#include <R.h>
#include <Rdefines.h>
#include "sources/EMGLLF.h"
-#include "sources/utils/io.h"
SEXP EMGLLF(
- SEXP M_,
- SEXP NIix_,
- SEXP alpha_,
- SEXP h_,
- SEXP epsilon_,
- SEXP maxiter_,
- SEXP symmNeighbs_,
- SEXP trace_
+ SEXP phiInit_,
+ SEXP rhoInit_,
+ SEXP piInit_,
+ SEXP gamInit_,
+ SEXP mini_,
+ SEXP maxi_,
+ SEXP gamma_,
+ SEXP lambda_,
+ SEXP X_,
+ SEXP Y_,
+ SEXP tau_
) {
- // get parameters
- double alpha = NUMERIC_VALUE(alpha_);
- double h = NUMERIC_VALUE(h_);
- double epsilon = NUMERIC_VALUE(epsilon_);
- int maxiter = INTEGER_VALUE(maxiter_);
- int symmNeighbs = LOGICAL_VALUE(symmNeighbs_);
- int trace = LOGICAL_VALUE(trace_);
-
- // extract infos from M and get associate pointer
- SEXP dim = getAttrib(M_, R_DimSymbol);
- int nrow = INTEGER(dim)[0];
- int ncol = INTEGER(dim)[1];
- // M is always given by columns: easier to process in rows
- double* pM = transpose(REAL(M_), nrow, ncol);
-
- // extract NIix list vectors in a jagged array
- int* lengthNIix = (int*)malloc(nrow*sizeof(int));
- int** NIix = (int**)malloc(nrow*sizeof(int*));
- for (int i=0; i<nrow; i++)
- {
- lengthNIix[i] = LENGTH(VECTOR_ELT(NIix_,i));
- SEXP tmp;
- PROTECT(tmp = AS_INTEGER(VECTOR_ELT(NIix_,i)));
- NIix[i] = (int*)malloc(lengthNIix[i]*sizeof(int));
- for (int j=0; j<lengthNIix[i]; j++)
- NIix[i][j] = INTEGER(tmp)[j];
- UNPROTECT(1);
- // WARNING: R indices start at 1,
- // so we must lower every index right now to avoid future bug
- for (int j=0; j<lengthNIix[i]; j++)
- NIix[i][j]--;
- }
-
- // Main call to core algorithm
- Parameters params = getVarsWithConvexOptim_core(
- pM, lengthNIix, NIix, nrow, ncol, alpha, h, epsilon, maxiter, symmNeighbs, trace);
-
- // free neighborhoods parameters arrays
- free(lengthNIix);
- for (int i=0; i<nrow; i++)
- free(NIix[i]);
- free(NIix);
-
- // copy matrix F into pF for output to R (1D matrices)
- SEXP f;
- PROTECT(f = allocMatrix(REALSXP, nrow, ncol));
- double* pF = REAL(f);
- for (int i=0; i<nrow; i++)
- {
- for (int j=0; j<ncol; j++)
- pF[i+nrow*j] = params.f[i][j];
- }
- // copy theta into pTheta for output to R
- SEXP theta;
- PROTECT(theta = allocVector(REALSXP, nrow));
- double* pTheta = REAL(theta);
- for (int i=0; i<nrow; i++)
- pTheta[i] = params.theta[i];
-
- // free params.f and params.theta
- free(params.theta);
- for (int i=0; i<nrow; i++)
- free(params.f[i]);
- free(params.f);
-
- // build return list with f and theta
- SEXP listParams, listNames;
- PROTECT(listParams = allocVector(VECSXP, 2));
- char* lnames[2] = {"f", "theta"}; //lists labels
- PROTECT(listNames = allocVector(STRSXP,2));
- for (int i=0; i<2; i++)
- SET_STRING_ELT(listNames,i,mkChar(lnames[i]));
- setAttrib(listParams, R_NamesSymbol, listNames);
- SET_VECTOR_ELT(listParams, 0, f);
- SET_VECTOR_ELT(listParams, 1, theta);
-
- UNPROTECT(4);
- return listParams;
-
-
-
-
-
-
-
-
// Get matrices dimensions
- const mwSize n = mxGetDimensions(prhs[8])[0];
- const mwSize p = mxGetDimensions(prhs[0])[0];
- const mwSize m = mxGetDimensions(prhs[0])[1];
- const mwSize k = mxGetDimensions(prhs[0])[2];
+ int n = INTEGER(getAttrib(X_, R_DimSymbol))[0];
+ SEXP dim = getAttrib(phiInit_, R_DimSymbol)
+ int p = INTEGER(dim)[0];
+ int m = INTEGER(dim)[1];
+ int k = INTEGER(dim)[2];
////////////
// INPUTS //
////////////
- // phiInit
- const mwSize* dimPhiInit = mxGetDimensions(prhs[0]);
- Real* brPhiInit = matlabToBrArray_real(mxGetPr(prhs[0]), dimPhiInit, 3);
-
- // rhoInit
- const mwSize* dimRhoInit = mxGetDimensions(prhs[1]);
- Real* brRhoInit = matlabToBrArray_real(mxGetPr(prhs[1]), dimRhoInit, 3);
-
- // piInit
- Real* piInit = mxGetPr(prhs[2]);
-
- // gamInit
- const mwSize* dimGamInit = mxGetDimensions(prhs[3]);
- Real* brGamInit = matlabToBrArray_real(mxGetPr(prhs[3]), dimGamInit, 2);
-
- // min number of iterations
- Int mini = ((Int*)mxGetData(prhs[4]))[0];
-
- // max number of iterations
- Int maxi = ((Int*)mxGetData(prhs[5]))[0];
-
- // gamma
- Real gamma = mxGetScalar(prhs[6]);
-
- // lambda
- Real lambda = mxGetScalar(prhs[7]);
-
- // X
- const mwSize* dimX = mxGetDimensions(prhs[8]);
- Real* brX = matlabToBrArray_real(mxGetPr(prhs[8]), dimX, 2);
-
- // Y
- const mwSize* dimY = mxGetDimensions(prhs[9]);
- Real* brY = matlabToBrArray_real(mxGetPr(prhs[9]), dimY, 2);
-
- // tau
- Real tau = mxGetScalar(prhs[10]);
+ // get scalar parameters
+ int mini = INTEGER_VALUE(mini_);
+ int maxi = INTEGER_VALUE(maxi_);
+ double gamma = NUMERIC_VALUE(gamma_);
+ double lambda = NUMERIC_VALUE(lambda_);
+ double tau = NUMERIC_VALUE(tau_);
+
+ // Get pointers from SEXP arrays ; WARNING: by columns !
