BNW using Octave instead of Matlab.

This version of BNW should perform the same as the original version. The only difference is that it uses Octave instead of Matlab when running BayesNet Toolbox during parameter learning.

I am calling this BNW_1.02. It can be accessed at:
compbio.uthsc.edu/BNW_1.02

1 files changed, 149 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/KPMtools/repmatC.c b/sourcecodes/bnt-master/KPMtools/repmatC.c
new file mode 100644
index 00000000..6062772c
--- /dev/null
+++ b/sourcecodes/bnt-master/KPMtools/repmatC.c
@@ -0,0 +1,149 @@
+/*
+mex -c mexutil.c
+mex repmat.c mexutil.obj
+to check for warnings:
+gcc -Wall -I/cygdrive/c/MATLAB6p1/extern/include -c repmat.c
+*/
+#include "mexutil.h"
+#include <string.h>
+
+/* repeat a block of memory rep times */
+void memrep(char *dest, size_t chunk, int rep)
+{
+#if 0
+  /* slow way */
+  int i;
+  char *p = dest;
+  for(i=1;i<rep;i++) {
+    p += chunk;
+    memcpy(p, dest, chunk);
+  }
+#else
+  /* fast way */
+  if(rep == 1) return;
+  memcpy(dest + chunk, dest, chunk); 
+  if(rep & 1) {
+    dest += chunk;
+    memcpy(dest + chunk, dest, chunk);
+  }
+  /* now repeat using a block twice as big */
+  memrep(dest, chunk<<1, rep>>1);
+#endif
+}
+
+void repmat(char *dest, const char *src, int ndim, int *destdimsize, 
+	    int *dimsize, const int *dims, int *rep) 
+{
+  int d = ndim-1;
+  int i, chunk;
+  /* copy the first repetition into dest */
+  if(d == 0) {
+    chunk = dimsize[0];
+    memcpy(dest,src,chunk);
+  }
+  else {
+    /* recursively repeat each slice of src */
+    for(i=0;i<dims[d];i++) {
+      repmat(dest + i*destdimsize[d-1], src + i*dimsize[d-1], 
+	     ndim-1, destdimsize, dimsize, dims, rep);
+    }
+    chunk = destdimsize[d-1]*dims[d];
+  }
+  /* copy the result rep-1 times */
+  memrep(dest,chunk,rep[d]);
+}
+
+void mexFunction(int nlhs, mxArray *plhs[],
+                 int nrhs, const mxArray *prhs[])
+{
+  const mxArray *srcmat;
+  int ndim, *dimsize, eltsize;
+  const int *dims;
+  int ndimdest, *destdims, *destdimsize;
+  char *src, *dest;
+  int *rep;
+  int i,nrep;
+  int extra_rep = 1;
+  int empty;
+
+  if(nrhs < 2) mexErrMsgTxt("Usage: xrepmat(A, [N M ...])");
+  srcmat = prhs[0];
+  if(mxIsSparse(srcmat)) {
+    mexErrMsgTxt("Sorry, can't handle sparse matrices yet.");
+  }
+  if(mxIsCell(srcmat)) {
+    mexErrMsgTxt("Sorry, can't handle cell arrays yet.");
+  }
+  ndim = mxGetNumberOfDimensions(srcmat);
+  dims = mxGetDimensions(srcmat);
+  eltsize = mxGetElementSize(srcmat);
+
+  /* compute dimension sizes */
+  dimsize = mxCalloc(ndim, sizeof(int));
+  dimsize[0] = eltsize*dims[0];
+  for(i=1;i<ndim;i++) dimsize[i] = dimsize[i-1]*dims[i];
+
+  /* determine repetition vector */
+  ndimdest = ndim;
+  if(nrhs == 2) {
+    nrep = mxGetN(prhs[1]);
+    if(nrep > ndimdest) ndimdest = nrep;
+    rep = mxCalloc(ndimdest, sizeof(int));
+    for(i=0;i<nrep;i++) {
+      double repv = mxGetPr(prhs[1])[i];
+      rep[i] = (int)repv;
+    }
+    if(nrep == 1) {
+      /* special behavior */
+      nrep = 2;
+      rep[1] = rep[0];
+    }
+  }
+  else {
+    nrep = nrhs-1;
+    if(nrep > ndimdest) ndimdest = nrep;
+    rep = mxCalloc(ndimdest, sizeof(int));
+    for(i=0;i<nrep;i++) {
+      rep[i] = (int)*mxGetPr(prhs[i+1]);
+    }
+  }
+  for(i=nrep;i<ndimdest;i++) rep[i] = 1;
+
+  /* compute output size */
+  destdims = mxCalloc(ndimdest, sizeof(int));
+  for(i=0;i<ndim;i++) destdims[i] = dims[i]*rep[i];
+  for(;i<ndimdest;i++) { 
+    destdims[i] = rep[i];
+    extra_rep *= rep[i];
+  }
+  destdimsize = mxCalloc(ndim, sizeof(int));
+  destdimsize[0] = eltsize*destdims[0];
+  for(i=1;i<ndim;i++) destdimsize[i] = destdimsize[i-1]*destdims[i];
+
+    
+  /* for speed, array should be uninitialized */
+  plhs[0] = mxCreateNumericArray(ndimdest, destdims, mxGetClassID(srcmat), 
+				  mxIsComplex(srcmat)?mxCOMPLEX:mxREAL);
+
+  /* if any rep[i] == 0, output should be empty array.
+     Added by KPM 11/13/02.
+  */
+  empty = 0;
+  for (i=0; i < nrep; i++) {
+    if (rep[i]==0) 
+      empty = 1;
+  }
+  if (empty) 
+    return;
+
+  src = (char*)mxGetData(srcmat);
+  dest = (char*)mxGetData(plhs[0]);
+  repmat(dest,src,ndim,destdimsize,dimsize,dims,rep);
+  if(ndimdest > ndim) memrep(dest,destdimsize[ndim-1],extra_rep);
+  if(mxIsComplex(srcmat)) {
+    src = (char*)mxGetPi(srcmat);
+    dest = (char*)mxGetPi(plhs[0]);
+    repmat(dest,src,ndim,destdimsize,dimsize,dims,rep);
+    if(ndimdest > ndim) memrep(dest,destdimsize[ndim-1],extra_rep);
+  }
+}