void compute_metrics(const Ty* X1, const Ty* X2, Ty* M, int d, int n1, int n2, int opcode, const mxArray *prhs[])
{
switch (opcode)
{
case 1:
cityblock(X1, X2, M, d, n1, n2);
break;
case 2:
mindiff(X1, X2, M, d, n1, n2);
break;
case 3:
maxdiff(X1, X2, M, d, n1, n2);
break;
case 4:
minkowski(X1, X2, M, d, n1, n2, *((const Ty*)mxGetData(prhs[3])));
break;
case 5:
intersect(X1, X2, M, d, n1, n2);
break;
case 6:
chisq(X1, X2, M, d, n1, n2);
break;
case 7:
kldiv(X1, X2, M, d, n1, n2);
break;
case 8:
jeffrey(X1, X2, M, d, n1, n2);
break;
}
}
// [[Rcpp::export]]
Rcpp::NumericMatrix DistMatrixMinkowskiMAT(Rcpp::NumericMatrix dists, double p, bool testNA){
int ncols = dists.ncol();
double dist_value = 0.0;
Rcpp::NumericMatrix dist_matrix(ncols,ncols);
// http://stackoverflow.com/questions/23748572/initializing-a-matrix-to-na-in-rcpp
std::fill( dist_matrix.begin(), dist_matrix.end(), Rcpp::NumericVector::get_na() );
for (int i = 0; i < ncols; i++){
for (int j = 0; j < ncols; j++){
if(Rcpp::NumericVector::is_na(dist_matrix(i,j))){
dist_value = minkowski(dists(Rcpp::_, i),dists(Rcpp::_, j), p, testNA);
dist_matrix(i,j) = dist_value;
dist_matrix(j,i) = dist_value;
}
}
}
return dist_matrix;
}
void main(int nar, char* ar[])
{
int i,j,k,l,m, n=0, num, nnn[4];
float*u; // ,*f;
double*f;
parlist par;
FILE *in,*out,*col,*grs;
char name[100];
char buffer[48];
float cpu[2];
clock_t t;
/* set default values */
par.sigma=2; par.seed=200294;
par.dim=intvector(1,3); par.dim[1]=64; par.dim[2]=32; par.dim[3]=16;
empty(&par.inname); empty(&par.outname);
empty(&par.colname); empty(&par.grsname);
par.length=1; par.nongauss=0; par.lo=-4; par.hi=4; par.bins=100;
par.med=0; par.pixel=1; par.normal=1; par.time=0;
/* work through arguments */
while(++n<nar){
if(ar[n][0]=='-'&&ar[n][1]){
switch(ar[n][1]) {
case'0' : par.grsname =READSTR; break;
case'1' : par.colname =READSTR; break;
case'L' : par.length =READINT; break;
case'N' : par.normal =0; break;
case'b' : par.bins =READINT; break;
case'g' : par.nongauss=READINT; break;
case'h' : par.hi =READFLT; break;
case'i' : par.inname =READSTR; break;
case'l' : par.lo =READFLT; break;
case'm' : par.med =READINT; break;
case'o' : par.outname =READSTR; break;
case'p' : par.pixel =READINT; break;
case'r' : par.seed =READINT; break;
case's' : par.sigma =READFLT; break;
case't' : par.time =1; break;
case'x' : par.dim[1] =READINT; break;
case'y' : par.dim[2] =READINT; break;
case'z' : par.dim[3] =READINT; break;
default : Explain(stderr,ar[0],&par);
}
}
else {
Explain(stderr,ar[0],&par);
}
}
par.a=1./(float)par.dim[1]; /* grid constant is used everywhere */
/* allocate some memory */
n=par.dim[1]*par.dim[2]*par.dim[3];
u=vector(0,2*n);
/* open input file and read data */
fileopenr(&in,par.inname);
/* printf("%s"," here 1a \n");
printf("size = %d\n",sizeof(in)); */
if(in) {
//f=vector(0,n);
f=doublevector(0,n);
fread((void*)buffer,sizeof(char),24,in);
if(n!=fread((void*)f,sizeof(double),n,in)) {
fprintf(stderr,"error when reading input!\n");
exit(99);
}
/* printf("f[0] %d\n",&f[0]);
printf("f[0]wert %g\n", f[0]);
printf("f[1]wert %g\n", f[1]);
printf("f[1]wert %g\n", f[2]);
printf("f[1]wert %g\n", f[3]); */
printf("---\n");
//for(i=0;i<n;i++) u[2*i]=f[i],u[2*i+1]=0;
for(i=0;i<n;i++) u[2*i]=(float)f[i],u[2*i+1]=0;
/* printf("u[0] %d\n",&u[0]);
printf("u[0]wert %g\n", u[0]);
printf("f[0] %d\n",&f[0]);
printf("f[0]wert %g\n", f[0]);
printf("u[1] %d\n",&u[1]);
printf("u[1]wert %g\n", u[1]);
printf("f[1] %d\n",&f[1]);
printf("f[1]wert %g\n", f[1]);
printf("%s"," here 1c \n"); */
//free_vector(f,0,n);
free_doublevector(f,0,n);
/* printf("%s"," here 1d \n");
printf("par.sigma = %g\n",par.sigma); */
if(par.sigma>0) fourn(u-1,par.dim,3,1);
}
/* printf("%s"," here 1e \n"); */
fileclose(in);
/* printf("%s"," here 1 \n"); */
/* open output files */
fileopenw(&out,par.outname);
/* printf("%s"," here 2 \n"); */
cpu[0]=cpu[1]=0;
for(num=0; num<par.length; num++) {
/* random field in Fourier space */
if(par.time) t=clock();
if(!in) randomfield(u,&par);
if(par.time) cpu[0]+=(clock()-t)/(float)CLOCKS_PER_SEC;
/* convolution and normalization */
if(par.time) t=clock();
if(par.sigma>0) convolution(u,&par);
if(par.sigma>0) fourn(u-1,par.dim,3,-1);
normalize(u,&par);
if(par.time) cpu[0]+=(clock()-t)/(float)CLOCKS_PER_SEC;
/* printf("%s"," here 2c \n");*/
/* perform statistics */
if(par.time) t=clock();
minkowski(out,u,&par);
if(par.time) cpu[1]+=(clock()-t)/(float)CLOCKS_PER_SEC;
}
/* printf("%s"," here 3 \n"); */
if(par.time)
fprintf(stderr,"CPU: %13s%13s\n"
" %8.2f sec %8.2f sec\n",
"fields","minkowski",cpu[0],cpu[1]);
/* output xpm bitmap data */
fileopenw(&col,par.colname); if(col) picture(1,col,u,&par); fileclose(col);
fileopenw(&grs,par.grsname); if(grs) picture(0,grs,u,&par); fileclose(grs);
/* finish */
fileclose(out);
free_vector(u,0,2*n);
exit(0);
}