+ double* phiInit = REAL(phiInit_);
+ double* rhoInit = REAL(rhoInit_);
+ double* piInit = REAL(piInit_);
+ double* gamInit = REAL(gamInit_);
+ double* X = REAL(X_);
+ double* Y = REAL(Y_);
/////////////
// OUTPUTS //
/////////////
- // phi
- const mwSize dimPhi[] = {dimPhiInit[0], dimPhiInit[1], dimPhiInit[2]};
- plhs[0] = mxCreateNumericArray(3,dimPhi,mxDOUBLE_CLASS,mxREAL);
- Real* phi = mxGetPr(plhs[0]);
-
- // rho
- const mwSize dimRho[] = {dimRhoInit[0], dimRhoInit[1], dimRhoInit[2]};
- plhs[1] = mxCreateNumericArray(3,dimRho,mxDOUBLE_CLASS,mxREAL);
- Real* rho = mxGetPr(plhs[1]);
-
- // pi
- plhs[2] = mxCreateNumericMatrix(k,1,mxDOUBLE_CLASS,mxREAL);
- Real* pi = mxGetPr(plhs[2]);
-
- // LLF
- plhs[3] = mxCreateNumericMatrix(maxi,1,mxDOUBLE_CLASS,mxREAL);
- Real* LLF = mxGetPr(plhs[3]);
-
- // S
- const mwSize dimS[] = {p, m, k};
- plhs[4] = mxCreateNumericArray(3,dimS,mxDOUBLE_CLASS,mxREAL);
- Real* S = mxGetPr(plhs[4]);
+ SEXP phi, rho, pi, LLF, S, dimPhiS, dimRho;
+ PROTECT(dimPhiS = allocVector(INTSXP, 3));
+ int* pDimPhiS = INTEGER(dimPhiS);
+ pDimPhiS[0] = p; pDimPhiS[1] = m; pDimPhiS[2] = k;
+ PROTECT(dimRho = allocVector(INTSXP, 3));
+ int* pDimRho = INTEGER(dimRho);
+ pDimRho[0] = m; pDimRho[1] = m; pDimRho[2] = k;
+ PROTECT(phi = allocArray(REALSXP, dimPhiS));
+ PROTECT(rho = allocArray(REALSXP, dimRho));
+ PROTECT(pi = allocVector(REALSXP, k));
+ PROTECT(LLF = allocVector(REALSXP, maxi-mini+1));
+ PROTECT(S = allocArray(REALSXP, dimPhiS));
+ double* pPhi=REAL(phi), pRho=REAL(rho), pPi=REAL(pi), pLLF=REAL(LLF), pS=REAL(S);
////////////////////
// Call to EMGLLF //
////////////////////
- EMGLLF(brPhiInit,brRhoInit,piInit,brGamInit,mini,maxi,gamma,lambda,brX,brY,tau,
- phi,rho,pi,LLF,S,
+ EMGLLF(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,tau,
+ pPhi,pRho,pPi,pLLF,pS,
n,p,m,k);
-
- free(brPhiInit);
- free(brRhoInit);
- free(brGamInit);
- free(brX);
- free(brY);
-
-
-
-
-
+ // Build list from OUT params and return it
+ SEXP listParams, listNames;
+ PROTECT(listParams = allocVector(VECSXP, 5));
+ char* lnames[5] = {"phi", "rho", "pi", "LLF", "S"}; //lists labels
+ PROTECT(listNames = allocVector(STRSXP,5));
+ for (int i=0; i<5; i++)
+ SET_STRING_ELT(listNames,i,mkChar(lnames[i]));
+ setAttrib(listParams, R_NamesSymbol, listNames);
+ SET_ARRAY_ELT(listParams, 0, phi);
+ SET_ARRAY_ELT(listParams, 1, rho);
+ SET_MATRIX_ELT(listParams, 2, pi);
+ SET_VECTOR_ELT(listParams, 3, LLF);
+ SET_ARRAY_ELT(listParams, 4, S);
+ UNPROTECT(9);
+ return listParams;
}
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