+++ /dev/null
-#include "ioutils.h"
-#include "EMGLLF.h"
-#include <mex.h>
-
-// nlhs, nrhs: resp. numbers of out and in parameters.
-// plhs: array of out parameters, each being a mxArray
-// plhs: array of in parameters (immutable), each being a mxArray
-//
-// MATLAB translates a call [A,B] = fun(C,D) into mexFunction(2,{A,B},2,{C,D}).
-// Then mxArrayS are adapted to be passed to a regular C function,
-// and the results are translated back to mxArrayS into plhs.
-void mexFunction(
- int nlhs,
- mxArray* plhs[],
- int nrhs,
- const mxArray* prhs[])
-{
- // Basic sanity checks
- if (nrhs!=11)
- mexErrMsgIdAndTxt("select:EMGLLF:nrhs","11 inputs required.");
- if (nlhs!=5)
- mexErrMsgIdAndTxt("select:EMGLLF:nlhs","5 outputs required.");
-
- // 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];
-
- ////////////
- // 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]);
-
- /////////////
- // 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]);
-
- ////////////////////
- // Call to EMGLLF //
- ////////////////////
-
- EMGLLF(brPhiInit,brRhoInit,piInit,brGamInit,mini,maxi,gamma,lambda,brX,brY,tau,
- phi,rho,pi,LLF,S,
- n,p,m,k);
-
- free(brPhiInit);
- free(brRhoInit);
- free(brGamInit);
- free(brX);
- free(brY);
-
- //post-processing: convert by-rows outputs to MATLAB matrices
- Real* mlPhi = brToMatlabArray_real(phi, dimPhi, 3);
- copyArray(mlPhi, phi, dimPhi[0]*dimPhi[1]*dimPhi[2]);
- free(mlPhi);
-
- Real* mlRho = brToMatlabArray_real(rho, dimRho, 3);
- copyArray(mlRho, rho, dimRho[0]*dimRho[1]*dimRho[2]);
- free(mlRho);
-
- Real* mlS = brToMatlabArray_real(S, dimS, 3);
- copyArray(mlS, S, dimS[0]*dimS[1]*dimS[2]);
- free(mlS);
-}
--- /dev/null
+#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_
+) {
+ // 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];
+
+ ////////////
+ // 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]);
+
+ /////////////
+ // 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]);
+
+ ////////////////////
+ // Call to EMGLLF //
+ ////////////////////
+
+ EMGLLF(brPhiInit,brRhoInit,piInit,brGamInit,mini,maxi,gamma,lambda,brX,brY,tau,
+ phi,rho,pi,LLF,S,
+ n,p,m,k);
+
+ free(brPhiInit);
+ free(brRhoInit);
+ free(brGamInit);
+ free(brX);
+ free(brY);
+
+
+
+
+
+
+
+}
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