source code as you receive it, in any medium, provided that you 81 | conspicuously and appropriately publish on each copy an appropriate 82 | copyright notice and disclaimer of warranty; keep intact all the 83 | notices that refer to this License and to the absence of any warranty; 84 | and give any other recipients of the Program a copy of this License 85 | along with the Program. 86 | 87 | You may charge a fee for the physical act of transferring a copy, and 88 | you may at your option offer warranty protection in exchange for a fee. 89 | 90 | 2. You may modify your copy or copies of the Program or any portion 91 | of it, thus forming a work based on the Program, and copy and 92 | distribute such modifications or work under the terms of Section 1 93 | above, provided that you also meet all of these conditions: 94 | 95 | a) You must cause the modified files to carry prominent notices 96 | stating that you changed the files and the date of any change. 97 | 98 | b) You must cause any work that you distribute or publish, that in 99 | whole or in part contains or is derived from the Program or any 100 | part thereof, to be licensed as a whole at no charge to all third 101 | parties under the terms of this License. 102 | 103 | c) If the modified program normally reads commands interactively 104 | when run, you must cause it, when started running for such 105 | interactive use in the most ordinary way, to print or display an 106 | announcement including an appropriate copyright notice and a 107 | notice that there is no warranty (or else, saying that you provide 108 | a warranty) and that users may redistribute the program under 109 | these conditions, and telling the user how to view a copy of this 110 | License. (Exception: if the Program itself is interactive but 111 | does not normally print such an announcement, your work based on 112 | the Program is not required to print an announcement.) 113 | 114 | These requirements apply to the modified work as a whole. If 115 | identifiable sections of that work are not derived from the Program, 116 | and can be reasonably considered independent and separate works in 117 | themselves, then this License, and its terms, do not apply to those 118 | sections when you distribute them as separate works. But when you 119 | distribute the same sections as part of a whole which is a work based 120 | on the Program, the distribution of the whole must be on the terms of 121 | this License, whose permissions for other licensees extend to the 122 | entire whole, and thus to each and every part regardless of who wrote it. 123 | 124 | Thus, it is not the intent of this section to claim rights or contest 125 | your rights to work written entirely by you; rather, the intent is to 126 | exercise the right to control the distribution of derivative or 127 | collective works based on the Program. 128 | 129 | In addition, mere aggregation of another work not based on the Program 130 | with the Program (or with a work based on the Program) on a volume of 131 | a storage or distribution medium does not bring the other work under 132 | the scope of this License. 133 | 134 | 3. You may copy and distribute the Program (or a work based on it, 135 | under Section 2) in object code or executable form under the terms of 136 | Sections 1 and 2 above provided that you also do one of the following: 137 | 138 | a) Accompany it with the complete corresponding machine-readable 139 | source code, which must be distributed under the terms of Sections 140 | 1 and 2 above on a medium customarily used for software interchange; or, 141 | 142 | b) Accompany it with a written offer, valid for at least three 143 | years, to give any third party, for a charge no more than your 144 | cost of physically performing source distribution, a complete 145 | machine-readable copy of the corresponding source code, to be 146 | distributed under the terms of Sections 1 and 2 above on a medium 147 | customarily used for software interchange; or, 148 | 149 | c) Accompany it with the information you received as to the offer 150 | to distribute corresponding source code. (This alternative is 151 | allowed only for noncommercial distribution and only if you 152 | received the program in object code or executable form with such 153 | an offer, in accord with Subsection b above.) 154 | 155 | The source code for a work means the preferred form of the work for 156 | making modifications to it. For an executable work, complete source 157 | code means all the source code for all modules it contains, plus any 158 | associated interface definition files, plus the scripts used to 159 | control compilation and installation of the executable. However, as a 160 | special exception, the source code distributed need not include 161 | anything that is normally distributed (in either source or binary 162 | form) with the major components (compiler, kernel, and so on) of the 163 | operating system on which the executable runs, unless that component 164 | itself accompanies the executable. 165 | 166 | If distribution of executable or object code is made by offering 167 | access to copy from a designated place, then offering equivalent 168 | access to copy the source code from the same place counts as 169 | distribution of the source code, even though third parties are not 170 | compelled to copy the source along with the object code. 171 | 172 | 4. You may not copy, modify, sublicense, or distribute the Program 173 | except as expressly provided under this License. Any attempt 174 | otherwise to copy, modify, sublicense or distribute the Program is 175 | void, and will automatically terminate your rights under this License. 176 | However, parties who have received copies, or rights, from you under 177 | this License will not have their licenses terminated so long as such 178 | parties remain in full compliance. 179 | 180 | 5. You are not required to accept this License, since you have not 181 | signed it. However, nothing else grants you permission to modify or 182 | distribute the Program or its derivative works. These actions are 183 | prohibited by law if you do not accept this License. Therefore, by 184 | modifying or distributing the Program (or any work based on the 185 | Program), you indicate your acceptance of this License to do so, and 186 | all its terms and conditions for copying, distributing or modifying 187 | the Program or works based on it. 188 | 189 | 6. Each time you redistribute the Program (or any work based on the 190 | Program), the recipient automatically receives a license from the 191 | original licensor to copy, distribute or modify the Program subject to 192 | these terms and conditions. You may not impose any further 193 | restrictions on the recipients' exercise of the rights granted herein. 194 | You are not responsible for enforcing compliance by third parties to 195 | this License. 196 | 197 | 7. If, as a consequence of a court judgment or allegation of patent 198 | infringement or for any other reason (not limited to patent issues), 199 | conditions are imposed on you (whether by court order, agreement or 200 | otherwise) that contradict the conditions of this License, they do not 201 | excuse you from the conditions of this License. If you cannot 202 | distribute so as to satisfy simultaneously your obligations under this 203 | License and any other pertinent obligations, then as a consequence you 204 | may not distribute the Program at all. For example, if a patent 205 | license would not permit royalty-free redistribution of the Program by 206 | all those who receive copies directly or indirectly through you, then 207 | the only way you could satisfy both it and this License would be to 208 | refrain entirely from distribution of the Program. 