X-Git-Url: https://git.auder.net/?a=blobdiff_plain;f=src%2Fadapters%2Fa.EMGLLF.c;h=0df00bdaa9fcde3bc6b556227e39a8affdcbe493;hb=09ab3c164abb566764e86a175b5973241e708fd6;hp=241a09f52bbc4a76701fe60407d894c20905015f;hpb=cb51adb811037428129ac947a5f7999c8c4539ae;p=valse.git

diff --git a/src/adapters/a.EMGLLF.c b/src/adapters/a.EMGLLF.c
index 241a09f..0df00bd 100644
--- a/src/adapters/a.EMGLLF.c
+++ b/src/adapters/a.EMGLLF.c
@@ -1,197 +1,86 @@
 #include <R.h>
 #include <Rdefines.h>
-#include "sources/EMGLLF.h"
-#include "sources/utils/io.h"
+#include "EMGLLF.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_core(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_VECTOR_ELT(listParams, 0, phi);
+	SET_VECTOR_ELT(listParams, 1, rho);
+	SET_VECTOR_ELT(listParams, 2, pi);
+	SET_VECTOR_ELT(listParams, 3, LLF);
+	SET_VECTOR_ELT(listParams, 4, S);
 
+	UNPROTECT(9);
+	return listParams;
 }