209 | 210 | If any portion of this section is held invalid or unenforceable under 211 | any particular circumstance, the balance of the section is intended to 212 | apply and the section as a whole is intended to apply in other 213 | circumstances. 214 | 215 | It is not the purpose of this section to induce you to infringe any 216 | patents or other property right claims or to contest validity of any 217 | such claims; this section has the sole purpose of protecting the 218 | integrity of the free software distribution system, which is 219 | implemented by public license practices. Many people have made 220 | generous contributions to the wide range of software distributed 221 | through that system in reliance on consistent application of that 222 | system; it is up to the author/donor to decide if he or she is willing 223 | to distribute software through any other system and a licensee cannot 224 | impose that choice. 225 | 226 | This section is intended to make thoroughly clear what is believed to 227 | be a consequence of the rest of this License. 228 | 229 | 8. If the distribution and/or use of the Program is restricted in 230 | certain countries either by patents or by copyrighted interfaces, the 231 | original copyright holder who places the Program under this License 232 | may add an explicit geographical distribution limitation excluding 233 | those countries, so that distribution is permitted only in or among 234 | countries not thus excluded. In such case, this License incorporates 235 | the limitation as if written in the body of this License. 236 | 237 | 9. The Free Software Foundation may publish revised and/or new versions 238 | of the General Public License from time to time. Such new versions will 239 | be similar in spirit to the present version, but may differ in detail to 240 | address new problems or concerns. 241 | 242 | Each version is given a distinguishing version number. If the Program 243 | specifies a version number of this License which applies to it and "any 244 | later version", you have the option of following the terms and conditions 245 | either of that version or of any later version published by the Free 246 | Software Foundation. If the Program does not specify a version number of 247 | this License, you may choose any version ever published by the Free Software 248 | Foundation. 249 | 250 | 10. If you wish to incorporate parts of the Program into other free 251 | programs whose distribution conditions are different, write to the author 252 | to ask for permission. For software which is copyrighted by the Free 253 | Software Foundation, write to the Free Software Foundation; we sometimes 254 | make exceptions for this. Our decision will be guided by the two goals 255 | of preserving the free status of all derivatives of our free software and 256 | of promoting the sharing and reuse of software generally. 257 | 258 | NO WARRANTY 259 | 260 | 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY 261 | FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN 262 | OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES 263 | PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED 264 | OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF 265 | MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS 266 | TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE 267 | PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, 268 | REPAIR OR CORRECTION. 269 | 270 | 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 271 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR 272 | REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, 273 | INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 274 | OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED 275 | TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY 276 | YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER 277 | PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE 278 | POSSIBILITY OF SUCH DAMAGES. 279 | 280 | END OF TERMS AND CONDITIONS 281 | 282 | How to Apply These Terms to Your New Programs 283 | 284 | If you develop a new program, and you want it to be of the greatest 285 | possible use to the public, the best way to achieve this is to make it 286 | free software which everyone can redistribute and change under these terms. 287 | 288 | To do so, attach the following notices to the program. It is safest 289 | to attach them to the start of each source file to most effectively 290 | convey the exclusion of warranty; and each file should have at least 291 | the "copyright" line and a pointer to where the full notice is found. 292 | 293 | {description} 294 | Copyright (C) {year} {fullname} 295 | 296 | This program is free software; you can redistribute it and/or modify 297 | it under the terms of the GNU General Public License as published by 298 | the Free Software Foundation; either version 2 of the License, or 299 | (at your option) any later version. 300 | 301 | This program is distributed in the hope that it will be useful, 302 | but WITHOUT ANY WARRANTY; without even the implied warranty of 303 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 304 | GNU General Public License for more details. 305 | 306 | You should have received a copy of the GNU General Public License along 307 | with this program; if not, write to the Free Software Foundation, Inc., 308 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. 309 | 310 | Also add information on how to contact you by electronic and paper mail. 311 | 312 | If the program is interactive, make it output a short notice like this 313 | when it starts in an interactive mode: 314 | 315 | Gnomovision version 69, Copyright (C) year name of author 316 | Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 317 | This is free software, and you are welcome to redistribute it 318 | under certain conditions; type `show c' for details. 319 | 320 | The hypothetical commands `show w' and `show c' should show the appropriate 321 | parts of the General Public License. Of course, the commands you use may 322 | be called something other than `show w' and `show c'; they could even be 323 | mouse-clicks or menu items--whatever suits your program. 324 | 325 | You should also get your employer (if you work as a programmer) or your 326 | school, if any, to sign a "copyright disclaimer" for the program, if 327 | necessary. Here is a sample; alter the names: 328 | 329 | Yoyodyne, Inc., hereby disclaims all copyright interest in the program 330 | `Gnomovision' (which makes passes at compilers) written by James Hacker. 331 | 332 | {signature of Ty Coon}, 1 April 1989 333 | Ty Coon, President of Vice 334 | 335 | This General Public License does not permit incorporating your program into 336 | proprietary programs. If your program is a subroutine library, you may 337 | consider it more useful to permit linking proprietary applications with the 338 | library. If this is what you want to do, use the GNU Lesser General 339 | Public License instead of this License. 340 | 341 | --------------------------------------------------------------------------------